Attachment 62220 Details for Bug 93053 – emboss_again.diff

[patch] emboss_again.diff

emboss_again.diff (text/plain; charset=us-ascii), 285.76 KB, created by Fernan Aguero on 2006-03-28 20:50:44 UTC

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Creator: Fernan Aguero

Created: 2006-03-28 20:50:44 UTC

Size: 285.76 KB

patch

obsolete

>diff -ruN /usr/ports/biology/emboss/Makefile emboss/Makefile
>--- /usr/ports/biology/emboss/Makefile	Wed Mar  1 20:11:41 2006
>+++ emboss/Makefile	Thu Mar 16 18:37:01 2006
>@@ -6,14 +6,15 @@
> #
> 
> PORTNAME=	emboss
>-PORTVERSION=	2.10.0
>-PORTREVISION=	1
>+PORTVERSION=	3.0.0
> CATEGORIES=	biology
>-MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
>+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
>@@ -28,11 +29,12 @@
> USE_SUBMAKE=	yes
> USE_GMAKE=	yes
> GNU_CONFIGURE=	yes
>+USE_AUTOTOOLS=	libtool:15
> INSTALLS_SHLIB=	yes
> USE_XLIB=	yes
> USE_MOTIF=	yes
>-USE_REINPLACE=	yes
>-PKGMESSAGE=	${WRKDIR}/pkg-message
>+SUB_FILES=	pkg-message
>+SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
> 
> DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
> DATADIR=	${PREFIX}/share/${PORTNAME:U}
>@@ -43,20 +45,17 @@
> post-patch:
> .if !defined(NOPORTDOCS)
> .for DIR in ${DOC_DIRS}
>-	${REINPLACE_CMD} -e \
>+	@ ${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:
>-	@ cd ${WRKSRC} && \
>-	${SED} -e 's#%%PREFIX%%#${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)
>+	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
> 	@ ${CAT} ${PKGMESSAGE}
>-.endif
> 
> .include <bsd.port.mk>
>diff -ruN /usr/ports/biology/emboss/distinfo emboss/distinfo
>--- /usr/ports/biology/emboss/distinfo	Wed Jan 25 11:31:47 2006
>+++ emboss/distinfo	Thu Jan 19 15:37:47 2006
>@@ -1,3 +1,3 @@
>-MD5 (EMBOSS-2.10.0.tar.gz) = 4a48388ced7021a8ffece5166c40a364
>-SHA256 (EMBOSS-2.10.0.tar.gz) = 1d3a8d84ff9c4f77d81b88c9e7c33517a232e7797eb2b761729f97898aa34a8f
>-SIZE (EMBOSS-2.10.0.tar.gz) = 16262124
>+MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
>+SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
>+SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
>diff -ruN /usr/ports/biology/emboss/files/patch-ajindex.c emboss/files/patch-ajindex.c
>--- /usr/ports/biology/emboss/files/patch-ajindex.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-ajindex.c	Mon Jan 23 12:18:51 2006
>@@ -0,0 +1,5134 @@
>+--- 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;
>++}
>++
>diff -ruN /usr/ports/biology/emboss/files/patch-ajindex.h emboss/files/patch-ajindex.h
>--- /usr/ports/biology/emboss/files/patch-ajindex.h	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-ajindex.h	Mon Jan 23 12:18:57 2006
>@@ -0,0 +1,170 @@
>+--- 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
>+ 
>diff -ruN /usr/ports/biology/emboss/files/patch-ajpdb.c emboss/files/patch-ajpdb.c
>--- /usr/ports/biology/emboss/files/patch-ajpdb.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-ajpdb.c	Mon Jan 23 12:20:04 2006
>@@ -0,0 +1,67 @@
>+--- 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 */
>diff -ruN /usr/ports/biology/emboss/files/patch-ajseqdb.c emboss/files/patch-ajseqdb.c
>--- /usr/ports/biology/emboss/files/patch-ajseqdb.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-ajseqdb.c	Mon Jan 23 12:21:36 2006
