Attachment #62221 for bug #93053




#

PORTNAME=	emboss
PORTVERSION=	3.0.0
PORTREVISION=	1
CATEGORIES=	biology
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTNAME=	${PORTNAME:U}-${PORTVERSION}
DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
DIST_SUBDIR=	${PORTNAME}

MAINTAINER=	fernan@iib.unsam.edu.ar
COMMENT=	A collection of open source tools for genetic sequence analysis


CONFLICTS=	qmail-ldap2-* digest-*

PREFIX?=	${LOCALBASE}/emboss
NO_MTREE=	yes
USE_SUBMAKE=	yes
USE_GMAKE=	yes
GNU_CONFIGURE=	yes
USE_AUTOTOOLS=	libtool:15
INSTALLS_SHLIB=	yes
USE_XLIB=	yes
USE_MOTIF=	yes
SUB_FILES=	pkg-message
SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}

DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
DATADIR=	${PREFIX}/share/${PORTNAME:U}

post-patch:
.if !defined(NOPORTDOCS)
.for DIR in ${DOC_DIRS}
	@ ${REINPLACE_CMD} -e \
	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
	  ${WRKSRC}/${DIR}/Makefile.in
.endfor
.endif

pre-install:
	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}

post-install:
	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
	${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
.if !defined(BATCH)
	@ ${CAT} ${PKGMESSAGE}
.endif

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)emboss/distinfo (-3 / +3 lines)
1	MD5 (EMBOSS-2.10.0.tar.gz) = 4a48388ced7021a8ffece5166c40a364	1	MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
2	SHA256 (EMBOSS-2.10.0.tar.gz) = 1d3a8d84ff9c4f77d81b88c9e7c33517a232e7797eb2b761729f97898aa34a8f	2	SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
3	SIZE (EMBOSS-2.10.0.tar.gz) = 16262124	3	SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908




--- ajax/ajindex.c.orig	Mon Jan 23 12:17:02 2006
+++ ajax/ajindex.c	Thu Dec 22 13:12:27 2005
@@ -22,7 +22,6 @@
 
 
 
-
 static AjPBtpage  btreeCacheLocate(const AjPBtcache cache, ajlong page);
 static AjPBtpage  btreeCacheLruUnlink(AjPBtcache cache);
 static void       btreeCacheUnlink(AjPBtcache cache, AjPBtpage cpage);
@@ -35,10 +34,14 @@
 				    AjBool isread);
 static AjPBtpage  btreeFindINode(AjPBtcache cache, AjPBtpage page,
 				 const char *item);
+static AjPBtpage  btreeSecFindINode(AjPBtcache cache, AjPBtpage page,
+				    const char *item);
 
 
 static AjPBtpage  btreePageFromKey(AjPBtcache cache, unsigned char *buf,
 				   const char *item);
+static AjPBtpage  btreeSecPageFromKey(AjPBtcache cache, unsigned char *buf,
+				      const char *item);
 static ajint      btreeNumInBucket(AjPBtcache cache, ajlong pageno);
 static AjPBucket  btreeReadBucket(AjPBtcache cache, ajlong pageno);
 static void       btreeWriteBucket(AjPBtcache cache, const AjPBucket bucket,
@@ -55,6 +58,7 @@
 				 AjPStr const *keys, const ajlong *ptrs,
 				 ajint nkeys);
 static AjBool     btreeNodeIsFull(const AjPBtcache cache, AjPBtpage page);
+static AjBool     btreeNodeIsFullSec(const AjPBtcache cache, AjPBtpage page);
 static void       btreeInsertNonFull(AjPBtcache cache, AjPBtpage page,
 				     const AjPStr key, ajlong less,
 				     ajlong greater);
@@ -87,6 +91,8 @@
 
 
 
+
+
 #if 0
 static AjPBtpage  btreeTraverseLeaves(AjPBtcache cache, AjPBtpage thys);
 static void       btreeJoinLeaves(AjPBtcache cache);
@@ -168,6 +174,63 @@
 static ajint         btreeDbnoCompare(const void *a, const void *b);
 
 
+static AjPBtMem      btreeAllocPriArray(AjPBtcache cache);
+static void          btreeDeallocPriArray(AjPBtcache cache, AjPBtMem node);
+static AjPBtMem      btreeAllocSecArray(AjPBtcache cache);
+static void          btreeDeallocSecArray(AjPBtcache cache, AjPBtMem node);
+
+
+
+static void          btreeAddToHybBucket(AjPBtcache cache, ajlong pageno,
+					 const AjPBtHybrid id);
+static AjPBtpage     btreeHybFindINode(AjPBtcache cache, AjPBtpage page,
+				       const char *item);
+static AjPBtpage     btreeHybPageFromKey(AjPBtcache cache,
+					 unsigned char *buf, const char *key);
+static ajlong        btreeHybInsertShift(AjPBtcache cache, AjPBtpage *retpage,
+					 const char *key);
+static AjBool        btreeHybReorderBuckets(AjPBtcache cache, AjPBtpage leaf);
+static AjPBtpage     btreeHybSplitLeaf(AjPBtcache cache, AjPBtpage spage);
+static void          btreeHybInsertKey(AjPBtcache cache, AjPBtpage page,
+				       const AjPStr key, ajlong less,
+				       ajlong greater);
+static void          btreeHybSplitRoot(AjPBtcache cache);
+static void          btreeHybDupInsert(AjPBtcache cache, AjPBtHybrid hyb,
+				       AjPBtId btid);
+static void          btreeGetNumKeys(AjPBtcache cache, unsigned char *buf,
+				     ajlong **keys, ajlong **ptrs);
+static void          btreeWriteNumNode(AjPBtcache cache, AjPBtpage spage,
+				       const ajlong *keys, const ajlong *ptrs,
+				       ajint nkeys);
+static AjPNumBucket  btreeReadNumBucket(AjPBtcache cache, ajlong pageno);
+static void          btreeNumBucketDel(AjPNumBucket *thys);
+static void          btreeAddToNumBucket(AjPBtcache cache, ajlong pageno,
+					 const AjPBtNumId num);
+static AjPBtpage     btreeNumFindINode(AjPBtcache cache, AjPBtpage page,
+				       const ajlong item);
+static AjPBtpage     btreeNumPageFromKey(AjPBtcache cache, unsigned char *buf,
+					 const ajlong key);
+static ajint         btreeNumInNumBucket(AjPBtcache cache, ajlong pageno);
+static AjBool        btreeReorderNumBuckets(AjPBtcache cache, AjPBtpage leaf);
+static AjPNumBucket  btreeNumBucketNew(ajint n);
+static ajint         btreeNumIdCompare(const void *a, const void *b);
+static AjBool        btreeNumNodeIsFull(const AjPBtcache cache,
+					AjPBtpage page);
+static void          btreeNumInsertNonFull(AjPBtcache cache, AjPBtpage page,
+					   const ajlong key, ajlong less,
+					   ajlong greater);
+static void          btreeNumInsertKey(AjPBtcache cache, AjPBtpage page,
+				       const ajlong key, ajlong less,
+				       ajlong greater);
+static void          btreeNumSplitRoot(AjPBtcache cache);
+static void          btreeNumKeyShift(AjPBtcache cache, AjPBtpage tpage);
+static ajlong        btreeNumInsertShift(AjPBtcache cache, AjPBtpage *retpage,
+					 ajlong key);
+static AjPBtpage     btreeNumSplitLeaf(AjPBtcache cache, AjPBtpage spage);
+
+
+
+
 
 
 
@@ -196,11 +259,14 @@
 {
     FILE *fp;
     AjPBtcache cache = NULL;
+#if 0
 #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
     struct stat64 buf;
 #else
     struct stat buf;
 #endif
+#endif
+
     ajlong filelen = 0L;
 
     AjPStr fn = NULL;
@@ -213,12 +279,18 @@
 	return NULL;
 
 
+    /* Commented out pending database updating */
+#if 0
+    if(strcmp(mode,"r"))
+    {
 #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
-    if(!stat64(file, &buf))
+	if(!stat64(fn->Ptr, &buf))
 #else
-    if(!stat(file, &buf))
+	    if(!stat(fn->Ptr, &buf))
 #endif
-	filelen = buf.st_size;
+		filelen = buf.st_size;
+    }
+#endif    
 
     AJNEW0(cache);
 
@@ -244,6 +316,13 @@
     cache->totsize    = filelen;
     cache->cachesize  = cachesize;
 
+    cache->bmem = NULL;
+    cache->tmem = NULL;
+
+    cache->bsmem = NULL;
+    cache->tsmem = NULL;
+
+
     /* Add slevel, sorder and snperbucket ???? */
 
     ajStrDel(&fn);
@@ -808,7 +887,7 @@
     root = btreeCacheLocate(cache,0L);
 
     if(!root)
-	ajFatal("Something has unlocked the PRI root cache page\n");
+	ajFatal("The PRI root cache page has been unlocked\n");
     
     if(!cache->level)
 	return root;
@@ -863,6 +942,48 @@
 
 
 
+/* @funcstatic btreeSecFindINode *************************************************
+**
+** Recursive search for insert node in a secondary tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] page
+** @param [r] item [const char*] key to search for 
+**
+** @return [AjPBtpage] leaf node where item should be inserted
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeSecFindINode(AjPBtcache cache, AjPBtpage page,
+				 const char *item)
+{
+    AjPBtpage ret = NULL;
+    AjPBtpage pg  = NULL;
+
+    unsigned char *buf = NULL;
+    ajint status       = 0;
+    ajint ival         = 0;
+
+    /* ajDebug("In btreeSecFindINode\n"); */
+    
+    ret = page;
+    buf = page->buf;
+    GBT_NODETYPE(buf,&ival);
+    if(ival != BT_LEAF)
+    {
+	status = ret->dirty;
+	ret->dirty = BT_LOCK;	/* Lock in case of lots of overflow pages */
+	pg = btreeSecPageFromKey(cache,buf,item);
+	ret->dirty = status;
+	ret = btreeSecFindINode(cache,pg,item);
+    }
+    
+    return ret;
+}
+
+
+
+
 /* @funcstatic btreePageFromKey *******************************************
 **
 ** Return next lower index page given a key
@@ -928,6 +1049,71 @@
 
 
 
+/* @funcstatic btreeSecPageFromKey *******************************************
+**
+** Return next lower index page given a key in a secondary tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] buf [unsigned char *] page buffer
+** @param [r] key [const char *] key to search for 
+**
+** @return [AjPBtpage] pointer to a page
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeSecPageFromKey(AjPBtcache cache, unsigned char *buf,
+				     const char *key)
+{
+    unsigned char *rootbuf = NULL;
+    ajint nkeys = 0;
+    ajint order = 0;
+    ajint i;
+    
+    ajlong blockno = 0L;
+    AjPStr *karray = NULL;
+    ajlong *parray = NULL;
+    AjPBtpage page = NULL;
+    
+    /* ajDebug("In btreePageFromKey\n"); */
+    
+    rootbuf = buf;
+
+
+    GBT_NKEYS(rootbuf,&nkeys);
+    order = cache->sorder;
+
+    AJCNEW0(karray,order);
+    AJCNEW0(parray,order);
+    for(i=0;i<order;++i)
+	karray[i] = ajStrNew();
+
+    btreeGetKeys(cache,rootbuf,&karray,&parray);
+    i = 0;
+    while(i!=nkeys && strcmp(key,karray[i]->Ptr)>=0)
+	++i;
+    if(i==nkeys)
+    {
+	if(strcmp(key,karray[i-1]->Ptr)<0)
+	    blockno = parray[i-1];
+	else
+	    blockno = parray[i];
+    }
+    else
+	blockno = parray[i];
+
+    for(i=0;i<order;++i)
+	ajStrDel(&karray[i]);
+    AJFREE(karray);
+    AJFREE(parray);
+
+    page =  ajBtreeCacheRead(cache,blockno);
+
+    return page;
+}
+
+
+
+
 /* @func ajBtreeIdNew *********************************************
 **
 ** Constructor for index bucket ID informationn
@@ -1617,6 +1803,36 @@
 
 
 
+/* @funcstatic btreeNodeIsFullSec *****************************************
+**
+** Tests whether a secondary node is full of keys
+**
+** @param [r] cache [const AjPBtcache] cache
+** @param [u] page [AjPBtpage] original page
+**
+** @return [AjBool] true if full
+** @@
+******************************************************************************/
+
+static AjBool btreeNodeIsFullSec(const AjPBtcache cache, AjPBtpage page)
+{
+    unsigned char *buf = NULL;
+    ajint nkeys = 0;
+
+    /* ajDebug("In btreeNodeIsFull\n"); */
+
+    buf = page->buf;
+    GBT_NKEYS(buf,&nkeys);
+
+    if(nkeys == cache->sorder - 1)
+	return ajTrue;
+
+    return ajFalse;
+}
+
+
+
+
 /* @funcstatic btreeInsertNonFull *****************************************
 **
 ** Insert a key into a non-full node
@@ -2289,6 +2505,25 @@
 
 
 
+/* @funcstatic btreeNumIdCompare *******************************************
+**
+** Comparison function for ajListSort
+**
+** @param [r] a [const void*] ID 1
+** @param [r] b [const void*] ID 2
+**
+** @return [ajint] 0 = bases match
+** @@
+******************************************************************************/
+
+static ajint btreeNumIdCompare(const void *a, const void *b)
+{
+    return (*(AjPBtNumId*)a)->offset - (*(AjPBtNumId*)b)->offset;
+}
+
+
+
+
 /* @funcstatic btreeWriteNode *******************************************
 **
 ** Write an internal node
@@ -2999,8 +3234,7 @@
     rno = totalkeys - lno;
 
     maxnperbucket = nperbucket >> 1;
-    if(!maxnperbucket)
-	++maxnperbucket;
+    ++maxnperbucket;
 
     cbucket = btreeBucketNew(maxnperbucket);
 
@@ -5729,7 +5963,17 @@
     {
 	bentries = buckets[i]->Nentries;
 	for(j=0;j<bentries;++j)
-	    ajListPush(list,(void *)buckets[i]->Ids[j]);
+	{
+	    if(!buckets[i]->Ids[j]->dups)
+		ajListPush(list,(void *)buckets[i]->Ids[j]);
+	    else
+	    {
+		ajBtreeHybLeafList(cache,buckets[i]->Ids[j]->offset,
+				   buckets[i]->Ids[j]->id,list);
+		ajBtreeIdDel(&buckets[i]->Ids[j]);
+	    }
+	}
+	
 	AJFREE(buckets[i]->keylen);
 	AJFREE(buckets[i]->Ids);
 	AJFREE(buckets[i]);
@@ -6273,6 +6517,7 @@
 **
 ** @param [r] filename [const char*] file name
 ** @param [r] indexdir [const char*] index file directory
+** @param [r] directory [const char*] file directory
 ** @param [w] seqfiles [AjPStr**] sequence file names
 ** @param [w] reffiles [AjPStr**] reference file names (if any)
 
@@ -6282,6 +6527,7 @@
 ******************************************************************************/
 
 ajint ajBtreeReadEntries(const char *filename, const char *indexdir,
+			 const char *directory,
 			 AjPStr **seqfiles, AjPStr **reffiles)
 {
     AjPStr line = NULL;
@@ -6292,6 +6538,8 @@
 
     AjPStr seqname = NULL;
     AjPStr refname = NULL;
+    AjPStr tseqname = NULL;
+    AjPStr trefname = NULL;
     
     AjPFile inf   = NULL;
     char p;
@@ -6303,6 +6551,9 @@
     line    = ajStrNew();
     list    = ajListNew();
     reflist = ajListNew();
+
+    tseqname = ajStrNew();
+    trefname = ajStrNew();
     
     fn = ajStrNew();
     ajFmtPrintS(&fn,"%s/%s",indexdir,filename);
@@ -6329,7 +6580,8 @@
 	while(ajFileReadLine(inf, &line))
 	{
 	    seqname = ajStrNew();
-	    ajFmtScanS(line,"%S",&seqname);
+	    ajFmtScanS(line,"%S",&tseqname);
+	    ajFmtPrintS(&seqname,"%s/%S",directory,tseqname);
 	    ajListPushApp(list,(void *)seqname);
 	}
 
@@ -6342,7 +6594,9 @@
 	{
 	    seqname = ajStrNew();
 	    refname = ajStrNew();
-	    ajFmtScanS(line,"%S%S",&seqname,&refname);
+	    ajFmtScanS(line,"%S%S",&tseqname,&trefname);
+	    ajFmtPrintS(&seqname,"%s/%S",directory,tseqname);
+	    ajFmtPrintS(&refname,"%s/%S",directory,trefname);
 	    ajListPushApp(list,(void *)seqname);
 	    ajListPushApp(reflist,(void *)refname);
 	}
@@ -6357,6 +6611,11 @@
     ajListDel(&reflist);
     ajStrDel(&line);
     ajStrDel(&fn);
+
+    ajStrDel(&tseqname);
+    ajStrDel(&trefname);
+    
+
     ajFileClose(&inf);
 
     return entries;
@@ -6967,7 +7226,7 @@
 	pripage = btreeCacheLocate(cache,0L);
 	pripage->dirty = BT_LOCK;
 
-	ajDebug("Created secondary tree at block %d\n",(ajint)secrootpage);
+	/* ajDebug("Created 2ry tree at block %d\n",(ajint)secrootpage); */
     }
     else
     {
@@ -7776,8 +8035,7 @@
     rno = totalkeys - lno;
 
     maxnperbucket = nperbucket >> 1;
-    if(!maxnperbucket)
-	++maxnperbucket;
+    ++maxnperbucket;
 
     cbucket = btreePriBucketNew(maxnperbucket);
 
@@ -8230,11 +8488,13 @@
 {
     FILE *fp;
     AjPBtcache cache = NULL;
+#if 0
 #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
     struct stat64 buf;
 #else
     struct stat buf;
 #endif
+#endif
     ajlong filelen = 0L;
 
     AjPStr fn = NULL;
@@ -8246,13 +8506,18 @@
     if(!fp)
 	return NULL;
 
-
+    /* Commented out pending database updating */
+#if 0
+    if(strcmp(mode,"r"))
+    {
 #if defined (HAVE64) && !defined(_OSF_SOURCE) && !defined(_AIX) && !defined(__hpux) && !defined(__ppc__) && !defined(__FreeBSD__)
-    if(!stat64(file, &buf))
+	if(!stat64(fn->Ptr, &buf))
 #else
-    if(!stat(file, &buf))
+	    if(!stat(fn->Ptr, &buf))
+#endif
+		filelen = buf.st_size;
+    }
 #endif
-	filelen = buf.st_size;
 
     AJNEW0(cache);
 
@@ -8283,6 +8548,12 @@
     cache->snperbucket = sfill;
     cache->count = count;
     cache->kwlimit = kwlimit;
+
+    cache->bmem = NULL;
+    cache->tmem = NULL;
+
+    cache->bsmem = NULL;
+    cache->tsmem = NULL;
     
     ajStrDel(&fn);
     
@@ -8456,8 +8727,7 @@
     rno = totalkeys - lno;
 
     maxnperbucket = nperbucket >> 1;
-    if(!maxnperbucket)
-	++maxnperbucket;
+    ++maxnperbucket;
 
     cbucket = btreeSecBucketNew(maxnperbucket);
 
@@ -9070,7 +9340,7 @@
     if(!cache->slevel)
 	return root;
     
-    ret = btreeFindINode(cache,root,key);
+    ret = btreeSecFindINode(cache,root,key);
 
     return ret;
 }
@@ -9694,7 +9964,7 @@
     
     /* ajDebug("In btreeInsertKeySec\n"); */
 
-    if(!btreeNodeIsFull(cache,page))
+    if(!btreeNodeIsFullSec(cache,page))
     {
 	btreeInsertNonFullSec(cache,page,key,less,greater);
 	return;
@@ -10572,7 +10842,7 @@
 
     list = ajListNew();
 
-    order = cache->order;
+    order = cache->sorder;
 