>@@ -0,0 +1,195 @@
>+--- 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;
>diff -ruN /usr/ports/biology/emboss/files/patch-dbxfasta.c emboss/files/patch-dbxfasta.c
>--- /usr/ports/biology/emboss/files/patch-dbxfasta.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-dbxfasta.c	Mon Jan 23 12:23:34 2006
>@@ -0,0 +1,89 @@
>+--- 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;
>diff -ruN /usr/ports/biology/emboss/files/patch-dbxflat.c emboss/files/patch-dbxflat.c
>--- /usr/ports/biology/emboss/files/patch-dbxflat.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-dbxflat.c	Mon Jan 23 12:23:51 2006
>@@ -0,0 +1,146 @@
>+--- 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;
>diff -ruN /usr/ports/biology/emboss/files/patch-dbxgcg.c emboss/files/patch-dbxgcg.c
>--- /usr/ports/biology/emboss/files/patch-dbxgcg.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-dbxgcg.c	Mon Jan 23 12:24:04 2006
>@@ -0,0 +1,96 @@
>+--- 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;
>diff -ruN /usr/ports/biology/emboss/files/patch-embindex.c emboss/files/patch-embindex.c
>--- /usr/ports/biology/emboss/files/patch-embindex.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-embindex.c	Mon Jan 23 12:25:40 2006
>@@ -0,0 +1,115 @@
>+--- 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);
>+     }
>diff -ruN /usr/ports/biology/emboss/files/patch-embindex.h emboss/files/patch-embindex.h
>--- /usr/ports/biology/emboss/files/patch-embindex.h	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-embindex.h	Mon Jan 23 12:25:48 2006
>@@ -0,0 +1,96 @@
>+--- 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;
>diff -ruN /usr/ports/biology/emboss/files/patch-emboss.default.template emboss/files/patch-emboss.default.template
>--- /usr/ports/biology/emboss/files/patch-emboss.default.template	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-emboss.default.template	Wed Feb  8 00:44:31 2006
>@@ -0,0 +1,20 @@
>+--- 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'
>diff -ruN /usr/ports/biology/emboss/files/patch-marscan.c emboss/files/patch-marscan.c
>--- /usr/ports/biology/emboss/files/patch-marscan.c	Wed Dec 31 21:00:00 1969
>+++ emboss/files/patch-marscan.c	Mon Jan 23 11:37:24 2006
>@@ -0,0 +1,72 @@
>+--- 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);
>diff -ruN /usr/ports/biology/emboss/files/pkg-message.in emboss/files/pkg-message.in
>--- /usr/ports/biology/emboss/files/pkg-message.in	Wed Dec 31 21:00:00 1969
>+++ emboss/files/pkg-message.in	Wed Feb  8 14:12:12 2006
>@@ -0,0 +1,27 @@
>+=============================================================================
>+
>+ 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.
>+
>+=============================================================================
>diff -ruN /usr/ports/biology/emboss/files/pre-install.in emboss/files/pre-install.in
>--- /usr/ports/biology/emboss/files/pre-install.in	Wed Dec 31 21:00:00 1969
>+++ emboss/files/pre-install.in	Wed Jan 25 15:06:47 2006
>@@ -0,0 +1,21 @@
>+===============================================================================
>+
>+ 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).