     AJCNEW0(karray,order);
     AJCNEW0(parray,order);
@@ -11724,3 +11994,4580 @@
     return (*(AjPBtId*)a)->dbno -
 		  (*(AjPBtId*)b)->dbno;
 }
+
+
+
+
+
+
+
+
+/* @func ajBtreeHybNew *********************************************
+**
+** Constructor for index bucket ID informationn
+**
+**
+** @return [AjPBtHybrid] Index ID object
+** @@
+******************************************************************************/
+
+AjPBtHybrid ajBtreeHybNew(void)
+{
+    AjPBtHybrid Id = NULL;
+
+    /* ajDebug("In ajBtreeHybNew\n"); */
+
+    AJNEW0(Id);
+    Id->key1 = ajStrNew();
+    Id->dbno = 0;
+    Id->dups = 0;
+    Id->offset = 0L;
+    Id->refoffset = 0L;
+    Id->treeblock = 0L;    
+
+    return Id;
+}
+
+
+
+
+/* @func ajBtreeHybDel *********************************************
+**
+** Destructor for index bucket ID information
+**
+** @param [w] thys [AjPBtHybrid*] index ID object
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+void ajBtreeHybDel(AjPBtHybrid *thys)
+{
+    AjPBtHybrid Id = NULL;
+
+    /* ajDebug("In ajBtreeIdDel\n"); */
+
+    if(!thys || !*thys)
+	return;
+    Id = *thys;
+    
+    ajStrDel(&Id->key1);
+    AJFREE(Id);
+    *thys = NULL;
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeAllocPriArray *******************************************
+**
+** Allocate karray and parray arrays for a primary key
+**
+** @param [rw] cache [AjPBtcache] cache
+**
+** @return [AjPBtMem] memory node
+** @@
+******************************************************************************/
+
+static AjPBtMem btreeAllocPriArray(AjPBtcache cache)
+{
+    AjPBtMem node = NULL;
+    ajint i;
+    ajint limit;
+    AjPBtMem p = NULL;
+
+    limit = cache->order;
+    if(!cache->bmem)
+    {
+        AJNEW0(node);
+        cache->bmem = node;
+        cache->tmem = node;
+        node->prev = NULL;
+        node->next = NULL;
+        node->used = ajTrue;
+        AJCNEW0(node->karray,limit);
+        AJCNEW0(node->parray,limit);
+        AJCNEW0(node->overflows,limit);
+        for(i=0;i<limit;++i)
+            node->karray[i] = ajStrNew();
+
+        return node;
+    }
+
+    if(!cache->bmem->used)
+    {
+        cache->bmem->used = ajTrue;
+
+        if(cache->bmem->next)
+        {
+            p = cache->bmem->next;
+
+            cache->tmem->next = cache->bmem;
+            cache->bmem->next = NULL;
+
+            cache->bmem->prev = cache->tmem;
+
+            cache->tmem = cache->bmem;
+
+            cache->bmem = p;
+            cache->bmem->prev = NULL;
+
+	    memset(cache->tmem->parray,0,sizeof(ajlong)*limit);
+	    
+	    return cache->tmem;
+        }
+
+	memset(cache->bmem->parray,0,sizeof(ajlong)*limit);
+	
+        return cache->bmem;
+    }
+
+
+    AJNEW0(node);
+    node->used = ajTrue;
+    node->next = NULL;
+    node->prev = cache->tmem;
+    cache->tmem->next = node;
+    cache->tmem = node;
+
+    AJCNEW0(node->karray,limit);
+    AJCNEW0(node->parray,limit);
+    AJCNEW0(node->overflows,limit);
+    for(i=0;i<limit;++i)
+        node->karray[i] = ajStrNew();
+
+    return node;
+}
+
+
+
+
+/* @funcstatic btreeDeallocPriArray *******************************************
+**
+** Deallocate karray and parray arrays for a primary key
+**
+** @param [rw] cache [AjPBtcache] cache
+** @param [rw] node [AjPBtMem] node
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeDeallocPriArray(AjPBtcache cache, AjPBtMem node)
+{
+    node->used = ajFalse;
+    if(!node->prev)
+        return;
+
+    node->prev->next = node->next;
+    if(node->next)
+        node->next->prev = node->prev;
+    else
+        cache->tmem = node->prev;
+
+    node->next = cache->bmem;
+    cache->bmem->prev = node;
+    cache->bmem = node;
+    node->prev = NULL;
+
+    return;
+}
+
+
+
+
+
+/* @funcstatic btreeAllocSecArray *******************************************
+**
+** Allocate karray and parray arrays for a primary key
+**
+** @param [rw] cache [AjPBtcache] cache
+**
+** @return [AjPBtMem] memory node
+** @@
+******************************************************************************/
+
+static AjPBtMem btreeAllocSecArray(AjPBtcache cache)
+{
+    AjPBtMem node = NULL;
+    ajint i;
+    ajint limit;
+    AjPBtMem p = NULL;
+
+    limit = cache->sorder;
+    if(!cache->bsmem)
+    {
+        AJNEW0(node);
+        cache->bsmem = node;
+        cache->tsmem = node;
+        node->prev = NULL;
+        node->next = NULL;
+        node->used = ajTrue;
+        AJCNEW0(node->karray,limit);
+        AJCNEW0(node->parray,limit);
+        AJCNEW0(node->overflows,limit);
+        for(i=0;i<limit;++i)
+            node->karray[i] = ajStrNew();
+
+        return node;
+    }
+
+    if(!cache->bsmem->used)
+    {
+        cache->bsmem->used = ajTrue;
+
+        if(cache->bsmem->next)
+        {
+            p = cache->bsmem->next;
+
+            cache->tsmem->next = cache->bsmem;
+            cache->bsmem->next = NULL;
+
+            cache->bsmem->prev = cache->tsmem;
+
+            cache->tsmem = cache->bsmem;
+
+            cache->bsmem = p;
+            cache->bsmem->prev = NULL;
+
+	    memset(cache->tsmem->parray,0,sizeof(ajlong)*limit);
+	    return cache->tsmem;
+        }
+
+	memset(cache->bsmem->parray,0,sizeof(ajlong)*limit);
+        return cache->bsmem;
+    }
+
+    AJNEW0(node);
+    node->used = ajTrue;
+    node->next = NULL;
+    node->prev = cache->tsmem;
+    cache->tsmem->next = node;
+    cache->tsmem = node;
+
+    AJCNEW0(node->karray,limit);
+    AJCNEW0(node->parray,limit);
+    AJCNEW0(node->overflows,limit);
+    for(i=0;i<limit;++i)
+        node->karray[i] = ajStrNew();
+
+    return node;
+}
+
+
+
+
+/* @funcstatic btreeDeallocSecArray *******************************************
+**
+** Deallocate karray and parray arrays for a primary key
+**
+** @param [rw] cache [AjPBtcache] cache
+** @param [rw] node [AjPBtMem] node
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeDeallocSecArray(AjPBtcache cache, AjPBtMem node)
+{
+    node->used = ajFalse;
+    if(!node->prev)
+        return;
+
+    node->prev->next = node->next;
+    if(node->next)
+        node->next->prev = node->prev;
+    else
+        cache->tsmem = node->prev;
+
+    node->next = cache->bsmem;
+    cache->bsmem->prev = node;
+    cache->bsmem = node;
+    node->prev = NULL;
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeAddToHybBucket *******************************************
+**
+** Add an ID to a bucket
+** Only called if there is room in the bucket
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] pageno [ajlong] page number of bucket
+** @param [r] id [const AjPBtId] ID info
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeAddToHybBucket(AjPBtcache cache, ajlong pageno,
+				const AjPBtHybrid hyb)
+{
+    AjPBucket bucket = NULL;
+    AjPBtId   destid = NULL;
+    
+    ajint nentries;
+    
+    /* ajDebug("In btreeAddToHybBucket\n"); */
+
+    bucket   = btreeReadBucket(cache,pageno);
+    nentries = bucket->Nentries;
+
+
+    /* Reading a bucket always gives one extra ID position */
+    bucket->Ids[nentries] = ajBtreeIdNew();
+    destid = bucket->Ids[nentries];
+
+    ajStrAssS(&destid->id,hyb->key1);
+    destid->dbno      = hyb->dbno;
+    destid->offset    = hyb->offset;
+    destid->refoffset = hyb->refoffset;
+    destid->dups      = hyb->dups;
+    
+    ++bucket->Nentries;
+
+    btreeWriteBucket(cache,bucket,pageno);
+
+    btreeBucketDel(&bucket);
+    
+    return;
+}
+
+
+
+
+/* @func ajBtreeHybFindInsert ***********************************************
+**
+** Find the node that should contain a new key for insertion
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] key [const char*] key to search for 
+**
+** @return [AjPBtpage] leaf node where item should be inserted
+** @@
+******************************************************************************/
+
+AjPBtpage ajBtreeHybFindInsert(AjPBtcache cache, const char *key)
+{
+    AjPBtpage root = NULL;
+    AjPBtpage ret  = NULL;
+
+    /* ajDebug("In ajBtreeHybFindInsert\n"); */
+
+    /* The root node should always be in the cache (BT_LOCKed) */
+    root = btreeCacheLocate(cache,0L);
+
+    if(!root)
+	ajFatal("The PRI root cache page has been unlocked\n");
+    
+    if(!cache->level)
+	return root;
+    
+    ret = btreeHybFindINode(cache,root,key);
+    
+    return ret;
+}
+
+
+
+
+/* @funcstatic btreeHybFindINode *********************************************
+**
+** Recursive search for insert node
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] page
+** @param [r] item [const char*] key to search for 
+**
+** @return [AjPBtpage] leaf node where item should be inserted
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeHybFindINode(AjPBtcache cache, AjPBtpage page,
+				 const char *item)
+{
+    AjPBtpage ret = NULL;
+    AjPBtpage pg  = NULL;
+
+    unsigned char *buf = NULL;
+    ajint status       = 0;
+    ajint ival         = 0;
+
+    /* ajDebug("In btreeHybFindINode\n"); */
+    
+    ret = page;
+    buf = page->buf;
+    GBT_NODETYPE(buf,&ival);
+    if(ival != BT_LEAF)
+    {
+	status = ret->dirty;
+	ret->dirty = BT_LOCK;	/* Lock in case of lots of overflow pages */
+	pg = btreeHybPageFromKey(cache,buf,item);
+	ret->dirty = status;
+	ret = btreeHybFindINode(cache,pg,item);
+    }
+    
+    return ret;
+}
+
+
+
+
+/* @funcstatic btreeHybPageFromKey *******************************************
+**
+** Return next lower index page given a key
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] buf [unsigned char *] page buffer
+** @param [r] key [const char *] key to search for 
+**
+** @return [AjPBtpage] pointer to a page
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeHybPageFromKey(AjPBtcache cache, unsigned char *buf,
+				     const char *key)
+{
+    unsigned char *rootbuf = NULL;
+    ajint nkeys = 0;
+    ajint order = 0;
+    ajint i;
+    
+    ajlong blockno = 0L;
+    AjPStr *karray = NULL;
+    ajlong *parray = NULL;
+    AjPBtpage page = NULL;
+    AjPBtMem arrays = NULL;
+    
+    /* ajDebug("In btreeHybPageFromKey\n"); */
+    
+    rootbuf = buf;
+
+
+    GBT_NKEYS(rootbuf,&nkeys);
+    order = cache->order;
+
+    arrays = btreeAllocPriArray(cache);
+    karray = arrays->karray;
+    parray = arrays->parray;
+
+    btreeGetKeys(cache,rootbuf,&karray,&parray);
+    i = 0;
+    while(i!=nkeys && strcmp(key,karray[i]->Ptr)>=0)
+	++i;
+    if(i==nkeys)
+    {
+	if(strcmp(key,karray[i-1]->Ptr)<0)
+	    blockno = parray[i-1];
+	else
+	    blockno = parray[i];
+    }
+    else
+	blockno = parray[i];
+
+    btreeDeallocPriArray(cache,arrays);
+
+    page =  ajBtreeCacheRead(cache,blockno);
+
+    return page;
+}
+
+
+
+
+/* @funcstatic btreeHybInsertShift ********************************************
+**
+** Rebalance buckets on insertion
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] retpage [AjPBtpage*] page
+** @param [r] key [const char *] key
+**
+** @return [ajlong] bucket block or 0L if shift not posible 
+** @@
+******************************************************************************/
+
+static ajlong btreeHybInsertShift(AjPBtcache cache, AjPBtpage *retpage,
+				  const char *key)
+{
+    unsigned char *tbuf = NULL;
+    unsigned char *pbuf = NULL;
+    unsigned char *sbuf = NULL;
+
+    AjPBtpage ppage = NULL;
+    AjPBtpage spage = NULL;
+    AjPBtpage tpage = NULL;
+
+    ajint tkeys = 0;
+    ajint pkeys = 0;
+    ajint skeys = 0;
+    ajint order = 0;
+    
+    ajint i;
+    ajint n;
+    
+    ajlong parent  = 0L;
+    ajlong blockno = 0L;
+    
+    AjPStr *kTarray = NULL;
+    AjPStr *kParray = NULL;
+    AjPStr *kSarray = NULL;
+    ajlong *pTarray = NULL;
+    ajlong *pParray = NULL;
+    ajlong *pSarray = NULL;
+
+    AjPStr *karray = NULL;
+    ajlong *parray = NULL;
+
+    ajint ppos    = 0;
+    ajint pkeypos = 0;
+    ajint minsize = 0;
+
+    AjPBtMem arrays1 = NULL;
+    AjPBtMem arrays2 = NULL;
+    AjPBtMem arrays3 = NULL;
+    
+    /* ajDebug("In btreeHybInsertShift\n"); */
+
+
+    tpage = *retpage;
+
+    tbuf = tpage->buf;
+
+    GBT_PREV(tbuf,&parent);
+    GBT_NKEYS(tbuf,&tkeys);
+
+    order = cache->order;
+    minsize = order / 2;
+    if(order % 2)
+	++minsize;
+
+    if(tkeys <= minsize)
+	return 0L;
+
+    ppage = ajBtreeCacheRead(cache,parent);
+    
+    pbuf = ppage->buf;
+    GBT_NKEYS(pbuf,&pkeys);
+    
+
+    arrays1 = btreeAllocPriArray(cache);
+    kParray = arrays1->karray;
+    pParray = arrays1->parray;
+
+    arrays2 = btreeAllocPriArray(cache);
+    kSarray = arrays2->karray;
+    pSarray = arrays2->parray;
+
+    arrays3 = btreeAllocPriArray(cache);
+    kTarray = arrays3->karray;
+    pTarray = arrays3->parray;
+    
+
+    btreeGetKeys(cache,pbuf,&kParray,&pParray);
+
+    i=0;
+    while(i!=pkeys && strcmp(key,kParray[i]->Ptr)>=0)
+	++i;
+    pkeypos = i;
+    
+    if(i==pkeys)
+    {
+	if(strcmp(key,kParray[i-1]->Ptr)<0)
+	    ppos = i-1;
+	else
+	    ppos = i;
+    }
+    else
+	ppos = i;
+
+    
+    if(ppos) /* There is another leaf to the left */
+    {
+	spage = ajBtreeCacheRead(cache,pParray[ppos-1]);
+	sbuf = spage->buf;
+	GBT_NKEYS(sbuf,&skeys);
+    }
+
+    if(i && skeys != order-1) /* There is space in the left leaf */
+    {
+	/* ajDebug("Left shift\n"); */
+	btreeGetKeys(cache,tbuf,&kTarray,&pTarray);
+	if(skeys)
+	    btreeGetKeys(cache,sbuf,&kSarray,&pSarray);
+
+	i = 0;
+	while(pParray[i] != tpage->pageno)
+	    ++i;
+	--i;
+
+	pkeypos = i;
+
+	ajStrAssS(&kSarray[skeys],kParray[pkeypos]);
+	pSarray[skeys+1] = pTarray[0];
+	++skeys;
+	--tkeys;
+	ajStrAssS(&kParray[pkeypos],kTarray[0]);
+	for(i=0;i<tkeys;++i)
+	{
+	    ajStrAssS(&kTarray[i],kTarray[i+1]);
+	    pTarray[i] = pTarray[i+1];
+	}
+	pTarray[i] = pTarray[i+1];
+	pTarray[i+1] = 0L;
+	
+	btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
+	btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
+	btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
+	if(!ppage->pageno)
+	    ppage->dirty = BT_LOCK;
+
+	i = 0;
+	while(i!=pkeys && strcmp(key,kParray[i]->Ptr)>=0)
+	    ++i;
+	if(i==pkeys)
+	{
+	    if(strcmp(key,kParray[i-1]->Ptr)<0)
+		blockno = pParray[i-1];
+	    else
+		blockno = pParray[i];
+	}
+	else
+	    blockno = pParray[i];
+
+	if(blockno == spage->pageno)
+	{
+	    *retpage = spage;
+	    karray = kSarray;
+	    parray = pSarray;
+	    n = skeys;
+	}
+	else
+	{
+	    karray = kTarray;
+	    parray = pTarray;
+	    n = tkeys;
+	}
+	
+
+	i = 0;
+	while(i!=n && strcmp(key,karray[i]->Ptr)>=0)
+	    ++i;
+	if(i==n)
+	{
+	    if(strcmp(key,karray[i-1]->Ptr)<0)
+		blockno = parray[i-1];
+	    else
+		blockno = parray[i];
+	}
+	else
+	    blockno = parray[i];
+
+	btreeDeallocPriArray(cache,arrays1);
+	btreeDeallocPriArray(cache,arrays2);
+	btreeDeallocPriArray(cache,arrays3);
+
+	/* ajDebug("... returns blockno (a) %Ld\n",blockno); */
+
+	return blockno;
+    }
+    
+
+    if(ppos != pkeys)	/* There is a right node */
+    {
+	spage = ajBtreeCacheRead(cache,pParray[ppos+1]);
+	sbuf = spage->buf;
+	GBT_NKEYS(sbuf,&skeys);
+    }
+
+
+    /* Space in the right leaf */
+    if(ppos != pkeys && skeys != order-1)
+    {
+	/* ajDebug("Right shift\n"); */
+	btreeGetKeys(cache,tbuf,&kTarray,&pTarray);
+	btreeGetKeys(cache,sbuf,&kSarray,&pSarray);
+
+	i = 0;
+	while(pParray[i] != tpage->pageno)
+	    ++i;
+	pkeypos = i;
+	
+	pSarray[skeys+1] = pSarray[skeys];
+	for(i=skeys-1;i>-1;--i)
+	{
+	    ajStrAssS(&kSarray[i+1],kSarray[i]);
+	    pSarray[i+1] = pSarray[i];
+	}
+	ajStrAssS(&kSarray[0],kParray[pkeypos]);
+	pSarray[0] = pTarray[tkeys];
+	ajStrAssS(&kParray[pkeypos],kTarray[tkeys-1]);
+	++skeys;
+	--tkeys;
+	pTarray[tkeys+1] = 0L;
+	
+	btreeWriteNode(cache,spage,kSarray,pSarray,skeys);
+	btreeWriteNode(cache,tpage,kTarray,pTarray,tkeys);
+	btreeWriteNode(cache,ppage,kParray,pParray,pkeys);
+	if(!ppage->pageno)
+	    ppage->dirty = BT_LOCK;
+
+	i = 0;
+	while(i!=pkeys && strcmp(key,kParray[i]->Ptr)>=0)
+	    ++i;
+	if(i==pkeys)
+	{
+	    if(strcmp(key,kParray[i-1]->Ptr)<0)
+		blockno = pParray[i-1];
+	    else
+		blockno = pParray[i];
+	}
+	else
+	    blockno = pParray[i];
+
+	if(blockno == spage->pageno)
+	{
+	    *retpage = spage;
+	    karray = kSarray;
+	    parray = pSarray;
+	    n = skeys;
+	}
+	else
+	{
+	    karray = kTarray;
+	    parray = pTarray;
+	    n = tkeys;
+	}
+	
+	i = 0;
+	while(i!=n && strcmp(key,karray[i]->Ptr)>=0)
+	    ++i;
+	if(i==n)
+	{
+	    if(strcmp(key,karray[i-1]->Ptr)<0)
+		blockno = parray[i-1];
+	    else
+		blockno = parray[i];
+	}
+	else
+	    blockno = parray[i];
+
+	btreeDeallocPriArray(cache,arrays1);
+	btreeDeallocPriArray(cache,arrays2);
+	btreeDeallocPriArray(cache,arrays3);
+
+	/* ajDebug("... returns blockno (b) %Ld\n",blockno); */
+	
+	return blockno;
+    }
+
+
+    btreeDeallocPriArray(cache,arrays1);
+    btreeDeallocPriArray(cache,arrays2);
+    btreeDeallocPriArray(cache,arrays3);
+
+    /* ajDebug("... returns 0L\n"); */
+
+    return 0L;
+}
+
+
+
+
+/* @funcstatic btreeHybReorderBuckets *****************************************
+**
+** Re-order leaf buckets
+** Must only be called if one of the buckets is full
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] leaf [AjPBtpage] leaf page
+**
+** @return [AjBool] true if reorder was successful i.e. leaf not full
+** @@
+******************************************************************************/
+
+static AjBool btreeHybReorderBuckets(AjPBtcache cache, AjPBtpage leaf)
+{
+    ajint nkeys = 0;
+    unsigned char *lbuf = NULL;
+    AjPBucket *buckets  = NULL;
+    AjPStr *keys        = NULL;
+    ajlong *ptrs        = NULL;
+    ajlong *overflows   = NULL;
+    AjPBtMem arrays     = NULL;
+
+    ajint i = 0;
+    ajint j = 0;
+    
+    ajint order;
+    ajint bentries      = 0;
+    ajint totalkeys     = 0;
+    ajint nperbucket    = 0;
+    ajint maxnperbucket = 0;
+    ajint count         = 0;
+    ajint totkeylen     = 0;
+    ajint keylimit      = 0;
+    ajint bucketn       = 0;
+    ajint bucketlimit   = 0;
+    ajint nodetype      = 0;
+    
+    AjPList idlist    = NULL;
+    ajint   dirtysave = 0;
+    AjPBtId bid       = NULL;
+    AjPBucket cbucket = NULL;
+    AjPBtId cid       = NULL;
+
+    ajint   v = 0;
+    
+    /* ajDebug("In btreeHybReorderBuckets\n"); */
+
+    dirtysave = leaf->dirty;
+
+    leaf->dirty = BT_LOCK;
+    lbuf = leaf->buf;
+
+    GBT_NODETYPE(lbuf,&nodetype);
+
+    order = cache->order;
+    nperbucket = cache->nperbucket;
+    
+
+    /* Read keys/ptrs */
+    arrays    = btreeAllocPriArray(cache);
+    keys      = arrays->karray;
+    ptrs      = arrays->parray;
+    overflows = arrays->overflows;
+
+    btreeGetKeys(cache,lbuf,&keys,&ptrs);
+
+    GBT_NKEYS(lbuf,&nkeys);
+
+
+    if(!nkeys)
+	ajFatal("BucketReorder: Attempt to reorder empty leaf");
+
+    for(i=0;i<nkeys;++i)
+	totalkeys += btreeNumInBucket(cache,ptrs[i]);
+    totalkeys += btreeNumInBucket(cache,ptrs[i]);
+
+    /* Set the number of entries per bucket to approximately half full */
+    maxnperbucket = nperbucket >> 1;
+
+    if(!maxnperbucket)
+	++maxnperbucket;
+
+    /* Work out the number of new buckets needed */
+    bucketn = (totalkeys / maxnperbucket);
+    if(totalkeys % maxnperbucket)
+	++bucketn;
+    
+    if(bucketn > order)
+    {
+	btreeDeallocPriArray(cache,arrays);
+
+	leaf->dirty = dirtysave;
+	return ajFalse;
+    }
+    
+
+    /* Read buckets */
+    AJCNEW0(buckets,nkeys+1);
+    keylimit = nkeys + 1;
+    
+    for(i=0;i<keylimit;++i)
+	buckets[i] = btreeReadBucket(cache,ptrs[i]);
+
+
+    /* Read IDs from all buckets and push to list and sort (increasing id) */
+    idlist  = ajListNew();
+    
+    for(i=0;i<keylimit;++i)
+    {
+	overflows[i] = buckets[i]->Overflow;
+	bentries = buckets[i]->Nentries;
+	for(j=0;j<bentries;++j)
+	    ajListPush(idlist,(void *)buckets[i]->Ids[j]);
+	
+	AJFREE(buckets[i]->keylen);
+	AJFREE(buckets[i]->Ids);
+	AJFREE(buckets[i]);
+    }
+    ajListSort(idlist,btreeIdCompare);
+    AJFREE(buckets);
+
+    cbucket = btreeBucketNew(maxnperbucket);
+    bucketlimit = bucketn - 1;
+    
+    for(i=0;i<bucketlimit;++i)
+    {
+	cbucket->Overflow = overflows[i];
+	cbucket->Nentries = 0;
+
+	count = 0;
+	while(count!=maxnperbucket)
+	{
+	    ajListPop(idlist,(void **)&bid);
+	    
+	    cid = cbucket->Ids[count];
+	    ajStrAssS(&cid->id,bid->id);
+	    cid->dbno = bid->dbno;
+	    cid->dups = bid->dups;
+	    cid->offset = bid->offset;
+	    cid->refoffset = bid->refoffset;
+	    
+	    cbucket->keylen[count] = BT_BUCKIDLEN(bid->id);
+	    ++cbucket->Nentries;
+	    ++count;
+	    ajBtreeIdDel(&bid);
+	}
+
+
+	ajListPeek(idlist,(void **)&bid);
+	ajStrAssS(&keys[i],bid->id);
+
+	totkeylen += ajStrLen(bid->id);
+
+	if(!ptrs[i])
+	    ptrs[i] = cache->totsize;
+	btreeWriteBucket(cache,cbucket,ptrs[i]);
+    }
+
+
+    /* Deal with greater-than bucket */
+
+    cbucket->Overflow = overflows[i];
+    cbucket->Nentries = 0;
+
+    count = 0;
+    while(ajListPop(idlist,(void **)&bid))
+    {
+	cid = cbucket->Ids[count];
+	ajStrAssS(&cid->id,bid->id);
+	cid->dbno = bid->dbno;
+	cid->dups = bid->dups;
+	cid->offset = bid->offset;
+	cid->refoffset = bid->refoffset;
+	
+	++cbucket->Nentries;
+	++count;
+	ajBtreeIdDel(&bid);
+    }
+    
+    
+    if(!ptrs[i])
+	ptrs[i] = cache->totsize;
+    btreeWriteBucket(cache,cbucket,ptrs[i]);
+
+    cbucket->Nentries = maxnperbucket;
+    btreeBucketDel(&cbucket);
+
+    /* Now write out a modified leaf with new keys/ptrs */
+
+    nkeys = bucketn - 1;
+    v = nkeys;
+    SBT_NKEYS(lbuf,v);
+    v = totkeylen;
+    SBT_TOTLEN(lbuf,v);
+
+    btreeWriteNode(cache,leaf,keys,ptrs,nkeys);
+
+    leaf->dirty = BT_DIRTY;
+    if(nodetype == BT_ROOT)
+	leaf->dirty = BT_LOCK;
+
+    btreeDeallocPriArray(cache,arrays);
+    
+    btreeBucketDel(&cbucket);
+    ajListDel(&idlist);
+
+    return ajTrue;
+}
+
+
+
+
+/* @funcstatic btreeHybSplitLeaf *********************************************
+**
+** Split a leaf and propagate up if necessary
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] spage [AjPBtpage] page
+**
+** @return [AjPBtpage] pointer to a parent page
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeHybSplitLeaf(AjPBtcache cache, AjPBtpage spage)
+{
+    ajint nkeys     = 0;
+    ajint order     = 0;
+    ajint totalkeys = 0;
+    ajint bentries  = 0;
+    ajint keylimit  = 0;
+    ajint nodetype  = 0;
+
+    ajint rootnodetype  = 0;
+    
+    ajint i;
+    ajint j;
+    
+    AjPBtpage lpage = NULL;
+    AjPBtpage rpage = NULL;
+    AjPBtpage page  = NULL;
+    
+    AjPStr mediankey  = NULL;
+    ajlong mediangtr  = 0L;
+    ajlong medianless = 0L;
+    
+
+    AjPBtId bid = NULL;
+    AjPBtId cid = NULL;
+
+    unsigned char *buf  = NULL;
+    unsigned char *lbuf = NULL;
+    unsigned char *rbuf = NULL;
+
+    AjPList idlist = NULL;
+
+    AjPBucket *buckets = NULL;
+    AjPBucket cbucket  = NULL;
+    
+    AjPStr *karray = NULL;
+    ajlong *parray = NULL;
+    AjPBtMem arrays     = NULL;
+    
+    ajint keypos = 0;
+    ajint lno    = 0;
+    ajint rno    = 0;
+
+    ajint bucketlimit   = 0;
+    ajint maxnperbucket = 0;
+    ajint nperbucket    = 0;
+    ajint bucketn       = 0;
+    ajint count         = 0;
+    ajint totkeylen     = 0;
+    
+    ajlong lblockno = 0L;
+    ajlong rblockno = 0L;
+    ajlong prev     = 0L;
+    ajlong overflow = 0L;
+    ajlong prevsave = 0L;
+
+    ajlong zero = 0L;
+    ajlong join = 0L;
+    
+    ajlong lv = 0L;
+    ajint  v  = 0;
+    
+    /* ajDebug("In btreeHybSplitLeaf\n"); */
+
+    order = cache->order;
+    nperbucket = cache->nperbucket;
+
+    mediankey = ajStrNew();
+
+    arrays    = btreeAllocPriArray(cache);
+    karray    = arrays->karray;
+    parray    = arrays->parray;
+
+
+    buf = spage->buf;
+    lbuf = buf;
+
+    GBT_NKEYS(buf,&nkeys);
+
+    for(i=nkeys+1; i<order; ++i)
+	parray[i] = 0L;
+
+    GBT_NODETYPE(buf,&rootnodetype);
+
+    if(rootnodetype == BT_ROOT)
+    {
+	/* ajDebug("Splitting root node\n"); */
+	lblockno = cache->totsize;
+	lpage = ajBtreeCacheWrite(cache,lblockno);
+	lpage->pageno = cache->totsize;
+	cache->totsize += cache->pagesize;
+	lbuf = lpage->buf;
+	lv = prev;
+	SBT_PREV(lbuf,lv);
+    }
+    else
+    {
+	lblockno = spage->pageno;
+	lpage = spage;
+    }
+
+    lpage->dirty = BT_LOCK;
+
+
+    rblockno = cache->totsize;
+    rpage = ajBtreeCacheWrite(cache,rblockno);
+    rpage->pageno = cache->totsize;
+    rpage->dirty = BT_LOCK;
+    cache->totsize += cache->pagesize;
+    rbuf = rpage->buf;
+
+
+    if(rootnodetype == BT_ROOT)
+    {
+	lv = zero;
+	SBT_RIGHT(rbuf,lv);
+	lv = zero;
+	SBT_LEFT(lbuf,lv);
+    }
+    else
+    {
+	GBT_RIGHT(lbuf,&join);
+	lv = join;
+	SBT_RIGHT(rbuf,lv);
+    }
+    lv = lblockno;
+    SBT_LEFT(rbuf,lv);
+    lv = rblockno;
+    SBT_RIGHT(lbuf,lv);
+
+
+    btreeGetKeys(cache,buf,&karray,&parray);
+
+
+    keylimit = nkeys+1;
+    AJCNEW0(buckets,keylimit);
+    for(i=0;i<keylimit;++i)
+	buckets[i] = btreeReadBucket(cache,parray[i]);
+
+    idlist = ajListNew();
+    for(i=0;i<keylimit;++i)
+    {
+	bentries = buckets[i]->Nentries;
+	for(j=0;j<bentries;++j)
+	    ajListPush(idlist,(void *)buckets[i]->Ids[j]);
+	AJFREE(buckets[i]->keylen);
+	AJFREE(buckets[i]->Ids);
+	AJFREE(buckets[i]);
+    }
+    ajListSort(idlist,btreeIdCompare);
+    AJFREE(buckets);
+
+
+    totalkeys = ajListLength(idlist);
+
+    keypos = totalkeys / 2;
+
+    lno = keypos;
+    rno = totalkeys - lno;
+
+    maxnperbucket = nperbucket >> 1;
+    ++maxnperbucket;
+
+    cbucket = btreeBucketNew(maxnperbucket);
+
+    bucketn = lno / maxnperbucket;
+    if(lno % maxnperbucket)
+	++bucketn;
+    bucketlimit = bucketn - 1;
+
+
+    totkeylen = 0;
+    count = 0;
+    for(i=0;i<bucketlimit;++i)
+    {
+	cbucket->Nentries = 0;
+	for(j=0;j<maxnperbucket;++j)
+	{
+	    ajListPop(idlist,(void **)&bid);
+	    
+	    cid = cbucket->Ids[j];
+	    ajStrAssS(&cid->id,bid->id);
+	    cid->dbno = bid->dbno;
+	    cid->dups = bid->dups;
+	    cid->offset = bid->offset;
+	    cid->refoffset = bid->refoffset;
+	    
+	    cbucket->keylen[j] = BT_BUCKIDLEN(bid->id);
+	    ++count;
+	    ++cbucket->Nentries;
+	    ajBtreeIdDel(&bid);
+	}
+	ajListPeek(idlist,(void **)&bid);
+	
+	ajStrAssS(&karray[i],bid->id);
+	totkeylen += ajStrLen(bid->id);
+
+	if(!parray[i])
+	    parray[i] = cache->totsize;
+	btreeWriteBucket(cache,cbucket,parray[i]);
+    }
+
+    cbucket->Nentries = 0;
+
+    j = 0;
+    while(count != lno)
+    {
+	ajListPop(idlist,(void **)&bid);
+	cid = cbucket->Ids[j];
+	++j;
+	++count;
+
+	ajStrAssS(&cid->id,bid->id);
+	cid->dbno = bid->dbno;
+	cid->dups = bid->dups;
+	cid->offset = bid->offset;
+	cid->refoffset = bid->refoffset;
+	
+	++cbucket->Nentries;
+	ajBtreeIdDel(&bid);
+    }
+
+    if(!parray[i])
+	parray[i] = cache->totsize;
+    btreeWriteBucket(cache,cbucket,parray[i]);
+
+    nkeys = bucketn - 1;
+    v = nkeys;
+    SBT_NKEYS(lbuf,v);
+    v = totkeylen;
+    SBT_TOTLEN(lbuf,v);
+    nodetype = BT_LEAF;
+    v = nodetype;
+    SBT_NODETYPE(lbuf,v);
+    lpage->dirty = BT_DIRTY;
+
+    GBT_PREV(lbuf,&prevsave);
+
+    btreeWriteNode(cache,lpage,karray,parray,nkeys);
+
+    ajListPeek(idlist,(void **)&bid);
+    ajStrAssS(&mediankey,bid->id);
+
+    totkeylen = 0;
+    bucketn = rno / maxnperbucket;
+    if(rno % maxnperbucket)
+	++bucketn;
+    bucketlimit = bucketn - 1;
+
+    for(i=0;i<bucketlimit;++i)
+    {
+	cbucket->Nentries = 0;
+	for(j=0;j<maxnperbucket;++j)
+	{
+	    ajListPop(idlist,(void **)&bid);
+	    
+	    cid = cbucket->Ids[j];
+	    ajStrAssS(&cid->id,bid->id);
+	    cid->dbno = bid->dbno;
+	    cid->dups = bid->dups;
+	    cid->offset = bid->offset;
+	    cid->refoffset = bid->refoffset;
+	    
+	    cbucket->keylen[j] = BT_BUCKIDLEN(bid->id);
+	    ++cbucket->Nentries;
+	    ajBtreeIdDel(&bid);
+	}
+
+	ajListPeek(idlist,(void **)&bid);
+	ajStrAssS(&karray[i],bid->id);
+	totkeylen += ajStrLen(bid->id);
+
+	parray[i] = cache->totsize;
+	btreeWriteBucket(cache,cbucket,parray[i]);
+    }
+
+    cbucket->Nentries = 0;
+
+    j = 0;
+    while(ajListPop(idlist,(void**)&bid))
+    {
+	cid = cbucket->Ids[j];
+	++j;
+
+	ajStrAssS(&cid->id,bid->id);
+	cid->dbno = bid->dbno;
+	cid->dups = bid->dups;
+	cid->offset = bid->offset;
+	cid->refoffset = bid->refoffset;
+	
+	++cbucket->Nentries;
+	ajBtreeIdDel(&bid);
+    }
+    
+    parray[i] = cache->totsize;
+    btreeWriteBucket(cache,cbucket,parray[i]);
+
+    nkeys = bucketn - 1;
+
+    v = nkeys;
+    SBT_NKEYS(rbuf,v);
+    v = totkeylen;
+    SBT_TOTLEN(rbuf,v);
+    nodetype = BT_LEAF;
+    v = nodetype;
+    SBT_NODETYPE(rbuf,v);
+    lv = prevsave;
+    SBT_PREV(rbuf,lv);
+    lv = overflow;
+    SBT_OVERFLOW(rbuf,lv);
+
+    btreeWriteNode(cache,rpage,karray,parray,nkeys);
+    rpage->dirty = BT_DIRTY;
+
+    cbucket->Nentries = maxnperbucket;
+    btreeBucketDel(&cbucket);
+    ajListDel(&idlist);
+
+
+
+    medianless = lblockno;
+    mediangtr  = rblockno;
+
+
+    if(rootnodetype == BT_ROOT)
+    {
+	ajStrAssS(&karray[0],mediankey);
+	parray[0]=lblockno;
+	parray[1]=rblockno;
+	nkeys = 1;
+	btreeWriteNode(cache,spage,karray,parray,nkeys);	
+	spage->dirty = BT_LOCK;
+
+	btreeDeallocPriArray(cache,arrays);
+
+	ajStrDel(&mediankey);
+	++cache->level;
+	return spage;
+    }
+
+
+    btreeDeallocPriArray(cache,arrays);
+
+    page = ajBtreeCacheRead(cache,prevsave);
+    btreeHybInsertKey(cache,page,mediankey,medianless,mediangtr);
+    ajStrDel(&mediankey);
+
+    page = ajBtreeCacheRead(cache,prevsave);
+
+    return page;
+}
+
+
+
+
+/* @funcstatic btreeHybInsertKey *****************************************
+**
+** Insert a key into a potentially full node
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] original page
+** @param [r] key [const AjPStr] key to insert
+** @param [r] less [ajlong] less-than pointer
+** @param [r] greater [ajlong] greater-than pointer
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeHybInsertKey(AjPBtcache cache, AjPBtpage page,
+			      const AjPStr key, ajlong less, ajlong greater)
+{
+    unsigned char *lbuf = NULL;
+    unsigned char *rbuf = NULL;
+    unsigned char *tbuf = NULL;
+    AjPStr *karray      = NULL;
+    ajlong *parray      = NULL;
+    AjPStr *tkarray     = NULL;
+    ajlong *tparray     = NULL;
+
+    AjPBtMem arrays1    = NULL;
+    AjPBtMem arrays2    = NULL;
+
+    ajint nkeys    = 0;
+    ajint order    = 0;
+    ajint keypos   = 0;
+    ajint rkeyno   = 0;
+    
+    ajint i = 0;
+    ajint n = 0;
+    
+    ajint nodetype  = 0;
+    AjPBtpage ipage = NULL;
+    AjPBtpage lpage = NULL;
+    AjPBtpage rpage = NULL;
+    AjPBtpage tpage = NULL;
+
+    ajlong blockno  = 0L;
+    ajlong rblockno = 0L;
+    ajlong lblockno = 0L;
+    AjPStr mediankey  = NULL;
+    ajlong medianless = 0L;
+    ajlong mediangtr  = 0L;
+    ajlong overflow   = 0L;
+    ajlong prev       = 0L;
+    ajint  totlen     = 0;
+    
+    ajlong lv = 0L;
+    ajint  v  = 0;
+    
+    /* ajDebug("In btreeHybInsertKey\n"); */
+
+    if(!btreeNodeIsFull(cache,page))
+    {
+	btreeInsertNonFull(cache,page,key,less,greater);
+	return;
+    }
+    
+    order = cache->order;
+    lbuf = page->buf;
+    GBT_NODETYPE(lbuf,&nodetype);
+    page->dirty = BT_LOCK;
+
+    if(nodetype == BT_ROOT)
+    {
+	arrays1   = btreeAllocPriArray(cache);
+	karray    = arrays1->karray;
+	parray    = arrays1->parray;
+
+	btreeHybSplitRoot(cache);
+
+	if(page->pageno)
+	    page->dirty = BT_DIRTY;
+	btreeGetKeys(cache,lbuf,&karray,&parray);
+
+	if(strcmp(key->Ptr,karray[0]->Ptr)<0)
+	    blockno = parray[0];
+	else
+	    blockno = parray[1];
+	ipage = ajBtreeCacheRead(cache,blockno);
+	btreeInsertNonFull(cache,ipage,key,less,greater);
+
+	btreeDeallocPriArray(cache,arrays1);
+	return;
+    }
+
+
+    arrays1   = btreeAllocPriArray(cache);
+    karray    = arrays1->karray;
+    parray    = arrays1->parray;
+
+    arrays2   = btreeAllocPriArray(cache);
+    tkarray   = arrays2->karray;
+    tparray   = arrays2->parray;
+
+    mediankey = ajStrNew();
+    
+    lpage = page;
+    lbuf = lpage->buf;
+    
+    btreeGetKeys(cache,lbuf,&karray,&parray);
+
+    GBT_BLOCKNUMBER(lbuf,&lblockno);
+    rblockno = cache->totsize;
+    rpage = ajBtreeCacheWrite(cache,rblockno);
+    rpage->dirty = BT_LOCK;
+    rpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+    rbuf = rpage->buf;
+    lv = rblockno;
+    SBT_BLOCKNUMBER(rbuf,lv);
+
+    
+    GBT_PREV(lbuf,&prev);
+    lv = prev;
+    SBT_PREV(rbuf,lv);
+
+    nkeys = order - 1;
+    keypos = nkeys / 2;
+    if(!(nkeys % 2))
+	--keypos;
+
+    ajStrAssS(&mediankey,karray[keypos]);
+    medianless = lblockno;
+    mediangtr  = rblockno;
+
+
+    GBT_NODETYPE(lbuf,&nodetype);
+    v = nodetype;
+    SBT_NODETYPE(rbuf,v);
+    lv = overflow;
+    SBT_OVERFLOW(rbuf,lv);
+
+
+    totlen = 0;
+    for(i=0;i<keypos;++i)
+    {
+	ajStrAssS(&tkarray[i],karray[i]);
+	totlen += ajStrLen(karray[i]);
+	tparray[i] = parray[i];
+    }
+    tparray[i] = parray[i];
+    v = totlen;
+    SBT_TOTLEN(lbuf,v);
+    n = i;
+    v = n;
+    SBT_NKEYS(lbuf,v);
+    btreeWriteNode(cache,lpage,tkarray,tparray,i);
+
+
+
+    for(i=0;i<n+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = lblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+
+    totlen = 0;
+    for(i=keypos+1;i<nkeys;++i)
+    {
+	ajStrAssS(&tkarray[i-(keypos+1)],karray[i]);
+	totlen += ajStrLen(karray[i]);
+	tparray[i-(keypos+1)] = parray[i];
+    }
+    tparray[i-(keypos+1)] = parray[i];
+    v = totlen;
+    SBT_TOTLEN(rbuf,v);
+    rkeyno = (nkeys-keypos) - 1;
+    v = rkeyno;
+    SBT_NKEYS(rbuf,v);
+    rpage->dirty = BT_DIRTY;
+    btreeWriteNode(cache,rpage,tkarray,tparray,rkeyno);
+
+
+    for(i=0;i<rkeyno+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = rblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+
+    ipage = rpage;
+    if(strcmp(key->Ptr,mediankey->Ptr)<0)
+	ipage = lpage;
+
+    btreeInsertNonFull(cache,ipage,key,less,greater);
+
+
+    btreeDeallocPriArray(cache,arrays1);
+    btreeDeallocPriArray(cache,arrays2);
+
+    ipage = ajBtreeCacheRead(cache,prev);
+
+    btreeHybInsertKey(cache,ipage,mediankey,medianless,mediangtr);
+    ajStrDel(&mediankey);
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeHybSplitRoot *****************************************
+**
+** Split the root node
+**
+** @param [u] cache [AjPBtcache] cache
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeHybSplitRoot(AjPBtcache cache)
+{
+    AjPBtpage rootpage = NULL;
+    AjPBtpage rpage    = NULL;
+    AjPBtpage lpage    = NULL;
+    AjPBtpage tpage    = NULL;
+
+    AjPStr *karray     = NULL;
+    AjPStr *tkarray    = NULL;
+    ajlong *parray     = NULL;
+    ajlong *tparray    = NULL;
+    AjPBtMem arrays1   = NULL;
+    AjPBtMem arrays2   = NULL;
+
+    ajint order     = 0;
+    ajint nkeys     = 0;
+    ajint keypos    = 0;
+    
+    ajlong rblockno = 0L;
+    ajlong lblockno = 0L;
+    
+    AjPStr key = NULL;
+    ajint  i;
+
+    unsigned char *rootbuf = NULL;
+    unsigned char *rbuf    = NULL;
+    unsigned char *lbuf    = NULL;
+    unsigned char *tbuf    = NULL;
+    
+    ajint nodetype  = 0;
+    ajlong overflow = 0L;
+    ajlong zero     = 0L;
+    ajint totlen    = 0;
+    ajint rkeyno    = 0;
+    ajint n         = 0;
+
+    ajlong lv = 0L;
+    ajint  v  = 0;
+    
+    
+    /* ajDebug("In btreeHybSplitRoot\n"); */
+
+    order = cache->order;
+
+    arrays1   = btreeAllocPriArray(cache);
+    karray    = arrays1->karray;
+    parray    = arrays1->parray;
+
+    arrays2   = btreeAllocPriArray(cache);
+    tkarray   = arrays2->karray;
+    tparray   = arrays2->parray;
+
+    key = ajStrNew();
+
+    rootpage = btreeCacheLocate(cache,0L);
+    if(!rootpage)
+	ajFatal("Root page has been unlocked 1");
+    
+    rootbuf = rootpage->buf;
+
+    nkeys = order - 1;
+
+    keypos = nkeys / 2;
+    if(!(nkeys % 2))
+	--keypos;
+
+
+    rblockno = cache->totsize;
+    rpage = ajBtreeCacheWrite(cache,rblockno);
+    rpage->dirty = BT_LOCK;
+    rpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+
+    lblockno = cache->totsize;
+    lpage = ajBtreeCacheWrite(cache,lblockno);
+    lpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+
+    lv = rblockno;
+    SBT_BLOCKNUMBER(rpage->buf,lv);
+    lv = lblockno;
+    SBT_BLOCKNUMBER(lpage->buf,lv);
+
+    if(!cache->level)
+    {
+	lv = zero;
+	SBT_LEFT(lpage->buf,lv);
+	lv = rblockno;
+	SBT_RIGHT(lpage->buf,lv);
+	lv = lblockno;
+	SBT_LEFT(rpage->buf,lv);
+	lv = zero;
+	SBT_RIGHT(rpage->buf,lv);
+    }
+
+    btreeGetKeys(cache,rootbuf,&karray,&parray);
+
+    /* Get key for root node and write new root node */
+    ajStrAssS(&tkarray[0],karray[keypos]);
+    tparray[0] = lblockno;
+    tparray[1] = rblockno;
+    
+
+    n = 1;
+    v = n;
+    SBT_NKEYS(rootbuf,v);
+    btreeWriteNode(cache,rootpage,tkarray,tparray,1);
+    rootpage->dirty = BT_LOCK;
+
+    rbuf = rpage->buf;
+    lbuf = lpage->buf;
+    
+    if(cache->level)
+	nodetype = BT_INTERNAL;
+    else
+	nodetype = BT_LEAF;
+
+    v = nodetype;
+    SBT_NODETYPE(rbuf,v);
+    v = nodetype;
+    SBT_NODETYPE(lbuf,v);
+    lv = overflow;
+    SBT_OVERFLOW(rbuf,lv);
+    lv = overflow;
+    SBT_PREV(rbuf,lv);
+    lv = overflow;
+    SBT_OVERFLOW(lbuf,lv);
+    lv = overflow;
+    SBT_PREV(lbuf,lv);
+
+    totlen = 0;
+    for(i=0;i<keypos;++i)
+    {
+	ajStrAssS(&tkarray[i],karray[i]);
+	totlen += ajStrLen(karray[i]);
+	tparray[i] = parray[i];
+    }
+    tparray[i] = parray[i];
+    v = totlen;
+    SBT_TOTLEN(lbuf,v);
+    n = i;
+    v = n;
+    SBT_NKEYS(lbuf,v);
+    btreeWriteNode(cache,lpage,tkarray,tparray,i);
+
+    for(i=0;i<n+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = lblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+    totlen = 0;
+    for(i=keypos+1;i<nkeys;++i)
+    {
+	ajStrAssS(&tkarray[i-(keypos+1)],karray[i]);
+	totlen += ajStrLen(karray[i]);
+	tparray[i-(keypos+1)] = parray[i];
+    }
+    tparray[i-(keypos+1)] = parray[i];
+    v = totlen;
+    SBT_TOTLEN(rbuf,v);
+    rkeyno = (nkeys-keypos) - 1;
+    v = rkeyno;
+    SBT_NKEYS(rbuf,v);
+    rpage->dirty = BT_DIRTY;
+    btreeWriteNode(cache,rpage,tkarray,tparray,rkeyno);
+
+    for(i=0;i<rkeyno+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = rblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+
+    btreeDeallocPriArray(cache,arrays1);
+    btreeDeallocPriArray(cache,arrays2);
+
+    ++cache->level;
+
+    ajStrDel(&key);
+    
+    return;
+}
+
+
+
+
+/* @func ajBtreeHybInsertId *********************************************
+**
+** Insert an ID structure into the tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] id [const AjPBtId] Id object
+**
+** @return [void] pointer to a page
+** @@
+******************************************************************************/
+
+void ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb)
+{
+    AjPBtpage spage   = NULL;
+    AjPBtpage parent  = NULL;
+    AjPStr key        = NULL;
+    const char *ckey  = NULL;
+    AjPBucket lbucket = NULL;
+    AjPBucket rbucket = NULL;
+    AjPBucket bucket  = NULL;
+    ajlong lblockno = 0L;
+    ajlong rblockno = 0L;
+    ajlong blockno  = 0L;
+    ajlong shift    = 0L;
+
+    ajint nkeys = 0;
+    ajint order = 0;
+
+    ajint nodetype = 0;
+    ajint nentries = 0;
+    
+    AjPStr *karray = NULL;
+    ajlong *parray = NULL;
+    AjPBtMem arrays = NULL;
+    AjBool found = ajFalse;
+    AjPBtId btid = NULL;
+    
+    ajint i;
+    ajint n;
+    
+    unsigned char *buf = NULL;
+
+    /* ajDebug("In ajBtreeHybInsertId\n"); */
+
+    key = ajStrNew();
+    
+
+    ajStrAssS(&key,hyb->key1);
+    if(!ajStrLen(key))
+    {
+	ajStrDel(&key);
+	return;
+    }
+
+    ckey = ajStrStr(key);
+    spage = ajBtreeHybFindInsert(cache,ckey);
+    buf = spage->buf;
+
+    GBT_NKEYS(buf,&nkeys);
+    GBT_NODETYPE(buf,&nodetype);
+    
+    order = cache->order;
+
+    arrays = btreeAllocPriArray(cache);
+    karray = arrays->karray;
+    parray = arrays->parray;
+    
+    if(!nkeys)
+    {
+	lbucket  = btreeBucketNew(0);
+	rbucket  = btreeBucketNew(0);
+
+	lblockno = cache->totsize;
+	btreeWriteBucket(cache,lbucket,lblockno);
+
+	rblockno = cache->totsize;
+	btreeWriteBucket(cache,rbucket,rblockno);	
+
+	parray[0] = lblockno;
+	parray[1] = rblockno;
+	ajStrAssS(karray,key);
+	
+	btreeWriteNode(cache,spage,karray,parray,1);
+
+	btreeBucketDel(&lbucket);
+	btreeBucketDel(&rbucket);
+
+	btreeAddToHybBucket(cache,rblockno,hyb);
+
+	btreeDeallocPriArray(cache,arrays);
+
+	ajStrDel(&key);
+
+	return;
+    }
+
+
+    /* Search to see whether entry exists */
+    
+    btreeGetKeys(cache,buf,&karray,&parray);
+
+    i=0;
+    while(i!=nkeys && strcmp(key->Ptr,karray[i]->Ptr)>=0)
+	++i;
+    if(i==nkeys)
+    {
+	if(strcmp(key->Ptr,karray[i-1]->Ptr)<0)
+	    blockno = parray[i-1];
+	else
+	    blockno = parray[i];
+    }
+    else
+	blockno = parray[i];
+
+
+    bucket = btreeReadBucket(cache,blockno);
+    
+    nentries = bucket->Nentries;
+    
+    found = ajFalse;
+
+    for(i=0;i<nentries;++i)
+	if(!strcmp(hyb->key1->Ptr,bucket->Ids[i]->id->Ptr))
+	{
+	    found = ajTrue;
+	    break;
+	}
+    
+
+    if(found)
+    {
+	btid = bucket->Ids[i];
+
+	btreeHybDupInsert(cache,hyb,btid);
+
+	btreeWriteBucket(cache,bucket,blockno);
+	btreeBucketDel(&bucket);
+
+	btreeDeallocPriArray(cache,arrays);
+
+	ajStrDel(&key);
+	
+	return;
+    }
+    else
+	btreeBucketDel(&bucket);
+
+    if(nodetype != BT_ROOT)
+	if((shift = btreeHybInsertShift(cache,&spage,key->Ptr)))
+	    blockno = shift;
+
+    buf = spage->buf;
+
+    n = btreeNumInBucket(cache,blockno);
+
+    if(n == cache->nperbucket)
+    {
+	if(btreeHybReorderBuckets(cache,spage))
+	{
+	    GBT_NKEYS(buf,&nkeys);	    
+	    btreeGetKeys(cache,buf,&karray,&parray);
+
+	    i=0;
+	    while(i!=nkeys && strcmp(key->Ptr,karray[i]->Ptr)>=0)
+		++i;
+
+	    if(i==nkeys)
+	    {
+		if(strcmp(key->Ptr,karray[i-1]->Ptr)<0)
+		    blockno = parray[i-1];
+		else
+		    blockno = parray[i];
+	    }
+	    else
+		blockno = parray[i];
+	}
+	else
+	{
+	    parent = btreeHybSplitLeaf(cache,spage);
+	    spage  = ajBtreeHybFindInsert(cache,ckey);
+	    buf = spage->buf;
+
+	    btreeGetKeys(cache,buf,&karray,&parray);
+
+	    GBT_NKEYS(buf,&nkeys);
+	    i=0;
+	    while(i!=nkeys && strcmp(key->Ptr,karray[i]->Ptr)>=0)
+		++i;
+
+	    if(i==nkeys)
+	    {
+		if(strcmp(key->Ptr,karray[i-1]->Ptr)<0)
+		    blockno = parray[i-1];
+		else
+		    blockno = parray[i];
+	    }
+	    else
+		blockno = parray[i];
+
+	}
+    }
+
+
+    btreeAddToHybBucket(cache,blockno,hyb);
+
+    ++cache->count;
+
+    btreeDeallocPriArray(cache,arrays);
+
+    ajStrDel(&key);
+
+    return;
+}
+
+
+
+
+static void btreeHybDupInsert(AjPBtcache cache, AjPBtHybrid hyb,
+			      AjPBtId btid)
+{
+    AjPBtpage page;
+    AjPBtpage rpage;
+    ajlong secrootpage = 0L;
+    unsigned char *buf;
+    ajlong right = 0L;
+    AjPBtNumId num = NULL;
+
+    /* ajDebug("In btreeHybDupInsert\n"); */
+
+    if(!btid->dups)
+    {
+	btid->dups = 1;
+	AJNEW0(num);
+	
+	num->offset    = btid->offset;
+	num->refoffset = btid->refoffset;
+	num->dbno      = btid->dbno;
+
+	secrootpage = cache->totsize;
+
+	btid->offset = secrootpage;
+
+	ajBtreeCreateRootNode(cache,secrootpage);
+	cache->secrootblock = secrootpage;
+	page = ajBtreeCacheWrite(cache,secrootpage);
+	page->dirty = BT_DIRTY;
+	ajBtreeCacheSync(cache,secrootpage);
+	page->dirty = BT_LOCK;
+	
+	rpage = btreeCacheLocate(cache, 0L);
+	rpage->dirty = BT_LOCK;
+
+	cache->slevel = 0;
+
+	ajBtreeInsertNum(cache,num,page);
+
+	num->offset    = hyb->offset;
+	num->refoffset = hyb->refoffset;
+	num->dbno      = hyb->dbno;
+
+	ajBtreeInsertNum(cache,num,page);
+	++btid->dups;
+
+	AJFREE(num);
+
+	return;
+    }
+    else
+    {
+	cache->secrootblock = btid->offset;
+	page = ajBtreeCacheWrite(cache,cache->secrootblock);
+	page->dirty = BT_LOCK;
+	buf = page->buf;
+	GBT_RIGHT(buf,&right);
+	cache->slevel = (ajint) right;
+
+	AJNEW0(num);
+	
+	num->offset    = hyb->offset;
+	num->refoffset = hyb->refoffset;
+	num->dbno      = hyb->dbno;
+	
+	ajBtreeInsertNum(cache,num,page);
+
+	AJFREE(num);
+	
+	++btid->dups;
+    }
+    
+
+    page->dirty = BT_DIRTY;
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeGetNumKeys *********************************************
+**
+** Get Keys and Pointers from an internal node
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] buf [unsigned char *] page buffer
+** @param [w] keys [ajlong **] keys
+** @param [w] ptrs [ajlong**] ptrs
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeGetNumKeys(AjPBtcache cache, unsigned char *buf,
+			    ajlong **keys, ajlong **ptrs)
+{
+    ajlong *karray = NULL;
+    ajlong *parray = NULL;
+    
+    ajint nkeys = 0;
+    unsigned char *pptr = NULL;
+    ajint    i;
+
+    /* ajDebug("In btreeGetNumKeys\n"); */
+
+
+    karray = *keys;
+    parray = *ptrs;
+
+    pptr = PBT_KEYLEN(buf);
+    GBT_NKEYS(buf,&nkeys);
+    if(!nkeys)
+	ajFatal("GetNumKeys: No keys in node");
+
+    for(i=0;i<nkeys;++i)
+    {
+	BT_GETAJLONG(pptr,&karray[i]);
+	pptr += sizeof(ajlong);
+    }
+
+    for(i=0;i<nkeys;++i)
+    {
+	BT_GETAJLONG(pptr,&parray[i]);
+	pptr += sizeof(ajlong);
+    }
+    
+    BT_GETAJLONG(pptr,&parray[i]);
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeWriteNumNode *******************************************
+**
+** Write an internal node
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] spage [AjPBtpage] buffer
+** @param [r] keys [AjPStr const *] keys
+** @param [r] ptrs [const ajlong*] page pointers
+** @param [r] nkeys [ajint] number of keys
+
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeWriteNumNode(AjPBtcache cache, AjPBtpage spage,
+			      const ajlong *keys, const ajlong *ptrs,
+			      ajint nkeys)
+{
+    unsigned char *pptr   = NULL;
+    unsigned char *buf;
+    
+    ajint tnkeys = 0;
+
+    ajlong aspace   = 0L;
+    ajlong lv       = 0L;
+    ajlong overflow = 0L;
+    ajint i;
+
+
+    /* ajDebug("In btreeWriteNumNode\n"); */
+
+    buf = spage->buf;
+
+    tnkeys = nkeys;
+    SBT_NKEYS(buf,tnkeys);
+
+    pptr = PBT_KEYLEN(buf);
+    aspace = 2 * nkeys * sizeof(ajlong) + sizeof(ajlong);
+    if((pptr+aspace)-buf > cache->pagesize)
+	ajFatal("WriteNumNode: too many keys for available pagesize");
+
+    for(i=0;i<nkeys;++i)
+    {
+	lv = keys[i];
+	BT_SETAJLONG(pptr,lv);
+	pptr += sizeof(ajlong);
+    }
+
+    for(i=0;i<nkeys;++i)
+    {
+	lv = ptrs[i];
+	BT_SETAJLONG(pptr,lv);
+	pptr += sizeof(ajlong);
+    }
+    
+    lv = ptrs[i];
+    BT_SETAJLONG(pptr,lv);
+
+    spage->dirty = BT_DIRTY;
+
+    overflow = 0L;
+    SBT_OVERFLOW(buf,overflow);
+
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeWriteNumBucket *******************************************
+**
+** Write index bucket object to the cache given a disc page number
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] bucket [const AjPBucket] bucket
+** @param [r] pageno [ajlong] page number
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeWriteNumBucket(AjPBtcache cache, const AjPNumBucket bucket,
+			     ajlong pageno)
+{
+    AjPBtpage page      = NULL;
+    unsigned char *buf  = NULL;
+    unsigned char *pptr = NULL;
+
+    ajint   v   = 0;
+    ajint   i   = 0;
+    ajlong lv   = 0L;
+    ajint  nentries = 0;
+    ajlong overflow = 0L;
+
+    /* ajDebug("In btreeWriteNumBucket\n"); */
+
+    if(pageno == cache->totsize)
+    {
+	page = ajBtreeCacheWrite(cache,pageno);
+	page->pageno = cache->totsize;
+	cache->totsize += cache->pagesize;
+	buf = page->buf;
+	overflow = 0L;
+	lv = overflow;
+	SBT_BUCKOVERFLOW(buf,lv);
+    }
+    else
+    {
+	page = ajBtreeCacheRead(cache,pageno);
+	buf = page->buf;
+	GBT_BUCKOVERFLOW(buf,&overflow);
+    }
+
+    v = BT_BUCKET;
+    SBT_BUCKNODETYPE(buf,v);
+    page->dirty = BT_LOCK;
+
+    nentries = bucket->Nentries;
+    v = nentries;
+    SBT_BUCKNENTRIES(buf,v);
+    
+    pptr = PBT_BUCKKEYLEN(buf);
+
+    for(i=0;i<nentries;++i)
+    {
+	lv = bucket->NumId[i]->offset;
+	BT_SETAJLONG(pptr,lv);
+	pptr += sizeof(ajlong);
+	lv = bucket->NumId[i]->refoffset;
+	BT_SETAJLONG(pptr,lv);
+	pptr += sizeof(ajlong);
+	v = bucket->NumId[i]->dbno;
+	BT_SETAJINT(pptr,v);
+	pptr += sizeof(ajint);
+    }
+    
+    lv = 0L;
+    SBT_BUCKOVERFLOW(buf,lv);
+    page->dirty = BT_DIRTY;
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeReadNumBucket *********************************************
+**
+** Constructor for index bucket given a disc page number
+** Creates one empty key slot for possible addition
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] pageno [ajlong] page number
+**
+** @return [AjPNumBucket] bucket
+** @@
+******************************************************************************/
+
+static AjPNumBucket btreeReadNumBucket(AjPBtcache cache, ajlong pageno)
+{
+    AjPNumBucket bucket    = NULL;
+    AjPBtpage page      = NULL;
+    unsigned char *buf  = NULL;
+    unsigned char *pptr = NULL;
+    ajint  nodetype  = 0;
+    ajint  nentries  = 0;
+    ajlong overflow  = 0L;
+    ajint  dirtysave = 0;
+    
+    ajint  i;
+    
+    /* ajDebug("In btreeReadNumBucket\n"); */
+
+    if(pageno == cache->secrootblock)
+	ajFatal("ReadNumBucket: cannot read bucket from a root page");
+
+    page = ajBtreeCacheRead(cache,pageno);
+    dirtysave = page->dirty;
+    page->dirty = BT_LOCK;
+    buf = page->buf;
+
+    GBT_BUCKNODETYPE(buf,&nodetype);
+    if(nodetype != BT_BUCKET)
+	ajFatal("ReadNumBucket: Nodetype mismatch. Not bucket (%d)",nodetype);
+
+    GBT_BUCKNENTRIES(buf,&nentries);
+    if(nentries > cache->snperbucket)
+	ajFatal("ReadNumBucket: Bucket too full");
+
+    GBT_BUCKOVERFLOW(buf,&overflow);
+
+    AJNEW0(bucket);
+    bucket->NodeType = nodetype;
+    bucket->Nentries = nentries;
+    bucket->Overflow = overflow;
+
+    AJCNEW0(bucket->NumId,nentries+1);
+    for(i=0;i<nentries;++i)
+	AJNEW0(bucket->NumId[i]);
+    
+
+    pptr = PBT_BUCKKEYLEN(buf);
+
+    for(i=0;i<nentries;++i)
+    {
+	BT_GETAJLONG(pptr,&bucket->NumId[i]->offset);
+	pptr += sizeof(ajlong);
+	BT_GETAJLONG(pptr,&bucket->NumId[i]->refoffset);
+	pptr += sizeof(ajlong);
+	BT_GETAJINT(pptr,&bucket->NumId[i]->dbno);
+	pptr += sizeof(ajint);
+    }
+    
+    page->dirty = dirtysave;
+
+    return bucket;
+}
+
+
+
+
+/* @funcstatic btreeNumBucketDel *********************************************
+**
+** Delete a bucket object
+**
+** @param [w] thys [AjPNumBucket*] bucket
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeNumBucketDel(AjPNumBucket *thys)
+{
+    AjPNumBucket pthis = NULL;
+    int i;
+    
+    
+    /* ajDebug("In btreeNumBucketDel\n"); */
+
+    if(!thys || !*thys)
+	return;
+
+    pthis = *thys;
+
+    if(pthis->Nentries)
+    {
+	for(i=0;i<pthis->Nentries;++i)
+	    AJFREE(pthis->NumId[i]);
+    
+	AJFREE(pthis->NumId);
+    }
+    
+    
+    AJFREE(pthis);
+
+    *thys = NULL;
+
+    return;
+}
+
+
+
+
+/* @func ajBtreeNumFindInsert ***********************************************
+**
+** Find the node that should contain a new key for insertion
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] key [const ajlong] key to search for 
+**
+** @return [AjPBtpage] leaf node where item should be inserted
+** @@
+******************************************************************************/
+
+AjPBtpage ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key)
+{
+    AjPBtpage root = NULL;
+    AjPBtpage ret  = NULL;
+
+    /* ajDebug("In ajBtreeNumFindInsert\n"); */
+
+    /* The root node should always be in the cache (BT_LOCKed) */
+    root = btreeCacheLocate(cache,cache->secrootblock);
+
+    /* ajDebug("cache->slevel = %d root=%d\n",cache->slevel,(ajint)root); */
+    
+
+    if(!cache->slevel)
+	return root;
+    
+    ret = btreeNumFindINode(cache,root,key);
+
+    return ret;
+}
+
+
+
+
+/* @funcstatic btreeNumFindINode **********************************************
+**
+** Recursive search for insert node in a secondary tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] page
+** @param [r] item [const ajlong] key to search for 
+**
+** @return [AjPBtpage] leaf node where item should be inserted
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeNumFindINode(AjPBtcache cache, AjPBtpage page,
+				   const ajlong item)
+{
+    AjPBtpage ret = NULL;
+    AjPBtpage pg  = NULL;
+
+    unsigned char *buf = NULL;
+    ajint status       = 0;
+    ajint ival         = 0;
+
+    /* ajDebug("In btreeNumFindINode\n"); */
+    
+    ret = page;
+    buf = page->buf;
+    GBT_NODETYPE(buf,&ival);
+    if(ival != BT_LEAF)
+    {
+	status = ret->dirty;
+	ret->dirty = BT_LOCK;	/* Lock in case of lots of overflow pages */
+	pg = btreeNumPageFromKey(cache,buf,item);
+	ret->dirty = status;
+	ret = btreeNumFindINode(cache,pg,item);
+    }
+    
+    return ret;
+}
+
+
+
+
+/* @funcstatic btreeNumPageFromKey *******************************************
+**
+** Return next lower index page given a key in a secondary tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] buf [unsigned char *] page buffer
+** @param [r] key [const ajlong] key to search for 
+**
+** @return [AjPBtpage] pointer to a page
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeNumPageFromKey(AjPBtcache cache, unsigned char *buf,
+				     const ajlong key)
+{
+    unsigned char *rootbuf = NULL;
+    ajint nkeys = 0;
+    ajint order = 0;
+    ajint i;
+    
+    ajlong blockno = 0L;
+    ajlong *karray = NULL;
+    ajlong *parray = NULL;
+    AjPBtpage page = NULL;
+    AjPBtMem array = NULL;
+
+    /* ajDebug("In btreeNumPageFromKey\n"); */
+    
+    rootbuf = buf;
+
+
+    GBT_NKEYS(rootbuf,&nkeys);
+    order = cache->sorder;
+
+    array = btreeAllocSecArray(cache);
+    karray = array->overflows;
+    parray = array->parray;
+    
+    btreeGetNumKeys(cache,rootbuf,&karray,&parray);
+    i = 0;
+    while(i!=nkeys && key >= karray[i])
+	++i;
+    if(i==nkeys)
+    {
+	if(key < karray[i-1])
+	    blockno = parray[i-1];
+	else
+	    blockno = parray[i];
+    }
+    else
+	blockno = parray[i];
+
+    btreeDeallocSecArray(cache,array);
+
+    page =  ajBtreeCacheRead(cache,blockno);
+
+    return page;
+}
+
+
+
+
+/* @funcstatic btreeAddToNumBucket *******************************************
+**
+** Add offset info to a bucket
+** Only called if there is room in the bucket
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] pageno [ajlong] page number of bucket
+** @param [r] num [const AjPBtNumId] ID info
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeAddToNumBucket(AjPBtcache cache, ajlong pageno,
+				const AjPBtNumId num)
+{
+    AjPNumBucket bucket = NULL;
+    ajint nentries;
+    
+    /* ajDebug("In btreeAddToNumBucket\n"); */
+
+    bucket   = btreeReadNumBucket(cache,pageno);
+
+    nentries = bucket->Nentries;
+
+    /* Reading a bucket always gives one extra ID position */
+
+    AJNEW0(bucket->NumId[nentries]);
+    bucket->NumId[nentries]->offset    = num->offset;
+    bucket->NumId[nentries]->refoffset = num->refoffset;
+    bucket->NumId[nentries]->dbno      = num->dbno;
+
+    
+    ++bucket->Nentries;
+
+    btreeWriteNumBucket(cache,bucket,pageno);
+
+    btreeNumBucketDel(&bucket);
+    
+    return;
+}
+
+
+
+
+/* @funcstatic btreeNumInNumBucket *******************************************
+**
+** Return number of entries in a bucket
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] pageno [ajlong] page number
+**
+** @return [ajint] Number of entries in bucket
+** @@
+******************************************************************************/
+
+static ajint btreeNumInNumBucket(AjPBtcache cache, ajlong pageno)
+{
+    AjPBtpage page     = NULL;
+    unsigned char *buf = NULL;
+    ajint  nodetype    = 0;
+    ajint  nentries    = 0;
+    
+    /* ajDebug("In btreeNumInNumBucket\n"); */
+    
+    if(pageno == cache->secrootblock)
+	ajFatal("NumInNumBucket: Attempt to read bucket from root page\n");
+
+    page  = ajBtreeCacheRead(cache,pageno);
+
+    buf = page->buf;
+
+    GBT_BUCKNODETYPE(buf,&nodetype);
+    if(nodetype != BT_BUCKET)
+	ajFatal("NumInNumBucket: NodeType mismatch. Not bucket (%d)",
+		nodetype);
+    
+    GBT_BUCKNENTRIES(buf,&nentries);
+
+    return nentries;
+}
+
+
+
+
+/* @funcstatic btreeNumBucketNew *********************************************
+**
+** Construct a bucket object
+**
+** @param [r] n [ajint] Number of IDs
+**
+** @return [AjPBucket] initialised disc block cache structure
+** @@
+******************************************************************************/
+
+static AjPNumBucket btreeNumBucketNew(ajint n)
+{
+    AjPNumBucket bucket = NULL;
+    ajint i;
+
+    /* ajDebug("In btreeNumBucketNew\n"); */
+    
+    AJNEW0(bucket);
+
+    if(n)
+    {
+	AJCNEW0(bucket->NumId,n);
+	for(i=0;i<n;++i)
+	    AJNEW0(bucket->NumId[i]);
+    }
+
+    bucket->NodeType = BT_BUCKET;
+    bucket->Nentries = n;
+    bucket->Overflow = 0L;
+    
+    return bucket;
+}
+
+
+
+
+/* @funcstatic btreeReorderNumBuckets *****************************************
+**
+** Re-order leaf buckets
+** Must only be called if one of the buckets is full
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] leaf [AjPBtpage] leaf page
+**
+** @return [AjBool] true if reorder was successful i.e. leaf not full
+** @@
+******************************************************************************/
+
+static AjBool btreeReorderNumBuckets(AjPBtcache cache, AjPBtpage leaf)
+{
+    ajint nkeys = 0;
+    unsigned char *lbuf = NULL;
+
+    ajlong *keys        = NULL;
+    ajlong *ptrs        = NULL;
+
+    AjPNumBucket *buckets  = NULL;
+    
+    ajint i = 0;
+    ajint j = 0;
+    
+    ajint order;
+    ajint bentries      = 0;
+    ajint totalkeys     = 0;
+    ajint nperbucket    = 0;
+    ajint maxnperbucket = 0;
+    ajint count         = 0;
+    ajint keylimit      = 0;
+    ajint bucketn       = 0;
+    ajint bucketlimit   = 0;
+    ajint nodetype      = 0;
+    
+    AjPList idlist    = NULL;
+    ajint   dirtysave = 0;
+    AjPBtNumId bid       = NULL;
+    AjPNumBucket cbucket = NULL;
+    AjPBtNumId cid       = NULL;
+
+    ajint   v = 0;
+    AjPBtMem array = NULL;
+    
+    /* ajDebug("In btreeReorderNumBuckets\n"); */
+
+    dirtysave = leaf->dirty;
+
+    leaf->dirty = BT_LOCK;
+    lbuf = leaf->buf;
+
+    GBT_NODETYPE(lbuf,&nodetype);
+
+    order = cache->sorder;
+    nperbucket = cache->snperbucket;
+    
+
+    array = btreeAllocSecArray(cache);
+    keys  = array->overflows;
+    ptrs  = array->parray;
+
+    /* Read keys/ptrs */
+
+    btreeGetNumKeys(cache,lbuf,&keys,&ptrs);
+
+    GBT_NKEYS(lbuf,&nkeys);
+
+
+    if(!nkeys)
+	ajFatal("NumBucketReorder: Attempt to reorder empty leaf");
+
+    for(i=0;i<nkeys;++i)
+	totalkeys += btreeNumInNumBucket(cache,ptrs[i]);
+    totalkeys += btreeNumInNumBucket(cache,ptrs[i]);
+
+    /* Set the number of entries per bucket to approximately half full */
+    maxnperbucket = nperbucket >> 1;
+
+    if(!maxnperbucket)
+	++maxnperbucket;
+
+    /* Work out the number of new buckets needed */
+    bucketn = (totalkeys / maxnperbucket);
+    if(totalkeys % maxnperbucket)
+	++bucketn;
+    
+    if(bucketn > order)
+    {
+	btreeDeallocSecArray(cache,array);
+	
+	leaf->dirty = dirtysave;
+	return ajFalse;
+    }
+    
+
+    /* Read buckets */
+    AJCNEW0(buckets,nkeys+1);
+    keylimit = nkeys + 1;
+    
+    for(i=0;i<keylimit;++i)
+	buckets[i] = btreeReadNumBucket(cache,ptrs[i]);
+
+
+    /* Read IDs from all buckets and push to list and sort (increasing id) */
+    idlist  = ajListNew();
+    
+    for(i=0;i<keylimit;++i)
+    {
+	bentries = buckets[i]->Nentries;
+	for(j=0;j<bentries;++j)
+	    ajListPush(idlist,(void *)buckets[i]->NumId[j]);
+	
+	AJFREE(buckets[i]->NumId);
+	AJFREE(buckets[i]);
+    }
+    ajListSort(idlist,btreeNumIdCompare);
+    AJFREE(buckets);
+
+    cbucket = btreeNumBucketNew(maxnperbucket);
+    bucketlimit = bucketn - 1;
+    
+    for(i=0;i<bucketlimit;++i)
+    {
+	cbucket->Nentries = 0;
+
+	count = 0;
+	while(count!=maxnperbucket)
+	{
+	    ajListPop(idlist,(void **)&bid);
+	    
+	    cid = cbucket->NumId[count];
+	    cid->dbno = bid->dbno;
+	    cid->offset = bid->offset;
+	    cid->refoffset = bid->refoffset;
+	    
+	    ++cbucket->Nentries;
+	    ++count;
+	    AJFREE(bid);
+	}
+
+
+	ajListPeek(idlist,(void **)&bid);
+	keys[i] = bid->offset;
+
+	if(!ptrs[i])
+	    ptrs[i] = cache->totsize;
+	btreeWriteNumBucket(cache,cbucket,ptrs[i]);
+    }
+
+
+    /* Deal with greater-than bucket */
+
+    cbucket->Nentries = 0;
+
+    count = 0;
+    while(ajListPop(idlist,(void **)&bid))
+    {
+	cid = cbucket->NumId[count];
+	cid->dbno = bid->dbno;
+	cid->offset = bid->offset;
+	cid->refoffset = bid->refoffset;
+	
+	++cbucket->Nentries;
+	++count;
+	AJFREE(bid);
+    }
+    
+    
+    if(!ptrs[i])
+	ptrs[i] = cache->totsize;
+    btreeWriteNumBucket(cache,cbucket,ptrs[i]);
+
+    cbucket->Nentries = maxnperbucket;
+    btreeNumBucketDel(&cbucket);
+
+    /* Now write out a modified leaf with new keys/ptrs */
+
+    nkeys = bucketn - 1;
+    v = nkeys;
+    SBT_NKEYS(lbuf,v);
+
+    btreeWriteNumNode(cache,leaf,keys,ptrs,nkeys);
+
+    leaf->dirty = BT_DIRTY;
+    if(nodetype == BT_ROOT)
+	leaf->dirty = BT_LOCK;
+    
+    btreeDeallocSecArray(cache,array);
+
+    ajListDel(&idlist);
+
+    return ajTrue;
+}
+
+
+
+
+/* @funcstatic btreeNumNodeIsFull *****************************************
+**
+** Tests whether a node is full of keys
+**
+** @param [r] cache [const AjPBtcache] cache
+** @param [u] page [AjPBtpage] original page
+**
+** @return [AjBool] true if full
+** @@
+******************************************************************************/
+
+static AjBool btreeNumNodeIsFull(const AjPBtcache cache, AjPBtpage page)
+{
+    unsigned char *buf = NULL;
+    ajint nkeys = 0;
+
+    /* ajDebug("In btreeNumNodeIsFull\n"); */
+
+    buf = page->buf;
+    GBT_NKEYS(buf,&nkeys);
+
+    if(nkeys == cache->sorder - 1)
+	return ajTrue;
+
+    return ajFalse;
+}
+
+
+
+
+/* @funcstatic btreeNumInsertNonFull *****************************************
+**
+** Insert a key into a non-full node
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] original page
+** @param [r] key [const ajlong] key to insert
+** @param [r] less [ajlong] less-than pointer
+** @param [r] greater [ajlong] greater-than pointer
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeNumInsertNonFull(AjPBtcache cache, AjPBtpage page,
+				  const ajlong key, ajlong less,
+				  ajlong greater)
+{
+    unsigned char *buf = NULL;
+    ajlong *karray     = NULL;
+    ajlong *parray     = NULL;
+    ajint nkeys  = 0;
+    ajint order  = 0;
+    ajint ipos   = 0;
+    ajint i;
+    ajint count  = 0;
+
+    ajlong lv = 0L;
+    ajint  v  = 0;
+    AjPBtMem array = NULL;    
+
+    AjPBtpage ppage = NULL;
+    ajlong pageno   = 0L;
+
+    ajint nodetype = 0;
+    
+    /* ajDebug("In btreeNumInsertNonFull\n"); */
+
+    order = cache->sorder;
+
+    array = btreeAllocSecArray(cache);
+    karray  = array->overflows;
+    parray  = array->parray;
+
+
+    buf = page->buf;
+    GBT_NKEYS(buf,&nkeys);
+    GBT_NODETYPE(buf,&nodetype);
+    
+    btreeGetNumKeys(cache,buf,&karray,&parray);
+
+    i = 0;
+    while(i!=nkeys && key >= karray[i])
+	++i;
+
+    ipos = i;
+
+    count = nkeys - ipos;
+    
+
+    if(ipos == nkeys)
+    {
+	karray[ipos] = key;
+	parray[ipos+1] = greater;
+	parray[ipos]   = less;
+    }
+    else
+    {
+	parray[nkeys+1] = parray[nkeys];
+
+	for(i=nkeys-1; count>0; --count, --i)
+	{
+	    karray[i+1] = karray[i];
+	    parray[i+1] = parray[i];
+	}
+
+	karray[ipos] = key;
+	parray[ipos] = less;
+	parray[ipos+1] = greater;
+    }
+
+    ++nkeys;
+    v = nkeys;
+    SBT_NKEYS(buf,v);
+
+    btreeWriteNumNode(cache,page,karray,parray,nkeys);
+    if(nodetype == BT_ROOT)
+	page->dirty = BT_LOCK;
+
+    pageno = page->pageno;
+    ppage = ajBtreeCacheRead(cache,less);
+    lv = pageno;
+    SBT_PREV(ppage->buf,lv);
+    ppage->dirty = BT_DIRTY;
+    ppage = ajBtreeCacheRead(cache,greater);
+    lv = pageno;
+    SBT_PREV(ppage->buf,lv);
+    ppage->dirty = BT_DIRTY;
+    
+
+    btreeDeallocSecArray(cache,array);
+
+    if(nodetype != BT_ROOT)
+	btreeNumKeyShift(cache,page);
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeNumInsertKey **********************************************
+**
+** Insert a key into a potentially full node
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] page [AjPBtpage] original page
+** @param [r] key [const ajlong] key to insert
+** @param [r] less [ajlong] less-than pointer
+** @param [r] greater [ajlong] greater-than pointer
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeNumInsertKey(AjPBtcache cache, AjPBtpage page,
+			      const ajlong key, ajlong less, ajlong greater)
+{
+    unsigned char *lbuf = NULL;
+    unsigned char *rbuf = NULL;
+    unsigned char *tbuf = NULL;
+    ajlong *karray      = NULL;
+    ajlong *parray      = NULL;
+    ajlong *tkarray     = NULL;
+    ajlong *tparray     = NULL;
+    ajint nkeys    = 0;
+    ajint order    = 0;
+    ajint keypos   = 0;
+    ajint rkeyno   = 0;
+    
+    ajint i = 0;
+    ajint n = 0;
+    
+    ajint nodetype  = 0;
+    AjPBtpage ipage = NULL;
+    AjPBtpage lpage = NULL;
+    AjPBtpage rpage = NULL;
+    AjPBtpage tpage = NULL;
+
+    ajlong blockno  = 0L;
+    ajlong rblockno = 0L;
+    ajlong lblockno = 0L;
+    ajlong mediankey  = 0L;
+    ajlong medianless = 0L;
+    ajlong mediangtr  = 0L;
+    ajlong overflow   = 0L;
+    ajlong prev       = 0L;
+    ajint  totlen     = 0;
+    
+    ajlong lv = 0L;
+    ajint  v  = 0;
+    AjPBtMem array  = NULL;    
+    AjPBtMem array2 = NULL;    
+    
+    /* ajDebug("In btreeNumInsertKey\n"); */
+
+    if(!btreeNumNodeIsFull(cache,page))
+    {
+	btreeNumInsertNonFull(cache,page,key,less,greater);
+	return;
+    }
+    
+    order = cache->sorder;
+    lbuf = page->buf;
+    GBT_NODETYPE(lbuf,&nodetype);
+    page->dirty = BT_LOCK;
+
+    if(nodetype == BT_ROOT)
+    {
+	array = btreeAllocSecArray(cache);
+	karray  = array->overflows;
+	parray  = array->parray;
+
+	btreeNumSplitRoot(cache);
+
+	if(page->pageno)
+	    page->dirty = BT_DIRTY;
+	btreeGetNumKeys(cache,lbuf,&karray,&parray);
+
+	if(key < karray[0])
+	    blockno = parray[0];
+	else
+	    blockno = parray[1];
+	ipage = ajBtreeCacheRead(cache,blockno);
+	btreeNumInsertNonFull(cache,ipage,key,less,greater);
+
+	btreeDeallocSecArray(cache,array);
+	return;
+    }
+
+
+    array = btreeAllocSecArray(cache);
+    karray  = array->overflows;
+    parray  = array->parray;
+    
+    array2 = btreeAllocSecArray(cache);
+    tkarray  = array2->overflows;
+    tparray  = array2->parray;
+
+    
+    lpage = page;
+    lbuf = lpage->buf;
+    
+    btreeGetNumKeys(cache,lbuf,&karray,&parray);
+
+    GBT_BLOCKNUMBER(lbuf,&lblockno);
+    rblockno = cache->totsize;
+    rpage = ajBtreeCacheWrite(cache,rblockno);
+    rpage->dirty = BT_LOCK;
+    rpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+    rbuf = rpage->buf;
+    lv = rblockno;
+    SBT_BLOCKNUMBER(rbuf,lv);
+
+    
+    GBT_PREV(lbuf,&prev);
+    lv = prev;
+    SBT_PREV(rbuf,lv);
+
+    nkeys = order - 1;
+    keypos = nkeys / 2;
+    if(!(nkeys % 2))
+	--keypos;
+
+    mediankey = karray[keypos];
+    medianless = lblockno;
+    mediangtr  = rblockno;
+
+
+    GBT_NODETYPE(lbuf,&nodetype);
+    v = nodetype;
+    SBT_NODETYPE(rbuf,v);
+    lv = overflow;
+    SBT_OVERFLOW(rbuf,lv);
+
+
+    totlen = 0;
+    for(i=0;i<keypos;++i)
+    {
+	tkarray[i] = karray[i];
+	tparray[i] = parray[i];
+    }
+    tparray[i] = parray[i];
+
+    n = i;
+    v = n;
+    SBT_NKEYS(lbuf,v);
+    btreeWriteNumNode(cache,lpage,tkarray,tparray,i);
+
+
+
+    for(i=0;i<n+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = lblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+
+    totlen = 0;
+    for(i=keypos+1;i<nkeys;++i)
+    {
+	tkarray[i-(keypos+1)] = karray[i];
+	tparray[i-(keypos+1)] = parray[i];
+    }
+    tparray[i-(keypos+1)] = parray[i];
+
+    rkeyno = (nkeys-keypos) - 1;
+    v = rkeyno;
+    SBT_NKEYS(rbuf,v);
+    rpage->dirty = BT_DIRTY;
+    btreeWriteNumNode(cache,rpage,tkarray,tparray,rkeyno);
+
+
+    for(i=0;i<rkeyno+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = rblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+
+    ipage = rpage;
+    if(key < mediankey)
+	ipage = lpage;
+
+    btreeNumInsertNonFull(cache,ipage,key,less,greater);
+
+
+    btreeDeallocSecArray(cache,array);
+    btreeDeallocSecArray(cache,array2);
+
+    ipage = ajBtreeCacheRead(cache,prev);
+
+    btreeNumInsertKey(cache,ipage,mediankey,medianless,mediangtr);
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeNumSplitRoot *****************************************
+**
+** Split s secondary root node
+**
+** @param [u] cache [AjPBtcache] cache
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeNumSplitRoot(AjPBtcache cache)
+{
+    AjPBtpage rootpage = NULL;
+    AjPBtpage rpage    = NULL;
+    AjPBtpage lpage    = NULL;
+    AjPBtpage tpage    = NULL;
+
+    ajlong *karray  = NULL;
+    ajlong *tkarray = NULL;
+    ajlong *parray  = NULL;
+    ajlong *tparray = NULL;
+
+    ajint order  = 0;
+    ajint nkeys  = 0;
+    ajint keypos = 0;
+    
+    ajlong rblockno = 0L;
+    ajlong lblockno = 0L;
+
+    ajlong right;
+    
+    ajint  i;
+
+    unsigned char *rootbuf = NULL;
+    unsigned char *rbuf    = NULL;
+    unsigned char *lbuf    = NULL;
+    unsigned char *tbuf    = NULL;
+    
+    ajint nodetype  = 0;
+    ajlong overflow = 0L;
+    ajlong zero     = 0L;
+    ajint rkeyno    = 0;
+    ajint n         = 0;
+
+    ajlong lv = 0L;
+    ajint  v  = 0;
+
+    AjPBtMem array  = NULL;    
+    AjPBtMem array2 = NULL;    
+    
+    
+    /* ajDebug("In btreeNumSplitRoot\n"); */
+
+    order = cache->sorder;
+
+    array = btreeAllocSecArray(cache);
+    karray  = array->overflows;
+    parray  = array->parray;
+    
+    array2 = btreeAllocSecArray(cache);
+    tkarray  = array2->overflows;
+    tparray  = array2->parray;
+
+
+    rootpage = btreeCacheLocate(cache,cache->secrootblock);
+    rootbuf = rootpage->buf;
+
+    nkeys = order - 1;
+
+    keypos = nkeys / 2;
+    if(!(nkeys % 2))
+	--keypos;
+
+
+    rblockno = cache->totsize;
+    rpage = ajBtreeCacheWrite(cache,rblockno);
+    rpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+    rpage->dirty = BT_LOCK;
+    
+    lblockno = cache->totsize;
+    lpage = ajBtreeCacheWrite(cache,lblockno);
+    lpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+
+    lv = rblockno;
+    SBT_BLOCKNUMBER(rpage->buf,lv);
+    lv = lblockno;
+    SBT_BLOCKNUMBER(lpage->buf,lv);
+
+    /* Comment this next block out after the beta test */
+    if(!cache->slevel)
+    {
+	fprintf(stderr,"btreeSplitRootSec: Shouldn't get here\n");
+	exit(0);
+	lv = zero;
+	SBT_LEFT(lpage->buf,lv);
+	lv = rblockno;
+	SBT_RIGHT(lpage->buf,lv);
+	lv = lblockno;
+	SBT_LEFT(rpage->buf,lv);
+	lv = zero;
+	SBT_RIGHT(rpage->buf,lv);
+    }
+
+    btreeGetNumKeys(cache,rootbuf,&karray,&parray);
+
+    /* Get key for root node and write new root node */
+    tkarray[0] = karray[keypos];
+    tparray[0] = lblockno;
+    tparray[1] = rblockno;
+    
+
+    n = 1;
+    v = n;
+    SBT_NKEYS(rootbuf,v);
+    btreeWriteNumNode(cache,rootpage,tkarray,tparray,1);
+    right = (ajlong)(cache->slevel + 1);
+    SBT_RIGHT(rootbuf,right);
+
+    rootpage->dirty = BT_LOCK;
+
+    rbuf = rpage->buf;
+    lbuf = lpage->buf;
+    
+    if(cache->slevel)
+	nodetype = BT_INTERNAL;
+    else
+	nodetype = BT_LEAF;
+
+    v = nodetype;
+    SBT_NODETYPE(rbuf,v);
+    v = nodetype;
+    SBT_NODETYPE(lbuf,v);
+    lv = overflow;
+    SBT_OVERFLOW(rbuf,lv);
+    lv = cache->secrootblock;
+    SBT_PREV(rbuf,lv);
+    lv = overflow;
+    SBT_OVERFLOW(lbuf,lv);
+    lv = cache->secrootblock;
+    SBT_PREV(lbuf,lv);
+
+    for(i=0;i<keypos;++i)
+    {
+	tkarray[i] = karray[i];
+	tparray[i] = parray[i];
+    }
+    tparray[i] = parray[i];
+
+    n = i;
+    v = n;
+    SBT_NKEYS(lbuf,v);
+    btreeWriteNumNode(cache,lpage,tkarray,tparray,i);
+
+    for(i=0;i<n+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = lblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+    for(i=keypos+1;i<nkeys;++i)
+    {
+	tkarray[i-(keypos+1)] = karray[i];
+	tparray[i-(keypos+1)] = parray[i];
+    }
+    tparray[i-(keypos+1)] = parray[i];
+
+    rkeyno = (nkeys-keypos) - 1;
+    v = rkeyno;
+    SBT_NKEYS(rbuf,v);
+    rpage->dirty = BT_DIRTY;
+    btreeWriteNumNode(cache,rpage,tkarray,tparray,rkeyno);
+
+    for(i=0;i<rkeyno+1;++i)
+    {
+	tpage = ajBtreeCacheRead(cache,tparray[i]);
+	tbuf = tpage->buf;
+	lv = rblockno;
+	SBT_PREV(tbuf,lv);
+	tpage->dirty = BT_DIRTY;
+    }
+
+
+    ++cache->slevel;
+
+    btreeDeallocSecArray(cache,array);
+    btreeDeallocSecArray(cache,array2);
+    
+    return;
+}
+
+
+
+
+/* @funcstatic btreeNumKeyShift ********************************************
+**
+** Rebalance Nodes on insertion
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] tpage [AjPBtpage] page
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+static void btreeNumKeyShift(AjPBtcache cache, AjPBtpage tpage)
+{
+    unsigned char *tbuf = NULL;
+    unsigned char *pbuf = NULL;
+    unsigned char *sbuf = NULL;
+    unsigned char *buf  = NULL;
+
+    AjPBtpage ppage = NULL;
+    AjPBtpage spage = NULL;
+    AjPBtpage page  = NULL;
+
+    ajint tkeys = 0;
+    ajint pkeys = 0;
+    ajint skeys = 0;
+    ajint order = 0;
+    
+    ajint i;
+    
+    ajlong parent  = 0L;
+    
+    ajlong *kTarray = NULL;
+    ajlong *kParray = NULL;
+    ajlong *kSarray = NULL;
+    ajlong *pTarray = NULL;
+    ajlong *pParray = NULL;
+    ajlong *pSarray = NULL;
+
+    ajint pkeypos = 0;
+    ajint minsize = 0;
+
+    ajlong lv = 0L;
+
+    AjPBtMem array  = NULL;    
+    AjPBtMem array2 = NULL;    
+    AjPBtMem array3 = NULL;    
+    
+    /* ajDebug("In btreeNumKeyShift\n"); */
+    
+    tbuf = tpage->buf;
+
+    GBT_PREV(tbuf,&parent);
+    GBT_NKEYS(tbuf,&tkeys);
+
+    order = cache->sorder;
+    minsize = order / 2;
+    if(order % 2)
+	++minsize;
+
+    if(tkeys <= minsize)
+	return;
+
+    
+    ppage = ajBtreeCacheRead(cache,parent);
+    pbuf = ppage->buf;
+    GBT_NKEYS(pbuf,&pkeys);
+    
+    array = btreeAllocSecArray(cache);
+    kParray  = array->overflows;
+    pParray  = array->parray;
+    
+    array2 = btreeAllocSecArray(cache);
+    kSarray  = array2->overflows;
+    pSarray  = array2->parray;
+
+    array3 = btreeAllocSecArray(cache);
+    kTarray  = array3->overflows;
+    pTarray  = array3->parray;
+
+
+    btreeGetNumKeys(cache,tbuf,&kTarray,&pTarray);
+    GBT_NKEYS(tbuf,&tkeys);
+
+
+    btreeGetNumKeys(cache,pbuf,&kParray,&pParray);
+    i=0;
+    while(pParray[i] != tpage->pageno)
+	++i;
+
+    if(i) /* There is another leaf to the left */
+    {
+	pkeypos = i-1;
+	spage = ajBtreeCacheRead(cache,pParray[pkeypos]);
+	sbuf = spage->buf;
+	GBT_NKEYS(sbuf,&skeys);
+	
+    }
+
+    if(i && skeys != order-1) /* There is space in the left leaf */
+    {
+	if(skeys)
+	    btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
+
+	kSarray[skeys] = kParray[pkeypos];
+	pSarray[skeys+1] = pTarray[0];
+	++skeys;
+	--tkeys;
+	kParray[pkeypos] = kTarray[0];
+	for(i=0;i<tkeys;++i)
+	{
+	    kTarray[i] = kTarray[i+1];
+	    pTarray[i] = pTarray[i+1];
+	}
+	pTarray[i] = pTarray[i+1];
+	pTarray[i+1] = 0L;
+	
+	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
+	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
+	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
+	if(!ppage->pageno)
+	    ppage->dirty = BT_LOCK;
+
+	page = ajBtreeCacheRead(cache,pSarray[skeys]);
+	buf = page->buf;
+	lv = spage->pageno;
+	SBT_PREV(buf,lv);
+	page->dirty = BT_DIRTY;
+
+
+	btreeDeallocSecArray(cache,array);
+	btreeDeallocSecArray(cache,array2);
+	btreeDeallocSecArray(cache,array3);
+
+	return;
+    }
+
+
+
+    if(i != pkeys)	/* There is a right node */
+    {
+	pkeypos = i;
+	spage = ajBtreeCacheRead(cache,pParray[pkeypos+1]);
+	sbuf = spage->buf;
+	GBT_NKEYS(sbuf,&skeys);
+    }
+
+
+    if(i != pkeys && skeys != order-1) /* Space in the right node */
+    {
+	if(skeys)
+	    btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
+
+	pSarray[skeys+1] = pSarray[skeys];
+	for(i=skeys-1;i>-1;--i)
+	{
+	    kSarray[i+1] = kSarray[i];
+	    pSarray[i+1] = pSarray[i];
+	}
+	kSarray[0] = kParray[pkeypos];
+	pSarray[0] = pTarray[tkeys];
+	kParray[pkeypos] = kTarray[tkeys-1];
+	++skeys;
+	--tkeys;
+	pTarray[tkeys+1] = 0L;
+	
+	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
+	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
+	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
+	if(!ppage->pageno)
+	    ppage->dirty = BT_LOCK;
+
+	page = ajBtreeCacheRead(cache,pSarray[0]);
+	buf = page->buf;
+	lv = spage->pageno;
+	SBT_PREV(buf,lv);
+	page->dirty = BT_DIRTY;
+
+	btreeDeallocSecArray(cache,array);
+	btreeDeallocSecArray(cache,array2);
+	btreeDeallocSecArray(cache,array3);
+
+	return;
+    }
+
+
+    btreeDeallocSecArray(cache,array);
+    btreeDeallocSecArray(cache,array2);
+    btreeDeallocSecArray(cache,array3);
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeNumInsertShift ********************************************
+**
+** Rebalance buckets on insertion
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] retpage [AjPBtpage*] page
+** @param [r] key [const ajlong] key
+**
+** @return [ajlong] bucket block or 0L if shift not posible 
+** @@
+******************************************************************************/
+
+static ajlong btreeNumInsertShift(AjPBtcache cache, AjPBtpage *retpage,
+				  ajlong key)
+{
+    unsigned char *tbuf = NULL;
+    unsigned char *pbuf = NULL;
+    unsigned char *sbuf = NULL;
+
+    AjPBtpage ppage = NULL;
+    AjPBtpage spage = NULL;
+    AjPBtpage tpage = NULL;
+
+    ajint tkeys = 0;
+    ajint pkeys = 0;
+    ajint skeys = 0;
+    ajint order = 0;
+    
+    ajint i;
+    ajint n;
+    
+    ajlong parent  = 0L;
+    ajlong blockno = 0L;
+    
+    ajlong *kTarray = NULL;
+    ajlong *kParray = NULL;
+    ajlong *kSarray = NULL;
+    ajlong *pTarray = NULL;
+    ajlong *pParray = NULL;
+    ajlong *pSarray = NULL;
+
+    ajlong *karray = NULL;
+    ajlong *parray = NULL;
+
+    ajint ppos    = 0;
+    ajint pkeypos = 0;
+    ajint minsize = 0;
+
+    AjPBtMem array  = NULL;    
+    AjPBtMem array2 = NULL;    
+    AjPBtMem array3 = NULL;    
+
+
+    
+    /* ajDebug("In btreeNumInsertShift\n"); */
+
+
+    tpage = *retpage;
+
+    tbuf = tpage->buf;
+
+    GBT_PREV(tbuf,&parent);
+    GBT_NKEYS(tbuf,&tkeys);
+
+
+    order = cache->sorder;
+    minsize = order / 2;
+    if(order % 2)
+	++minsize;
+
+    if(tkeys <= minsize)
+	return 0L;
+
+    ppage = ajBtreeCacheRead(cache,parent);
+
+
+    
+    pbuf = ppage->buf;
+    GBT_NKEYS(pbuf,&pkeys);
+
+    
+    array = btreeAllocSecArray(cache);
+    kParray  = array->overflows;
+    pParray  = array->parray;
+    
+    array2 = btreeAllocSecArray(cache);
+    kSarray  = array2->overflows;
+    pSarray  = array2->parray;
+
+    array3 = btreeAllocSecArray(cache);
+    kTarray  = array3->overflows;
+    pTarray  = array3->parray;
+
+
+    btreeGetNumKeys(cache,pbuf,&kParray,&pParray);
+
+    i=0;
+    while(i!=pkeys && key >= kParray[i])
+	++i;
+    pkeypos = i;
+    
+    if(i==pkeys)
+    {
+	if(key < kParray[i-1])
+	    ppos = i-1;
+	else
+	    ppos = i;
+    }
+    else
+	ppos = i;
+
+    
+    if(ppos) /* There is another leaf to the left */
+    {
+	spage = ajBtreeCacheRead(cache,pParray[ppos-1]);
+	sbuf = spage->buf;
+	GBT_NKEYS(sbuf,&skeys);
+    }
+
+    if(i && skeys != order-1) /* There is space in the left leaf */
+    {
+	/* ajDebug("Left shift\n"); */
+	btreeGetNumKeys(cache,tbuf,&kTarray,&pTarray);
+	if(skeys)
+	    btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
+
+	i = 0;
+	while(pParray[i] != tpage->pageno)
+	    ++i;
+	--i;
+
+	pkeypos = i;
+
+	kSarray[skeys] = kParray[pkeypos];
+	pSarray[skeys+1] = pTarray[0];
+	++skeys;
+	--tkeys;
+	kParray[pkeypos] = kTarray[0];
+	for(i=0;i<tkeys;++i)
+	{
+	    kTarray[i] = kTarray[i+1];
+	    pTarray[i] = pTarray[i+1];
+	}
+	pTarray[i] = pTarray[i+1];
+	pTarray[i+1] = 0L;
+	
+	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
+	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
+	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
+	if(!ppage->pageno)
+	    ppage->dirty = BT_LOCK;
+
+	i = 0;
+	while(i!=pkeys && key >= kParray[i])
+	    ++i;
+	if(i==pkeys)
+	{
+	    if(key < kParray[i-1])
+		blockno = pParray[i-1];
+	    else
+		blockno = pParray[i];
+	}
+	else
+	    blockno = pParray[i];
+
+	if(blockno == spage->pageno)
+	{
+	    *retpage = spage;
+	    karray = kSarray;
+	    parray = pSarray;
+	    n = skeys;
+	}
+	else
+	{
+	    karray = kTarray;
+	    parray = pTarray;
+	    n = tkeys;
+	}
+	
+
+	i = 0;
+	while(i!=n && key >= karray[i])
+	    ++i;
+	if(i==n)
+	{
+	    if(key < karray[i-1])
+		blockno = parray[i-1];
+	    else
+		blockno = parray[i];
+	}
+	else
+	    blockno = parray[i];
+
+	btreeDeallocSecArray(cache,array);
+	btreeDeallocSecArray(cache,array2);
+	btreeDeallocSecArray(cache,array3);
+
+	/* ajDebug("... returns blockno (a) %Ld\n",blockno); */
+
+	return blockno;
+    }
+    
+
+    if(ppos != pkeys)	/* There is a right node */
+    {
+	spage = ajBtreeCacheRead(cache,pParray[ppos+1]);
+	sbuf = spage->buf;
+	GBT_NKEYS(sbuf,&skeys);
+    }
+
+
+    /* Space in the right leaf */
+    if(ppos != pkeys && skeys != order-1)
+    {
+	/* ajDebug("Right shift\n"); */
+	btreeGetNumKeys(cache,tbuf,&kTarray,&pTarray);
+	btreeGetNumKeys(cache,sbuf,&kSarray,&pSarray);
+
+	i = 0;
+	while(pParray[i] != tpage->pageno)
+	    ++i;
+	pkeypos = i;
+	
+	pSarray[skeys+1] = pSarray[skeys];
+	for(i=skeys-1;i>-1;--i)
+	{
+	    kSarray[i+1] = kSarray[i];
+	    pSarray[i+1] = pSarray[i];
+	}
+	kSarray[0] = kParray[pkeypos];
+	pSarray[0] = pTarray[tkeys];
+	kParray[pkeypos] = kTarray[tkeys-1];
+	++skeys;
+	--tkeys;
+	pTarray[tkeys+1] = 0L;
+	
+	btreeWriteNumNode(cache,spage,kSarray,pSarray,skeys);
+	btreeWriteNumNode(cache,tpage,kTarray,pTarray,tkeys);
+	btreeWriteNumNode(cache,ppage,kParray,pParray,pkeys);
+	if(!ppage->pageno)
+	    ppage->dirty = BT_LOCK;
+
+	i = 0;
+	while(i!=pkeys && key >= kParray[i])
+	    ++i;
+	if(i==pkeys)
+	{
+	    if(key < kParray[i-1])
+		blockno = pParray[i-1];
+	    else
+		blockno = pParray[i];
+	}
+	else
+	    blockno = pParray[i];
+
+	if(blockno == spage->pageno)
+	{
+	    *retpage = spage;
+	    karray = kSarray;
+	    parray = pSarray;
+	    n = skeys;
+	}
+	else
+	{
+	    karray = kTarray;
+	    parray = pTarray;
+	    n = tkeys;
+	}
+	
+	i = 0;
+	while(i!=n && key >= karray[i])
+	    ++i;
+	if(i==n)
+	{
+	    if(key < karray[i-1])
+		blockno = parray[i-1];
+	    else
+		blockno = parray[i];
+	}
+	else
+	    blockno = parray[i];
+
+	btreeDeallocSecArray(cache,array);
+	btreeDeallocSecArray(cache,array2);
+	btreeDeallocSecArray(cache,array3);
+
+	/* ajDebug("... returns blockno (b) %Ld\n",blockno); */
+	
+	return blockno;
+    }
+
+
+    btreeDeallocSecArray(cache,array);
+    btreeDeallocSecArray(cache,array2);
+    btreeDeallocSecArray(cache,array3);
+
+    /* ajDebug("... returns 0L\n"); */
+
+    return 0L;
+}
+
+
+
+
+void ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page)
+{
+    unsigned char *buf = NULL;
+    ajint order;
+    AjPBtMem array = NULL;
+    ajlong key;
+    AjPBtpage spage  = NULL;
+    AjPBtpage parent = NULL;
+    ajint nkeys = 0;
+    ajint nodetype = 0;
+    ajlong *karray = NULL;
+    ajlong *parray = NULL;
+    AjPNumBucket lbucket = NULL;
+    AjPNumBucket rbucket = NULL;
+    ajlong lblockno;
+    ajlong rblockno;
+    ajlong blockno;
+    ajlong shift;
+    ajint n;
+    ajint i;
+
+    /* ajDebug("In ajBtreeInsertNum\n"); */
+
+    key = num->offset;
+
+    spage = ajBtreeNumFindInsert(cache,key);
+    buf = spage->buf;
+
+    GBT_NKEYS(buf,&nkeys);
+    GBT_NODETYPE(buf,&nodetype);
+
+    order = cache->sorder;
+
+    array = btreeAllocSecArray(cache);
+    karray = array->overflows;
+    parray = array->parray;
+
+    if(!nkeys)
+    {
+	lbucket = btreeNumBucketNew(0);
+	rbucket = btreeNumBucketNew(0);
+
+	lblockno = cache->totsize;
+	btreeWriteNumBucket(cache,lbucket,lblockno);
+	rblockno = cache->totsize;
+	btreeWriteNumBucket(cache,rbucket,rblockno);
+
+	parray[0] = lblockno;
+	parray[1] = rblockno;
+	karray[0] = key;
+
+	btreeWriteNumNode(cache,spage,karray,parray,1);
+
+	btreeNumBucketDel(&lbucket);
+	btreeNumBucketDel(&rbucket);
+
+	btreeAddToNumBucket(cache,rblockno,num);
+
+	btreeDeallocSecArray(cache,array);
+
+	return;
+    }
+
+
+    btreeGetNumKeys(cache,buf,&karray,&parray);
+    i=0;
+    while(i != nkeys && key >= karray[i])
+	++i;
+    if(i==nkeys)
+    {
+	if(key < karray[i-1])
+	    blockno = parray[i-1];
+	else
+	    blockno = parray[i];
+    }
+    else
+	blockno = parray[i];
+
+    if(nodetype != BT_ROOT)
+	if((shift = btreeNumInsertShift(cache,&spage,key)))
+	    blockno = shift;
+
+
+    buf = spage->buf;
+    n = btreeNumInNumBucket(cache,blockno);
+
+    if(n == cache->snperbucket)
+    {
+	if(btreeReorderNumBuckets(cache,spage))
+	{
+	    GBT_NKEYS(buf,&nkeys);
+	    btreeGetNumKeys(cache,buf,&karray,&parray);
+	    i=0;
+	    while(i != nkeys && key >= karray[i])
+		++i;
+	    if(i==nkeys)
+	    {
+		if(key < karray[i-1])
+		    blockno = parray[i-1];
+		else
+		    blockno = parray[i];
+	    }
+	    else
+		blockno = parray[i];
+	}
+	else
+	{
+	    parent = btreeNumSplitLeaf(cache,spage);
+	    spage = ajBtreeNumFindInsert(cache,key);
+	    buf = spage->buf;
+
+	    btreeGetNumKeys(cache,buf,&karray,&parray);
+	    GBT_NKEYS(buf,&nkeys);
+	
+	    i=0;
+	    while(i != nkeys && key >= karray[i])
+		++i;
+	    if(i==nkeys)
+	    {
+		if(key < karray[i-1])
+		    blockno = parray[i-1];
+		else
+		    blockno = parray[i];
+	    }
+	    else
+		blockno = parray[i];
+	}
+    }
+
+    btreeAddToNumBucket(cache,blockno,num);
+
+    btreeDeallocSecArray(cache,array);
+
+    ++cache->count;
+
+    return;
+}
+
+
+
+
+/* @funcstatic btreeNumSplitLeaf *********************************************
+**
+** Split a leaf and propagate up if necessary
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [u] spage [AjPBtpage] page
+**
+** @return [AjPBtpage] pointer to a parent page
+** @@
+******************************************************************************/
+
+static AjPBtpage btreeNumSplitLeaf(AjPBtcache cache, AjPBtpage spage)
+{
+    ajint nkeys     = 0;
+    ajint order     = 0;
+    ajint totalkeys = 0;
+    ajint bentries  = 0;
+    ajint keylimit  = 0;
+    ajint nodetype  = 0;
+
+    ajint rootnodetype = 0;
+    
+    ajint i;
+    ajint j;
+    
+    AjPBtpage lpage = NULL;
+    AjPBtpage rpage = NULL;
+    AjPBtpage page  = NULL;
+    
+    ajlong mediankey  = 0L;
+    ajlong mediangtr  = 0L;
+    ajlong medianless = 0L;
+
+    AjPBtNumId bid = NULL;
+
+    unsigned char *buf  = NULL;
+    unsigned char *lbuf = NULL;
+    unsigned char *rbuf = NULL;
+
+    AjPList idlist = NULL;
+
+    AjPNumBucket *buckets = NULL;
+    AjPNumBucket cbucket  = NULL;
+    
+    ajlong *karray = NULL;
+    ajlong *parray = NULL;
+    
+    ajint keypos = 0;
+    ajint lno    = 0;
+    ajint rno    = 0;
+
+    ajint bucketlimit   = 0;
+    ajint maxnperbucket = 0;
+    ajint nperbucket    = 0;
+    ajint bucketn       = 0;
+    ajint count         = 0;
+    
+    ajlong lblockno = 0L;
+    ajlong rblockno = 0L;
+    ajlong overflow = 0L;
+    ajlong prevsave = 0L;
+    
+    ajlong zero = 0L;
+    ajlong join = 0L;
+    
+    ajlong lv = 0L;
+    ajint  v  = 0;
+
+    AjPBtMem array = NULL;
+    
+    
+    /* ajDebug("In btreeNumSplitLeaf\n"); */
+
+    order = cache->sorder;
+    nperbucket = cache->snperbucket;
+
+    array = btreeAllocSecArray(cache);
+    karray = array->overflows;
+    parray = array->parray;
+
+    buf = spage->buf;
+    lbuf = buf;
+
+    GBT_NKEYS(buf,&nkeys);
+    GBT_NODETYPE(buf,&rootnodetype);
+
+    if(rootnodetype == BT_ROOT)
+    {
+	/* ajDebug("Root leaf splitting\n"); */
+	lblockno = cache->totsize;
+	lpage = ajBtreeCacheWrite(cache,lblockno);
+	lpage->pageno = cache->totsize;
+	cache->totsize += cache->pagesize;
+	lbuf = lpage->buf;
+	lv = cache->secrootblock;
+	SBT_PREV(lbuf,lv);
+    }
+    else
+    {
+	lblockno = spage->pageno;
+	lpage = spage;
+    }
+
+    lpage->dirty = BT_LOCK;
+
+    rblockno = cache->totsize;
+    rpage = ajBtreeCacheWrite(cache,rblockno);
+    rpage->pageno = cache->totsize;
+    cache->totsize += cache->pagesize;
+    rbuf = rpage->buf;
+    rpage->dirty = BT_LOCK;
+
+    if(rootnodetype == BT_ROOT)
+    {
+	lv = zero;
+	SBT_RIGHT(rbuf,lv);
+	lv = zero;
+	SBT_LEFT(lbuf,lv);
+    }
+    else
+    {
+	GBT_RIGHT(lbuf,&join);
+	lv = join;
+	SBT_RIGHT(rbuf,lv);
+    }
+    lv = lblockno;
+    SBT_LEFT(rbuf,lv);
+    lv = rblockno;
+    SBT_RIGHT(lbuf,lv);
+
+
+    btreeGetNumKeys(cache,buf,&karray,&parray);
+
+
+    keylimit = nkeys+1;
+    AJCNEW0(buckets,keylimit);
+    for(i=0;i<keylimit;++i)
+	buckets[i] = btreeReadNumBucket(cache,parray[i]);
+
+    idlist = ajListNew();
+    for(i=0;i<keylimit;++i)
+    {
+	bentries = buckets[i]->Nentries;
+	for(j=0;j<bentries;++j)
+	    ajListPush(idlist,(void *)buckets[i]->NumId[j]);
+	AJFREE(buckets[i]->NumId);
+	AJFREE(buckets[i]);
+    }
+
+
+
+    ajListSort(idlist,btreeNumIdCompare);
+    AJFREE(buckets);
+
+    totalkeys = ajListLength(idlist);
+
+    keypos = totalkeys / 2;
+
+    lno = keypos;
+    rno = totalkeys - lno;
+
+    maxnperbucket = nperbucket >> 1;
+    ++maxnperbucket;
+
+    cbucket = btreeNumBucketNew(maxnperbucket);
+
+    bucketn = lno / maxnperbucket;
+    if(lno % maxnperbucket)
+	++bucketn;
+    bucketlimit = bucketn - 1;
+
+
+    count = 0;
+    for(i=0;i<bucketlimit;++i)
+    {
+	cbucket->Nentries = 0;
+	for(j=0;j<maxnperbucket;++j)
+	{
+	    ajListPop(idlist,(void **)&bid);
+
+	    cbucket->NumId[j]->offset    = bid->offset;
+	    cbucket->NumId[j]->refoffset = bid->refoffset;
+	    cbucket->NumId[j]->dbno      = bid->dbno;
+	    
+	    ++count;
+	    ++cbucket->Nentries;
+	    AJFREE(bid);
+	}
+	ajListPeek(idlist,(void **)&bid);
+
+	karray[i] = bid->offset;
+
+	if(!parray[i])
+	    parray[i] = cache->totsize;
+	btreeWriteNumBucket(cache,cbucket,parray[i]);
+    }
+
+    cbucket->Nentries = 0;
+
+    j = 0;
+    while(count != lno)
+    {
+	ajListPop(idlist,(void **)&bid);
+
+	cbucket->NumId[j]->offset    = bid->offset;
+	cbucket->NumId[j]->refoffset = bid->refoffset;
+	cbucket->NumId[j]->dbno      = bid->dbno;
+
+	++j;
+	++count;
+
+
+	++cbucket->Nentries;
+	AJFREE(bid);
+    }
+
+    if(!parray[i])
+	parray[i] = cache->totsize;
+    btreeWriteNumBucket(cache,cbucket,parray[i]);
+
+    nkeys = bucketn - 1;
+    v = nkeys;
+    SBT_NKEYS(lbuf,v);
+    nodetype = BT_LEAF;
+    v = nodetype;
+    SBT_NODETYPE(lbuf,v);
+    GBT_PREV(lbuf,&prevsave);
+    lpage->dirty = BT_DIRTY;
+    btreeWriteNumNode(cache,lpage,karray,parray,nkeys);
+
+    ajListPeek(idlist,(void **)&bid);
+    mediankey = bid->offset;
+
+    bucketn = rno / maxnperbucket;
+    if(rno % maxnperbucket)
+	++bucketn;
+    bucketlimit = bucketn - 1;
+
+    for(i=0;i<bucketlimit;++i)
+    {
+	cbucket->Nentries = 0;
+	for(j=0;j<maxnperbucket;++j)
+	{
+	    ajListPop(idlist,(void **)&bid);
+	    
+	    cbucket->NumId[j]->offset    = bid->offset;
+	    cbucket->NumId[j]->refoffset = bid->refoffset;
+	    cbucket->NumId[j]->dbno      = bid->dbno;
+	    
+	    ++cbucket->Nentries;
+	    AJFREE(bid);
+	}
+
+	ajListPeek(idlist,(void **)&bid);
+	karray[i] = bid->offset;
+
+	parray[i] = cache->totsize;
+	btreeWriteNumBucket(cache,cbucket,parray[i]);
+    }
+
+    cbucket->Nentries = 0;
+
+    j = 0;
+    while(ajListPop(idlist,(void**)&bid))
+    {
+	cbucket->NumId[j]->offset    = bid->offset;
+	cbucket->NumId[j]->refoffset = bid->refoffset;
+	cbucket->NumId[j]->dbno      = bid->dbno;
+	++j;
+
+
+	++cbucket->Nentries;
+	AJFREE(bid);
+    }
+    
+    parray[i] = cache->totsize;
+    btreeWriteNumBucket(cache,cbucket,parray[i]);
+
+    nkeys = bucketn - 1;
+
+    v = nkeys;
+    SBT_NKEYS(rbuf,v);
+    nodetype = BT_LEAF;
+    v = nodetype;
+    SBT_NODETYPE(rbuf,v);
+    lv = prevsave;
+    SBT_PREV(rbuf,lv);
+    lv = overflow;
+    SBT_OVERFLOW(rbuf,lv);
+    
+    btreeWriteNumNode(cache,rpage,karray,parray,nkeys);
+    rpage->dirty = BT_DIRTY;
+
+    cbucket->Nentries = maxnperbucket;
+    btreeNumBucketDel(&cbucket);
+    ajListDel(&idlist);
+
+
+
+    medianless = lblockno;
+    mediangtr  = rblockno;
+
+
+    if(rootnodetype == BT_ROOT)
+    {
+	karray[0] = mediankey;
+	parray[0]=lblockno;
+	parray[1]=rblockno;
+	nkeys = 1;
+	spage->dirty = BT_DIRTY;
+	btreeWriteNumNode(cache,spage,karray,parray,nkeys);	
+
+	++cache->slevel;
+	lv = cache->slevel;
+	SBT_RIGHT(buf,lv);
+	spage->dirty = BT_LOCK;
+
+	btreeDeallocSecArray(cache,array);
+
+	return spage;
+    }
+
+    btreeDeallocSecArray(cache,array);
+
+
+    page = ajBtreeCacheRead(cache,prevsave);
+    btreeNumInsertKey(cache,page,mediankey,medianless,mediangtr);
+
+
+    page = ajBtreeCacheRead(cache,prevsave);
+
+    return page;
+}
+
+
+
+
+/* @func ajBtreeFreePriArray *******************************************
+**
+** Free karray and parray arrays for a primary key
+**
+** @param [rw] cache [AjPBtcache] cache
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+void ajBtreeFreePriArray(AjPBtcache cache)
+{
+    AjPBtMem p;
+    AjPBtMem next;
+    ajint i;
+
+    /* ajDebug("In ajBtreeFreePriArray\n"); */
+    
+    if(!cache->bmem)
+	return;
+
+    p = cache->bmem;
+    next = p->next;
+    
+    while(next)
+    {
+	AJFREE(p->parray);
+	AJFREE(p->overflows);
+	for(i=0;i<cache->order;++i)
+	    ajStrDel(&p->karray[i]);
+	AJFREE(p->karray);
+	AJFREE(p);
+	p = next;
+	next = p->next;
+    }
+    
+
+    AJFREE(p->parray);
+    AJFREE(p->overflows);
+    for(i=0;i<cache->order;++i)
+	ajStrDel(&p->karray[i]);
+    AJFREE(p->karray);
+    AJFREE(p);
+    
+    cache->bmem = NULL;
+    cache->tmem = NULL;
+
+    return;
+}
+
+
+
+
+/* @func ajBtreeFreeSecArray *******************************************
+**
+** Free karray and parray arrays for a secondary key
+**
+** @param [rw] cache [AjPBtcache] cache
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+void ajBtreeFreeSecArray(AjPBtcache cache)
+{
+    AjPBtMem p;
+    AjPBtMem next;
+    ajint i;
+
+    /* ajDebug("In ajBtreeFreeSecArray\n"); */
+    
+    if(!cache->bsmem)
+	return;
+
+    p = cache->bsmem;
+    next = p->next;
+    
+    while(next)
+    {
+	AJFREE(p->parray);
+	AJFREE(p->overflows);
+	for(i=0;i<cache->sorder;++i)
+	    ajStrDel(&p->karray[i]);
+	AJFREE(p->karray);
+	AJFREE(p);
+	
+	p = next;
+	next = p->next;
+    }
+    
+
+    AJFREE(p->parray);
+    AJFREE(p->overflows);
+    for(i=0;i<cache->sorder;++i)
+	ajStrDel(&p->karray[i]);
+    AJFREE(p->karray);
+    AJFREE(p);
+
+    cache->bsmem = NULL;
+    cache->tsmem = NULL;
+
+    return;
+}
+
+
+
+
+/* @func ajBtreeHybLeafList ********************************************
+**
+** Read the leaves of a secondary hybrid tree
+**
+** @param [u] cache [AjPBtcache] cache
+** @param [r] rootblock [ajlong] root page of secondary tree
+** @param [r] idname [AjPStr] id name
+** @param [r] list [AjPList] list to add BtIDs to
+**
+** @return [void]
+** @@
+******************************************************************************/
+
+void ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock, AjPStr idname,
+			AjPList list)
+{
+    AjPBtId id = NULL;
+    
+    ajint order;
+    ajlong *karray;
+    ajlong *parray;
+    AjPBtpage page;
+    unsigned char *buf;
+    ajint nodetype;
+    ajint i;
+    ajint j;
+    ajlong level = 0L;
+    
+    AjPNumBucket bucket;
+    ajint nkeys;
+    ajlong right;
+    AjPBtMem array = NULL;
+
+    order = cache->sorder;
+
+    array = btreeAllocSecArray(cache);
+    karray = array->overflows;
+    parray = array->parray;
+
+    page = ajBtreeCacheRead(cache, rootblock);
+    buf = page->buf;
+
+    GBT_RIGHT(buf,&level);
+    cache->slevel = (ajint) level;
+
+    btreeGetNumKeys(cache,buf,&karray,&parray);
+    GBT_NODETYPE(buf,&nodetype);
+
+    while(nodetype != BT_LEAF && cache->slevel != 0)
+    {
+	page = ajBtreeCacheRead(cache,parray[0]);
+	buf = page->buf;
+	btreeGetNumKeys(cache,buf,&karray,&parray);
+	GBT_NODETYPE(buf,&nodetype);
+    }
+
+    do
+    {
+	GBT_NKEYS(buf,&nkeys);
+	for(i=0;i<nkeys+1;++i)
+	{
+	    bucket = btreeReadNumBucket(cache,parray[i]);
+	    for(j=0;j<bucket->Nentries;++j)
+	    {
+		id = ajBtreeIdNew();
+		ajStrAssS(&id->id,idname);
+		id->offset = bucket->NumId[j]->offset;
+		id->refoffset = bucket->NumId[j]->refoffset;
+		id->dbno = bucket->NumId[j]->dbno;
+		ajListPush(list, (void*)id);
+	    }
+	    btreeNumBucketDel(&bucket);
+	}
+
+	right = 0L;
+	if(cache->slevel)
+	{
+	    GBT_RIGHT(buf,&right);
+	    if(right)
+	    {
+		page = ajBtreeCacheRead(cache,right);
+		buf = page->buf;
+		btreeGetNumKeys(cache,buf,&karray,&parray);
+	    }
+	}
+    } while(right);
+
+    btreeDeallocSecArray(cache,array);
+
+    return;
+}
+