>+
>+===============================================================================
>diff -ruN /usr/ports/biology/emboss/pkg-message emboss/pkg-message
>--- /usr/ports/biology/emboss/pkg-message	Thu Apr 28 09:05:22 2005
>+++ emboss/pkg-message	Wed Dec 31 21:00:00 1969
>@@ -1,22 +0,0 @@
>---------------------------------------------------------------------------
>-
>-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/
>-
>---------------------------------------------------------------------------
>diff -ruN /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist
>--- /usr/ports/biology/emboss/pkg-plist	Wed Mar  1 20:11:41 2006
>+++ emboss/pkg-plist	Tue Mar 28 16:23:31 2006
>@@ -17,6 +17,7 @@
> bin/chips
> bin/cirdna
> bin/codcmp
>+bin/codcopy
> bin/coderet
> bin/compseq
> bin/cons
>@@ -24,12 +25,15 @@
> bin/cpgreport
> bin/cusp
> bin/cutgextract
>-bin/cutseq
> bin/dan
>+bin/cutseq
> bin/dbiblast
> bin/dbifasta
> bin/dbiflat
> bin/dbigcg
>+bin/dbxfasta
>+bin/dbxflat
>+bin/dbxgcg
> bin/degapseq
> bin/descseq
> bin/diffseq
>@@ -119,7 +123,6 @@
> bin/restover
> bin/restrict
> bin/revseq
>-bin/runJemboss.csh
> bin/seealso
> bin/seqmatchall
> bin/seqret
>@@ -135,11 +138,11 @@
> bin/sirna
> bin/sixpack
> bin/skipseq
>+bin/syco
> bin/splitter
> bin/stretcher
> bin/stssearch
> bin/supermatcher
>-bin/syco
> bin/tcode
> bin/textsearch
> bin/tfextract
>@@ -160,18 +163,30 @@
> bin/wordmatch
> bin/wossname
> bin/yank
>-etc/emboss.default.sample
>+bin/runJemboss.csh
>+include/drivers.h
>+include/pdf.h
>+include/plcore.h
>+include/plevent.h
>+include/plplotP.h
>+include/plxwd.h
>+include/metadefs.h
>+include/plConfig.h
>+include/pldebug.h
>+include/plplot.h
>+include/plstrm.h
>+include/plDevs.h
>+include/ajax.h
>+include/ajarch.h
>+include/ajdefine.h
> include/ajacd.h
> include/ajalign.h
>-include/ajarch.h
> include/ajarr.h
> include/ajassert.h
>-include/ajax.h
> include/ajbase.h
> include/ajcall.h
> include/ajcod.h
> include/ajdan.h
>-include/ajdefine.h
> include/ajdmx.h
> include/ajdomain.h
> include/ajexcept.h
>@@ -180,8 +195,8 @@
> include/ajfile.h
> include/ajfmt.h
> include/ajgraph.h
>-include/ajgraphstruct.h
> include/ajgraphxml.h
>+include/ajgraphstruct.h
> include/ajhist.h
> include/ajindex.h
> include/ajjava.h
>@@ -214,7 +229,14 @@
> include/ajtree.h
> include/ajutil.h
> include/ajvector.h
>-include/drivers.h
>+include/pcre.h
>+include/pcre_chartables.c
>+include/pcre_config.h
>+include/pcre_get.c
>+include/pcre_printint.c
>+include/pcre_internal.h
>+include/pcreposix.h
>+include/emboss.h
> include/embaln.h
> include/embcom.h
> include/embcons.h
>@@ -232,999 +254,234 @@
> include/embmisc.h
> include/embmol.h
> include/embnmer.h
>-include/emboss.h
> include/embpat.h
>-include/embpdb.h
> include/embprop.h
>+include/embpdb.h
> include/embread.h
>-include/embshow.h
> include/embsig.h
>+include/embshow.h