--- ajax/ajindex.h.orig	Mon Jan 23 12:17:10 2006
+++ ajax/ajindex.h	Thu Dec 22 13:12:32 2005
@@ -67,6 +67,23 @@
 } AjOBtNode;
 #define AjPBtNode AjOBtNode*
 
+
+
+
+typedef struct AjSBtMem
+{
+    struct AjSBtMem *next;
+    struct AjSBtMem *prev;
+    AjPStr *karray;
+    ajlong *parray;
+    ajlong *overflows;
+    AjBool used;
+} AjOBtMem;
+#define AjPBtMem AjOBtMem*
+
+
+
+
 /* @data AjPBtId ***************************************************
 **
 ** Btree ID
@@ -137,6 +154,54 @@
 
 
 
+/* @data AjPBtNumId ***************************************************
+**
+** Btree ID
+**
+** @attr id [AjPStr] Unique ID
+** @attr dbno [ajint] Database file number
+** @attr dups [ajint] Duplicates
+** @attr offset [ajlong] Offset within database file (ftello)
+** @attr refoffset [ajlong] Offset within reference database file (ftello)
+******************************************************************************/
+
+typedef struct AjSBtNumId
+{
+    ajint  dbno;
+    ajlong offset;
+    ajlong refoffset;
+} AjOBtNumId;
+#define AjPBtNumId AjOBtNumId*
+
+
+
+
+/* @data AjPNumBucket ***************************************************
+**
+** Offset bucket structure on disc
+**
+** Key, filenumber, ftell ID, subkey page (char*, ajint, ajlong, ajlong)
+**
+** @attr NodeType [ajint] Node type
+** @attr Nentries [ajint] Number of entries
+** @attr Overflow [ajlong] Offset to overflow block
+** @attr offset [ajlong*] file offsets
+** @attr refoffset [ajlong*] ref file offsets
+** @attr offset [ajint*] database numbers
+******************************************************************************/
+
+typedef struct AjSNumBucket
+{
+    ajint    NodeType;
+    ajint    Nentries;
+    ajlong   Overflow;
+    AjPBtNumId *NumId;
+} AjONumBucket;
+#define AjPNumBucket AjONumBucket*
+
+
+
+
 /* Database file name structure
 **
 ** ajint        order			Order of B+tree
@@ -387,6 +452,10 @@
 ** @attr snperbucket [ajint] Undocumented
 ** @attr secrootblock [ajlong] secondary tree root block
 ** @attr kwlimit [ajint] Max length of secondary key
+** @attr bmem [AjPBtMem] primary memory allocation MRU bottom
+** @attr bsmem [AjPBtMem] secondary memory allocation MRU bottom
+** @attr tmem [AjPBtMem] primary memory allocation MRU top
+** @attr tsmem [AjPBtMem] secondary memory allocation MRU top
 ******************************************************************************/
 
 typedef struct AjSBtCache
@@ -409,6 +478,12 @@
     ajint snperbucket;
     ajlong secrootblock;
     ajint  kwlimit;
+
+    AjPBtMem bmem;
+    AjPBtMem tmem;
+    AjPBtMem bsmem;
+    AjPBtMem tsmem;
+
 } AjOBtcache;
 #define AjPBtcache AjOBtcache*
 
@@ -511,6 +586,32 @@
 
 
 
+/* @data AjPBtHybrid ***************************************************
+**
+** Btree ID
+**
+** @attr key1 [AjPStr] Unique ID
+** @attr dbno [ajint] Database file number
+** @attr dups [ajint] Duplicates
+** @attr offset [ajlong] Offset within database file (ftello)** @attr refoffset [ajlong] Offset within reference database file (ftello)
+** @attr refoffset [ajlong] Offset within reference database file (ftello)
+** @attr treeblock [ajlong] Secondary tree root page
+******************************************************************************/
+
+typedef struct AjSBtHybrid
+{
+    AjPStr key1;
+    ajint  dbno;
+    ajint  dups;
+    ajlong offset;
+    ajlong refoffset;
+    ajlong treeblock;
+} AjOBtHybrid;
+#define AjPBtHybrid AjOBtHybrid*
+
+
+
+
 AjPBtcache ajBtreeCacheNewC(const char *file, const char *ext,
 			    const char *idir, const char *mode,
 			    ajint pagesize, ajint order, ajint fill,
@@ -553,7 +654,8 @@
 AjBool     ajBtreeReplaceId(AjPBtcache cache, const AjPBtId rid);
 
 ajint      ajBtreeReadEntries(const char *filename, const char *indexdir,
-		   	      AjPStr **seqfiles, AjPStr **reffiles);
+			      const char *directory,
+			      AjPStr **seqfiles, AjPStr **reffiles);
 void       ajBtreeInsertDupId(AjPBtcache cache, AjPBtId id);
 AjPList    ajBtreeDupFromKey(AjPBtcache cache, const char *key);
 
@@ -580,6 +682,21 @@
 void       ajBtreeInsertKeyword(AjPBtcache cache, const AjPBtPri pri);
 
 void       ajBtreeLockTest(AjPBtcache cache);
+
+
+
+AjPBtpage   ajBtreeHybFindInsert(AjPBtcache cache, const char *key);
+AjPBtpage   ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key);
+
+void        ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page);
+void        ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb);
+AjPBtHybrid ajBtreeHybNew(void);
+void        ajBtreeHybDel(AjPBtHybrid *thys);
+void        ajBtreeFreePriArray(AjPBtcache cache);
+void        ajBtreeFreeSecArray(AjPBtcache cache);
+void 	    ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock,
+			       AjPStr idname, AjPList list);
+
 
 #endif
 




--- ajax/ajpdb.c.orig	Mon Jan 23 12:19:22 2006
+++ ajax/ajpdb.c	Fri Aug 19 13:49:12 2005
@@ -1198,7 +1198,7 @@
     osstr = ajStrNew();
     xstr  = ajStrNew();
 
-    /* Start of main application loop */
+    /* Start of main loop */
     while(ajFileReadLine(inf,&line))
     {
 	if(ajStrPrefixC(line,"XX"))
@@ -1313,6 +1313,8 @@
 	    
 	    (ret)->Nchn = ncha;
 	    (ret)->Ngp  = ngrp;
+
+	    continue;
 	}
 	
 
@@ -1382,7 +1384,11 @@
 	    ajStrToken(&token,&handle,NULL);
 	    ajStrToInt(token,&mod);
 	    if((mode == 0) && (mod!=1))
-		break;
+	      {
+		/* break; */
+		/* Discard remaining AT lines */
+		while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"AT"));
+	      }
 
 	    /* Chain number */
 	    ajStrToken(&token,&handle,NULL);
@@ -1463,7 +1469,10 @@
 			    "jison@hgmp.mrc.ac.uk");
 	    }
 	    else
+	      {
 		ajListPushApp((ret)->Chains[chn-1]->Atoms,(void *)atom);
+	      }
+	    continue;
 	}
 	
 	/* Parse residue line */
@@ -1479,8 +1488,11 @@
 	    ajStrToken(&token,&handle,NULL);
 	    ajStrToInt(token,&mod);
 	    if((mode == 0) && (mod!=1))
-		break;
-
+	      {
+		/* break;*/
+		/* Discard remaining RE lines */
+		while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"RE"));
+	      }
 	    /* Chain number */
 	    ajStrToken(&token,&handle,NULL);
 	    ajStrToInt(token,&chn);
@@ -1585,6 +1597,8 @@
             ajStrToFloat(token,&residue->pol_rel);
 
 	    ajListPushApp((ret)->Chains[chn-1]->Residues,(void *)residue);  
+
+	    continue;
 	}
     }
     /* End of main application loop */




--- ajax/ajseqdb.c.orig	Mon Jan 23 12:20:25 2006
+++ ajax/ajseqdb.c	Thu Dec 22 13:12:57 2005
@@ -27,8 +27,7 @@
 ******************************************************************************/
 
 #include "ajax.h"
-#include "ajmem.h"
-#include "ajfile.h"
+
 #include "limits.h"
 #include <stdarg.h>
 #include <sys/types.h>
@@ -3055,13 +3054,13 @@
 
 
     if(qryd->do_id)
-        seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
+        seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
 
     if(qryd->do_ac)
-	seqEmbossOpenCache(qry,AC_EXTENSION,&qryd->accache);
+	seqEmbossOpenSecCache(qry,AC_EXTENSION,&qryd->accache);
 
     if(qryd->do_sv)
-	seqEmbossOpenCache(qry,SV_EXTENSION,&qryd->svcache);
+	seqEmbossOpenSecCache(qry,SV_EXTENSION,&qryd->svcache);
 
     if(qryd->do_kw)
     {
@@ -3073,14 +3072,14 @@
     if(qryd->do_de)
     {
 	if(!qryd->idcache)
-	    seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);	
+	    seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);	
 	seqEmbossOpenSecCache(qry,DE_EXTENSION,&qryd->decache);
     }
 
     if(qryd->do_tx)
     {
 	if(!qryd->idcache)
-	    seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);	
+	    seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);	
 	seqEmbossOpenSecCache(qry,TX_EXTENSION,&qryd->txcache);
     }
 
@@ -3149,6 +3148,7 @@
     if(qryd->nentries == -1)
 	qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
 					    ajStrStr(qry->IndexDir),
+					    ajStrStr(qry->Directory),
 					    &qryd->files,&qryd->reffiles);
 
     *cache = ajBtreeCacheNewC(ajStrStr(qry->DbAlias),ext,
@@ -3209,6 +3209,7 @@
     if(qryd->nentries == -1)
 	qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
 					    ajStrStr(qry->IndexDir),
+					    ajStrStr(qry->Directory),
 					    &qryd->files,&qryd->reffiles);
     
     
@@ -3270,6 +3271,7 @@
 
 
     n = ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
+			   qry->Directory->Ptr,
 			   &filestrings,&reffilestrings);
 
 
@@ -3365,7 +3367,13 @@
     {
 	    entry = ajBtreeIdFromKey(qryd->idcache,ajStrStr(qry->Id));
 	    if(entry)
-		ajListPushApp(qryd->List,(void *)entry);
+	    {
+		if(!entry->dups)
+		    ajListPushApp(qryd->List,(void *)entry);
+		else
+		    ajBtreeHybLeafList(qryd->idcache,entry->offset,
+				       entry->id,qryd->List);
+	    }
     }
     
 
@@ -3373,14 +3381,26 @@
     {
 	    entry = ajBtreeIdFromKey(qryd->accache,ajStrStr(qry->Acc));
 	    if(entry)
-		ajListPushApp(qryd->List,(void *)entry);
+	    {
+		if(!entry->dups)
+		    ajListPushApp(qryd->List,(void *)entry);
+		else
+		    ajBtreeHybLeafList(qryd->accache,entry->offset,
+				       entry->id,qryd->List);
+	    }
     }
 
     if((qryd->do_sv && !entry) && (qryd->do_sv && qryd->svcache))
     {
 	    entry = ajBtreeIdFromKey(qryd->svcache,ajStrStr(qry->Gi));
 	    if(entry)
-		ajListPushApp(qryd->List,(void *)entry);
+	    {
+		if(!entry->dups)
+		    ajListPushApp(qryd->List,(void *)entry);
+		else
+		    ajBtreeHybLeafList(qryd->svcache,entry->offset,
+				       entry->id,qryd->List);
+	    }
     }
 
     if(!ajListLength(qryd->List))
@@ -3512,13 +3532,25 @@
     qryd = qry->QryData;
 
     if(qryd->do_id && qryd->idcache)
+    {
+	ajBtreeFreeSecArray(qryd->idcache);
 	ajBtreeCacheDel(&qryd->idcache);
+    }
+    
 
     if(qryd->do_ac && qryd->accache)
+    {
+	ajBtreeFreeSecArray(qryd->accache);	
 	ajBtreeCacheDel(&qryd->accache);
+    }
+    
 
     if(qryd->do_sv && qryd->svcache)
+    {
+	ajBtreeFreeSecArray(qryd->svcache);	
 	ajBtreeCacheDel(&qryd->svcache);
+    }
+
 
     if(qryd->do_kw && qryd->kwcache)
 	ajBtreeCacheDel(&qryd->kwcache);
@@ -3608,7 +3640,14 @@
 		    ajStrToLower(&kwid);
 		    id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
 		    if(id)
-			ajListPushApp(qryd->List,(void *)id);
+		    {
+			if(!id->dups)
+			    ajListPushApp(qryd->List,(void *)id);
+			else
+			    ajBtreeHybLeafList(qryd->idcache,id->offset,
+					       id->id,qryd->List);
+		    }
+		    ajStrDel(&kwid);
 		}
 		ajListDel(&tlist);
 		ajBtreePriDel(&pri);
@@ -3637,7 +3676,13 @@
 		    ajStrToLower(&kwid);
 		    id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
 		    if(id)
-			ajListPushApp(qryd->List,(void *)id);
+		    {
+			if(!id->dups)
+			    ajListPushApp(qryd->List,(void *)id);
+			else
+			    ajBtreeHybLeafList(qryd->idcache,id->offset,
+					       id->id,qryd->List);
+		    }
 		    ajStrDel(&kwid);
 		}
 		ajListDel(&tlist);
@@ -3667,7 +3712,14 @@
 		    ajStrToLower(&kwid);
 		    id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
 		    if(id)
-			ajListPushApp(qryd->List,(void *)id);
+		    {
+			if(!id->dups)
+			    ajListPushApp(qryd->List,(void *)id);
+			else
+			    ajBtreeHybLeafList(qryd->idcache,id->offset,
+					       id->id,qryd->List);
+		    }
+		    ajStrDel(&kwid);
 		}
 		ajListDel(&tlist);
 		ajBtreePriDel(&pri);
@@ -3832,6 +3884,7 @@
 	qryd = qry->QryData;
 	i = -1;
 	ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
+			   qry->Directory->Ptr,
 			   &qryd->files,&qryd->reffiles);
 
 	seqin->Single = ajTrue;




--- emboss/dbxfasta.c.orig	Mon Jan 23 12:22:12 2006
+++ emboss/dbxfasta.c	Wed Jan  4 16:31:37 2006
@@ -2,7 +2,7 @@
 **
 ** Index flatfile databases
 **
-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
 ** @@
 **
 ** This program is free software; you can redistribute it and/or
@@ -77,6 +77,7 @@
     
     AjPBtId  idobj  = NULL;
     AjPBtPri priobj = NULL;
+    AjPBtHybrid hyb = NULL;
     
 
     AjPRegexp typeexp = NULL;
@@ -102,7 +103,8 @@
     
     idobj   = ajBtreeIdNew();
     priobj  = ajBtreePriNew();
-
+    hyb     = ajBtreeHybNew();
+    
 
     nfields = embBtreeSetFields(entry,fieldarray);
     embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
@@ -134,22 +136,22 @@
 	    if(entry->do_id)
 	    {
 		ajStrToLower(&entry->id);
-		ajStrAssS(&idobj->id,entry->id);
-		idobj->dbno = i;
-		idobj->offset = entry->fpos;
-		idobj->dups = 0;
-		ajBtreeInsertId(entry->idcache,idobj);
+		ajStrAssS(&hyb->key1,entry->id);
+		hyb->dbno = i;
+		hyb->offset = entry->fpos;
+		hyb->dups = 0;
+		ajBtreeHybInsertId(entry->idcache,hyb);
 	    }
 
 	    if(entry->do_accession)
                 while(ajListPop(entry->ac,(void **)&word))
                 {
 		    ajStrToLower(&word);
-                    ajStrAssS(&idobj->id,word);
-                    idobj->dbno = i;
-		    idobj->offset = entry->fpos;
-		    idobj->dups = 0;
-		    ajBtreeInsertId(entry->accache,idobj);
+                    ajStrAssS(&hyb->key1,word);
+                    hyb->dbno = i;
+		    hyb->offset = entry->fpos;
+		    hyb->dups = 0;
+		    ajBtreeHybInsertId(entry->accache,hyb);
 		    ajStrDel(&word);
                 }
 
@@ -157,11 +159,11 @@
                 while(ajListPop(entry->sv,(void **)&word))
                 {
 		    ajStrToLower(&word);
-                    ajStrAssS(&idobj->id,word);
-                    idobj->dbno = i;
-		    idobj->offset = entry->fpos;
-		    idobj->dups = 0;
-		    ajBtreeInsertId(entry->svcache,idobj);
+                    ajStrAssS(&hyb->key1,word);
+                    hyb->dbno = i;
+		    hyb->offset = entry->fpos;
+		    hyb->dups = 0;
+		    ajBtreeHybInsertId(entry->svcache,hyb);
 		    ajStrDel(&word);
                 }
 
@@ -197,7 +199,8 @@
 
     ajBtreeIdDel(&idobj);
     ajBtreePriDel(&priobj);
-
+    ajBtreeHybDel(&hyb);
+    
     ajExit();
 
     return 0;




--- emboss/dbxflat.c.orig	Mon Jan 23 12:22:23 2006
+++ emboss/dbxflat.c	Sun Jan  1 07:29:09 2006
@@ -2,7 +2,7 @@
 **
 ** Index flatfile databases
 **
-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
 ** @@
 **
 ** This program is free software; you can redistribute it and/or
@@ -106,6 +106,7 @@
     
     AjPBtId  idobj  = NULL;
     AjPBtPri priobj = NULL;
+    AjPBtHybrid hyb = NULL;
     
 
     embInit("dbxflat", argc, argv);
@@ -126,7 +127,8 @@
     
     idobj   = ajBtreeIdNew();
     priobj  = ajBtreePriNew();
-
+    hyb     = ajBtreeHybNew();
+    
 
     nfields = embBtreeSetFields(entry,fieldarray);
     embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
@@ -156,11 +158,11 @@
 	    if(entry->do_id)
 	    {
 		ajStrToLower(&entry->id);
-		ajStrAssS(&idobj->id,entry->id);
-		idobj->dbno = i;
-		idobj->offset = entry->fpos;
-		idobj->dups = 0;
-		ajBtreeInsertId(entry->idcache,idobj);
+		ajStrAssS(&hyb->key1,entry->id);
+		hyb->dbno = i;
+		hyb->offset = entry->fpos;
+		hyb->dups = 0;
+		ajBtreeHybInsertId(entry->idcache,hyb);
 	    }
 
 	    if(entry->do_accession)
@@ -168,11 +170,11 @@
                 while(ajListPop(entry->ac,(void **)&word))
                 {
 		    ajStrToLower(&word);
-                    ajStrAssS(&idobj->id,word);
-                    idobj->dbno = i;
-		    idobj->offset = entry->fpos;
-		    idobj->dups = 0;
-		    ajBtreeInsertId(entry->accache,idobj);
+                    ajStrAssS(&hyb->key1,word);
+                    hyb->dbno = i;
+		    hyb->offset = entry->fpos;
+		    hyb->dups = 0;
+		    ajBtreeHybInsertId(entry->accache,hyb);
 		    ajStrDel(&word);
                 }
 	    }
@@ -182,11 +184,11 @@
                 while(ajListPop(entry->sv,(void **)&word))
                 {
 		    ajStrToLower(&word);
-                    ajStrAssS(&idobj->id,word);
-                    idobj->dbno = i;
-		    idobj->offset = entry->fpos;
-		    idobj->dups = 0;
-		    ajBtreeInsertId(entry->svcache,idobj);
+                    ajStrAssS(&hyb->key1,word);
+                    hyb->dbno = i;
+		    hyb->offset = entry->fpos;
+		    hyb->dups = 0;
+		    ajBtreeHybInsertId(entry->svcache,hyb);
 		    ajStrDel(&word);
                 }
 	    }
@@ -231,15 +233,11 @@
 	    }
 	}
 	