> include/embword.h
>-include/metadefs.h
>-include/pcre.h
>-include/pcre_chartables.c
>-include/pcre_config.h
>-include/pcre_get.c
>-include/pcre_internal.h
>-include/pcre_printint.c
>-include/pcreposix.h
>-include/pdf.h
>-include/plConfig.h
>-include/plDevs.h
>-include/plcore.h
>-include/pldebug.h
>-include/plevent.h
>-include/plplot.h
>-include/plplotP.h
>-include/plstrm.h
>-include/plxwd.h
>-lib/libajax.a
>-lib/libajax.la
>+lib/libplplot.so.5
>+lib/libplplot.so
>+lib/libplplot.la
>+lib/libplplot.a
>+lib/libajax.so.3
> lib/libajax.so
>-lib/libajax.so.1
>-lib/libajaxg.a
>-lib/libajaxg.la
>+lib/libajax.la
>+lib/libajax.a
>+lib/libajaxg.so.3
> lib/libajaxg.so
>-lib/libajaxg.so.1
>-lib/libnucleus.a
>-lib/libnucleus.la
>+lib/libajaxg.la
>+lib/libajaxg.a
>+lib/libnucleus.so.3
> lib/libnucleus.so
>-lib/libnucleus.so.1
>-lib/libplplot.a
>-lib/libplplot.la
>-lib/libplplot.so
>-lib/libplplot.so.5
>-%%DATADIR%%/acd/aaindexextract.acd
>-%%DATADIR%%/acd/abiview.acd
>-%%DATADIR%%/acd/acdc.acd
>-%%DATADIR%%/acd/acdlog.acd
>-%%DATADIR%%/acd/acdpretty.acd
>-%%DATADIR%%/acd/acdtable.acd
>-%%DATADIR%%/acd/acdtrace.acd
>-%%DATADIR%%/acd/acdvalid.acd
>-%%DATADIR%%/acd/ajbad.acd
>-%%DATADIR%%/acd/ajfeatest.acd
>-%%DATADIR%%/acd/ajtest.acd
>-%%DATADIR%%/acd/antigenic.acd
>-%%DATADIR%%/acd/backtranseq.acd
>-%%DATADIR%%/acd/banana.acd
>-%%DATADIR%%/acd/biosed.acd
>-%%DATADIR%%/acd/btwisted.acd
>-%%DATADIR%%/acd/cai.acd
>-%%DATADIR%%/acd/chaos.acd
>-%%DATADIR%%/acd/charge.acd
>-%%DATADIR%%/acd/checktrans.acd
>-%%DATADIR%%/acd/chips.acd
>-%%DATADIR%%/acd/cirdna.acd
>-%%DATADIR%%/acd/codcmp.acd
>-%%DATADIR%%/acd/coderet.acd
>-%%DATADIR%%/acd/codes.english
>-%%DATADIR%%/acd/complex.acd
>-%%DATADIR%%/acd/compseq.acd
>-%%DATADIR%%/acd/cons.acd
>-%%DATADIR%%/acd/corbatest.acd
>-%%DATADIR%%/acd/cpgplot.acd
>-%%DATADIR%%/acd/cpgreport.acd
>-%%DATADIR%%/acd/cusp.acd
>-%%DATADIR%%/acd/cutgextract.acd
>-%%DATADIR%%/acd/cutseq.acd
>-%%DATADIR%%/acd/dan.acd
>-%%DATADIR%%/acd/dbiblast.acd
>-%%DATADIR%%/acd/dbifasta.acd
>-%%DATADIR%%/acd/dbiflat.acd
>-%%DATADIR%%/acd/dbigcg.acd
>-%%DATADIR%%/acd/degapseq.acd
>-%%DATADIR%%/acd/demoalign.acd
>-%%DATADIR%%/acd/demofeatures.acd
>-%%DATADIR%%/acd/demolist.acd
>-%%DATADIR%%/acd/demoreport.acd
>-%%DATADIR%%/acd/demosequence.acd
>-%%DATADIR%%/acd/demostring.acd
>-%%DATADIR%%/acd/demotable.acd
>-%%DATADIR%%/acd/descseq.acd
>-%%DATADIR%%/acd/diffseq.acd
>-%%DATADIR%%/acd/digest.acd
>-%%DATADIR%%/acd/distmat.acd
>-%%DATADIR%%/acd/dotmatcher.acd
>-%%DATADIR%%/acd/dotpath.acd
>-%%DATADIR%%/acd/dottup.acd
>-%%DATADIR%%/acd/dreg.acd
>-%%DATADIR%%/acd/einverted.acd
>-%%DATADIR%%/acd/embossdata.acd
>-%%DATADIR%%/acd/embossversion.acd
>-%%DATADIR%%/acd/emma.acd
>-%%DATADIR%%/acd/emowse.acd
>-%%DATADIR%%/acd/entrails.acd
>-%%DATADIR%%/acd/entret.acd
>-%%DATADIR%%/acd/epestfind.acd
>-%%DATADIR%%/acd/eprimer3.acd
>-%%DATADIR%%/acd/equicktandem.acd
>-%%DATADIR%%/acd/est2genome.acd
>-%%DATADIR%%/acd/etandem.acd
>-%%DATADIR%%/acd/extractfeat.acd
>-%%DATADIR%%/acd/extractseq.acd
>-%%DATADIR%%/acd/findkm.acd
>-%%DATADIR%%/acd/freak.acd
>-%%DATADIR%%/acd/fuzznuc.acd
>-%%DATADIR%%/acd/fuzzpro.acd
>-%%DATADIR%%/acd/fuzztran.acd
>-%%DATADIR%%/acd/garnier.acd
>-%%DATADIR%%/acd/geecee.acd
>-%%DATADIR%%/acd/getorf.acd
>-%%DATADIR%%/acd/giep.acd
>-%%DATADIR%%/acd/groups.standard
>-%%DATADIR%%/acd/helixturnhelix.acd
>-%%DATADIR%%/acd/histogramtest.acd
>-%%DATADIR%%/acd/hmoment.acd
>-%%DATADIR%%/acd/iep.acd
>-%%DATADIR%%/acd/infoalign.acd
>-%%DATADIR%%/acd/infoseq.acd
>-%%DATADIR%%/acd/intconv.acd
>-%%DATADIR%%/acd/isochore.acd
>-%%DATADIR%%/acd/kmrsplitter.acd
>-%%DATADIR%%/acd/kmrunion.acd
>-%%DATADIR%%/acd/knowntypes.standard
>-%%DATADIR%%/acd/lindna.acd
>-%%DATADIR%%/acd/listor.acd
>-%%DATADIR%%/acd/marscan.acd
>-%%DATADIR%%/acd/maskfeat.acd
>-%%DATADIR%%/acd/maskseq.acd
>-%%DATADIR%%/acd/matcher.acd
>-%%DATADIR%%/acd/megamerger.acd
>-%%DATADIR%%/acd/merger.acd
>-%%DATADIR%%/acd/msbar.acd
>-%%DATADIR%%/acd/mwcontam.acd
>-%%DATADIR%%/acd/mwfilter.acd
>-%%DATADIR%%/acd/needle.acd
>-%%DATADIR%%/acd/newcoils.acd
>-%%DATADIR%%/acd/newcpgreport.acd
>-%%DATADIR%%/acd/newcpgseek.acd
>-%%DATADIR%%/acd/newseq.acd
>-%%DATADIR%%/acd/noreturn.acd
>-%%DATADIR%%/acd/notseq.acd
>-%%DATADIR%%/acd/nthseq.acd
>-%%DATADIR%%/acd/octanol.acd
>-%%DATADIR%%/acd/oddcomp.acd
>-%%DATADIR%%/acd/palindrome.acd
>-%%DATADIR%%/acd/pasteseq.acd
>-%%DATADIR%%/acd/patmatdb.acd
>-%%DATADIR%%/acd/patmatmotifs.acd
>-%%DATADIR%%/acd/patmattest.acd
>-%%DATADIR%%/acd/pepcoil.acd
>-%%DATADIR%%/acd/pepinfo.acd
>-%%DATADIR%%/acd/pepnet.acd
>-%%DATADIR%%/acd/pepstats.acd
>-%%DATADIR%%/acd/pepwheel.acd
>-%%DATADIR%%/acd/pepwindow.acd
>-%%DATADIR%%/acd/pepwindowall.acd
>-%%DATADIR%%/acd/plotcon.acd
>-%%DATADIR%%/acd/plotorf.acd
>-%%DATADIR%%/acd/polydot.acd
>-%%DATADIR%%/acd/preg.acd
>-%%DATADIR%%/acd/prettyplot.acd
>-%%DATADIR%%/acd/prettyseq.acd
>-%%DATADIR%%/acd/prima.acd
>-%%DATADIR%%/acd/primers.acd
>-%%DATADIR%%/acd/primersearch.acd
>-%%DATADIR%%/acd/printsextract.acd
>-%%DATADIR%%/acd/profit.acd
>-%%DATADIR%%/acd/prophecy.acd
>-%%DATADIR%%/acd/prophet.acd
>-%%DATADIR%%/acd/prosextract.acd
>-%%DATADIR%%/acd/pscan.acd
>-%%DATADIR%%/acd/psiphi.acd
>-%%DATADIR%%/acd/rebaseextract.acd
>-%%DATADIR%%/acd/recoder.acd
>-%%DATADIR%%/acd/redata.acd
>-%%DATADIR%%/acd/remap.acd
>-%%DATADIR%%/acd/restover.acd
>-%%DATADIR%%/acd/restrict.acd
>-%%DATADIR%%/acd/revseq.acd
>-%%DATADIR%%/acd/sections.standard
>-%%DATADIR%%/acd/seealso.acd
>-%%DATADIR%%/acd/seqinfo.acd
>-%%DATADIR%%/acd/seqmatchall.acd
>-%%DATADIR%%/acd/seqret.acd
>-%%DATADIR%%/acd/seqretall.acd
>-%%DATADIR%%/acd/seqretallfeat.acd
>-%%DATADIR%%/acd/seqretset.acd
>-%%DATADIR%%/acd/seqretsingle.acd
>-%%DATADIR%%/acd/seqretsplit.acd