-
-
-
-
-
 	ajFileClose(&inf);
     }
     
 
+
     embBtreeDumpParameters(entry);
     embBtreeCloseCaches(entry);
     
@@ -256,7 +254,8 @@
 
     ajBtreeIdDel(&idobj);
     ajBtreePriDel(&priobj);
-
+    ajBtreeHybDel(&hyb);
+    
     ajExit();
 
     return 0;
@@ -306,11 +305,13 @@
 	}
 
 	if(entry->do_sv)
-	    if(ajStrPrefixC(line,"SV"))
+	    if(ajStrPrefixC(line,"SV") ||
+	       ajStrPrefixC(line,"IV"))	/* emblcds database format */
 		embBtreeEmblAC(line,entry->sv);
 
 	if(entry->do_accession)
-	    if(ajStrPrefixC(line,"AC"))
+	    if(ajStrPrefixC(line,"AC") ||
+	       ajStrPrefixC(line,"PA"))	/* emblcds database format */
 		embBtreeEmblAC(line,entry->ac);
 	
 	if(entry->do_keyword)
@@ -356,12 +357,10 @@
     
     line = ajStrNewC("");
     sumline = ajStrNew();
+
     
     while(!ajStrPrefixC(line,"//") && ret)
     {
-	pos = ajFileTell(inf);
-	
-	
 	if(ajStrPrefixC(line,"LOCUS"))
 	{
 	    entry->fpos = pos;
@@ -423,7 +422,7 @@
 	    }
 	
 
-
+	pos = ajFileTell(inf);
 
 	if(!ajFileReadLine(inf,&line))
 	    ret = ajFalse;




--- emboss/dbxgcg.c.orig	Mon Jan 23 12:22:30 2006
+++ emboss/dbxgcg.c	Thu Dec 22 13:13:18 2005
@@ -2,7 +2,7 @@
 **
 ** Index flatfile databases
 **
-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
 ** @@
 **
 ** This program is free software; you can redistribute it and/or
@@ -136,6 +136,7 @@
     
     AjPBtId  idobj  = NULL;
     AjPBtPri priobj = NULL;
+    AjPBtHybrid hyb = NULL;
     
 
     embInit("dbxgcg", argc, argv);
@@ -156,7 +157,8 @@
     
     idobj   = ajBtreeIdNew();
     priobj  = ajBtreePriNew();
-
+    hyb     = ajBtreeHybNew();
+    
 
     nfields = embBtreeSetFields(entry,fieldarray);
     embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
@@ -204,12 +206,12 @@
 	    if(entry->do_id)
 	    {
 		ajStrToLower(&entry->id);
-		ajStrAssS(&idobj->id,entry->id);
-		idobj->dbno = i;
-		idobj->offset = entry->fpos;
-		idobj->refoffset = entry->reffpos;
-		idobj->dups = 0;
-		ajBtreeInsertId(entry->idcache,idobj);
+		ajStrAssS(&hyb->key1,entry->id);
+		hyb->dbno = i;
+		hyb->offset = entry->fpos;
+		hyb->refoffset = entry->reffpos;
+		hyb->dups = 0;
+		ajBtreeHybInsertId(entry->idcache,hyb);
 	    }
 
 	    if(entry->do_accession)
@@ -217,12 +219,12 @@
                 while(ajListPop(entry->ac,(void **)&word))
                 {
 		    ajStrToLower(&word);
-                    ajStrAssS(&idobj->id,word);
-                    idobj->dbno = i;
-		    idobj->offset = entry->fpos;
-		    idobj->refoffset = entry->reffpos;
-		    idobj->dups = 0;
-		    ajBtreeInsertId(entry->accache,idobj);
+                    ajStrAssS(&hyb->key1,word);
+                    hyb->dbno = i;
+		    hyb->offset = entry->fpos;
+		    hyb->refoffset = entry->reffpos;
+		    hyb->dups = 0;
+		    ajBtreeHybInsertId(entry->accache,hyb);
 		    ajStrDel(&word);
                 }
 	    }
@@ -232,12 +234,12 @@
                 while(ajListPop(entry->sv,(void **)&word))
                 {
 		    ajStrToLower(&word);
-                    ajStrAssS(&idobj->id,word);
-                    idobj->dbno = i;
-		    idobj->offset = entry->fpos;
-		    idobj->refoffset = entry->reffpos;
-		    idobj->dups = 0;
-		    ajBtreeInsertId(entry->svcache,idobj);
+                    ajStrAssS(&hyb->key1,word);
+                    hyb->dbno = i;
+		    hyb->offset = entry->fpos;
+		    hyb->refoffset = entry->reffpos;
+		    hyb->dups = 0;
+		    ajBtreeHybInsertId(entry->svcache,hyb);
 		    ajStrDel(&word);
                 }
 	    }
@@ -303,7 +305,8 @@
 
     ajBtreeIdDel(&idobj);
     ajBtreePriDel(&priobj);
-
+    ajBtreeHybDel(&hyb);
+    
     ajExit();
 
     return 0;




--- nucleus/embindex.c.orig	Mon Jan 23 12:24:54 2006
+++ nucleus/embindex.c	Thu Dec 22 13:12:38 2005
@@ -973,15 +973,14 @@
 	if(!do_ref)
 	{
 	    ajListPop(entry->files,(void **)&tmpstr);
-	    ajFmtPrintF(entfile,"%S%S\n",entry->directory,tmpstr);
+	    ajFmtPrintF(entfile,"%S\n",tmpstr);
 	    ajListPushApp(entry->files,(void *)tmpstr);
 	}
 	else
 	{
 	    ajListPop(entry->files,(void **)&tmpstr);
 	    ajListPop(entry->reffiles,(void **)&refstr);
-	    ajFmtPrintF(entfile,"%S%S %S%S\n",entry->directory,tmpstr,
-			entry->directory,refstr);
+	    ajFmtPrintF(entfile,"%S %S\n",tmpstr, refstr);
 	    ajListPushApp(entry->files,(void *)tmpstr);
 	    ajListPushApp(entry->reffiles,(void *)refstr);
 	}
@@ -1150,7 +1149,15 @@
     entry->desecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
     entry->txsecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
 
+    entry->idsecorder = (entry->pagesize - 60) / 24;
+    entry->idsecfill  = (entry->pagesize - 60) / 20;
 
+    entry->acsecorder = (entry->pagesize - 60) / 24;
+    entry->acsecfill  = (entry->pagesize - 60) / 20;
+
+    entry->svsecorder = (entry->pagesize - 60) / 24;
+    entry->svsecfill  = (entry->pagesize - 60) / 20;
+    
     ajStrDel(&value);
 
     return;
@@ -1183,28 +1190,38 @@
 
     if(entry->do_id)
     {
-	entry->idcache = ajBtreeCacheNewC(basenam,ID_EXTENSION,idir,"w+",
-					  entry->pagesize, entry->idorder,
-					  entry->idfill, level,
-					  entry->cachesize);
+	entry->idcache = ajBtreeSecCacheNewC(basenam,ID_EXTENSION,idir,"w+",
+					     entry->pagesize, entry->idorder,
+					     entry->idfill, level,
+					     entry->cachesize,
+					     entry->idsecorder, slevel,
+					     entry->idsecfill, count,
+					     entry->kwlen);
 	ajBtreeCreateRootNode(entry->idcache,0L);
     }
 
     if(entry->do_accession)
     {
-	entry->accache = ajBtreeCacheNewC(basenam,AC_EXTENSION,idir,"w+",
-					  entry->pagesize, entry->acorder,
-					  entry->acfill, level,
-					  entry->cachesize);
+	entry->accache = ajBtreeSecCacheNewC(basenam,AC_EXTENSION,idir,"w+",
+					     entry->pagesize,
+					     entry->acorder, entry->acfill,
+					     level,
+					     entry->cachesize,
+					     entry->acsecorder, slevel,
+					     entry->acsecfill, count,
+					     entry->kwlen);
 	ajBtreeCreateRootNode(entry->accache,0L);
     }
 
     if(entry->do_sv)
     {
-	entry->svcache = ajBtreeCacheNewC(basenam,SV_EXTENSION,idir,"w+",
-					  entry->pagesize, entry->svorder,
-					  entry->svfill, level,
-					  entry->cachesize);
+	entry->svcache = ajBtreeSecCacheNewC(basenam,SV_EXTENSION,idir,"w+",
+					     entry->pagesize, entry->svorder,
+					     entry->svfill, level,
+					     entry->cachesize,
+					     entry->svsecorder, slevel,
+					     entry->svsecfill, count,
+					     entry->kwlen);
 	ajBtreeCreateRootNode(entry->svcache,0L);
     }
 
@@ -1270,18 +1287,27 @@
 
     if(entry->do_id)
     {
+	ajBtreeFreePriArray(entry->idcache);
+	ajBtreeFreeSecArray(entry->idcache);
+
 	ajBtreeCacheSync(entry->idcache,0L);
 	ajBtreeCacheDel(&entry->idcache);
     }
 
     if(entry->do_accession)
     {
+	ajBtreeFreePriArray(entry->accache);
+	ajBtreeFreeSecArray(entry->accache);
+
 	ajBtreeCacheSync(entry->accache,0L);
 	ajBtreeCacheDel(&entry->accache);
     }
 
     if(entry->do_sv)
     {
+	ajBtreeFreePriArray(entry->svcache);
+	ajBtreeFreeSecArray(entry->svcache);
+
 	ajBtreeCacheSync(entry->svcache,0L);
 	ajBtreeCacheDel(&entry->svcache);
     }




--- nucleus/embindex.h.orig	Mon Jan 23 12:24:46 2006
+++ nucleus/embindex.h	Thu Dec 22 13:12:44 2005
@@ -16,6 +16,76 @@
 #define BTREE_DEF_CACHESIZE 100
 #define BTREE_DEF_PAGESIZE  2048
 
+/* @data EmbPBtreeEntry *******************************************************
+**
+** Index tree entries
+**
+** @alias EmbSBtreeEntry
+**
+** @attr do_id [AjBool] Undocumented
+** @attr do_accession [AjBool] Undocumented
+** @attr do_sv [AjBool] Undocumented
+** @attr do_description [AjBool] Undocumented
+** @attr do_keyword [AjBool] Undocumented
+** @attr do_taxonomy [AjBool] Undocumented
+** @attr dbname [AjPStr] Undocumented
+** @attr dbrs [AjPStr] Undocumented
+** @attr release [AjPStr] Undocumented
+** @attr date [AjPStr] Undocumented
+** @attr dbtype [AjPStr] Undocumented
+** @attr directory [AjPStr] Undocumented
+** @attr idirectory [AjPStr] Undocumented
+** @attr files [AjPList] Undocumented
+** @attr reffiles [AjPList] Undocumented
+** @attr nfiles [ajint] Undocumented
+** @attr cachesize [ajint] Undocumented
+** @attr pagesize [ajint] Undocumented
+** @attr idlen [ajint] Undocumented
+** @attr aclen [ajint] Undocumented
+** @attr svlen [ajint] Undocumented
+** @attr kwlen [ajint] Undocumented
+** @attr delen [ajint] Undocumented
+** @attr txlen [ajint] Undocumented
+** @attr idorder [ajint] Undocumented
+** @attr idfill [ajint] Undocumented
+** @attr idsecorder [ajint] Undocumented
+** @attr idsecfill [ajint] Undocumented
+** @attr acorder [ajint] Undocumented
+** @attr acfill [ajint] Undocumented
+** @attr acsecorder [ajint] Undocumented
+** @attr acsecfill [ajint] Undocumented
+** @attr svorder [ajint] Undocumented
+** @attr svfill [ajint] Undocumented
+** @attr svsecorder [ajint] Undocumented
+** @attr svsecfill [ajint] Undocumented
+** @attr kworder [ajint] Undocumented
+** @attr kwfill [ajint] Undocumented
+** @attr kwsecorder [ajint] Undocumented
+** @attr kwsecfill [ajint] Undocumented
+** @attr deorder [ajint] Undocumented
+** @attr defill [ajint] Undocumented
+** @attr desecorder [ajint] Undocumented
+** @attr desecfill [ajint] Undocumented
+** @attr txorder [ajint] Undocumented
+** @attr txfill [ajint] Undocumented
+** @attr txsecorder [ajint] Undocumented
+** @attr txsecfill [ajint] Undocumented
+** @attr idcache [AjPBtcache] Undocumented
+** @attr accache [AjPBtcache] Undocumented
+** @attr svcache [AjPBtcache] Undocumented
+** @attr kwcache [AjPBtcache] Undocumented
+** @attr decache [AjPBtcache] Undocumented
+** @attr txcache [AjPBtcache] Undocumented
+** @attr fpos [ajlong] Undocumented
+** @attr reffpos [ajlong] Undocumented
+** @attr id [AjPStr] Undocumented
+** @attr ac [AjPList] Undocumented
+** @attr sv [AjPList] Undocumented
+** @attr tx [AjPList] Undocumented
+** @attr kw [AjPList] Undocumented
+** @attr de [AjPList] Undocumented
+******************************************************************************/
+
 typedef struct EmbSBtreeEntry
 {
     AjBool do_id;
@@ -48,10 +118,16 @@
 
     ajint idorder;
     ajint idfill;
+    ajint idsecorder;
+    ajint idsecfill;
     ajint acorder;
     ajint acfill;
+    ajint acsecorder;
+    ajint acsecfill;
     ajint svorder;
     ajint svfill;
+    ajint svsecorder;
+    ajint svsecfill;
 
     ajint kworder;
     ajint kwfill;




--- emboss/emboss.default.template.orig	Wed Feb  8 00:43:42 2006
+++ emboss/emboss.default.template	Wed Feb  8 00:40:34 2006
@@ -4,7 +4,7 @@
 # By default this is /usr/local/share/EMBOSS/test but the directory can
 # be changed with --prefix when you configure EMBOSS.
 
-# SET emboss_tempdata path_to_directory_$EMBOSS/test
+# SET emboss_tempdata %%DATADIR%%/test
 
 # Proxy - set this if any databases are accessed through a proxy web server.
 # Turn off in the DB definition with proxy: ":" for any
@@ -15,7 +15,7 @@
 # Logfile - set this to a file that any user can append to
 # and EMBOSS applications will automatically write log information
 
-# SET emboss_logfile /packages/emboss/emboss/log
+# SET emboss_logfile /var/log/emboss.log
 
 # Pagesize - this is the size of disc page blocks and is
 # required by the 'dbx' indexing programs and 'method: emboss'




--- emboss/marscan.c.orig	Mon Jan 23 11:36:36 2006
+++ emboss/marscan.c	Mon Jan 23 08:56:35 2006
@@ -1,7 +1,7 @@
 /* @source marscan application
 **
 ** Finds MAR/SAR sites in nucleic sequences
-** @author: Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
+** @author Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
 ** @@
 **
 ** This program is free software; you can redistribute it and/or
@@ -249,33 +249,41 @@
 			 amino8rev, carboxyl8rev, buf8rev, off8rev,
 			 sotable8rev, solimit8rev, regexp8rev, skipm8rev,
 			 &hits8rev, m8rev, &tidy8rev);
+	ajDebug("Marscan '%S' hits %d:%d %d:%d\n", seqname,
+		hits16, hits16rev,
+		hits8, hits8rev);
+
+	/* initialise the output feature table */
+	tab = ajFeattableNewDna(seqname);
+
+	/*
+	**  append reverse lists to forward lists and sort them by match
+	**  position
+	*/
 
-	if((hits16 || hits16rev) && (hits8 || hits8rev))
+	if(hits8 || hits8rev)
 	{
-	    /*
-	    **  append reverse lists to forward lists and sort them by match
-	    **  position
-	    */
 	    ajListPushList(l8, &l8rev);
 	    ajListSort(l8, embPatRestrictStartCompare);
-
+	}
+	if((hits16 || hits16rev))
+	{
 	    ajListPushList(l16, &l16rev);
 	    ajListSort(l16, embPatRestrictStartCompare);
 
-	    /* initialise the output feature table */
-	    if(!tab)
-		tab = ajFeattableNewDna(seqname);
-
-	    /*
-	    **  find pairs of hits within the required distance and output
-	    **  the results
-	    */
-	    marscan_stepdown(l16, l8, &tab);
-
-	    /* write features and tidy up */
-	    ajReportWrite(report, tab, seq);
-	    ajFeattableDel(&tab);
 	}
+
+
+	/*
+	**  find pairs of hits within the required distance and output
+	**  the results
+	*/
+	marscan_stepdown(l16, l8, &tab);
+
+	ajDebug("Marscan reportwrite '%S'\n", seqname);
+	/* write features and tidy up */
+	ajReportWrite(report, tab, seq);
+	ajFeattableDel(&tab);
 
         while(ajListPop(l16,(void **)&aptr))
             embMatMatchDel(&aptr);




=============================================================================

 The EMBOSS suite has been successfully installed under
 %%PREFIX%%

 To run EMBOSS programs make sure that %%PREFIX%%/bin is in your PATH.

 In order to see graphical output from some EMBOSS programs, you will 
 need to set the following environment variable in your shell:

 set PLPLOT_LIB to: "%%PREFIX%%/share/EMBOSS"

 A sample configuration file has been installed in
 %%DATADIR%%/emboss.default.template

 This must be renamed to emboss.default and edited to suit your site 
 and requirements.

 A .embossrc file in a user's home directory overrides settings in the
 system-wide emboss.default.

 Additional third party applications for EMBOSS can be installed from the
 biology/embassy port. Remember, though that if you installed EMBOSS in a 
 PREFIX other than the default, you will have to install EMBASSY into this 
 same PREFIX.

=============================================================================




===============================================================================

 ATENTION!!!

 The EMBOSS port is currently affected by a CONFLICTS condition.
 If you install the port in the default prefix
 PREFIX = LOCALBASE = %%LOCALBASE%%
 it will conflict with other ports that install applications with the 
 same name, in the same places. 

 It is highly recommended that you install EMBOSS to a different prefix,
 for example PREFIX=%%LOCALBASE%%/emboss
 In this case, all of the documentation and examples will be installed 
 within this PREFIX. 

 If you still choose to install EMBOSS on the default prefix, do note 
 that documentation, examples and shared data will not be installed 
 in the usual places for a FreeBSD port (i.e. docs in
 PREFIX/share/EMBOSS/doc instead of in PREFIX/share/doc/EMBOSS).

===============================================================================




--------------------------------------------------------------------------

The EMBOSS suite has been successfully installed.

In order to see graphical output from some EMBOSS programs, you will need to
set the following environment variable in your shell startup file:

- set PLPLOT_LIB to:     "%%PREFIX%%/share/EMBOSS"

NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
emboss.default.sample.  This must be renamed to emboss.default and edited
to suit your site and its requirements.

A .embossrc in a user's home directory overrides settings in the
system-wide emboss.default.

Online EMBOSS documentation is available at:
	http://www.uk.embnet.org/Software/EMBOSS/userdoc.html
	http://www.uk.embnet.org/Software/EMBOSS/Doc/
  http://emboss.sourceforge.net/docs/