>-%%DATADIR%%/acd/seqrettype.acd
>-%%DATADIR%%/acd/showalign.acd
>-%%DATADIR%%/acd/showdb.acd
>-%%DATADIR%%/acd/showfeat.acd
>-%%DATADIR%%/acd/showorf.acd
>-%%DATADIR%%/acd/showseq.acd
>-%%DATADIR%%/acd/shuffleseq.acd
>-%%DATADIR%%/acd/sigcleave.acd
>-%%DATADIR%%/acd/silent.acd
>-%%DATADIR%%/acd/sirna.acd
>-%%DATADIR%%/acd/sixpack.acd
>-%%DATADIR%%/acd/skipseq.acd
>-%%DATADIR%%/acd/splitter.acd
>-%%DATADIR%%/acd/stretcher.acd
>-%%DATADIR%%/acd/stssearch.acd
>-%%DATADIR%%/acd/supermatcher.acd
>-%%DATADIR%%/acd/syco.acd
>-%%DATADIR%%/acd/tcode.acd
>-%%DATADIR%%/acd/testplot.acd
>-%%DATADIR%%/acd/textsearch.acd
>-%%DATADIR%%/acd/tfextract.acd
>-%%DATADIR%%/acd/tfm.acd
>-%%DATADIR%%/acd/tfscan.acd
>-%%DATADIR%%/acd/tmap.acd
>-%%DATADIR%%/acd/tranalign.acd
>-%%DATADIR%%/acd/transeq.acd
>-%%DATADIR%%/acd/treetypedisplay.acd
>-%%DATADIR%%/acd/trimest.acd
>-%%DATADIR%%/acd/trimseq.acd
>-%%DATADIR%%/acd/twofeat.acd
>-%%DATADIR%%/acd/union.acd
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
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>+%%PORTDOCS%%%%DOCSDIR%%/programs/html/libscan.html
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/matgen3d.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorecmapdir.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggenlig.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscanlig.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt
>@@ -1627,25 +810,21 @@
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/clique.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcopy.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/comparator.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/consense.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/contactalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactcount.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contml.txt
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> %%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/crystalball.txt
>@@ -1657,21 +836,15 @@
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxfasta.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxflat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxgcg.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnacomp.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnadist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnainvar.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnaml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnamlk.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapars.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dollop.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dolpenny.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt
>@@ -1696,6 +869,7 @@
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt
>@@ -1732,7 +906,6 @@