--------------------------------------------------------------------------

Lines 17-22 Link Here

(-)emboss/pkg-plist (-1392 / +1478 lines)
17	bin/chips	17	bin/chips
18	bin/cirdna	18	bin/cirdna
19	bin/codcmp	19	bin/codcmp
		20	bin/codcopy
20	bin/coderet	21	bin/coderet
21	bin/compseq	22	bin/compseq
22	bin/cons	23	bin/cons
Lines 24-35 Link Here
24	bin/cpgreport	25	bin/cpgreport
25	bin/cusp	26	bin/cusp
26	bin/cutgextract	27	bin/cutgextract
27	bin/cutseq
28	bin/dan	28	bin/dan
		29	bin/cutseq
29	bin/dbiblast	30	bin/dbiblast
30	bin/dbifasta	31	bin/dbifasta
31	bin/dbiflat	32	bin/dbiflat
32	bin/dbigcg	33	bin/dbigcg
		34	bin/dbxfasta
		35	bin/dbxflat
		36	bin/dbxgcg
33	bin/degapseq	37	bin/degapseq
34	bin/descseq	38	bin/descseq
35	bin/diffseq	39	bin/diffseq
Lines 119-125 Link Here
119	bin/restover	123	bin/restover
120	bin/restrict	124	bin/restrict
121	bin/revseq	125	bin/revseq
122	bin/runJemboss.csh
123	bin/seealso	126	bin/seealso
124	bin/seqmatchall	127	bin/seqmatchall
125	bin/seqret	128	bin/seqret
Lines 135-145 Link Here
135	bin/sirna	138	bin/sirna
136	bin/sixpack	139	bin/sixpack
137	bin/skipseq	140	bin/skipseq
		141	bin/syco
138	bin/splitter	142	bin/splitter
139	bin/stretcher	143	bin/stretcher
140	bin/stssearch	144	bin/stssearch
141	bin/supermatcher	145	bin/supermatcher
142	bin/syco
143	bin/tcode	146	bin/tcode
144	bin/textsearch	147	bin/textsearch
145	bin/tfextract	148	bin/tfextract
Lines 160-177 Link Here
160	bin/wordmatch	163	bin/wordmatch
161	bin/wossname	164	bin/wossname
162	bin/yank	165	bin/yank
163	etc/emboss.default.sample	166	bin/runJemboss.csh
		167	include/drivers.h
		168	include/pdf.h
		169	include/plcore.h
		170	include/plevent.h
		171	include/plplotP.h
		172	include/plxwd.h
		173	include/metadefs.h
		174	include/plConfig.h
		175	include/pldebug.h
		176	include/plplot.h
		177	include/plstrm.h
		178	include/plDevs.h
		179	include/ajax.h
		180	include/ajarch.h
		181	include/ajdefine.h
164	include/ajacd.h	182	include/ajacd.h
165	include/ajalign.h	183	include/ajalign.h
166	include/ajarch.h
167	include/ajarr.h	184	include/ajarr.h
168	include/ajassert.h	185	include/ajassert.h
169	include/ajax.h
170	include/ajbase.h	186	include/ajbase.h
171	include/ajcall.h	187	include/ajcall.h
172	include/ajcod.h	188	include/ajcod.h
173	include/ajdan.h	189	include/ajdan.h
174	include/ajdefine.h
175	include/ajdmx.h	190	include/ajdmx.h
176	include/ajdomain.h	191	include/ajdomain.h
177	include/ajexcept.h	192	include/ajexcept.h
Lines 180-187 Link Here
180	include/ajfile.h	195	include/ajfile.h
181	include/ajfmt.h	196	include/ajfmt.h
182	include/ajgraph.h	197	include/ajgraph.h
183	include/ajgraphstruct.h
184	include/ajgraphxml.h	198	include/ajgraphxml.h
		199	include/ajgraphstruct.h
185	include/ajhist.h	200	include/ajhist.h
186	include/ajindex.h	201	include/ajindex.h
187	include/ajjava.h	202	include/ajjava.h
Lines 214-220 Link Here
214	include/ajtree.h	229	include/ajtree.h
215	include/ajutil.h	230	include/ajutil.h
216	include/ajvector.h	231	include/ajvector.h
217	include/drivers.h	232	include/pcre.h
		233	include/pcre_chartables.c
		234	include/pcre_config.h
		235	include/pcre_get.c
		236	include/pcre_printint.c
		237	include/pcre_internal.h
		238	include/pcreposix.h
		239	include/emboss.h
218	include/embaln.h	240	include/embaln.h
219	include/embcom.h	241	include/embcom.h
220	include/embcons.h	242	include/embcons.h
Lines 232-1230 Link Here
232	include/embmisc.h	254	include/embmisc.h
233	include/embmol.h	255	include/embmol.h
234	include/embnmer.h	256	include/embnmer.h
235	include/emboss.h
236	include/embpat.h	257	include/embpat.h
237	include/embpdb.h
238	include/embprop.h	258	include/embprop.h
		259	include/embpdb.h
239	include/embread.h	260	include/embread.h
240	include/embshow.h
241	include/embsig.h	261	include/embsig.h
		262	include/embshow.h
242	include/embword.h	263	include/embword.h
243	include/metadefs.h	264	lib/libplplot.so.5
244	include/pcre.h	265	lib/libplplot.so
245	include/pcre_chartables.c	266	lib/libplplot.la
246	include/pcre_config.h	267	lib/libplplot.a
247	include/pcre_get.c	268	lib/libajax.so.3
248	include/pcre_internal.h
249	include/pcre_printint.c
250	include/pcreposix.h
251	include/pdf.h
252	include/plConfig.h
253	include/plDevs.h
254	include/plcore.h
255	include/pldebug.h
256	include/plevent.h
257	include/plplot.h
258	include/plplotP.h
259	include/plstrm.h
260	include/plxwd.h
261	lib/libajax.a
262	lib/libajax.la
263	lib/libajax.so	269	lib/libajax.so
264	lib/libajax.so.1	270	lib/libajax.la
265	lib/libajaxg.a	271	lib/libajax.a
266	lib/libajaxg.la	272	lib/libajaxg.so.3
267	lib/libajaxg.so	273	lib/libajaxg.so
268	lib/libajaxg.so.1	274	lib/libajaxg.la
269	lib/libnucleus.a	275	lib/libajaxg.a
270	lib/libnucleus.la	276	lib/libnucleus.so.3
271	lib/libnucleus.so	277	lib/libnucleus.so
272	lib/libnucleus.so.1	278	lib/libnucleus.la
273	lib/libplplot.a	279	lib/libnucleus.a
274	lib/libplplot.la	280	%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
275	lib/libplplot.so	281	%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
276	lib/libplplot.so.5
277	%%DATADIR%%/acd/aaindexextract.acd
278	%%DATADIR%%/acd/abiview.acd
279	%%DATADIR%%/acd/acdc.acd
280	%%DATADIR%%/acd/acdlog.acd
281	%%DATADIR%%/acd/acdpretty.acd
282	%%DATADIR%%/acd/acdtable.acd
283	%%DATADIR%%/acd/acdtrace.acd
284	%%DATADIR%%/acd/acdvalid.acd
285	%%DATADIR%%/acd/ajbad.acd
286	%%DATADIR%%/acd/ajfeatest.acd
287	%%DATADIR%%/acd/ajtest.acd
288	%%DATADIR%%/acd/antigenic.acd
289	%%DATADIR%%/acd/backtranseq.acd
290	%%DATADIR%%/acd/banana.acd
291	%%DATADIR%%/acd/biosed.acd
292	%%DATADIR%%/acd/btwisted.acd
293	%%DATADIR%%/acd/cai.acd
294	%%DATADIR%%/acd/chaos.acd
295	%%DATADIR%%/acd/charge.acd
296	%%DATADIR%%/acd/checktrans.acd
297	%%DATADIR%%/acd/chips.acd
298	%%DATADIR%%/acd/cirdna.acd
299	%%DATADIR%%/acd/codcmp.acd
300	%%DATADIR%%/acd/coderet.acd
301	%%DATADIR%%/acd/codes.english
302	%%DATADIR%%/acd/complex.acd
303	%%DATADIR%%/acd/compseq.acd
304	%%DATADIR%%/acd/cons.acd
305	%%DATADIR%%/acd/corbatest.acd
306	%%DATADIR%%/acd/cpgplot.acd
307	%%DATADIR%%/acd/cpgreport.acd
308	%%DATADIR%%/acd/cusp.acd
309	%%DATADIR%%/acd/cutgextract.acd
310	%%DATADIR%%/acd/cutseq.acd
311	%%DATADIR%%/acd/dan.acd
312	%%DATADIR%%/acd/dbiblast.acd
313	%%DATADIR%%/acd/dbifasta.acd
314	%%DATADIR%%/acd/dbiflat.acd
315	%%DATADIR%%/acd/dbigcg.acd
316	%%DATADIR%%/acd/degapseq.acd
317	%%DATADIR%%/acd/demoalign.acd
318	%%DATADIR%%/acd/demofeatures.acd
319	%%DATADIR%%/acd/demolist.acd
320	%%DATADIR%%/acd/demoreport.acd
321	%%DATADIR%%/acd/demosequence.acd
322	%%DATADIR%%/acd/demostring.acd
323	%%DATADIR%%/acd/demotable.acd
324	%%DATADIR%%/acd/descseq.acd
325	%%DATADIR%%/acd/diffseq.acd
326	%%DATADIR%%/acd/digest.acd
327	%%DATADIR%%/acd/distmat.acd
328	%%DATADIR%%/acd/dotmatcher.acd
329	%%DATADIR%%/acd/dotpath.acd
330	%%DATADIR%%/acd/dottup.acd
331	%%DATADIR%%/acd/dreg.acd
332	%%DATADIR%%/acd/einverted.acd
333	%%DATADIR%%/acd/embossdata.acd
334	%%DATADIR%%/acd/embossversion.acd
335	%%DATADIR%%/acd/emma.acd
336	%%DATADIR%%/acd/emowse.acd
337	%%DATADIR%%/acd/entrails.acd
338	%%DATADIR%%/acd/entret.acd
339	%%DATADIR%%/acd/epestfind.acd
340	%%DATADIR%%/acd/eprimer3.acd
341	%%DATADIR%%/acd/equicktandem.acd
342	%%DATADIR%%/acd/est2genome.acd
343	%%DATADIR%%/acd/etandem.acd
344	%%DATADIR%%/acd/extractfeat.acd
345	%%DATADIR%%/acd/extractseq.acd
346	%%DATADIR%%/acd/findkm.acd
347	%%DATADIR%%/acd/freak.acd
348	%%DATADIR%%/acd/fuzznuc.acd
349	%%DATADIR%%/acd/fuzzpro.acd
350	%%DATADIR%%/acd/fuzztran.acd
351	%%DATADIR%%/acd/garnier.acd
352	%%DATADIR%%/acd/geecee.acd
353	%%DATADIR%%/acd/getorf.acd
354	%%DATADIR%%/acd/giep.acd
355	%%DATADIR%%/acd/groups.standard
356	%%DATADIR%%/acd/helixturnhelix.acd
357	%%DATADIR%%/acd/histogramtest.acd
358	%%DATADIR%%/acd/hmoment.acd
359	%%DATADIR%%/acd/iep.acd
360	%%DATADIR%%/acd/infoalign.acd
361	%%DATADIR%%/acd/infoseq.acd
362	%%DATADIR%%/acd/intconv.acd
363	%%DATADIR%%/acd/isochore.acd
364	%%DATADIR%%/acd/kmrsplitter.acd
365	%%DATADIR%%/acd/kmrunion.acd
366	%%DATADIR%%/acd/knowntypes.standard
367	%%DATADIR%%/acd/lindna.acd
368	%%DATADIR%%/acd/listor.acd
369	%%DATADIR%%/acd/marscan.acd
370	%%DATADIR%%/acd/maskfeat.acd
371	%%DATADIR%%/acd/maskseq.acd
372	%%DATADIR%%/acd/matcher.acd
373	%%DATADIR%%/acd/megamerger.acd
374	%%DATADIR%%/acd/merger.acd
375	%%DATADIR%%/acd/msbar.acd
376	%%DATADIR%%/acd/mwcontam.acd
377	%%DATADIR%%/acd/mwfilter.acd
378	%%DATADIR%%/acd/needle.acd
379	%%DATADIR%%/acd/newcoils.acd
380	%%DATADIR%%/acd/newcpgreport.acd
381	%%DATADIR%%/acd/newcpgseek.acd
382	%%DATADIR%%/acd/newseq.acd
383	%%DATADIR%%/acd/noreturn.acd
384	%%DATADIR%%/acd/notseq.acd
385	%%DATADIR%%/acd/nthseq.acd
386	%%DATADIR%%/acd/octanol.acd
387	%%DATADIR%%/acd/oddcomp.acd
388	%%DATADIR%%/acd/palindrome.acd
389	%%DATADIR%%/acd/pasteseq.acd
390	%%DATADIR%%/acd/patmatdb.acd
391	%%DATADIR%%/acd/patmatmotifs.acd
392	%%DATADIR%%/acd/patmattest.acd
393	%%DATADIR%%/acd/pepcoil.acd
394	%%DATADIR%%/acd/pepinfo.acd
395	%%DATADIR%%/acd/pepnet.acd
396	%%DATADIR%%/acd/pepstats.acd
397	%%DATADIR%%/acd/pepwheel.acd
398	%%DATADIR%%/acd/pepwindow.acd
399	%%DATADIR%%/acd/pepwindowall.acd
400	%%DATADIR%%/acd/plotcon.acd
401	%%DATADIR%%/acd/plotorf.acd
402	%%DATADIR%%/acd/polydot.acd
403	%%DATADIR%%/acd/preg.acd
404	%%DATADIR%%/acd/prettyplot.acd
405	%%DATADIR%%/acd/prettyseq.acd
406	%%DATADIR%%/acd/prima.acd
407	%%DATADIR%%/acd/primers.acd
408	%%DATADIR%%/acd/primersearch.acd
409	%%DATADIR%%/acd/printsextract.acd
410	%%DATADIR%%/acd/profit.acd
411	%%DATADIR%%/acd/prophecy.acd
412	%%DATADIR%%/acd/prophet.acd
413	%%DATADIR%%/acd/prosextract.acd
414	%%DATADIR%%/acd/pscan.acd
415	%%DATADIR%%/acd/psiphi.acd
416	%%DATADIR%%/acd/rebaseextract.acd
417	%%DATADIR%%/acd/recoder.acd
418	%%DATADIR%%/acd/redata.acd
419	%%DATADIR%%/acd/remap.acd
420	%%DATADIR%%/acd/restover.acd
421	%%DATADIR%%/acd/restrict.acd
422	%%DATADIR%%/acd/revseq.acd
423	%%DATADIR%%/acd/sections.standard
424	%%DATADIR%%/acd/seealso.acd
425	%%DATADIR%%/acd/seqinfo.acd
426	%%DATADIR%%/acd/seqmatchall.acd
427	%%DATADIR%%/acd/seqret.acd
428	%%DATADIR%%/acd/seqretall.acd
429	%%DATADIR%%/acd/seqretallfeat.acd
430	%%DATADIR%%/acd/seqretset.acd
431	%%DATADIR%%/acd/seqretsingle.acd
432	%%DATADIR%%/acd/seqretsplit.acd
433	%%DATADIR%%/acd/seqrettype.acd
434	%%DATADIR%%/acd/showalign.acd
435	%%DATADIR%%/acd/showdb.acd
436	%%DATADIR%%/acd/showfeat.acd
437	%%DATADIR%%/acd/showorf.acd
438	%%DATADIR%%/acd/showseq.acd
439	%%DATADIR%%/acd/shuffleseq.acd
440	%%DATADIR%%/acd/sigcleave.acd
441	%%DATADIR%%/acd/silent.acd
442	%%DATADIR%%/acd/sirna.acd
443	%%DATADIR%%/acd/sixpack.acd
444	%%DATADIR%%/acd/skipseq.acd
445	%%DATADIR%%/acd/splitter.acd
446	%%DATADIR%%/acd/stretcher.acd
447	%%DATADIR%%/acd/stssearch.acd
448	%%DATADIR%%/acd/supermatcher.acd
449	%%DATADIR%%/acd/syco.acd
450	%%DATADIR%%/acd/tcode.acd
451	%%DATADIR%%/acd/testplot.acd
452	%%DATADIR%%/acd/textsearch.acd
453	%%DATADIR%%/acd/tfextract.acd
454	%%DATADIR%%/acd/tfm.acd
455	%%DATADIR%%/acd/tfscan.acd
456	%%DATADIR%%/acd/tmap.acd
457	%%DATADIR%%/acd/tranalign.acd
458	%%DATADIR%%/acd/transeq.acd
459	%%DATADIR%%/acd/treetypedisplay.acd
460	%%DATADIR%%/acd/trimest.acd
461	%%DATADIR%%/acd/trimseq.acd
462	%%DATADIR%%/acd/twofeat.acd
463	%%DATADIR%%/acd/union.acd
464	%%DATADIR%%/acd/variables.standard
465	%%DATADIR%%/acd/vectorstrip.acd
466	%%DATADIR%%/acd/water.acd
467	%%DATADIR%%/acd/whichdb.acd
468	%%DATADIR%%/acd/wobble.acd
469	%%DATADIR%%/acd/wordcount.acd
470	%%DATADIR%%/acd/wordmatch.acd
471	%%DATADIR%%/acd/wossname.acd
472	%%DATADIR%%/acd/yank.acd
473	%%DATADIR%%/data/AAINDEX/dummyfile
474	%%DATADIR%%/data/CODONS/Eacc.cut
475	%%DATADIR%%/data/CODONS/Eadenovirus5.cut
476	%%DATADIR%%/data/CODONS/Eadenovirus7.cut
477	%%DATADIR%%/data/CODONS/Eaidlav.cut
478	%%DATADIR%%/data/CODONS/Eanasp.cut
479	%%DATADIR%%/data/CODONS/Eani.cut
480	%%DATADIR%%/data/CODONS/Eani_h.cut
481	%%DATADIR%%/data/CODONS/Eanidmit.cut
482	%%DATADIR%%/data/CODONS/Easn.cut
483	%%DATADIR%%/data/CODONS/Eath.cut
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601	%%DATADIR%%/data/CODONS/Esv40.cut
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669	%%DATADIR%%/data/EPAM150
670	%%DATADIR%%/data/EPAM160
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673	%%DATADIR%%/data/EPAM190
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863	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java
864	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java
865	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java
866	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java
867	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java
868	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java
869	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java
870	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java
871	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java
872	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignApplet.java
873	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignJFrame.java
874	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourJFrame.java
875	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourMenu.java
876	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourPanel.java
877	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Consensus.java
878	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ConsensusOptions.java
879	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GraphicSequenceCollection.java
880	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrame.java
881	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java
882	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java
883	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java
884	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java
885	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java
886	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequence.java
887	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java
888	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java
889	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Matrix.java
890	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java
891	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Paste.java
892	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PatternJFrame.java
893	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PlotConsensus.java
894	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java
895	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignment.java
896	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java
897	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintableJTable.java
898	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Sequence.java
899	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceJPanel.java
900	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceNameJButton.java
901	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceProperties.java
902	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceReader.java
903	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceSaver.java
904	%%DATADIR%%/jemboss/org/emboss/jemboss/graphics/Graph2DPlot.java
905	%%DATADIR%%/jemboss/org/emboss/jemboss/graphics/PrintPlot.java
906	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
907	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java
908	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
909	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Favorites.java
910	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
911	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.java
912	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
913	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
914	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
915	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
916	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java
917	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java
918	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
919	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
920	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
921	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java
922	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java
923	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
924	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java
925	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java
926	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java
927	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java
928	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java
929	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalTreeToolBar.java
930	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
931	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java
932	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java
933	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
934	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java
935	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
936	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
937	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java
938	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java
939	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
940	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
941	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
942	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java
943	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java
944	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java
945	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetOutFileCard.java
946	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java
947	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java
948	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java
949	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java
950	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java
951	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
952	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/OutputSequenceAttributes.java
953	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/SequenceFilter.java
954	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java
955	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java
956	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java
957	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java
958	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
959	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
960	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java
961	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
962	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java
963	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java
964	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
965	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
966	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
967	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java
968	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java
969	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultList.java
970	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
971	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
972	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
973	%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
974	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
975	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
976	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
977	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java
978	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java
979	%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
980	%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
981	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java
982	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
983	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
984	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
985	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
986	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
987	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
988	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
989	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
990	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
991	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
992	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
993	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
994	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
995	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
996	%%DATADIR%%/jemboss/readme.html
997	%%DATADIR%%/jemboss/resources/filemgr.html
998	%%DATADIR%%/jemboss/resources/jemboss.properties
999	%%DATADIR%%/jemboss/resources/readme.html
1000	%%DATADIR%%/jemboss/resources/readmeAlign.html
1001	%%DATADIR%%/jemboss/resources/readmeDNADraw.html
1002	%%DATADIR%%/jemboss/resources/results.html
1003	%%DATADIR%%/jemboss/resources/seqList.html
1004	%%DATADIR%%/jemboss/resources/version
1005	%%DATADIR%%/jemboss/runJemboss.sh
1006	%%DATADIR%%/jemboss/utils/README
1007	%%DATADIR%%/jemboss/utils/install-jemboss-server.sh
1008	%%DATADIR%%/jemboss/utils/keys.sh
1009	%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
1010	%%DATADIR%%/jemboss/utils/makeJNLP.sh
1011	%%DATADIR%%/jemboss/utils/makeJar.csh
1012	%%DATADIR%%/jemboss/utils/template.html
1013	%%DATADIR%%/plstnd5.fnt
1014	%%DATADIR%%/plxtnd5.fnt
1015	%%DATADIR%%/test/data/aaindex1.test
1016	%%DATADIR%%/test/data/aligna.dna
1017	%%DATADIR%%/test/data/aligna.prot
1018	%%DATADIR%%/test/data/alignapart.dna
1019	%%DATADIR%%/test/data/alignapart.prot
1020	%%DATADIR%%/test/data/alignb.dna
1021	%%DATADIR%%/test/data/alignb.prot
1022	%%DATADIR%%/test/data/cutg.codon
1023	%%DATADIR%%/test/data/dna.acedb
1024	%%DATADIR%%/test/data/dna.aln
1025	%%DATADIR%%/test/data/dna.asn1
1026	%%DATADIR%%/test/data/dna.codata
1027	%%DATADIR%%/test/data/dna.embl
1028	%%DATADIR%%/test/data/dna.fasta
1029	%%DATADIR%%/test/data/dna.fitch
1030	%%DATADIR%%/test/data/dna.gcg
1031	%%DATADIR%%/test/data/dna.gcg8
1032	%%DATADIR%%/test/data/dna.genbank
1033	%%DATADIR%%/test/data/dna.ig
1034	%%DATADIR%%/test/data/dna.m-acedb
1035	%%DATADIR%%/test/data/dna.m-codata
1036	%%DATADIR%%/test/data/dna.m-embl
1037	%%DATADIR%%/test/data/dna.m-fasta
1038	%%DATADIR%%/test/data/dna.m-fasta-long
1039	%%DATADIR%%/test/data/dna.m-ncbi
1040	%%DATADIR%%/test/data/dna.m-strider
1041	%%DATADIR%%/test/data/dna.msf
1042	%%DATADIR%%/test/data/dna.msf8
1043	%%DATADIR%%/test/data/dna.ncbi
1044	%%DATADIR%%/test/data/dna.phylip
1045	%%DATADIR%%/test/data/dna.phylip3
1046	%%DATADIR%%/test/data/dna.staden
1047	%%DATADIR%%/test/data/dna.strider
1048	%%DATADIR%%/test/data/dna.text
1049	%%DATADIR%%/test/data/feat.emft
1050	%%DATADIR%%/test/data/feat.fasta
1051	%%DATADIR%%/test/data/feat.pir
1052	%%DATADIR%%/test/data/mw1.dat
1053	%%DATADIR%%/test/data/mw2.dat
1054	%%DATADIR%%/test/data/mw3.dat
1055	%%DATADIR%%/test/data/paamir.pep
1056	%%DATADIR%%/test/data/pax6_cdna.fasta
1057	%%DATADIR%%/test/data/prints.test
1058	%%DATADIR%%/test/data/prosite.dat
1059	%%DATADIR%%/test/data/prosite.doc
1060	%%DATADIR%%/test/data/prot.acedb
1061	%%DATADIR%%/test/data/prot.codata
1062	%%DATADIR%%/test/data/prot.fasta
1063	%%DATADIR%%/test/data/prot.gcg
1064	%%DATADIR%%/test/data/prot.gcg8
1065	%%DATADIR%%/test/data/prot.ig
1066	%%DATADIR%%/test/data/prot.m-acedb
1067	%%DATADIR%%/test/data/prot.m-codata
1068	%%DATADIR%%/test/data/prot.m-fasta
1069	%%DATADIR%%/test/data/prot.m-nbrf
1070	%%DATADIR%%/test/data/prot.m-ncbi
1071	%%DATADIR%%/test/data/prot.m-swiss
1072	%%DATADIR%%/test/data/prot.nbrf
1073	%%DATADIR%%/test/data/prot.ncbi
1074	%%DATADIR%%/test/data/prot.swiss
1075	%%DATADIR%%/test/data/prot.text
1076	%%DATADIR%%/test/data/site.dat
1077	%%DATADIR%%/test/data/tranalign.pep
1078	%%DATADIR%%/test/data/tranalign.seq
1079	%%DATADIR%%/test/data/withrefm
1080	%%DATADIR%%/test/data/z83307.seq
1081	%%DATADIR%%/test/embl/acnum.hit
1082	%%DATADIR%%/test/embl/acnum.trg
1083	%%DATADIR%%/test/embl/des.hit
1084	%%DATADIR%%/test/embl/des.trg
1085	%%DATADIR%%/test/embl/division.lkp
1086	%%DATADIR%%/test/embl/entrynam.idx
1087	%%DATADIR%%/test/embl/est.dat
1088	%%DATADIR%%/test/embl/fun.dat
1089	%%DATADIR%%/test/embl/hum1.dat
1090	%%DATADIR%%/test/embl/inv.dat
1091	%%DATADIR%%/test/embl/keyword.hit
1092	%%DATADIR%%/test/embl/keyword.trg
1093	%%DATADIR%%/test/embl/pln.dat
1094	%%DATADIR%%/test/embl/pro.dat
1095	%%DATADIR%%/test/embl/rod.dat
1096	%%DATADIR%%/test/embl/seqvn.hit
1097	%%DATADIR%%/test/embl/seqvn.trg
1098	%%DATADIR%%/test/embl/sts.dat
1099	%%DATADIR%%/test/embl/taxon.hit
1100	%%DATADIR%%/test/embl/taxon.trg
1101	%%DATADIR%%/test/embl/vrl.dat
1102	%%DATADIR%%/test/embl/vrt.dat
1103	%%DATADIR%%/test/gb/acnum.hit
1104	%%DATADIR%%/test/gb/acnum.trg
1105	%%DATADIR%%/test/gb/ba.ref
1106	%%DATADIR%%/test/gb/ba.seq
1107	%%DATADIR%%/test/gb/des.hit
1108	%%DATADIR%%/test/gb/des.trg
1109	%%DATADIR%%/test/gb/division.lkp
1110	%%DATADIR%%/test/gb/entrynam.idx
1111	%%DATADIR%%/test/gb/htg.ref
1112	%%DATADIR%%/test/gb/htg.seq
1113	%%DATADIR%%/test/gb/keyword.hit
1114	%%DATADIR%%/test/gb/keyword.trg
1115	%%DATADIR%%/test/gb/seqvn.hit
1116	%%DATADIR%%/test/gb/seqvn.trg
1117	%%DATADIR%%/test/gb/taxon.hit
1118	%%DATADIR%%/test/gb/taxon.trg
1119	%%DATADIR%%/test/genbank/acnum.hit
1120	%%DATADIR%%/test/genbank/acnum.trg
1121	%%DATADIR%%/test/genbank/des.hit
1122	%%DATADIR%%/test/genbank/des.trg
1123	%%DATADIR%%/test/genbank/division.lkp
1124	%%DATADIR%%/test/genbank/entrynam.idx
1125	%%DATADIR%%/test/genbank/gbbct1.seq
1126	%%DATADIR%%/test/genbank/gbest1.seq
1127	%%DATADIR%%/test/genbank/gbinv1.seq
1128	%%DATADIR%%/test/genbank/gbpln1.seq
1129	%%DATADIR%%/test/genbank/gbpln2.seq
1130	%%DATADIR%%/test/genbank/gbpri1.seq
1131	%%DATADIR%%/test/genbank/gbrod1.seq
1132	%%DATADIR%%/test/genbank/gbsts1.seq
1133	%%DATADIR%%/test/genbank/gbvrl1.seq
1134	%%DATADIR%%/test/genbank/gbvrt.seq
1135	%%DATADIR%%/test/genbank/keyword.hit
1136	%%DATADIR%%/test/genbank/keyword.trg
1137	%%DATADIR%%/test/genbank/seqvn.hit
1138	%%DATADIR%%/test/genbank/seqvn.trg
1139	%%DATADIR%%/test/genbank/taxon.hit
1140	%%DATADIR%%/test/genbank/taxon.trg
1141	%%DATADIR%%/test/pir/acnum.hit
1142	%%DATADIR%%/test/pir/acnum.trg
1143	%%DATADIR%%/test/pir/des.hit
1144	%%DATADIR%%/test/pir/des.trg
1145	%%DATADIR%%/test/pir/division.lkp
1146	%%DATADIR%%/test/pir/entrynam.idx
1147	%%DATADIR%%/test/pir/keyword.hit
1148	%%DATADIR%%/test/pir/keyword.trg
1149	%%DATADIR%%/test/pir/pir1.header
1150	%%DATADIR%%/test/pir/pir1.names
1151	%%DATADIR%%/test/pir/pir1.numbers
1152	%%DATADIR%%/test/pir/pir1.offset
1153	%%DATADIR%%/test/pir/pir1.ref
1154	%%DATADIR%%/test/pir/pir1.seq
1155	%%DATADIR%%/test/pir/pir2.header
1156	%%DATADIR%%/test/pir/pir2.names
1157	%%DATADIR%%/test/pir/pir2.numbers
1158	%%DATADIR%%/test/pir/pir2.offset
1159	%%DATADIR%%/test/pir/pir2.ref
1160	%%DATADIR%%/test/pir/pir2.seq
1161	%%DATADIR%%/test/pir/pir3.header
1162	%%DATADIR%%/test/pir/pir3.names
1163	%%DATADIR%%/test/pir/pir3.numbers
1164	%%DATADIR%%/test/pir/pir3.offset
1165	%%DATADIR%%/test/pir/pir3.ref
1166	%%DATADIR%%/test/pir/pir3.seq
1167	%%DATADIR%%/test/pir/pir4.header
1168	%%DATADIR%%/test/pir/pir4.names
1169	%%DATADIR%%/test/pir/pir4.numbers
1170	%%DATADIR%%/test/pir/pir4.offset
1171	%%DATADIR%%/test/pir/pir4.ref
1172	%%DATADIR%%/test/pir/pir4.seq
1173	%%DATADIR%%/test/pir/taxon.hit
1174	%%DATADIR%%/test/pir/taxon.trg
1175	%%DATADIR%%/test/swiss/acnum.hit
1176	%%DATADIR%%/test/swiss/acnum.trg
1177	%%DATADIR%%/test/swiss/des.hit
1178	%%DATADIR%%/test/swiss/des.trg
1179	%%DATADIR%%/test/swiss/division.lkp
1180	%%DATADIR%%/test/swiss/entrynam.idx
1181	%%DATADIR%%/test/swiss/keyword.hit
1182	%%DATADIR%%/test/swiss/keyword.trg
1183	%%DATADIR%%/test/swiss/seq.dat
1184	%%DATADIR%%/test/swiss/seqvn.hit
1185	%%DATADIR%%/test/swiss/seqvn.trg
1186	%%DATADIR%%/test/swiss/taxon.hit
1187	%%DATADIR%%/test/swiss/taxon.trg
1188	%%DATADIR%%/test/swnew/acnum.hit
1189	%%DATADIR%%/test/swnew/acnum.trg
1190	%%DATADIR%%/test/swnew/des.hit
1191	%%DATADIR%%/test/swnew/des.trg
1192	%%DATADIR%%/test/swnew/division.lkp
1193	%%DATADIR%%/test/swnew/entrynam.idx
1194	%%DATADIR%%/test/swnew/keyword.hit
1195	%%DATADIR%%/test/swnew/keyword.trg
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1202	%%DATADIR%%/test/swnew/upd_seq.dat
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1204	%%DATADIR%%/test/wormpep/acnum.trg
1205	%%DATADIR%%/test/wormpep/des.hit
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1216	%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
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1225	%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz	296	%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
1226	%%PORTDOCS%%%%DOCSDIR%%/programs/html/aaindexextract.html	297	%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
		298	%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
		299	%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
		300	%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
		301	%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
		302	%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
		303	%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
		304	%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
		305	%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
		306	%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
		307	%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
		308	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
		309	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
		310	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
		311	%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
		312	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
		313	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
		314	%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
		315	%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
		316	%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
		317	%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
		318	%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
		319	%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
		320	%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
		321	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
		322	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
		323	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
		324	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
		325	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
		326	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
		327	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
		328	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
		329	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
		330	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
		331	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
		332	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
		333	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
		334	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
		335	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
		336	%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
		337	%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
		338	%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
		339	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
		340	%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
		341	%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
		342	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
		343	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
		344	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
		345	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
		346	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
		347	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
		348	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
		349	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
		350	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
		351	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
		352	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
		353	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
		354	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
		355	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
		356	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
		357	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
		358	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
		359	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
		360	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
		361	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
362	%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
363	%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
364	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
365	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
366	%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
367	%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
368	%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
369	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
370	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
371	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
372	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
373	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
374	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
375	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
376	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
377	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
378	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
379	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
380	%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
381	%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
382	%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
383	%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
384	%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
385	%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
386	%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
387	%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
388	%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
389	%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
390	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
391	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
392	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
393	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
394	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
395	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
396	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
397	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
398	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
399	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
400	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
401	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
402	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
403	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
404	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
405	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
406	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
407	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
408	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
409	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
410	%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
411	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
412	%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
413	%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
414	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
415	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
416	%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
417	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
418	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
419	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
420	%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
421	%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
422	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
423	%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
424	%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
425	%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
426	%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
427	%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
428	%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
429	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
430	%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
431	%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
432	%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
433	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
434	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
435	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
436	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
437	%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
438	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
439	%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
440	%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
441	%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
442	%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
443	%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
444	%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
445	%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
446	%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
447	%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
448	%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
449	%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
450	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
451	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
452	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
453	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
454	%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
455	%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
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1228	%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html	485	%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html
1229	%%PORTDOCS%%%%DOCSDIR%%/programs/html/acd_group.html	486	%%PORTDOCS%%%%DOCSDIR%%/programs/html/acd_group.html
1230	%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html	487	%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html
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1241	%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_local_group.html	499	%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_local_group.html
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1245	%%PORTDOCS%%%%DOCSDIR%%/programs/html/antigenic.html
1246	%%PORTDOCS%%%%DOCSDIR%%/programs/html/backtranseq.html	503	%%PORTDOCS%%%%DOCSDIR%%/programs/html/backtranseq.html
1247	%%PORTDOCS%%%%DOCSDIR%%/programs/html/banana.html	504	%%PORTDOCS%%%%DOCSDIR%%/programs/html/banana.html
1248	%%PORTDOCS%%%%DOCSDIR%%/programs/html/biosed.html	505	%%PORTDOCS%%%%DOCSDIR%%/programs/html/biosed.html
1249	%%PORTDOCS%%%%DOCSDIR%%/programs/html/btwisted.html	506	%%PORTDOCS%%%%DOCSDIR%%/programs/html/btwisted.html
1250	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cai.html	507	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cai.html
1251	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cathparse.html	508	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cathparse.html
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1255	%%PORTDOCS%%%%DOCSDIR%%/programs/html/checktrans.html	511	%%PORTDOCS%%%%DOCSDIR%%/programs/html/checktrans.html
1256	%%PORTDOCS%%%%DOCSDIR%%/programs/html/chips.html	512	%%PORTDOCS%%%%DOCSDIR%%/programs/html/chips.html
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1260	%%PORTDOCS%%%%DOCSDIR%%/programs/html/codcmp.html	514	%%PORTDOCS%%%%DOCSDIR%%/programs/html/codcmp.html
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1261	%%PORTDOCS%%%%DOCSDIR%%/programs/html/coderet.html	516	%%PORTDOCS%%%%DOCSDIR%%/programs/html/coderet.html
		517	%%PORTDOCS%%%%DOCSDIR%%/programs/html/comparator.html
1262	%%PORTDOCS%%%%DOCSDIR%%/programs/html/compseq.html	518	%%PORTDOCS%%%%DOCSDIR%%/programs/html/compseq.html
1263	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cons.html	519	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cons.html
1264	%%PORTDOCS%%%%DOCSDIR%%/programs/html/consense.html
1265	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contactalign.html	520	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contactalign.html
1266	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contactcount.html
1267	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contacts.html	521	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contacts.html
1268	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contml.html
1269	%%PORTDOCS%%%%DOCSDIR%%/programs/html/contrast.html
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1271	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.html	522	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.html
1272	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgreport.html	523	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgreport.html
1273	%%PORTDOCS%%%%DOCSDIR%%/programs/html/crystalball.html	524	%%PORTDOCS%%%%DOCSDIR%%/programs/html/crystalball.html
1274	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cusp.html	525	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cusp.html
1275	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutgextract.html	526	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutgextract.html
1276	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutseq.html	527	%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutseq.html
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1279	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiblast.html	529	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiblast.html
1280	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbifasta.html	530	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbifasta.html
1281	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiflat.html	531	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiflat.html
1282	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbigcg.html	532	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbigcg.html
		533	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbxfasta.html
		534	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbxflat.html
		535	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbxgcg.html
1283	%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseq.html	536	%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseq.html
1284	%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseqrunner.html	537	%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseqrunner.html
1285	%%PORTDOCS%%%%DOCSDIR%%/programs/html/descseq.html	538	%%PORTDOCS%%%%DOCSDIR%%/programs/html/descseq.html
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1287	%%PORTDOCS%%%%DOCSDIR%%/programs/html/digest.html	540	%%PORTDOCS%%%%DOCSDIR%%/programs/html/digest.html
1288	%%PORTDOCS%%%%DOCSDIR%%/programs/html/display_group.html	541	%%PORTDOCS%%%%DOCSDIR%%/programs/html/display_group.html
1289	%%PORTDOCS%%%%DOCSDIR%%/programs/html/distmat.html	542	%%PORTDOCS%%%%DOCSDIR%%/programs/html/distmat.html
1290	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnacomp.html
1291	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnadist.html
1292	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnainvar.html
1293	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnaml.html
1294	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnamlk.html
1295	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnapars.html
1296	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnapenny.html
1297	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dollop.html
1298	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dolpenny.html
1299	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainalign.html	543	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainalign.html
1300	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainer.html	544	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainer.html
1301	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainnr.html	545	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainnr.html
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1303	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainreso.html	547	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainreso.html
1304	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainseqs.html	548	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainseqs.html
1305	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainsse.html	549	%%PORTDOCS%%%%DOCSDIR%%/programs/html/domainsse.html
1306	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
1307	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.html	550	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.html
1308	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
1309	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.html	551	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.html
1310	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
1311	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.html	552	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.html
1312	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dreg.html	553	%%PORTDOCS%%%%DOCSDIR%%/programs/html/dreg.html
1313	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ealistat.html	554	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ealistat.html
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1339	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmsearch.html	580	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ehmmsearch.html
1340	%%PORTDOCS%%%%DOCSDIR%%/programs/html/einverted.html	581	%%PORTDOCS%%%%DOCSDIR%%/programs/html/einverted.html
1341	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ekitsch.html	582	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ekitsch.html
1342	%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
1343	%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
1344	%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossdata.html	583	%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossdata.html
1345	%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossversion.html	584	%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossversion.html
1346	%%PORTDOCS%%%%DOCSDIR%%/programs/html/emix.html	585	%%PORTDOCS%%%%DOCSDIR%%/programs/html/emix.html
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1363	%%PORTDOCS%%%%DOCSDIR%%/programs/html/etandem.html	602	%%PORTDOCS%%%%DOCSDIR%%/programs/html/etandem.html
1364	%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractfeat.html	603	%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractfeat.html
1365	%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractseq.html	604	%%PORTDOCS%%%%DOCSDIR%%/programs/html/extractseq.html
1366	%%PORTDOCS%%%%DOCSDIR%%/programs/html/factor.html
1367	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fclique.html	605	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fclique.html
1368	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fconsense.html	606	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fconsense.html
1369	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fcontml.html	607	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fcontml.html
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1387	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffitch.html	625	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffitch.html
1388	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffreqboot.html	626	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ffreqboot.html
1389	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fgendist.html	627	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fgendist.html
1390	%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
1391	%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.html	628	%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.html
1392	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fitch.html
1393	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fkitsch.html	629	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fkitsch.html
1394	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmix.html	630	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmix.html
1395	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmove.html	631	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fmove.html
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1414	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzztran.html	650	%%PORTDOCS%%%%DOCSDIR%%/programs/html/fuzztran.html
1415	%%PORTDOCS%%%%DOCSDIR%%/programs/html/garnier.html	651	%%PORTDOCS%%%%DOCSDIR%%/programs/html/garnier.html
1416	%%PORTDOCS%%%%DOCSDIR%%/programs/html/geecee.html	652	%%PORTDOCS%%%%DOCSDIR%%/programs/html/geecee.html
1417	%%PORTDOCS%%%%DOCSDIR%%/programs/html/gendist.html
1418	%%PORTDOCS%%%%DOCSDIR%%/programs/html/getorf.html	653	%%PORTDOCS%%%%DOCSDIR%%/programs/html/getorf.html
1419	%%PORTDOCS%%%%DOCSDIR%%/programs/html/groups.html	654	%%PORTDOCS%%%%DOCSDIR%%/programs/html/groups.html
1420	%%PORTDOCS%%%%DOCSDIR%%/programs/html/helixturnhelix.html	655	%%PORTDOCS%%%%DOCSDIR%%/programs/html/helixturnhelix.html
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1427	%%PORTDOCS%%%%DOCSDIR%%/programs/html/information_group.html	662	%%PORTDOCS%%%%DOCSDIR%%/programs/html/information_group.html
1428	%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoseq.html	663	%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoseq.html
1429	%%PORTDOCS%%%%DOCSDIR%%/programs/html/interface.html	664	%%PORTDOCS%%%%DOCSDIR%%/programs/html/interface.html
1430	%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
1431	%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.html	665	%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.html
1432	%%PORTDOCS%%%%DOCSDIR%%/programs/html/jembossctl.html	666	%%PORTDOCS%%%%DOCSDIR%%/programs/html/jembossctl.html
1433	%%PORTDOCS%%%%DOCSDIR%%/programs/html/kitsch.html
1434	%%PORTDOCS%%%%DOCSDIR%%/programs/html/libgen.html	667	%%PORTDOCS%%%%DOCSDIR%%/programs/html/libgen.html
1435	%%PORTDOCS%%%%DOCSDIR%%/programs/html/libscan.html	668	%%PORTDOCS%%%%DOCSDIR%%/programs/html/libscan.html
1436	%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif	669	%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
1437	%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html	670	%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
1438	%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html	671	%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
1439	%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html	672	%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
1440	%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html	673	%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
1441	%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html	674	%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
1442	%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html	675	%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
1443	%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html	676	%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
1444	%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html	677	%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
1445	%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html	678	%%PORTDOCS%%%%DOCSDIR%%/programs/text/matgen3d.txt
1446	%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html	679	%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
1447	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mix.html	680	%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
1448	%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html	681	%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
1449	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html	682	%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
1450	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html	683	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
1451	%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html	684	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
1452	%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html	685	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
1453	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html	686	%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
1454	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html	687	%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
1455	%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html	688	%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
1456	%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html	689	%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
1457	%%PORTDOCS%%%%DOCSDIR%%/programs/html/neighbor.html	690	%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
1458	%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html	691	%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
1459	%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html	692	%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
1460	%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html	693	%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
1461	%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html	694	%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
1462	%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html	695	%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
1463	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html	696	%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
1464	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html	697	%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
1465	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html	698	%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
1466	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html	699	%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
1467	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html	700	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
1468	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html	701	%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
1469	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html	702	%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
1470	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html	703	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
1471	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html	704	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
1472	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html	705	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
1473	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html	706	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
1474	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html	707	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
1475	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html	708	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
1476	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html	709	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
1477	%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html	710	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
1478	%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif	711	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
1479	%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html	712	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
1480	%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html	713	%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
1481	%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html	714	%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
1482	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html	715	%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
1483	%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html	716	%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
1484	%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html	717	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
1485	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html	718	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
1486	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html	719	%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
1487	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html	720	%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
1488	%%PORTDOCS%%%%DOCSDIR%%/programs/html/penny.html	721	%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
1489	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html	722	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
1490	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif	723	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
1491	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html	724	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
1492	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif	725	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
1493	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html	726	%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
1494	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html	727	%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
1495	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif	728	%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
1496	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html	729	%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
1497	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif	730	%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
1498	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html	731	%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
1499	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif	732	%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
1500	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html	733	%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
1501	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pestfind.html	734	%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
1502	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html	735	%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
1503	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html	736	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
1504	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html	737	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
1505	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html	738	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorecmapdir.txt
1506	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html	739	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
1507	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html	740	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
1508	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html	741	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
1509	%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html	742	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
1510	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif	743	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
1511	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html	744	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
1512	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif	745	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
1513	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif	746	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
1514	%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html	747	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
1515	%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif	748	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
1516	%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html	749	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
1517	%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html	750	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
1518	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif	751	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
1519	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif	752	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
1520	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html	753	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
1521	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html	754	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
1522	%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html	755	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
1523	%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html	756	%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
1524	%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html	757	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
1525	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html	758	%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
1526	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html	759	%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggenlig.txt
1527	%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html	760	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
1528	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protdist.html	761	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscanlig.txt
1529	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html	762	%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
1530	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html	763	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
1531	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html	764	%%PORTDOCS%%%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt
1532	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html	765	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
1533	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html	766	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
1534	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html	767	%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
1535	%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html	768	%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
1536	%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html	769	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
1537	%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html	770	%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
1538	%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html	771	%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
1539	%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html	772	%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
1540	%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html	773	%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
1541	%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html	774	%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
1542	%%PORTDOCS%%%%DOCSDIR%%/programs/html/restml.html	775	%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
1543	%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html	776	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
1544	%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html	777	%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
1545	%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html	778	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
1546	%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html	779	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
1547	%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html	780	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
1548	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html	781	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
1549	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html	782	%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
1550	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html	783	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
1551	%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html	784	%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
1552	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html	785	%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
1553	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html	786	%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
1554	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqboot.html	787	%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
1555	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html	788	%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
1556	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html	789	%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
1557	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html	790	%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
1558	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html	791	%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
1559	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html	792	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
1560	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html	793	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
1561	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html	794	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
1562	%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html	795	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
1563	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html	796	%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
1564	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
1565	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
1566	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
1567	%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
1568	%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
1569	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
1570	%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
1571	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
1572	%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
1573	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
1574	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
1575	%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
1576	%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
1577	%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
1578	%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
1579	%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
1580	%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
1581	%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
1582	%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
1583	%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
1584	%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.1.syco.gif
1585	%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
1586	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
1587	%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
1588	%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
1589	%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
1590	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
1591	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
1592	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
1593	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.1.tmap.gif
1594	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
1595	%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.gif
1596	%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
1597	%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
1598	%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
1599	%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
1600	%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
1601	%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
1602	%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
1603	%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
1604	%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
1605	%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
1606	%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
1607	%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
1608	%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
1609	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.1.wobble.gif
1610	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
1611	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
1612	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
1613	%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
1614	%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
1615	%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt	797	%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt
1616	%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt	798	%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt
1617	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt	799	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt
1618	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt	800	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt
1619	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt	801	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt
1620	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt	802	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt
		803	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
1621	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt	804	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt
1622	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt	805	%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt
1623	%%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt	806	%%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt
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1627	%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt	810	%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt
1628	%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt	811	%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt
1629	%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt	812	%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt
1630	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
1631	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt	813	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt
1632	%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt	814	%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt
1633	%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt	815	%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt
1634	%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt	816	%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt
1635	%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt	817	%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt
1636	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt	818	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt
1637	%%PORTDOCS%%%%DOCSDIR%%/programs/text/clique.txt
1638	%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt	819	%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt
		820	%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcopy.txt
1639	%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt	821	%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt
		822	%%PORTDOCS%%%%DOCSDIR%%/programs/text/comparator.txt
1640	%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt	823	%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt
1641	%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt	824	%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt
1642	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt	825	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt
1643	%%PORTDOCS%%%%DOCSDIR%%/programs/text/consense.txt
1644	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactalign.txt	826	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactalign.txt
1645	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactcount.txt
1646	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt	827	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt
1647	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contml.txt
1648	%%PORTDOCS%%%%DOCSDIR%%/programs/text/contrast.txt
1649	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt	828	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt
1650	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt	829	%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt
1651	%%PORTDOCS%%%%DOCSDIR%%/programs/text/crystalball.txt	830	%%PORTDOCS%%%%DOCSDIR%%/programs/text/crystalball.txt
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1657	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt	836	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt
1658	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt	837	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt
1659	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt	838	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt
		839	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxfasta.txt
		840	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxflat.txt
		841	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxgcg.txt
1660	%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt	842	%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
1661	%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt	843	%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt
1662	%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt	844	%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
1663	%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt	845	%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
1664	%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt	846	%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
1665	%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt	847	%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
1666	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnacomp.txt
1667	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnadist.txt
1668	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnainvar.txt
1669	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnaml.txt
1670	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnamlk.txt
1671	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapars.txt
1672	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapenny.txt
1673	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dollop.txt
1674	%%PORTDOCS%%%%DOCSDIR%%/programs/text/dolpenny.txt
1675	%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt	848	%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt
1676	%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt	849	%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt
1677	%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt	850	%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt
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1696	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt	869	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt
1697	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt	870	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt
1698	%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt	871	%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt
		872	%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
1699	%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt	873	%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt
1700	%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt	874	%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt
1701	%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt	875	%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt
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1732	%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt	906	%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
1733	%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt	907	%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
1734	%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt	908	%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
1735	%%PORTDOCS%%%%DOCSDIR%%/programs/text/factor.txt
1736	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt	909	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt
1737	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt	910	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt
1738	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt	911	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt
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1756	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt	929	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
1757	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt	930	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
1758	%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt	931	%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
1759	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fitch.txt
1760	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt	932	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
1761	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt	933	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
1762	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt	934	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
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1781	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt	953	%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
1782	%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt	954	%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
1783	%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt	955	%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
1784	%%PORTDOCS%%%%DOCSDIR%%/programs/text/gendist.txt
1785	%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt	956	%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
1786	%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt	957	%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
1787	%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt	958	%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt
1788	%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt	959	%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
1789	%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt	960	%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
1790	%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt	961	%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
1791	%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt	962	%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
1792	%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt	963	%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
1793	%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
1794	%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
1795	%%PORTDOCS%%%%DOCSDIR%%/programs/text/kitsch.txt
1796	%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
1797	%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
1798	%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
1799	%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
1800	%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
1801	%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
1802	%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
1803	%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
1804	%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
1805	%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
1806	%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
1807	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mix.txt
1808	%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
1809	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
1810	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
1811	%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
1812	%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
1813	%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
1814	%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
1815	%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
1816	%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
1817	%%PORTDOCS%%%%DOCSDIR%%/programs/text/neighbor.txt
1818	%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
1819	%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
1820	%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
1821	%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
1822	%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
1823	%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
1824	%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
1825	%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
1826	%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
1827	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
1828	%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
1829	%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
1830	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
1831	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
1832	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
1833	%%PORTDOCS%%%%DOCSDIR%%/programs/text/penny.txt
1834	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
1835	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
1836	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
1837	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
1838	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
1839	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
1840	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
1841	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pestfind.txt
1842	%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
1843	%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
1844	%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
1845	%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
1846	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
1847	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
1848	%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
1849	%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
1850	%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
1851	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
1852	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
1853	%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
1854	%%PORTDOCS%%%%DOCSDIR%%/programs/text/protdist.txt
1855	%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
1856	%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
1857	%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
1858	%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
1859	%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
1860	%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
1861	%%PORTDOCS%%%%DOCSDIR%%/programs/text/restml.txt
1862	%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
1863	%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
1864	%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
1865	%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
1866	%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
1867	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
1868	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
1869	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
1870	%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
1871	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
1872	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
1873	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqboot.txt
1874	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
1875	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
1876	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
1877	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
1878	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
1879	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
1880	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
1881	%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
1882	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
1883	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
1884	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
1885	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
1886	%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
1887	%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
1888	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
1889	%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
1890	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
1891	%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
1892	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
1893	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
1894	%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
1895	%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
1896	%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
1897	%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
1898	%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
1899	%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
1900	%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
1901	%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
1902	%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
1903	%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
1904	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
1905	%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
1906	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
1907	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
1908	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
1909	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
1910	%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
1911	%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
1912	%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
1913	%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
1914	%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
1915	%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
1916	%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
1917	%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
1918	%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
1919	%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
1920	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
1921	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
1922	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
1923	%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
1924	%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
1925	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt	964	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
1926	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt	965	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
1927	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt	966	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
1928	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz	967	%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
1929	%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials	968	%%DATADIR%%/plstnd5.fnt
1930	%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text	969	%%DATADIR%%/plxtnd5.fnt
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1034	%%DATADIR%%/acd/sixpack.acd
1035	%%DATADIR%%/acd/skipseq.acd
1036	%%DATADIR%%/acd/tfm.acd
1037	%%DATADIR%%/acd/splitter.acd
1038	%%DATADIR%%/acd/stretcher.acd
1039	%%DATADIR%%/acd/stssearch.acd
1040	%%DATADIR%%/acd/supermatcher.acd
1041	%%DATADIR%%/acd/syco.acd
1042	%%DATADIR%%/acd/tcode.acd
1043	%%DATADIR%%/acd/testplot.acd
1044	%%DATADIR%%/acd/textsearch.acd
1045	%%DATADIR%%/acd/tfextract.acd
1046	%%DATADIR%%/acd/tfscan.acd
1047	%%DATADIR%%/acd/tmap.acd
1048	%%DATADIR%%/acd/tranalign.acd
1049	%%DATADIR%%/acd/transeq.acd
1050	%%DATADIR%%/acd/treetypedisplay.acd
1051	%%DATADIR%%/acd/trimest.acd
1052	%%DATADIR%%/acd/trimseq.acd
1053	%%DATADIR%%/acd/twofeat.acd
1054	%%DATADIR%%/acd/union.acd
1055	%%DATADIR%%/acd/vectorstrip.acd
1056	%%DATADIR%%/acd/water.acd
1057	%%DATADIR%%/acd/whichdb.acd
1058	%%DATADIR%%/acd/wobble.acd
1059	%%DATADIR%%/acd/wordcount.acd
1060	%%DATADIR%%/acd/wordmatch.acd
1061	%%DATADIR%%/acd/wossname.acd
1062	%%DATADIR%%/acd/yank.acd
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1065	%%DATADIR%%/acd/knowntypes.standard
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1067	%%DATADIR%%/acd/variables.standard
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1070	%%DATADIR%%/acd/acdc.acd
1071	%%DATADIR%%/acd/acdlog.acd
1072	%%DATADIR%%/acd/acdpretty.acd
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1074	%%DATADIR%%/acd/acdtrace.acd
1075	%%DATADIR%%/acd/acdvalid.acd
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1077	%%DATADIR%%/acd/ajfeatest.acd
1078	%%DATADIR%%/acd/ajtest.acd
1079	%%DATADIR%%/acd/antigenic.acd
1080	%%DATADIR%%/acd/backtranseq.acd
1081	%%DATADIR%%/acd/cai.acd
1082	%%DATADIR%%/acd/banana.acd
1083	%%DATADIR%%/acd/biosed.acd
1084	%%DATADIR%%/acd/btwisted.acd
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1088	%%DATADIR%%/acd/chips.acd
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1091	%%DATADIR%%/acd/codcopy.acd
1092	%%DATADIR%%/acd/coderet.acd
1093	%%DATADIR%%/acd/complex.acd
1094	%%DATADIR%%/acd/compseq.acd
1095	%%DATADIR%%/acd/cons.acd
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1098	%%DATADIR%%/acd/cpgreport.acd
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1267	%%DATADIR%%/data/CODONS/Etobac.cut
1268	%%DATADIR%%/data/CODONS/Etobac_chl.cut
1269	%%DATADIR%%/data/CODONS/Etrybr.cut
1270	%%DATADIR%%/data/CODONS/Etrycr.cut
1271	%%DATADIR%%/data/CODONS/Evibch.cut
1272	%%DATADIR%%/data/CODONS/Ewheat.cut
1273	%%DATADIR%%/data/CODONS/Exenla.cut
1274	%%DATADIR%%/data/CODONS/Eyeast.cut
1275	%%DATADIR%%/data/CODONS/Eyeast_cai.cut
1276	%%DATADIR%%/data/CODONS/Eyeast_high.cut
1277	%%DATADIR%%/data/CODONS/Eyeast_mit.cut
1278	%%DATADIR%%/data/CODONS/Eyeren.cut
1279	%%DATADIR%%/data/CODONS/Eyerpe.cut
1280	%%DATADIR%%/data/CODONS/Eacc.cut
1281	%%DATADIR%%/data/CODONS/Eadenovirus5.cut
1282	%%DATADIR%%/data/CODONS/Eadenovirus7.cut
1283	%%DATADIR%%/data/CODONS/Eaidlav.cut
1284	%%DATADIR%%/data/CODONS/Eani.cut
1285	%%DATADIR%%/data/CODONS/Eani_h.cut
1286	%%DATADIR%%/data/CODONS/Eanidmit.cut
1287	%%DATADIR%%/data/CODONS/Easn.cut
1288	%%DATADIR%%/data/CODONS/Eath.cut
1289	%%DATADIR%%/data/CODONS/Eatu.cut
1290	%%DATADIR%%/data/CODONS/Eavi.cut
1291	%%DATADIR%%/data/CODONS/Ef1.cut
1292	%%DATADIR%%/data/CODONS/Ebja.cut
1293	%%DATADIR%%/data/CODONS/Ebly.cut
1294	%%DATADIR%%/data/CODONS/Ebme.cut
1295	%%DATADIR%%/data/CODONS/Ebmo.cut
1296	%%DATADIR%%/data/CODONS/Ebna.cut
1297	%%DATADIR%%/data/CODONS/Ebov.cut
1298	%%DATADIR%%/data/CODONS/Ebovsp.cut
1299	%%DATADIR%%/data/CODONS/Ebst.cut
1300	%%DATADIR%%/data/CODONS/Ebsu.cut
1301	%%DATADIR%%/data/CODONS/Ebsu_h.cut
1302	%%DATADIR%%/data/CODONS/Ecac.cut
1303	%%DATADIR%%/data/CODONS/Ecal.cut
1304	%%DATADIR%%/data/CODONS/Eccr.cut
1305	%%DATADIR%%/data/CODONS/Ecel.cut
1306	%%DATADIR%%/data/CODONS/Echi.cut
1307	%%DATADIR%%/data/CODONS/Echicken.cut
1308	%%DATADIR%%/data/CODONS/Echisp.cut
1309	%%DATADIR%%/data/CODONS/Echk.cut
1310	%%DATADIR%%/data/CODONS/Echmp.cut
1311	%%DATADIR%%/data/CODONS/Echnt.cut
1312	%%DATADIR%%/data/CODONS/Echos.cut
1313	%%DATADIR%%/data/CODONS/Echzm.cut
1314	%%DATADIR%%/data/CODONS/Echzmrubp.cut
1315	%%DATADIR%%/data/CODONS/Ecpx.cut
1316	%%DATADIR%%/data/CODONS/Ecre.cut
1317	%%DATADIR%%/data/CODONS/Ecrisp.cut
1318	%%DATADIR%%/data/CODONS/Ectr.cut
1319	%%DATADIR%%/data/CODONS/Eddi.cut
1320	%%DATADIR%%/data/CODONS/Eddi_h.cut
1321	%%DATADIR%%/data/CODONS/Edog.cut
1322	%%DATADIR%%/data/CODONS/Edro.cut
1323	%%DATADIR%%/data/CODONS/Edro_h.cut
1324	%%DATADIR%%/data/CODONS/Edrosophila.cut
1325	%%DATADIR%%/data/CODONS/Eeca.cut
1326	%%DATADIR%%/data/CODONS/Eeco.cut
1327	%%DATADIR%%/data/CODONS/Eeco_h.cut
1328	%%DATADIR%%/data/CODONS/Efish.cut
1329	%%DATADIR%%/data/CODONS/Efmdvpolyp.cut
1330	%%DATADIR%%/data/CODONS/Eham.cut
1331	%%DATADIR%%/data/CODONS/Ehha.cut
1332	%%DATADIR%%/data/CODONS/Ehin.cut
1333	%%DATADIR%%/data/CODONS/Ehma.cut
1334	%%DATADIR%%/data/CODONS/Ehum.cut
1335	%%DATADIR%%/data/CODONS/Ekla.cut
1336	%%DATADIR%%/data/CODONS/Ekpn.cut
1337	%%DATADIR%%/data/CODONS/Ella.cut
1338	%%DATADIR%%/data/CODONS/Emac.cut
1339	%%DATADIR%%/data/CODONS/Emam_h.cut
1340	%%DATADIR%%/data/CODONS/Emixlg.cut
1341	%%DATADIR%%/data/CODONS/Emsa.cut
1342	%%DATADIR%%/data/CODONS/Emse.cut
1343	%%DATADIR%%/data/CODONS/Emta.cut
1344	%%DATADIR%%/data/CODONS/Emtu.cut
1345	%%DATADIR%%/data/CODONS/Emus.cut
1346	%%DATADIR%%/data/CODONS/Emussp.cut
1347	%%DATADIR%%/data/CODONS/Emva.cut
1348	%%DATADIR%%/data/CODONS/Emze.cut
1349	%%DATADIR%%/data/CODONS/Emzecp.cut
1350	%%DATADIR%%/data/CODONS/Encr.cut
1351	%%DATADIR%%/data/CODONS/Eneu.cut
1352	%%DATADIR%%/data/CODONS/Engo.cut
1353	%%DATADIR%%/data/CODONS/Eoncsp.cut
1354	%%DATADIR%%/data/CODONS/Epae.cut
1355	%%DATADIR%%/data/CODONS/Epet.cut
1356	%%DATADIR%%/data/CODONS/Epfa.cut
1357	%%DATADIR%%/data/CODONS/Ephix174.cut
1358	%%DATADIR%%/data/CODONS/Ephv.cut
1359	%%DATADIR%%/data/CODONS/Ephy.cut
1360	%%DATADIR%%/data/CODONS/Epolyomaa2.cut
1361	%%DATADIR%%/data/CODONS/Epombe.cut
1362	%%DATADIR%%/data/CODONS/Epombecai.cut
1363	%%DATADIR%%/data/CODONS/Epot.cut
1364	%%DATADIR%%/data/CODONS/Eppu.cut
1365	%%DATADIR%%/data/CODONS/Epse.cut
1366	%%DATADIR%%/data/CODONS/Epsy.cut
1367	%%DATADIR%%/data/CODONS/Epvu.cut
1368	%%DATADIR%%/data/CODONS/Erab.cut
1369	%%DATADIR%%/data/CODONS/Erabbit.cut
1370	%%DATADIR%%/data/CODONS/Erabsp.cut
1371	%%DATADIR%%/data/CODONS/Eratsp.cut
1372	%%DATADIR%%/data/CODONS/Erca.cut
1373	%%DATADIR%%/data/CODONS/Erhm.cut
1374	%%DATADIR%%/data/CODONS/Eric.cut
1375	%%DATADIR%%/data/CODONS/Erle.cut
1376	%%DATADIR%%/data/CODONS/Erme.cut
1377	%%DATADIR%%/data/CODONS/Ersp.cut
1378	%%DATADIR%%/data/CODONS/Esalsp.cut
1379	%%DATADIR%%/data/CODONS/Esau.cut
1380	%%DATADIR%%/data/CODONS/Esco.cut
1381	%%DATADIR%%/data/CODONS/Esgi.cut
1382	%%DATADIR%%/data/CODONS/Eshp.cut
1383	%%DATADIR%%/data/CODONS/Eshpsp.cut
1384	%%DATADIR%%/data/CODONS/Esli.cut
1385	%%DATADIR%%/data/CODONS/Eslm.cut
1386	%%DATADIR%%/data/CODONS/Esma.cut
1387	%%DATADIR%%/data/CODONS/Esmi.cut
1388	%%DATADIR%%/data/CODONS/Esmu.cut
1389	%%DATADIR%%/data/CODONS/Esoy.cut
1390	%%DATADIR%%/data/CODONS/Espi.cut
1391	%%DATADIR%%/data/CODONS/Espn.cut
1392	%%DATADIR%%/data/CODONS/Espo.cut
1393	%%DATADIR%%/data/CODONS/Espo_h.cut
1394	%%DATADIR%%/data/CODONS/Espu.cut
1395	%%DATADIR%%/data/CODONS/Esta.cut
1396	%%DATADIR%%/data/CODONS/Esty.cut
1397	%%DATADIR%%/data/CODONS/Esus.cut
1398	%%DATADIR%%/data/CODONS/Esv40.cut
1399	%%DATADIR%%/data/CODONS/Esyhsp.cut
1400	%%DATADIR%%/data/CODONS/Esynsp.cut
1401	%%DATADIR%%/data/CODONS/Etbr.cut
1402	%%DATADIR%%/data/CODONS/Etcr.cut
1403	%%DATADIR%%/data/CODONS/Eter.cut
1404	%%DATADIR%%/data/CODONS/Etetsp.cut
1405	%%DATADIR%%/data/CODONS/Etob.cut
1406	%%DATADIR%%/data/CODONS/Etobcp.cut
1407	%%DATADIR%%/data/CODONS/Etom.cut
1408	%%DATADIR%%/data/CODONS/Etrb.cut
1409	%%DATADIR%%/data/CODONS/Evco.cut
1410	%%DATADIR%%/data/CODONS/Ewht.cut
1411	%%DATADIR%%/data/CODONS/Exel.cut
1412	%%DATADIR%%/data/CODONS/Exenopus.cut
1413	%%DATADIR%%/data/CODONS/Eyeastcai.cut
1414	%%DATADIR%%/data/CODONS/Eyen.cut
1415	%%DATADIR%%/data/CODONS/Eysc.cut
1416	%%DATADIR%%/data/CODONS/Eysc_h.cut
1417	%%DATADIR%%/data/CODONS/Eyscmt.cut
1418	%%DATADIR%%/data/CODONS/Eysp.cut
1419	%%DATADIR%%/data/CODONS/Ezebrafish.cut
1420	%%DATADIR%%/data/CODONS/Ezma.cut
1421	%%DATADIR%%/data/REBASE/dummyfile
1422	%%DATADIR%%/data/PRINTS/dummyfile
1423	%%DATADIR%%/data/PROSITE/dummyfile
1424	%%DATADIR%%/data/EBLOSUM30
1425	%%DATADIR%%/data/EBLOSUM35
1426	%%DATADIR%%/data/EBLOSUM40
1427	%%DATADIR%%/data/EBLOSUM45
1428	%%DATADIR%%/data/EBLOSUM50
1429	%%DATADIR%%/data/EBLOSUM55
1430	%%DATADIR%%/data/EBLOSUM60
1431	%%DATADIR%%/data/EBLOSUM62
1432	%%DATADIR%%/data/EBLOSUM62-12
1433	%%DATADIR%%/data/EBLOSUM65
1434	%%DATADIR%%/data/EBLOSUM70
1435	%%DATADIR%%/data/EBLOSUM75
1436	%%DATADIR%%/data/EBLOSUM80
1437	%%DATADIR%%/data/EBLOSUM85
1438	%%DATADIR%%/data/EBLOSUM90
1439	%%DATADIR%%/data/EBLOSUMN
1440	%%DATADIR%%/data/EDNAFULL
1441	%%DATADIR%%/data/EDNAMAT
1442	%%DATADIR%%/data/EGC.0
1443	%%DATADIR%%/data/EGC.1
1444	%%DATADIR%%/data/EGC.10
1445	%%DATADIR%%/data/EGC.11
1446	%%DATADIR%%/data/EGC.12
1447	%%DATADIR%%/data/EGC.13
1448	%%DATADIR%%/data/EGC.14
1449	%%DATADIR%%/data/EGC.15
1450	%%DATADIR%%/data/EGC.16
1451	%%DATADIR%%/data/EGC.2
1452	%%DATADIR%%/data/EGC.21
1453	%%DATADIR%%/data/EGC.22
1454	%%DATADIR%%/data/EGC.23
1455	%%DATADIR%%/data/EGC.3
1456	%%DATADIR%%/data/EGC.4
1457	%%DATADIR%%/data/EGC.5
1458	%%DATADIR%%/data/EGC.6
1459	%%DATADIR%%/data/EGC.9
1460	%%DATADIR%%/data/EGC.index
1461	%%DATADIR%%/data/EGC.txt
1462	%%DATADIR%%/data/ENUC.4.2
1463	%%DATADIR%%/data/ENUC.4.4
1464	%%DATADIR%%/data/EPAM10
1465	%%DATADIR%%/data/EPAM100
1466	%%DATADIR%%/data/EPAM110
1467	%%DATADIR%%/data/EPAM120
1468	%%DATADIR%%/data/EPAM130
1469	%%DATADIR%%/data/EPAM140
1470	%%DATADIR%%/data/EPAM150
1471	%%DATADIR%%/data/EPAM160
1472	%%DATADIR%%/data/EPAM170
1473	%%DATADIR%%/data/EPAM180
1474	%%DATADIR%%/data/EPAM190
1475	%%DATADIR%%/data/EPAM20
1476	%%DATADIR%%/data/EPAM200
1477	%%DATADIR%%/data/EPAM210
1478	%%DATADIR%%/data/EPAM220
1479	%%DATADIR%%/data/EPAM230
1480	%%DATADIR%%/data/EPAM240
1481	%%DATADIR%%/data/EPAM250
1482	%%DATADIR%%/data/EPAM260
1483	%%DATADIR%%/data/EPAM270
1484	%%DATADIR%%/data/EPAM280
1485	%%DATADIR%%/data/EPAM290
1486	%%DATADIR%%/data/EPAM30
1487	%%DATADIR%%/data/EPAM300
1488	%%DATADIR%%/data/EPAM310
1489	%%DATADIR%%/data/EPAM320
1490	%%DATADIR%%/data/EPAM330
1491	%%DATADIR%%/data/EPAM340
1492	%%DATADIR%%/data/EPAM350
1493	%%DATADIR%%/data/EPAM360
1494	%%DATADIR%%/data/EPAM370
1495	%%DATADIR%%/data/EPAM380
1496	%%DATADIR%%/data/EPAM390
1497	%%DATADIR%%/data/EPAM40
1498	%%DATADIR%%/data/EPAM400
1499	%%DATADIR%%/data/EPAM410
1500	%%DATADIR%%/data/EPAM420
1501	%%DATADIR%%/data/EPAM430
1502	%%DATADIR%%/data/EPAM440
1503	%%DATADIR%%/data/EPAM450
1504	%%DATADIR%%/data/EPAM460
1505	%%DATADIR%%/data/EPAM470
1506	%%DATADIR%%/data/EPAM480
1507	%%DATADIR%%/data/EPAM490
1508	%%DATADIR%%/data/EPAM50
1509	%%DATADIR%%/data/EPAM500
1510	%%DATADIR%%/data/EPAM60
1511	%%DATADIR%%/data/EPAM70
1512	%%DATADIR%%/data/EPAM80
1513	%%DATADIR%%/data/EPAM90
1514	%%DATADIR%%/data/Eaa_acc_surface.dat
1515	%%DATADIR%%/data/Eaa_hydropathy.dat
1516	%%DATADIR%%/data/Eaa_properties.dat
1517	%%DATADIR%%/data/Eamino.dat
1518	%%DATADIR%%/data/Eangles.dat
1519	%%DATADIR%%/data/Eangles_tri.dat
1520	%%DATADIR%%/data/Eantigenic.dat
1521	%%DATADIR%%/data/Ebases.iub
1522	%%DATADIR%%/data/Edayhoff.freq
1523	%%DATADIR%%/data/Edna.melt
1524	%%DATADIR%%/data/Eembl.ior
1525	%%DATADIR%%/data/Eenergy.dat
1526	%%DATADIR%%/data/Efeatures.embl
1527	%%DATADIR%%/data/Efeatures.emboss
1528	%%DATADIR%%/data/Efeatures.gff
1529	%%DATADIR%%/data/Efeatures.pir
1530	%%DATADIR%%/data/Efeatures.protein
1531	%%DATADIR%%/data/Efeatures.swiss
1532	%%DATADIR%%/data/Efreqs.dat
1533	%%DATADIR%%/data/Ehet.dat
1534	%%DATADIR%%/data/Ehth.dat
1535	%%DATADIR%%/data/Ehth87.dat
1536	%%DATADIR%%/data/Ememe.dat
1537	%%DATADIR%%/data/Enakai.dat
1538	%%DATADIR%%/data/Epepcoil.dat
1539	%%DATADIR%%/data/Epk.dat
1540	%%DATADIR%%/data/Epprofile
1541	%%DATADIR%%/data/Eprior1.plib
1542	%%DATADIR%%/data/Eprior30.plib
1543	%%DATADIR%%/data/Erna.melt
1544	%%DATADIR%%/data/Esig.euk
1545	%%DATADIR%%/data/Esig.pro
1546	%%DATADIR%%/data/Etags.embl
1547	%%DATADIR%%/data/Etags.emboss
1548	%%DATADIR%%/data/Etags.gff
1549	%%DATADIR%%/data/Etags.pir
1550	%%DATADIR%%/data/Etags.protein
1551	%%DATADIR%%/data/Etags.swiss
1552	%%DATADIR%%/data/Etcode.dat
1553	%%DATADIR%%/data/Evdw.dat
1554	%%DATADIR%%/data/Ewhite-wimley.dat
1555	%%DATADIR%%/data/embossre.equ
1556	%%DATADIR%%/data/Emwfilter.dat
1557	%%DATADIR%%/data/Emass.dat
1558	%%DATADIR%%/data/Emassmod.dat
1559	%%DATADIR%%/data/Matrices.nucleotide
1560	%%DATADIR%%/data/Matrices.protein
1561	%%DATADIR%%/data/Matrices.proteinstructure
1562	%%DATADIR%%/emboss.default.template
1563	%%DATADIR%%/test/data/aaindex1.test
1564	%%DATADIR%%/test/data/prosite.dat
1565	%%DATADIR%%/test/data/prosite.doc
1566	%%DATADIR%%/test/data/prints.test
1567	%%DATADIR%%/test/data/withrefm
1568	%%DATADIR%%/test/data/site.dat
1569	%%DATADIR%%/test/data/cutg.codon
1570	%%DATADIR%%/test/data/dna.acedb
1571	%%DATADIR%%/test/data/dna.aln
1572	%%DATADIR%%/test/data/dna.asn1
1573	%%DATADIR%%/test/data/dna.codata
1574	%%DATADIR%%/test/data/dna.embl
1575	%%DATADIR%%/test/data/dna.fasta
1576	%%DATADIR%%/test/data/dna.fitch
1577	%%DATADIR%%/test/data/dna.gcg
1578	%%DATADIR%%/test/data/dna.gcg8
1579	%%DATADIR%%/test/data/dna.genbank
1580	%%DATADIR%%/test/data/dna.ig
1581	%%DATADIR%%/test/data/dna.m-acedb
1582	%%DATADIR%%/test/data/dna.m-codata
1583	%%DATADIR%%/test/data/dna.m-embl
1584	%%DATADIR%%/test/data/dna.m-fasta
1585	%%DATADIR%%/test/data/dna.m-fasta-long
1586	%%DATADIR%%/test/data/dna.m-ncbi
1587	%%DATADIR%%/test/data/dna.m-strider
1588	%%DATADIR%%/test/data/dna.msf
1589	%%DATADIR%%/test/data/dna.msf8
1590	%%DATADIR%%/test/data/dna.ncbi
1591	%%DATADIR%%/test/data/dna.phylip
1592	%%DATADIR%%/test/data/dna.phylip3
1593	%%DATADIR%%/test/data/dna.staden
1594	%%DATADIR%%/test/data/dna.strider
1595	%%DATADIR%%/test/data/dna.text
1596	%%DATADIR%%/test/data/feat.emft
1597	%%DATADIR%%/test/data/feat.fasta
1598	%%DATADIR%%/test/data/feat.pir
1599	%%DATADIR%%/test/data/mw1.dat
1600	%%DATADIR%%/test/data/mw2.dat
1601	%%DATADIR%%/test/data/mw3.dat
1602	%%DATADIR%%/test/data/paamir.pep
1603	%%DATADIR%%/test/data/pax6_cdna.fasta
1604	%%DATADIR%%/test/data/prot.acedb
1605	%%DATADIR%%/test/data/prot.codata
1606	%%DATADIR%%/test/data/prot.fasta
1607	%%DATADIR%%/test/data/prot.gcg
1608	%%DATADIR%%/test/data/prot.gcg8
1609	%%DATADIR%%/test/data/prot.ig
1610	%%DATADIR%%/test/data/prot.m-acedb
1611	%%DATADIR%%/test/data/prot.m-codata
1612	%%DATADIR%%/test/data/prot.m-fasta
1613	%%DATADIR%%/test/data/prot.m-nbrf
1614	%%DATADIR%%/test/data/prot.m-ncbi
1615	%%DATADIR%%/test/data/prot.m-swiss
1616	%%DATADIR%%/test/data/prot.nbrf
1617	%%DATADIR%%/test/data/prot.ncbi
1618	%%DATADIR%%/test/data/prot.swiss
1619	%%DATADIR%%/test/data/prot.text
1620	%%DATADIR%%/test/data/z83307.seq
1621	%%DATADIR%%/test/data/aligna.dna
1622	%%DATADIR%%/test/data/alignapart.dna
1623	%%DATADIR%%/test/data/alignb.dna
1624	%%DATADIR%%/test/data/aligna.prot
1625	%%DATADIR%%/test/data/alignapart.prot
1626	%%DATADIR%%/test/data/alignb.prot
1627	%%DATADIR%%/test/data/tranalign.pep
1628	%%DATADIR%%/test/data/tranalign.seq
1629	%%DATADIR%%/test/embl/acnum.hit
1630	%%DATADIR%%/test/embl/acnum.trg
1631	%%DATADIR%%/test/embl/division.lkp
1632	%%DATADIR%%/test/embl/entrynam.idx
1633	%%DATADIR%%/test/embl/seqvn.hit
1634	%%DATADIR%%/test/embl/seqvn.trg
1635	%%DATADIR%%/test/embl/des.hit
1636	%%DATADIR%%/test/embl/des.trg
1637	%%DATADIR%%/test/embl/keyword.hit
1638	%%DATADIR%%/test/embl/keyword.trg
1639	%%DATADIR%%/test/embl/taxon.hit
1640	%%DATADIR%%/test/embl/taxon.trg
1641	%%DATADIR%%/test/embl/est.dat
1642	%%DATADIR%%/test/embl/fun.dat
1643	%%DATADIR%%/test/embl/hum1.dat
1644	%%DATADIR%%/test/embl/inv.dat
1645	%%DATADIR%%/test/embl/pln.dat
1646	%%DATADIR%%/test/embl/pro.dat
1647	%%DATADIR%%/test/embl/rod.dat
1648	%%DATADIR%%/test/embl/sts.dat
1649	%%DATADIR%%/test/embl/vrl.dat
1650	%%DATADIR%%/test/embl/vrt.dat
1651	%%DATADIR%%/test/genbank/acnum.hit
1652	%%DATADIR%%/test/genbank/acnum.trg
1653	%%DATADIR%%/test/genbank/division.lkp
1654	%%DATADIR%%/test/genbank/entrynam.idx
1655	%%DATADIR%%/test/genbank/seqvn.hit
1656	%%DATADIR%%/test/genbank/seqvn.trg
1657	%%DATADIR%%/test/genbank/des.hit
1658	%%DATADIR%%/test/genbank/des.trg
1659	%%DATADIR%%/test/genbank/keyword.hit
1660	%%DATADIR%%/test/genbank/keyword.trg
1661	%%DATADIR%%/test/genbank/taxon.hit
1662	%%DATADIR%%/test/genbank/taxon.trg
1663	%%DATADIR%%/test/genbank/gbbct1.seq
1664	%%DATADIR%%/test/genbank/gbest1.seq
1665	%%DATADIR%%/test/genbank/gbinv1.seq
1666	%%DATADIR%%/test/genbank/gbpln1.seq
1667	%%DATADIR%%/test/genbank/gbpln2.seq
1668	%%DATADIR%%/test/genbank/gbpri1.seq
1669	%%DATADIR%%/test/genbank/gbrod1.seq
1670	%%DATADIR%%/test/genbank/gbsts1.seq
1671	%%DATADIR%%/test/genbank/gbvrl1.seq
1672	%%DATADIR%%/test/genbank/gbvrt.seq
1673	%%DATADIR%%/test/gb/acnum.hit
1674	%%DATADIR%%/test/gb/acnum.trg
1675	%%DATADIR%%/test/gb/division.lkp
1676	%%DATADIR%%/test/gb/entrynam.idx
1677	%%DATADIR%%/test/gb/seqvn.hit
1678	%%DATADIR%%/test/gb/seqvn.trg
1679	%%DATADIR%%/test/gb/des.hit
1680	%%DATADIR%%/test/gb/des.trg
1681	%%DATADIR%%/test/gb/keyword.hit
1682	%%DATADIR%%/test/gb/keyword.trg
1683	%%DATADIR%%/test/gb/taxon.hit
1684	%%DATADIR%%/test/gb/taxon.trg
1685	%%DATADIR%%/test/gb/ba.ref
1686	%%DATADIR%%/test/gb/ba.seq
1687	%%DATADIR%%/test/gb/htg.ref
1688	%%DATADIR%%/test/gb/htg.seq
1689	%%DATADIR%%/test/pir/acnum.hit
1690	%%DATADIR%%/test/pir/acnum.trg
1691	%%DATADIR%%/test/pir/division.lkp
1692	%%DATADIR%%/test/pir/entrynam.idx
1693	%%DATADIR%%/test/pir/des.hit
1694	%%DATADIR%%/test/pir/des.trg
1695	%%DATADIR%%/test/pir/keyword.hit
1696	%%DATADIR%%/test/pir/keyword.trg
1697	%%DATADIR%%/test/pir/taxon.hit
1698	%%DATADIR%%/test/pir/taxon.trg
1699	%%DATADIR%%/test/pir/pir1.header
1700	%%DATADIR%%/test/pir/pir1.names
1701	%%DATADIR%%/test/pir/pir1.numbers
1702	%%DATADIR%%/test/pir/pir1.offset
1703	%%DATADIR%%/test/pir/pir1.ref
1704	%%DATADIR%%/test/pir/pir1.seq
1705	%%DATADIR%%/test/pir/pir2.header
1706	%%DATADIR%%/test/pir/pir2.names
1707	%%DATADIR%%/test/pir/pir2.numbers
1708	%%DATADIR%%/test/pir/pir2.offset
1709	%%DATADIR%%/test/pir/pir2.ref
1710	%%DATADIR%%/test/pir/pir2.seq
1711	%%DATADIR%%/test/pir/pir3.header
1712	%%DATADIR%%/test/pir/pir3.names
1713	%%DATADIR%%/test/pir/pir3.numbers
1714	%%DATADIR%%/test/pir/pir3.offset
1715	%%DATADIR%%/test/pir/pir3.ref
1716	%%DATADIR%%/test/pir/pir3.seq
1717	%%DATADIR%%/test/pir/pir4.header
1718	%%DATADIR%%/test/pir/pir4.names
1719	%%DATADIR%%/test/pir/pir4.numbers
1720	%%DATADIR%%/test/pir/pir4.offset
1721	%%DATADIR%%/test/pir/pir4.ref
1722	%%DATADIR%%/test/pir/pir4.seq
1723	%%DATADIR%%/test/swiss/seq.dat
1724	%%DATADIR%%/test/swiss/acnum.hit
1725	%%DATADIR%%/test/swiss/acnum.trg
1726	%%DATADIR%%/test/swiss/division.lkp
1727	%%DATADIR%%/test/swiss/entrynam.idx
1728	%%DATADIR%%/test/swiss/seqvn.hit
1729	%%DATADIR%%/test/swiss/seqvn.trg
1730	%%DATADIR%%/test/swiss/des.hit
1731	%%DATADIR%%/test/swiss/des.trg
1732	%%DATADIR%%/test/swiss/keyword.hit
1733	%%DATADIR%%/test/swiss/keyword.trg
1734	%%DATADIR%%/test/swiss/taxon.hit
1735	%%DATADIR%%/test/swiss/taxon.trg
1736	%%DATADIR%%/test/swnew/acnum.hit
1737	%%DATADIR%%/test/swnew/acnum.trg
1738	%%DATADIR%%/test/swnew/division.lkp
1739	%%DATADIR%%/test/swnew/entrynam.idx
1740	%%DATADIR%%/test/swnew/seqvn.hit
1741	%%DATADIR%%/test/swnew/seqvn.trg
1742	%%DATADIR%%/test/swnew/des.hit
1743	%%DATADIR%%/test/swnew/des.trg
1744	%%DATADIR%%/test/swnew/keyword.hit
1745	%%DATADIR%%/test/swnew/keyword.trg
1746	%%DATADIR%%/test/swnew/taxon.hit
1747	%%DATADIR%%/test/swnew/taxon.trg
1748	%%DATADIR%%/test/swnew/new_seq.dat
1749	%%DATADIR%%/test/swnew/upd_ann.dat
1750	%%DATADIR%%/test/swnew/upd_seq.dat
1751	%%DATADIR%%/test/wormpep/wormpep
1752	%%DATADIR%%/test/wormpep/acnum.hit
1753	%%DATADIR%%/test/wormpep/acnum.trg
1754	%%DATADIR%%/test/wormpep/division.lkp
1755	%%DATADIR%%/test/wormpep/entrynam.idx
1756	%%DATADIR%%/test/wormpep/des.hit
1757	%%DATADIR%%/test/wormpep/des.trg
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1759	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html
1760	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html
1761	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileNode.html
1762	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileSaving.html
1763	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/BuildJembossForm.html
1764	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/ListFilePanel.html
1765	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SectionPanel.html
1766	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html
1767	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetOutFileCard.html
1768	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldFloat.DecimalNumberDocument.html
1769	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldFloat.html
1770	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.WholeNumberDocument.html
1771	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.html
1772	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldSink.html
1773	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html
1774	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html
1775	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.html
1776	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/FileChooser.html
1777	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.html
1778	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/OutputSequenceAttributes.html
1779	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/SequenceFilter.html
1780	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.html
1781	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/Database.html
1782	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/ProgList.HorizontalMenu.html
1783	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/ProgList.html
1784	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/Splash.html
1785	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/BuildProgramMenu.html
1786	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ResultsMenuBar.html
1787	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SetUpMenuBar.html
1788	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowResultSet.html
1789	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowSavedResults.html
1790	%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SwingWorker.html
1791	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationFields.html
1792	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationParam.html
1793	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/AcdFunResolve.html
1794	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/AcdVarResolve.html
1795	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/Ajax.html
1796	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/Dependent.html
1797	%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/ParseAcd.html
1798	%%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/JembossProcess.html
1799	%%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ListFile.html
1800	%%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ResultList.html
1801	%%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/RunEmbossApplication.html
1802	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/AuthPopup.html
1803	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/CallAjax.html
1804	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/GetWossname.html
1805	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/JembossRun.html
1806	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/JembossSoapException.html
1807	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/PendingResults.html
1808	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/PrivateRequest.html
1809	%%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/ResListView.html
1810	%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html
1811	%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html
1812	%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossLogo.html
1813	%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossParams.html
1814	%%DATADIR%%/jemboss/api/allclasses-frame.html
1815	%%DATADIR%%/jemboss/api/deprecated-list.html
1816	%%DATADIR%%/jemboss/api/getClasses.pl
1817	%%DATADIR%%/jemboss/api/help-doc.html
1818	%%DATADIR%%/jemboss/api/index-all.html
1819	%%DATADIR%%/jemboss/api/index.html
1820	%%DATADIR%%/jemboss/api/makeDocs.csh
1821	%%DATADIR%%/jemboss/api/overview-tree.html
1822	%%DATADIR%%/jemboss/api/package-list
1823	%%DATADIR%%/jemboss/api/packages.html
1824	%%DATADIR%%/jemboss/api/serialized-form.html
1825	%%DATADIR%%/jemboss/api/stylesheet.css
1826	%%DATADIR%%/jemboss/images/Backward_arrow_button.gif
1827	%%DATADIR%%/jemboss/images/Forward_arrow_button.gif
1828	%%DATADIR%%/jemboss/images/Go_button.gif
1829	%%DATADIR%%/jemboss/images/Information_button.gif
1830	%%DATADIR%%/jemboss/images/Jemboss_logo_greyback.gif
1831	%%DATADIR%%/jemboss/images/Jemboss_logo_large.gif
1832	%%DATADIR%%/jemboss/images/Jemboss_logo_small.gif
1833	%%DATADIR%%/jemboss/images/Job_manager_button.gif
1834	%%DATADIR%%/jemboss/images/Refresh_button.gif
1835	%%DATADIR%%/jemboss/images/Refresh_button2.gif
1836	%%DATADIR%%/jemboss/lib/axis/axis-ant.jar
1837	%%DATADIR%%/jemboss/lib/axis/axis.jar
1838	%%DATADIR%%/jemboss/lib/axis/commons-discovery.jar
1839	%%DATADIR%%/jemboss/lib/axis/commons-logging.jar
1840	%%DATADIR%%/jemboss/lib/axis/jaxrpc.jar
1841	%%DATADIR%%/jemboss/lib/axis/log4j-1.2.8.jar
1842	%%DATADIR%%/jemboss/lib/axis/saaj.jar
1843	%%DATADIR%%/jemboss/lib/axis/servlet.jar
1844	%%DATADIR%%/jemboss/lib/axis/wsdl4j.jar
1845	%%DATADIR%%/jemboss/lib/README
1846	%%DATADIR%%/jemboss/lib/activation.jar
1847	%%DATADIR%%/jemboss/lib/jakarta-regexp-1.2.jar
1848	%%DATADIR%%/jemboss/lib/mail.jar
1849	%%DATADIR%%/jemboss/lib/xerces.jar
1850	%%DATADIR%%/jemboss/lib/jalview.jar
1851	%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar
1852	%%DATADIR%%/jemboss/lib/grout.jar
1853	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignApplet.java
1854	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java
1855	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignJFrame.java
1856	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Matrix.java
1857	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourJFrame.java
1858	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java
1859	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourMenu.java
1860	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PatternJFrame.java
1861	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourPanel.java
1862	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PlotConsensus.java
1863	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Consensus.java
1864	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java
1865	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/ConsensusOptions.java
1866	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java
1867	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GraphicSequenceCollection.java
1868	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignment.java
1869	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Paste.java
1870	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java
1871	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Sequence.java
1872	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrame.java
1873	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceJPanel.java
1874	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java
1875	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceNameJButton.java
1876	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java
1877	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceProperties.java
1878	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java
1879	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceReader.java
1880	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java
1881	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceSaver.java
1882	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequence.java
1883	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java
1884	%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintableJTable.java
1885	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java
1886	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java
1887	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java
1888	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java
1889	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java
1890	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java
1891	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java
1892	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java
1893	%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java
1894	%%DATADIR%%/jemboss/org/emboss/jemboss/graphics/Graph2DPlot.java
1895	%%DATADIR%%/jemboss/org/emboss/jemboss/graphics/PrintPlot.java
1896	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
1897	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java
1898	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java
1899	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java
1900	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java
1901	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
1902	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java
1903	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java
1904	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java
1905	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalTreeToolBar.java
1906	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
1907	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java
1908	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java
1909	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java
1910	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetOutFileCard.java
1911	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java
1912	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java
1913	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java
1914	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
1915	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
1916	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
1917	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
1918	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
1919	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java
1920	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java
1921	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java
1922	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java
1923	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java
1924	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
1925	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/OutputSequenceAttributes.java
1926	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/SequenceFilter.java
1927	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java
1928	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java
1929	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java
1930	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
1931	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
1932	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
1933	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
1934	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java
1935	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
1936	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
1937	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java
1938	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java
1939	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
1940	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
1941	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java
1942	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java
1943	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
1944	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
1945	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Favorites.java
1946	%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.java
1947	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
1948	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
1949	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java
1950	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
1951	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
1952	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java
1953	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
1954	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java
1955	%%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java
1956	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
1957	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java
1958	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java
1959	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultList.java
1960	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
1961	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
1962	%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
1963	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java
1964	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
1965	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java
1966	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
1967	%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
1968	%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
1969	%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
1970	%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
1971	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java
1972	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
1973	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
1974	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
1975	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
1976	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
1977	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
1978	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
1979	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
1980	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
1981	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
1982	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
1983	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
1984	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
1985	%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
1986	%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
1987	%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
1988	%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java
1989	%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
1990	%%DATADIR%%/jemboss/resources/jemboss.properties
1991	%%DATADIR%%/jemboss/resources/readme.html
1992	%%DATADIR%%/jemboss/resources/readmeAlign.html
1993	%%DATADIR%%/jemboss/resources/readmeDNADraw.html
1994	%%DATADIR%%/jemboss/resources/results.html
1995	%%DATADIR%%/jemboss/resources/version
1996	%%DATADIR%%/jemboss/resources/filemgr.html
1997	%%DATADIR%%/jemboss/resources/seqList.html
1998	%%DATADIR%%/jemboss/utils/install-jemboss-server.sh
1999	%%DATADIR%%/jemboss/utils/keys.sh
2000	%%DATADIR%%/jemboss/utils/makeJar.csh
2001	%%DATADIR%%/jemboss/utils/makeJNLP.sh
2002	%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
2003	%%DATADIR%%/jemboss/utils/template.html
2004	%%DATADIR%%/jemboss/utils/README
2005	%%DATADIR%%/jemboss/LICENSE
2006	%%DATADIR%%/jemboss/readme.html
2007	%%DATADIR%%/jemboss/runJemboss.sh
2008	%%DATADIR%%/jemboss/README
2009	%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
1931	%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html	2010	%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
		2011	%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
1932	%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs	2012	%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
1933	%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals	2013	%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
1934	%%PORTDOCS%%@dirrm %%DOCSDIR%%	2014	%%PORTDOCS%%@dirrm %%DOCSDIR%%
1935	@dirrm %%DATADIR%%/test/wormpep	2015	@dirrm %%DATADIR%%/acd
1936	@dirrm %%DATADIR%%/test/swnew	2016	@dirrm %%DATADIR%%/data/AAINDEX
1937	@dirrm %%DATADIR%%/test/swiss	2017	@dirrm %%DATADIR%%/data/CODONS
1938	@dirrm %%DATADIR%%/test/pir	2018	@dirrm %%DATADIR%%/data/REBASE
		2019	@dirrm %%DATADIR%%/data/PRINTS
		2020	@dirrm %%DATADIR%%/data/PROSITE
		2021	@dirrmtry %%DATADIR%%/data
		2022	@dirrm %%DATADIR%%/test/data
		2023	@dirrm %%DATADIR%%/test/embl
1939	@dirrm %%DATADIR%%/test/genbank	2024	@dirrm %%DATADIR%%/test/genbank
1940	@dirrm %%DATADIR%%/test/gb	2025	@dirrm %%DATADIR%%/test/gb
1941	@dirrm %%DATADIR%%/test/embl	2026	@dirrm %%DATADIR%%/test/pir
1942	@dirrm %%DATADIR%%/test/data	2027	@dirrm %%DATADIR%%/test/swiss
		2028	@dirrm %%DATADIR%%/test/swnew
		2029	@dirrm %%DATADIR%%/test/wormpep
1943	@dirrm %%DATADIR%%/test	2030	@dirrm %%DATADIR%%/test
1944	@dirrm %%DATADIR%%/jemboss/utils
1945	@dirrm %%DATADIR%%/jemboss/resources
1946	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
1947	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
1948	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
1949	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
1950	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
1951	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
1952	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
1953	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
1954	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
1955	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
1956	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
1957	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
1958	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
1959	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
1960	@dirrm %%DATADIR%%/jemboss/org/emboss
1961	@dirrm %%DATADIR%%/jemboss/org
1962	@dirrm %%DATADIR%%/jemboss/lib/axis
1963	@dirrm %%DATADIR%%/jemboss/lib
1964	@dirrm %%DATADIR%%/jemboss/images
1965	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
1966	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
1967	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
1968	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
1969	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
1970	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
1971	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
1972	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree	2031	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree
		2032	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
		2033	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
		2034	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
1973	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui	2035	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui
		2036	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
		2037	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
		2038	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
		2039	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
1974	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss	2040	@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss
1975	@dirrm %%DATADIR%%/jemboss/api/org/emboss	2041	@dirrm %%DATADIR%%/jemboss/api/org/emboss
1976	@dirrm %%DATADIR%%/jemboss/api/org	2042	@dirrm %%DATADIR%%/jemboss/api/org
1977	@dirrm %%DATADIR%%/jemboss/api	2043	@dirrm %%DATADIR%%/jemboss/api
		2044	@dirrm %%DATADIR%%/jemboss/images
		2045	@dirrm %%DATADIR%%/jemboss/lib/axis
		2046	@dirrm %%DATADIR%%/jemboss/lib
		2047	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
		2048	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
		2049	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
		2050	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
		2051	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
		2052	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
		2053	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
		2054	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
		2055	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
		2056	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
		2057	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
		2058	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
		2059	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
		2060	@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
		2061	@dirrm %%DATADIR%%/jemboss/org/emboss
		2062	@dirrm %%DATADIR%%/jemboss/org
		2063	@dirrm %%DATADIR%%/jemboss/resources
		2064	@dirrm %%DATADIR%%/jemboss/utils
1978	@dirrm %%DATADIR%%/jemboss	2065	@dirrm %%DATADIR%%/jemboss
1979	@dirrm %%DATADIR%%/data/REBASE	2066	@dirrmtry %%DATADIR%%
1980	@dirrm %%DATADIR%%/data/PROSITE	2067	@dirrmtry bin
1981	@dirrm %%DATADIR%%/data/PRINTS	2068	@dirrmtry include
1982	@dirrm %%DATADIR%%/data/CODONS	2069	@dirrmtry lib
1983	@dirrm %%DATADIR%%/data/AAINDEX	2070	@dirrmtry share/doc
1984	@dirrm %%DATADIR%%/data	2071	@dirrmtry share
1985	@dirrm %%DATADIR%%/acd	2072
1986	@dirrm %%DATADIR%%