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/factor.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt
>@@ -1756,7 +929,6 @@
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fitch.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
>@@ -1781,206 +953,1120 @@
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/gendist.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
> %%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/kitsch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mix.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/neighbor.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/penny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pestfind.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/protdist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqboot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
> %%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
> %%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
> %%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
> %%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
>+%%DATADIR%%/plstnd5.fnt
>+%%DATADIR%%/plxtnd5.fnt
>+%%DATADIR%%/acd/needle.acd
>+%%DATADIR%%/acd/newcoils.acd
>+%%DATADIR%%/acd/newcpgreport.acd
>+%%DATADIR%%/acd/newcpgseek.acd
>+%%DATADIR%%/acd/newseq.acd
>+%%DATADIR%%/acd/noreturn.acd
>+%%DATADIR%%/acd/notseq.acd
>+%%DATADIR%%/acd/nthseq.acd
>+%%DATADIR%%/acd/octanol.acd
>+%%DATADIR%%/acd/oddcomp.acd
>+%%DATADIR%%/acd/palindrome.acd
>+%%DATADIR%%/acd/pasteseq.acd
>+%%DATADIR%%/acd/patmatdb.acd
>+%%DATADIR%%/acd/patmatmotifs.acd
>+%%DATADIR%%/acd/patmattest.acd
>+%%DATADIR%%/acd/pepcoil.acd
>+%%DATADIR%%/acd/pepinfo.acd
>+%%DATADIR%%/acd/pepnet.acd
>+%%DATADIR%%/acd/pepstats.acd
>+%%DATADIR%%/acd/pepwheel.acd
>+%%DATADIR%%/acd/pepwindow.acd
>+%%DATADIR%%/acd/pepwindowall.acd
>+%%DATADIR%%/acd/plotcon.acd
>+%%DATADIR%%/acd/plotorf.acd
>+%%DATADIR%%/acd/polydot.acd
>+%%DATADIR%%/acd/preg.acd
>+%%DATADIR%%/acd/prettyplot.acd
>+%%DATADIR%%/acd/prettyseq.acd
>+%%DATADIR%%/acd/prima.acd
>+%%DATADIR%%/acd/primers.acd
>+%%DATADIR%%/acd/primersearch.acd
>+%%DATADIR%%/acd/printsextract.acd
>+%%DATADIR%%/acd/profit.acd
>+%%DATADIR%%/acd/prophecy.acd
>+%%DATADIR%%/acd/prophet.acd
>+%%DATADIR%%/acd/prosextract.acd
>+%%DATADIR%%/acd/pscan.acd
>+%%DATADIR%%/acd/psiphi.acd
>+%%DATADIR%%/acd/rebaseextract.acd
>+%%DATADIR%%/acd/recoder.acd
>+%%DATADIR%%/acd/redata.acd
>+%%DATADIR%%/acd/remap.acd
>+%%DATADIR%%/acd/restover.acd
>+%%DATADIR%%/acd/revseq.acd
>+%%DATADIR%%/acd/restrict.acd
>+%%DATADIR%%/acd/seealso.acd
>+%%DATADIR%%/acd/seqinfo.acd
>+%%DATADIR%%/acd/seqmatchall.acd
>+%%DATADIR%%/acd/seqret.acd
>+%%DATADIR%%/acd/seqretall.acd
>+%%DATADIR%%/acd/seqretallfeat.acd
>+%%DATADIR%%/acd/seqretset.acd
>+%%DATADIR%%/acd/seqretsingle.acd
>+%%DATADIR%%/acd/seqretsplit.acd
>+%%DATADIR%%/acd/seqrettype.acd