Return to bug 93053

Lines 6-19 Link Here

(-)emboss/Makefile (-13 / +14 lines)
6	#	6	#
7		7
8	PORTNAME= emboss	8	PORTNAME= emboss
9	PORTVERSION= 2.10.0	9	PORTVERSION= 3.0.0
10	PORTREVISION= 1
11	CATEGORIES= biology	10	CATEGORIES= biology
12	MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \	11	MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \
		12	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
13	ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \	13	ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
14	ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/	14	ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
15	DISTNAME= ${PORTNAME:U}-${PORTVERSION}	15	DISTNAME= ${PORTNAME:U}-${PORTVERSION}
16	DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}	16	DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
		17	DIST_SUBDIR= ${PORTNAME}
17		18
18	MAINTAINER= fernan@iib.unsam.edu.ar	19	MAINTAINER= fernan@iib.unsam.edu.ar
19	COMMENT= A collection of open source tools for genetic sequence analysis	20	COMMENT= A collection of open source tools for genetic sequence analysis
Lines 25-38 Link Here
25		26
26	CONFLICTS= qmail-ldap2-* digest-*	27	CONFLICTS= qmail-ldap2-* digest-*
27		28
		29	PREFIX?= ${LOCALBASE}/emboss
		30	NO_MTREE= yes
28	USE_SUBMAKE= yes	31	USE_SUBMAKE= yes
29	USE_GMAKE= yes	32	USE_GMAKE= yes
30	GNU_CONFIGURE= yes	33	GNU_CONFIGURE= yes
		34	USE_AUTOTOOLS= libtool:15
31	INSTALLS_SHLIB= yes	35	INSTALLS_SHLIB= yes
32	USE_XLIB= yes	36	USE_XLIB= yes
33	USE_MOTIF= yes	37	USE_MOTIF= yes
34	USE_REINPLACE= yes	38	SUB_FILES= pkg-message
35	PKGMESSAGE= ${WRKDIR}/pkg-message	39	SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR}
36		40
37	DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:U}	41	DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:U}
38	DATADIR= ${PREFIX}/share/${PORTNAME:U}	42	DATADIR= ${PREFIX}/share/${PORTNAME:U}
Lines 43-62 Link Here
43	post-patch:	47	post-patch:
44	.if !defined(NOPORTDOCS)	48	.if !defined(NOPORTDOCS)
45	.for DIR in ${DOC_DIRS}	49	.for DIR in ${DOC_DIRS}
46	${REINPLACE_CMD} -e \	50	@ ${REINPLACE_CMD} -e \
47	's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \	51	's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
48	${WRKSRC}/${DIR}/Makefile.in	52	${WRKSRC}/${DIR}/Makefile.in
49	.endfor	53	.endfor
50	.endif	54	.endif
51		55
		56	pre-install:
		57	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
		58
52	post-install:	59	post-install:
53	@ cd ${WRKSRC} && \	60	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
54	${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
55	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
56	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
57	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
58	.if !defined(BATCH)
59	@ ${CAT} ${PKGMESSAGE}	61	@ ${CAT} ${PKGMESSAGE}
60	.endif
61		62
62	.include <bsd.port.mk>	63	.include <bsd.port.mk>

Line 0 Link Here

(-)emboss/files/patch-ajindex.h (+170 lines)
		1	--- ajax/ajindex.h.orig Mon Jan 23 12:17:10 2006
		2	+++ ajax/ajindex.h Thu Dec 22 13:12:32 2005
		3	@@ -67,6 +67,23 @@
		4	} AjOBtNode;
		5	#define AjPBtNode AjOBtNode*
		6
		7	+
		8	+
		9	+
		10	+typedef struct AjSBtMem
		11	+{
		12	+ struct AjSBtMem *next;
		13	+ struct AjSBtMem *prev;
		14	+ AjPStr *karray;
		15	+ ajlong *parray;
		16	+ ajlong *overflows;
		17	+ AjBool used;
		18	+} AjOBtMem;
		19	+#define AjPBtMem AjOBtMem*
		20	+
		21	+
		22	+
		23	+
		24	/* @data AjPBtId ***************************************************
		25	**
		26	** Btree ID
		27	@@ -137,6 +154,54 @@
		28
		29
		30
		31	+/* @data AjPBtNumId ***************************************************
		32	+**
		33	+** Btree ID
		34	+**
		35	+** @attr id [AjPStr] Unique ID
		36	+** @attr dbno [ajint] Database file number
		37	+** @attr dups [ajint] Duplicates
		38	+** @attr offset [ajlong] Offset within database file (ftello)
		39	+** @attr refoffset [ajlong] Offset within reference database file (ftello)
		40	+******************************************************************************/
		41	+
		42	+typedef struct AjSBtNumId
		43	+{
		44	+ ajint dbno;
		45	+ ajlong offset;
		46	+ ajlong refoffset;
		47	+} AjOBtNumId;
		48	+#define AjPBtNumId AjOBtNumId*
		49	+
		50	+
		51	+
		52	+
		53	+/* @data AjPNumBucket ***************************************************
		54	+**
		55	+** Offset bucket structure on disc
		56	+**
		57	+** Key, filenumber, ftell ID, subkey page (char*, ajint, ajlong, ajlong)
		58	+**
		59	+** @attr NodeType [ajint] Node type
		60	+** @attr Nentries [ajint] Number of entries
		61	+** @attr Overflow [ajlong] Offset to overflow block
		62	+** @attr offset [ajlong*] file offsets
		63	+** @attr refoffset [ajlong*] ref file offsets
		64	+** @attr offset [ajint*] database numbers
65	+******************************************************************************/
66	+
67	+typedef struct AjSNumBucket
68	+{
69	+ ajint NodeType;
70	+ ajint Nentries;
71	+ ajlong Overflow;
72	+ AjPBtNumId *NumId;
73	+} AjONumBucket;
74	+#define AjPNumBucket AjONumBucket*
75	+
76	+
77	+
78	+
79	/* Database file name structure
80	**
81	** ajint order Order of B+tree
82	@@ -387,6 +452,10 @@
83	** @attr snperbucket [ajint] Undocumented
84	** @attr secrootblock [ajlong] secondary tree root block
85	** @attr kwlimit [ajint] Max length of secondary key
86	+** @attr bmem [AjPBtMem] primary memory allocation MRU bottom
87	+** @attr bsmem [AjPBtMem] secondary memory allocation MRU bottom
88	+** @attr tmem [AjPBtMem] primary memory allocation MRU top
89	+** @attr tsmem [AjPBtMem] secondary memory allocation MRU top
90	******************************************************************************/
91
92	typedef struct AjSBtCache
93	@@ -409,6 +478,12 @@
94	ajint snperbucket;
95	ajlong secrootblock;
96	ajint kwlimit;
97	+
98	+ AjPBtMem bmem;
99	+ AjPBtMem tmem;
100	+ AjPBtMem bsmem;
101	+ AjPBtMem tsmem;
102	+
103	} AjOBtcache;
104	#define AjPBtcache AjOBtcache*
105
106	@@ -511,6 +586,32 @@
107
108
109
110	+/* @data AjPBtHybrid ***************************************************
111	+**
112	+** Btree ID
113	+**
114	+** @attr key1 [AjPStr] Unique ID
115	+** @attr dbno [ajint] Database file number
116	+** @attr dups [ajint] Duplicates
117	+ @attr offset [ajlong] Offset within database file (ftello) @attr refoffset [ajlong] Offset within reference database file (ftello)
118	+** @attr refoffset [ajlong] Offset within reference database file (ftello)
119	+** @attr treeblock [ajlong] Secondary tree root page
120	+******************************************************************************/
121	+
122	+typedef struct AjSBtHybrid
123	+{
124	+ AjPStr key1;
125	+ ajint dbno;
126	+ ajint dups;
127	+ ajlong offset;
128	+ ajlong refoffset;
129	+ ajlong treeblock;
130	+} AjOBtHybrid;
131	+#define AjPBtHybrid AjOBtHybrid*
132	+
133	+
134	+
135	+
136	AjPBtcache ajBtreeCacheNewC(const char file, const char ext,
137	const char idir, const char mode,
138	ajint pagesize, ajint order, ajint fill,
139	@@ -553,7 +654,8 @@
140	AjBool ajBtreeReplaceId(AjPBtcache cache, const AjPBtId rid);
141
142	ajint ajBtreeReadEntries(const char filename, const char indexdir,
143	- AjPStr seqfiles, AjPStr reffiles);
144	+ const char *directory,
145	+ AjPStr seqfiles, AjPStr reffiles);
146	void ajBtreeInsertDupId(AjPBtcache cache, AjPBtId id);
147	AjPList ajBtreeDupFromKey(AjPBtcache cache, const char *key);
148
149	@@ -580,6 +682,21 @@
150	void ajBtreeInsertKeyword(AjPBtcache cache, const AjPBtPri pri);
151
152	void ajBtreeLockTest(AjPBtcache cache);
153	+
154	+
155	+
156	+AjPBtpage ajBtreeHybFindInsert(AjPBtcache cache, const char *key);
157	+AjPBtpage ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key);
158	+
159	+void ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page);
160	+void ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb);
161	+AjPBtHybrid ajBtreeHybNew(void);
162	+void ajBtreeHybDel(AjPBtHybrid *thys);
163	+void ajBtreeFreePriArray(AjPBtcache cache);
164	+void ajBtreeFreeSecArray(AjPBtcache cache);
165	+void ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock,
166	+ AjPStr idname, AjPList list);
167	+
168
169	#endif
170

Line 0 Link Here

(-)emboss/files/patch-ajpdb.c (+67 lines)
		1	--- ajax/ajpdb.c.orig Mon Jan 23 12:19:22 2006
		2	+++ ajax/ajpdb.c Fri Aug 19 13:49:12 2005
		3	@@ -1198,7 +1198,7 @@
		4	osstr = ajStrNew();
		5	xstr = ajStrNew();
		6
		7	- /* Start of main application loop */
		8	+ /* Start of main loop */
		9	while(ajFileReadLine(inf,&line))
		10	{
		11	if(ajStrPrefixC(line,"XX"))
		12	@@ -1313,6 +1313,8 @@
		13
		14	(ret)->Nchn = ncha;
		15	(ret)->Ngp = ngrp;
		16	+
		17	+ continue;
		18	}
		19
		20
		21	@@ -1382,7 +1384,11 @@
		22	ajStrToken(&token,&handle,NULL);
		23	ajStrToInt(token,&mod);
		24	if((mode == 0) && (mod!=1))
		25	- break;
		26	+ {
		27	+ /* break; */
		28	+ /* Discard remaining AT lines */
		29	+ while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"AT"));
		30	+ }
		31
		32	/* Chain number */
		33	ajStrToken(&token,&handle,NULL);
		34	@@ -1463,7 +1469,10 @@
		35	"jison@hgmp.mrc.ac.uk");
		36	}
		37	else
		38	+ {
		39	ajListPushApp((ret)->Chains[chn-1]->Atoms,(void *)atom);
		40	+ }
		41	+ continue;
		42	}
		43
		44	/* Parse residue line */
		45	@@ -1479,8 +1488,11 @@
		46	ajStrToken(&token,&handle,NULL);
		47	ajStrToInt(token,&mod);
		48	if((mode == 0) && (mod!=1))
		49	- break;
		50	-
		51	+ {
		52	+ /* break;*/
		53	+ /* Discard remaining RE lines */
		54	+ while(ajFileReadLine(inf,&line) && ajStrPrefixC(line,"RE"));
		55	+ }
		56	/* Chain number */
		57	ajStrToken(&token,&handle,NULL);
		58	ajStrToInt(token,&chn);
		59	@@ -1585,6 +1597,8 @@
		60	ajStrToFloat(token,&residue->pol_rel);
		61
		62	ajListPushApp((ret)->Chains[chn-1]->Residues,(void *)residue);
		63	+
		64	+ continue;
65	}
66	}
67	/* End of main application loop */

Line 0 Link Here

(-)emboss/files/patch-ajseqdb.c (+195 lines)
		1	--- ajax/ajseqdb.c.orig Mon Jan 23 12:20:25 2006
		2	+++ ajax/ajseqdb.c Thu Dec 22 13:12:57 2005
		3	@@ -27,8 +27,7 @@
		4	******************************************************************************/
		5
		6	#include "ajax.h"
		7	-#include "ajmem.h"
		8	-#include "ajfile.h"
		9	+
		10	#include "limits.h"
		11	#include <stdarg.h>
		12	#include <sys/types.h>
		13	@@ -3055,13 +3054,13 @@
		14
		15
		16	if(qryd->do_id)
		17	- seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
		18	+ seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
		19
		20	if(qryd->do_ac)
		21	- seqEmbossOpenCache(qry,AC_EXTENSION,&qryd->accache);
		22	+ seqEmbossOpenSecCache(qry,AC_EXTENSION,&qryd->accache);
		23
		24	if(qryd->do_sv)
		25	- seqEmbossOpenCache(qry,SV_EXTENSION,&qryd->svcache);
		26	+ seqEmbossOpenSecCache(qry,SV_EXTENSION,&qryd->svcache);
		27
		28	if(qryd->do_kw)
		29	{
		30	@@ -3073,14 +3072,14 @@
		31	if(qryd->do_de)
		32	{
		33	if(!qryd->idcache)
		34	- seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
		35	+ seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
		36	seqEmbossOpenSecCache(qry,DE_EXTENSION,&qryd->decache);
		37	}
		38
		39	if(qryd->do_tx)
		40	{
		41	if(!qryd->idcache)
		42	- seqEmbossOpenCache(qry,ID_EXTENSION,&qryd->idcache);
		43	+ seqEmbossOpenSecCache(qry,ID_EXTENSION,&qryd->idcache);
		44	seqEmbossOpenSecCache(qry,TX_EXTENSION,&qryd->txcache);
		45	}
		46
		47	@@ -3149,6 +3148,7 @@
		48	if(qryd->nentries == -1)
		49	qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
		50	ajStrStr(qry->IndexDir),
		51	+ ajStrStr(qry->Directory),
		52	&qryd->files,&qryd->reffiles);
		53
		54	*cache = ajBtreeCacheNewC(ajStrStr(qry->DbAlias),ext,
		55	@@ -3209,6 +3209,7 @@
		56	if(qryd->nentries == -1)
		57	qryd->nentries = ajBtreeReadEntries(ajStrStr(qry->DbAlias),
		58	ajStrStr(qry->IndexDir),
		59	+ ajStrStr(qry->Directory),
		60	&qryd->files,&qryd->reffiles);
		61
		62
		63	@@ -3270,6 +3271,7 @@
		64
65
66	n = ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
67	+ qry->Directory->Ptr,
68	&filestrings,&reffilestrings);
69
70
71	@@ -3365,7 +3367,13 @@
72	{
73	entry = ajBtreeIdFromKey(qryd->idcache,ajStrStr(qry->Id));
74	if(entry)
75	- ajListPushApp(qryd->List,(void *)entry);
76	+ {
77	+ if(!entry->dups)
78	+ ajListPushApp(qryd->List,(void *)entry);
79	+ else
80	+ ajBtreeHybLeafList(qryd->idcache,entry->offset,
81	+ entry->id,qryd->List);
82	+ }
83	}
84
85
86	@@ -3373,14 +3381,26 @@
87	{
88	entry = ajBtreeIdFromKey(qryd->accache,ajStrStr(qry->Acc));
89	if(entry)
90	- ajListPushApp(qryd->List,(void *)entry);
91	+ {
92	+ if(!entry->dups)
93	+ ajListPushApp(qryd->List,(void *)entry);
94	+ else
95	+ ajBtreeHybLeafList(qryd->accache,entry->offset,
96	+ entry->id,qryd->List);
97	+ }
98	}
99
100	if((qryd->do_sv && !entry) && (qryd->do_sv && qryd->svcache))
101	{
102	entry = ajBtreeIdFromKey(qryd->svcache,ajStrStr(qry->Gi));
103	if(entry)
104	- ajListPushApp(qryd->List,(void *)entry);
105	+ {
106	+ if(!entry->dups)
107	+ ajListPushApp(qryd->List,(void *)entry);
108	+ else
109	+ ajBtreeHybLeafList(qryd->svcache,entry->offset,
110	+ entry->id,qryd->List);
111	+ }
112	}
113
114	if(!ajListLength(qryd->List))
115	@@ -3512,13 +3532,25 @@
116	qryd = qry->QryData;
117
118	if(qryd->do_id && qryd->idcache)
119	+ {
120	+ ajBtreeFreeSecArray(qryd->idcache);
121	ajBtreeCacheDel(&qryd->idcache);
122	+ }
123	+
124
125	if(qryd->do_ac && qryd->accache)
126	+ {
127	+ ajBtreeFreeSecArray(qryd->accache);
128	ajBtreeCacheDel(&qryd->accache);
129	+ }
130	+
131
132	if(qryd->do_sv && qryd->svcache)
133	+ {
134	+ ajBtreeFreeSecArray(qryd->svcache);
135	ajBtreeCacheDel(&qryd->svcache);
136	+ }
137	+
138
139	if(qryd->do_kw && qryd->kwcache)
140	ajBtreeCacheDel(&qryd->kwcache);
141	@@ -3608,7 +3640,14 @@
142	ajStrToLower(&kwid);
143	id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
144	if(id)
145	- ajListPushApp(qryd->List,(void *)id);
146	+ {
147	+ if(!id->dups)
148	+ ajListPushApp(qryd->List,(void *)id);
149	+ else
150	+ ajBtreeHybLeafList(qryd->idcache,id->offset,
151	+ id->id,qryd->List);
152	+ }
153	+ ajStrDel(&kwid);
154	}
155	ajListDel(&tlist);
156	ajBtreePriDel(&pri);
157	@@ -3637,7 +3676,13 @@
158	ajStrToLower(&kwid);
159	id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
160	if(id)
161	- ajListPushApp(qryd->List,(void *)id);
162	+ {
163	+ if(!id->dups)
164	+ ajListPushApp(qryd->List,(void *)id);
165	+ else
166	+ ajBtreeHybLeafList(qryd->idcache,id->offset,
167	+ id->id,qryd->List);
168	+ }
169	ajStrDel(&kwid);
170	}
171	ajListDel(&tlist);
172	@@ -3667,7 +3712,14 @@
173	ajStrToLower(&kwid);
174	id = ajBtreeIdFromKey(qryd->idcache,ajStrStr(kwid));
175	if(id)
176	- ajListPushApp(qryd->List,(void *)id);
177	+ {
178	+ if(!id->dups)
179	+ ajListPushApp(qryd->List,(void *)id);
180	+ else
181	+ ajBtreeHybLeafList(qryd->idcache,id->offset,
182	+ id->id,qryd->List);
183	+ }
184	+ ajStrDel(&kwid);
185	}
186	ajListDel(&tlist);
187	ajBtreePriDel(&pri);
188	@@ -3832,6 +3884,7 @@
189	qryd = qry->QryData;
190	i = -1;
191	ajBtreeReadEntries(qry->DbAlias->Ptr,qry->IndexDir->Ptr,
192	+ qry->Directory->Ptr,
193	&qryd->files,&qryd->reffiles);
194
195	seqin->Single = ajTrue;

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(-)emboss/files/patch-dbxfasta.c (+89 lines)
		1	--- emboss/dbxfasta.c.orig Mon Jan 23 12:22:12 2006
		2	+++ emboss/dbxfasta.c Wed Jan 4 16:31:37 2006
		3	@@ -2,7 +2,7 @@
		4	**
		5	** Index flatfile databases
		6	**
		7	-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
		8	+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
		9	** @@
		10	**
		11	** This program is free software; you can redistribute it and/or
		12	@@ -77,6 +77,7 @@
		13
		14	AjPBtId idobj = NULL;
		15	AjPBtPri priobj = NULL;
		16	+ AjPBtHybrid hyb = NULL;
		17
		18
		19	AjPRegexp typeexp = NULL;
		20	@@ -102,7 +103,8 @@
		21
		22	idobj = ajBtreeIdNew();
		23	priobj = ajBtreePriNew();
		24	-
		25	+ hyb = ajBtreeHybNew();
		26	+
		27
		28	nfields = embBtreeSetFields(entry,fieldarray);
		29	embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
		30	@@ -134,22 +136,22 @@
		31	if(entry->do_id)
		32	{
		33	ajStrToLower(&entry->id);
		34	- ajStrAssS(&idobj->id,entry->id);
		35	- idobj->dbno = i;
		36	- idobj->offset = entry->fpos;
		37	- idobj->dups = 0;
		38	- ajBtreeInsertId(entry->idcache,idobj);
		39	+ ajStrAssS(&hyb->key1,entry->id);
		40	+ hyb->dbno = i;
		41	+ hyb->offset = entry->fpos;
		42	+ hyb->dups = 0;
		43	+ ajBtreeHybInsertId(entry->idcache,hyb);
		44	}
		45
		46	if(entry->do_accession)
		47	while(ajListPop(entry->ac,(void **)&word))
		48	{
		49	ajStrToLower(&word);
		50	- ajStrAssS(&idobj->id,word);
		51	- idobj->dbno = i;
		52	- idobj->offset = entry->fpos;
		53	- idobj->dups = 0;
		54	- ajBtreeInsertId(entry->accache,idobj);
		55	+ ajStrAssS(&hyb->key1,word);
		56	+ hyb->dbno = i;
		57	+ hyb->offset = entry->fpos;
		58	+ hyb->dups = 0;
		59	+ ajBtreeHybInsertId(entry->accache,hyb);
		60	ajStrDel(&word);
		61	}
		62
		63	@@ -157,11 +159,11 @@
		64	while(ajListPop(entry->sv,(void **)&word))
65	{
66	ajStrToLower(&word);
67	- ajStrAssS(&idobj->id,word);
68	- idobj->dbno = i;
69	- idobj->offset = entry->fpos;
70	- idobj->dups = 0;
71	- ajBtreeInsertId(entry->svcache,idobj);
72	+ ajStrAssS(&hyb->key1,word);
73	+ hyb->dbno = i;
74	+ hyb->offset = entry->fpos;
75	+ hyb->dups = 0;
76	+ ajBtreeHybInsertId(entry->svcache,hyb);
77	ajStrDel(&word);
78	}
79
80	@@ -197,7 +199,8 @@
81
82	ajBtreeIdDel(&idobj);
83	ajBtreePriDel(&priobj);
84	-
85	+ ajBtreeHybDel(&hyb);
86	+
87	ajExit();
88
89	return 0;

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(-)emboss/files/patch-dbxflat.c (+146 lines)
		1	--- emboss/dbxflat.c.orig Mon Jan 23 12:22:23 2006
		2	+++ emboss/dbxflat.c Sun Jan 1 07:29:09 2006
		3	@@ -2,7 +2,7 @@
		4	**
		5	** Index flatfile databases
		6	**
		7	-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
		8	+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
		9	** @@
		10	**
		11	** This program is free software; you can redistribute it and/or
		12	@@ -106,6 +106,7 @@
		13
		14	AjPBtId idobj = NULL;
		15	AjPBtPri priobj = NULL;
		16	+ AjPBtHybrid hyb = NULL;
		17
		18
		19	embInit("dbxflat", argc, argv);
		20	@@ -126,7 +127,8 @@
		21
		22	idobj = ajBtreeIdNew();
		23	priobj = ajBtreePriNew();
		24	-
		25	+ hyb = ajBtreeHybNew();
		26	+
		27
		28	nfields = embBtreeSetFields(entry,fieldarray);
		29	embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
		30	@@ -156,11 +158,11 @@
		31	if(entry->do_id)
		32	{
		33	ajStrToLower(&entry->id);
		34	- ajStrAssS(&idobj->id,entry->id);
		35	- idobj->dbno = i;
		36	- idobj->offset = entry->fpos;
		37	- idobj->dups = 0;
		38	- ajBtreeInsertId(entry->idcache,idobj);
		39	+ ajStrAssS(&hyb->key1,entry->id);
		40	+ hyb->dbno = i;
		41	+ hyb->offset = entry->fpos;
		42	+ hyb->dups = 0;
		43	+ ajBtreeHybInsertId(entry->idcache,hyb);
		44	}
		45
		46	if(entry->do_accession)
		47	@@ -168,11 +170,11 @@
		48	while(ajListPop(entry->ac,(void **)&word))
		49	{
		50	ajStrToLower(&word);
		51	- ajStrAssS(&idobj->id,word);
		52	- idobj->dbno = i;
		53	- idobj->offset = entry->fpos;
		54	- idobj->dups = 0;
		55	- ajBtreeInsertId(entry->accache,idobj);
		56	+ ajStrAssS(&hyb->key1,word);
		57	+ hyb->dbno = i;
		58	+ hyb->offset = entry->fpos;
		59	+ hyb->dups = 0;
		60	+ ajBtreeHybInsertId(entry->accache,hyb);
		61	ajStrDel(&word);
		62	}
		63	}
		64	@@ -182,11 +184,11 @@
65	while(ajListPop(entry->sv,(void **)&word))
66	{
67	ajStrToLower(&word);
68	- ajStrAssS(&idobj->id,word);
69	- idobj->dbno = i;
70	- idobj->offset = entry->fpos;
71	- idobj->dups = 0;
72	- ajBtreeInsertId(entry->svcache,idobj);
73	+ ajStrAssS(&hyb->key1,word);
74	+ hyb->dbno = i;
75	+ hyb->offset = entry->fpos;
76	+ hyb->dups = 0;
77	+ ajBtreeHybInsertId(entry->svcache,hyb);
78	ajStrDel(&word);
79	}
80	}
81	@@ -231,15 +233,11 @@
82	}
83	}
84
85	-
86	-
87	-
88	-
89	-
90	ajFileClose(&inf);
91	}
92
93
94	+
95	embBtreeDumpParameters(entry);
96	embBtreeCloseCaches(entry);
97
98	@@ -256,7 +254,8 @@
99
100	ajBtreeIdDel(&idobj);
101	ajBtreePriDel(&priobj);
102	-
103	+ ajBtreeHybDel(&hyb);
104	+
105	ajExit();
106
107	return 0;
108	@@ -306,11 +305,13 @@
109	}
110
111	if(entry->do_sv)
112	- if(ajStrPrefixC(line,"SV"))
113	+ if(ajStrPrefixC(line,"SV") \|\|
114	+ ajStrPrefixC(line,"IV")) /* emblcds database format */
115	embBtreeEmblAC(line,entry->sv);
116
117	if(entry->do_accession)
118	- if(ajStrPrefixC(line,"AC"))
119	+ if(ajStrPrefixC(line,"AC") \|\|
120	+ ajStrPrefixC(line,"PA")) /* emblcds database format */
121	embBtreeEmblAC(line,entry->ac);
122
123	if(entry->do_keyword)
124	@@ -356,12 +357,10 @@
125
126	line = ajStrNewC("");
127	sumline = ajStrNew();
128	+
129
130	while(!ajStrPrefixC(line,"//") && ret)
131	{
132	- pos = ajFileTell(inf);
133	-
134	-
135	if(ajStrPrefixC(line,"LOCUS"))
136	{
137	entry->fpos = pos;
138	@@ -423,7 +422,7 @@
139	}
140
141
142	-
143	+ pos = ajFileTell(inf);
144
145	if(!ajFileReadLine(inf,&line))
146	ret = ajFalse;

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(-)emboss/files/patch-dbxgcg.c (+96 lines)
		1	--- emboss/dbxgcg.c.orig Mon Jan 23 12:22:30 2006
		2	+++ emboss/dbxgcg.c Thu Dec 22 13:13:18 2005
		3	@@ -2,7 +2,7 @@
		4	**
		5	** Index flatfile databases
		6	**
		7	-** @author: Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
		8	+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
		9	** @@
		10	**
		11	** This program is free software; you can redistribute it and/or
		12	@@ -136,6 +136,7 @@
		13
		14	AjPBtId idobj = NULL;
		15	AjPBtPri priobj = NULL;
		16	+ AjPBtHybrid hyb = NULL;
		17
		18
		19	embInit("dbxgcg", argc, argv);
		20	@@ -156,7 +157,8 @@
		21
		22	idobj = ajBtreeIdNew();
		23	priobj = ajBtreePriNew();
		24	-
		25	+ hyb = ajBtreeHybNew();
		26	+
		27
		28	nfields = embBtreeSetFields(entry,fieldarray);
		29	embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory,
		30	@@ -204,12 +206,12 @@
		31	if(entry->do_id)
		32	{
		33	ajStrToLower(&entry->id);
		34	- ajStrAssS(&idobj->id,entry->id);
		35	- idobj->dbno = i;
		36	- idobj->offset = entry->fpos;
		37	- idobj->refoffset = entry->reffpos;
		38	- idobj->dups = 0;
		39	- ajBtreeInsertId(entry->idcache,idobj);
		40	+ ajStrAssS(&hyb->key1,entry->id);
		41	+ hyb->dbno = i;
		42	+ hyb->offset = entry->fpos;
		43	+ hyb->refoffset = entry->reffpos;
		44	+ hyb->dups = 0;
		45	+ ajBtreeHybInsertId(entry->idcache,hyb);
		46	}
		47
		48	if(entry->do_accession)
		49	@@ -217,12 +219,12 @@
		50	while(ajListPop(entry->ac,(void **)&word))
		51	{
		52	ajStrToLower(&word);
		53	- ajStrAssS(&idobj->id,word);
		54	- idobj->dbno = i;
		55	- idobj->offset = entry->fpos;
		56	- idobj->refoffset = entry->reffpos;
		57	- idobj->dups = 0;
		58	- ajBtreeInsertId(entry->accache,idobj);
		59	+ ajStrAssS(&hyb->key1,word);
		60	+ hyb->dbno = i;
		61	+ hyb->offset = entry->fpos;
		62	+ hyb->refoffset = entry->reffpos;
		63	+ hyb->dups = 0;
		64	+ ajBtreeHybInsertId(entry->accache,hyb);
65	ajStrDel(&word);
66	}
67	}
68	@@ -232,12 +234,12 @@
69	while(ajListPop(entry->sv,(void **)&word))
70	{
71	ajStrToLower(&word);
72	- ajStrAssS(&idobj->id,word);
73	- idobj->dbno = i;
74	- idobj->offset = entry->fpos;
75	- idobj->refoffset = entry->reffpos;
76	- idobj->dups = 0;
77	- ajBtreeInsertId(entry->svcache,idobj);
78	+ ajStrAssS(&hyb->key1,word);
79	+ hyb->dbno = i;
80	+ hyb->offset = entry->fpos;
81	+ hyb->refoffset = entry->reffpos;
82	+ hyb->dups = 0;
83	+ ajBtreeHybInsertId(entry->svcache,hyb);
84	ajStrDel(&word);
85	}
86	}
87	@@ -303,7 +305,8 @@
88
89	ajBtreeIdDel(&idobj);
90	ajBtreePriDel(&priobj);
91	-
92	+ ajBtreeHybDel(&hyb);
93	+
94	ajExit();
95
96	return 0;

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(-)emboss/files/patch-embindex.c (+115 lines)
		1	--- nucleus/embindex.c.orig Mon Jan 23 12:24:54 2006
		2	+++ nucleus/embindex.c Thu Dec 22 13:12:38 2005
		3	@@ -973,15 +973,14 @@
		4	if(!do_ref)
		5	{
		6	ajListPop(entry->files,(void **)&tmpstr);
		7	- ajFmtPrintF(entfile,"%S%S\n",entry->directory,tmpstr);
		8	+ ajFmtPrintF(entfile,"%S\n",tmpstr);
		9	ajListPushApp(entry->files,(void *)tmpstr);
		10	}
		11	else
		12	{
		13	ajListPop(entry->files,(void **)&tmpstr);
		14	ajListPop(entry->reffiles,(void **)&refstr);
		15	- ajFmtPrintF(entfile,"%S%S %S%S\n",entry->directory,tmpstr,
		16	- entry->directory,refstr);
		17	+ ajFmtPrintF(entfile,"%S %S\n",tmpstr, refstr);
		18	ajListPushApp(entry->files,(void *)tmpstr);
		19	ajListPushApp(entry->reffiles,(void *)refstr);
		20	}
		21	@@ -1150,7 +1149,15 @@
		22	entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
		23	entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
		24
		25	+ entry->idsecorder = (entry->pagesize - 60) / 24;
		26	+ entry->idsecfill = (entry->pagesize - 60) / 20;
		27
		28	+ entry->acsecorder = (entry->pagesize - 60) / 24;
		29	+ entry->acsecfill = (entry->pagesize - 60) / 20;
		30	+
		31	+ entry->svsecorder = (entry->pagesize - 60) / 24;
		32	+ entry->svsecfill = (entry->pagesize - 60) / 20;
		33	+
		34	ajStrDel(&value);
		35
		36	return;
		37	@@ -1183,28 +1190,38 @@
		38
		39	if(entry->do_id)
		40	{
		41	- entry->idcache = ajBtreeCacheNewC(basenam,ID_EXTENSION,idir,"w+",
		42	- entry->pagesize, entry->idorder,
		43	- entry->idfill, level,
		44	- entry->cachesize);
		45	+ entry->idcache = ajBtreeSecCacheNewC(basenam,ID_EXTENSION,idir,"w+",
		46	+ entry->pagesize, entry->idorder,
		47	+ entry->idfill, level,
		48	+ entry->cachesize,
		49	+ entry->idsecorder, slevel,
		50	+ entry->idsecfill, count,
		51	+ entry->kwlen);
		52	ajBtreeCreateRootNode(entry->idcache,0L);
		53	}
		54
		55	if(entry->do_accession)
		56	{
		57	- entry->accache = ajBtreeCacheNewC(basenam,AC_EXTENSION,idir,"w+",
		58	- entry->pagesize, entry->acorder,
		59	- entry->acfill, level,
		60	- entry->cachesize);
		61	+ entry->accache = ajBtreeSecCacheNewC(basenam,AC_EXTENSION,idir,"w+",
		62	+ entry->pagesize,
		63	+ entry->acorder, entry->acfill,
		64	+ level,
65	+ entry->cachesize,
66	+ entry->acsecorder, slevel,
67	+ entry->acsecfill, count,
68	+ entry->kwlen);
69	ajBtreeCreateRootNode(entry->accache,0L);
70	}
71
72	if(entry->do_sv)
73	{
74	- entry->svcache = ajBtreeCacheNewC(basenam,SV_EXTENSION,idir,"w+",
75	- entry->pagesize, entry->svorder,
76	- entry->svfill, level,
77	- entry->cachesize);
78	+ entry->svcache = ajBtreeSecCacheNewC(basenam,SV_EXTENSION,idir,"w+",
79	+ entry->pagesize, entry->svorder,
80	+ entry->svfill, level,
81	+ entry->cachesize,
82	+ entry->svsecorder, slevel,
83	+ entry->svsecfill, count,
84	+ entry->kwlen);
85	ajBtreeCreateRootNode(entry->svcache,0L);
86	}
87
88	@@ -1270,18 +1287,27 @@
89
90	if(entry->do_id)
91	{
92	+ ajBtreeFreePriArray(entry->idcache);
93	+ ajBtreeFreeSecArray(entry->idcache);
94	+
95	ajBtreeCacheSync(entry->idcache,0L);
96	ajBtreeCacheDel(&entry->idcache);
97	}
98
99	if(entry->do_accession)
100	{
101	+ ajBtreeFreePriArray(entry->accache);
102	+ ajBtreeFreeSecArray(entry->accache);
103	+
104	ajBtreeCacheSync(entry->accache,0L);
105	ajBtreeCacheDel(&entry->accache);
106	}
107
108	if(entry->do_sv)
109	{
110	+ ajBtreeFreePriArray(entry->svcache);
111	+ ajBtreeFreeSecArray(entry->svcache);
112	+
113	ajBtreeCacheSync(entry->svcache,0L);
114	ajBtreeCacheDel(&entry->svcache);
115	}

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(-)emboss/files/patch-embindex.h (+96 lines)
		1	--- nucleus/embindex.h.orig Mon Jan 23 12:24:46 2006
		2	+++ nucleus/embindex.h Thu Dec 22 13:12:44 2005
		3	@@ -16,6 +16,76 @@
		4	#define BTREE_DEF_CACHESIZE 100
		5	#define BTREE_DEF_PAGESIZE 2048
		6
		7	+/* @data EmbPBtreeEntry *******************************************************
		8	+**
		9	+** Index tree entries
		10	+**
		11	+** @alias EmbSBtreeEntry
		12	+**
		13	+** @attr do_id [AjBool] Undocumented
		14	+** @attr do_accession [AjBool] Undocumented
		15	+** @attr do_sv [AjBool] Undocumented
		16	+** @attr do_description [AjBool] Undocumented
		17	+** @attr do_keyword [AjBool] Undocumented
		18	+** @attr do_taxonomy [AjBool] Undocumented
		19	+** @attr dbname [AjPStr] Undocumented
		20	+** @attr dbrs [AjPStr] Undocumented
		21	+** @attr release [AjPStr] Undocumented
		22	+** @attr date [AjPStr] Undocumented
		23	+** @attr dbtype [AjPStr] Undocumented
		24	+** @attr directory [AjPStr] Undocumented
		25	+** @attr idirectory [AjPStr] Undocumented
		26	+** @attr files [AjPList] Undocumented
		27	+** @attr reffiles [AjPList] Undocumented
		28	+** @attr nfiles [ajint] Undocumented
		29	+** @attr cachesize [ajint] Undocumented
		30	+** @attr pagesize [ajint] Undocumented
		31	+** @attr idlen [ajint] Undocumented
		32	+** @attr aclen [ajint] Undocumented
		33	+** @attr svlen [ajint] Undocumented
		34	+** @attr kwlen [ajint] Undocumented
		35	+** @attr delen [ajint] Undocumented
		36	+** @attr txlen [ajint] Undocumented
		37	+** @attr idorder [ajint] Undocumented
		38	+** @attr idfill [ajint] Undocumented
		39	+** @attr idsecorder [ajint] Undocumented
		40	+** @attr idsecfill [ajint] Undocumented
		41	+** @attr acorder [ajint] Undocumented
		42	+** @attr acfill [ajint] Undocumented
		43	+** @attr acsecorder [ajint] Undocumented
		44	+** @attr acsecfill [ajint] Undocumented
		45	+** @attr svorder [ajint] Undocumented
		46	+** @attr svfill [ajint] Undocumented
		47	+** @attr svsecorder [ajint] Undocumented
		48	+** @attr svsecfill [ajint] Undocumented
		49	+** @attr kworder [ajint] Undocumented
		50	+** @attr kwfill [ajint] Undocumented
		51	+** @attr kwsecorder [ajint] Undocumented
		52	+** @attr kwsecfill [ajint] Undocumented
		53	+** @attr deorder [ajint] Undocumented
		54	+** @attr defill [ajint] Undocumented
		55	+** @attr desecorder [ajint] Undocumented
		56	+** @attr desecfill [ajint] Undocumented
		57	+** @attr txorder [ajint] Undocumented
		58	+** @attr txfill [ajint] Undocumented
		59	+** @attr txsecorder [ajint] Undocumented
		60	+** @attr txsecfill [ajint] Undocumented
		61	+** @attr idcache [AjPBtcache] Undocumented
		62	+** @attr accache [AjPBtcache] Undocumented
		63	+** @attr svcache [AjPBtcache] Undocumented
		64	+** @attr kwcache [AjPBtcache] Undocumented
65	+** @attr decache [AjPBtcache] Undocumented
66	+** @attr txcache [AjPBtcache] Undocumented
67	+** @attr fpos [ajlong] Undocumented
68	+** @attr reffpos [ajlong] Undocumented
69	+** @attr id [AjPStr] Undocumented
70	+** @attr ac [AjPList] Undocumented
71	+** @attr sv [AjPList] Undocumented
72	+** @attr tx [AjPList] Undocumented
73	+** @attr kw [AjPList] Undocumented
74	+** @attr de [AjPList] Undocumented
75	+******************************************************************************/
76	+
77	typedef struct EmbSBtreeEntry
78	{
79	AjBool do_id;
80	@@ -48,10 +118,16 @@
81
82	ajint idorder;
83	ajint idfill;
84	+ ajint idsecorder;
85	+ ajint idsecfill;
86	ajint acorder;
87	ajint acfill;
88	+ ajint acsecorder;
89	+ ajint acsecfill;
90	ajint svorder;
91	ajint svfill;
92	+ ajint svsecorder;
93	+ ajint svsecfill;
94
95	ajint kworder;
96	ajint kwfill;

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(-)emboss/files/patch-emboss.default.template (+20 lines)
	1	--- emboss/emboss.default.template.orig Wed Feb 8 00:43:42 2006
	2	+++ emboss/emboss.default.template Wed Feb 8 00:40:34 2006
	3	@@ -4,7 +4,7 @@
	4	# By default this is /usr/local/share/EMBOSS/test but the directory can
	5	# be changed with --prefix when you configure EMBOSS.
	6
	7	-# SET emboss_tempdata path_to_directory_$EMBOSS/test
	8	+# SET emboss_tempdata %%DATADIR%%/test
	9
	10	# Proxy - set this if any databases are accessed through a proxy web server.
	11	# Turn off in the DB definition with proxy: ":" for any
	12	@@ -15,7 +15,7 @@
	13	# Logfile - set this to a file that any user can append to
	14	# and EMBOSS applications will automatically write log information
	15
	16	-# SET emboss_logfile /packages/emboss/emboss/log
	17	+# SET emboss_logfile /var/log/emboss.log
	18
	19	# Pagesize - this is the size of disc page blocks and is
	20	# required by the 'dbx' indexing programs and 'method: emboss'

Line 0 Link Here

(-)emboss/files/patch-marscan.c (+72 lines)
		1	--- emboss/marscan.c.orig Mon Jan 23 11:36:36 2006
		2	+++ emboss/marscan.c Mon Jan 23 08:56:35 2006
		3	@@ -1,7 +1,7 @@
		4	/* @source marscan application
		5	**
		6	** Finds MAR/SAR sites in nucleic sequences
		7	-** @author: Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
		8	+** @author Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
		9	** @@
		10	**
		11	** This program is free software; you can redistribute it and/or
		12	@@ -249,33 +249,41 @@
		13	amino8rev, carboxyl8rev, buf8rev, off8rev,
		14	sotable8rev, solimit8rev, regexp8rev, skipm8rev,
		15	&hits8rev, m8rev, &tidy8rev);
		16	+ ajDebug("Marscan '%S' hits %d:%d %d:%d\n", seqname,
		17	+ hits16, hits16rev,
		18	+ hits8, hits8rev);
		19	+
		20	+ /* initialise the output feature table */
		21	+ tab = ajFeattableNewDna(seqname);
		22	+
		23	+ /*
		24	+ ** append reverse lists to forward lists and sort them by match
		25	+ ** position
		26	+ */
		27
		28	- if((hits16 \|\| hits16rev) && (hits8 \|\| hits8rev))
		29	+ if(hits8 \|\| hits8rev)
		30	{
		31	- /*
		32	- ** append reverse lists to forward lists and sort them by match
		33	- ** position
		34	- */
		35	ajListPushList(l8, &l8rev);
		36	ajListSort(l8, embPatRestrictStartCompare);
		37	-
		38	+ }
		39	+ if((hits16 \|\| hits16rev))
		40	+ {
		41	ajListPushList(l16, &l16rev);
		42	ajListSort(l16, embPatRestrictStartCompare);
		43
		44	- /* initialise the output feature table */
		45	- if(!tab)
		46	- tab = ajFeattableNewDna(seqname);
		47	-
		48	- /*
		49	- ** find pairs of hits within the required distance and output
		50	- ** the results
		51	- */
		52	- marscan_stepdown(l16, l8, &tab);
		53	-
		54	- /* write features and tidy up */
		55	- ajReportWrite(report, tab, seq);
		56	- ajFeattableDel(&tab);
		57	}
		58	+
		59	+
		60	+ /*
		61	+ ** find pairs of hits within the required distance and output
		62	+ ** the results
		63	+ */
		64	+ marscan_stepdown(l16, l8, &tab);
65	+
66	+ ajDebug("Marscan reportwrite '%S'\n", seqname);
67	+ /* write features and tidy up */
68	+ ajReportWrite(report, tab, seq);
69	+ ajFeattableDel(&tab);
70
71	while(ajListPop(l16,(void **)&aptr))
72	embMatMatchDel(&aptr);

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(-)emboss/files/pkg-message.in (+27 lines)
	1	=============================================================================
	2
	3	The EMBOSS suite has been successfully installed under
	4	%%PREFIX%%
	5
	6	To run EMBOSS programs make sure that %%PREFIX%%/bin is in your PATH.
	7
	8	In order to see graphical output from some EMBOSS programs, you will
	9	need to set the following environment variable in your shell:
	10
	11	set PLPLOT_LIB to: "%%PREFIX%%/share/EMBOSS"
	12
	13	A sample configuration file has been installed in
	14	%%DATADIR%%/emboss.default.template
	15
	16	This must be renamed to emboss.default and edited to suit your site
	17	and requirements.
	18
	19	A .embossrc file in a user's home directory overrides settings in the
	20	system-wide emboss.default.
	21
	22	Additional third party applications for EMBOSS can be installed from the
	23	biology/embassy port. Remember, though that if you installed EMBOSS in a
	24	PREFIX other than the default, you will have to install EMBASSY into this
	25	same PREFIX.
	26
	27	=============================================================================

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(-)emboss/files/pre-install.in (+21 lines)
	1	===============================================================================
	2
	3	ATENTION!!!
	4
	5	The EMBOSS port is currently affected by a CONFLICTS condition.
	6	If you install the port in the default prefix
	7	PREFIX = LOCALBASE = %%LOCALBASE%%
	8	it will conflict with other ports that install applications with the
	9	same name, in the same places.
	10
	11	It is highly recommended that you install EMBOSS to a different prefix,
	12	for example PREFIX=%%LOCALBASE%%/emboss
	13	In this case, all of the documentation and examples will be installed
	14	within this PREFIX.
	15
	16	If you still choose to install EMBOSS on the default prefix, do note
	17	that documentation, examples and shared data will not be installed
	18	in the usual places for a FreeBSD port (i.e. docs in
	19	PREFIX/share/EMBOSS/doc instead of in PREFIX/share/doc/EMBOSS).
	20
	21	===============================================================================

Lines 1-22 Link Here

(-)emboss/pkg-message (-22 lines)
1	--------------------------------------------------------------------------
2
3	The EMBOSS suite has been successfully installed.
4
5	In order to see graphical output from some EMBOSS programs, you will need to
6	set the following environment variable in your shell startup file:
7
8	- set PLPLOT_LIB to: "%%PREFIX%%/share/EMBOSS"
9
10	NB: A sample configuration file has been installed to %%PREFIX%%/etc as
11	emboss.default.sample. This must be renamed to emboss.default and edited
12	to suit your site and its requirements.
13
14	A .embossrc in a user's home directory overrides settings in the
15	system-wide emboss.default.
16
17	Online EMBOSS documentation is available at:
18	http://www.uk.embnet.org/Software/EMBOSS/userdoc.html
19	http://www.uk.embnet.org/Software/EMBOSS/Doc/
20	http://emboss.sourceforge.net/docs/
21
22	--------------------------------------------------------------------------