>+%%DATADIR%%/acd/showalign.acd
>+%%DATADIR%%/acd/showdb.acd
>+%%DATADIR%%/acd/showfeat.acd
>+%%DATADIR%%/acd/showorf.acd
>+%%DATADIR%%/acd/showseq.acd
>+%%DATADIR%%/acd/shuffleseq.acd
>+%%DATADIR%%/acd/sigcleave.acd
>+%%DATADIR%%/acd/silent.acd
>+%%DATADIR%%/acd/sirna.acd
>+%%DATADIR%%/acd/sixpack.acd
>+%%DATADIR%%/acd/skipseq.acd
>+%%DATADIR%%/acd/tfm.acd
>+%%DATADIR%%/acd/splitter.acd
>+%%DATADIR%%/acd/stretcher.acd
>+%%DATADIR%%/acd/stssearch.acd
>+%%DATADIR%%/acd/supermatcher.acd
>+%%DATADIR%%/acd/syco.acd
>+%%DATADIR%%/acd/tcode.acd
>+%%DATADIR%%/acd/testplot.acd
>+%%DATADIR%%/acd/textsearch.acd
>+%%DATADIR%%/acd/tfextract.acd
>+%%DATADIR%%/acd/tfscan.acd
>+%%DATADIR%%/acd/tmap.acd
>+%%DATADIR%%/acd/tranalign.acd
>+%%DATADIR%%/acd/transeq.acd
>+%%DATADIR%%/acd/treetypedisplay.acd
>+%%DATADIR%%/acd/trimest.acd
>+%%DATADIR%%/acd/trimseq.acd
>+%%DATADIR%%/acd/twofeat.acd
>+%%DATADIR%%/acd/union.acd
>+%%DATADIR%%/acd/vectorstrip.acd
>+%%DATADIR%%/acd/water.acd
>+%%DATADIR%%/acd/whichdb.acd
>+%%DATADIR%%/acd/wobble.acd
>+%%DATADIR%%/acd/wordcount.acd
>+%%DATADIR%%/acd/wordmatch.acd
>+%%DATADIR%%/acd/wossname.acd
>+%%DATADIR%%/acd/yank.acd
>+%%DATADIR%%/acd/codes.english
>+%%DATADIR%%/acd/groups.standard
>+%%DATADIR%%/acd/knowntypes.standard
>+%%DATADIR%%/acd/sections.standard
>+%%DATADIR%%/acd/variables.standard
>+%%DATADIR%%/acd/aaindexextract.acd
>+%%DATADIR%%/acd/abiview.acd
>+%%DATADIR%%/acd/acdc.acd
>+%%DATADIR%%/acd/acdlog.acd
>+%%DATADIR%%/acd/acdpretty.acd
>+%%DATADIR%%/acd/acdtable.acd
>+%%DATADIR%%/acd/acdtrace.acd
>+%%DATADIR%%/acd/acdvalid.acd
>+%%DATADIR%%/acd/ajbad.acd
>+%%DATADIR%%/acd/ajfeatest.acd
>+%%DATADIR%%/acd/ajtest.acd
>+%%DATADIR%%/acd/antigenic.acd
>+%%DATADIR%%/acd/backtranseq.acd
>+%%DATADIR%%/acd/cai.acd
>+%%DATADIR%%/acd/banana.acd
>+%%DATADIR%%/acd/biosed.acd
>+%%DATADIR%%/acd/btwisted.acd
>+%%DATADIR%%/acd/chaos.acd
>+%%DATADIR%%/acd/charge.acd
>+%%DATADIR%%/acd/checktrans.acd
>+%%DATADIR%%/acd/chips.acd
>+%%DATADIR%%/acd/cirdna.acd
>+%%DATADIR%%/acd/codcmp.acd
>+%%DATADIR%%/acd/codcopy.acd
>+%%DATADIR%%/acd/coderet.acd
>+%%DATADIR%%/acd/complex.acd
>+%%DATADIR%%/acd/compseq.acd
>+%%DATADIR%%/acd/cons.acd
>+%%DATADIR%%/acd/corbatest.acd
>+%%DATADIR%%/acd/cpgplot.acd
>+%%DATADIR%%/acd/cpgreport.acd
>+%%DATADIR%%/acd/cusp.acd
>+%%DATADIR%%/acd/cutgextract.acd
>+%%DATADIR%%/acd/cutseq.acd
>+%%DATADIR%%/acd/dan.acd
>+%%DATADIR%%/acd/dbiblast.acd
>+%%DATADIR%%/acd/dbifasta.acd
>+%%DATADIR%%/acd/dbiflat.acd
>+%%DATADIR%%/acd/dbigcg.acd
>+%%DATADIR%%/acd/dbxfasta.acd
>+%%DATADIR%%/acd/dbxflat.acd
>+%%DATADIR%%/acd/dbxgcg.acd
>+%%DATADIR%%/acd/degapseq.acd
>+%%DATADIR%%/acd/demoalign.acd
>+%%DATADIR%%/acd/demofeatures.acd
>+%%DATADIR%%/acd/demolist.acd
>+%%DATADIR%%/acd/demoreport.acd
>+%%DATADIR%%/acd/demosequence.acd
>+%%DATADIR%%/acd/demostring.acd
>+%%DATADIR%%/acd/demotable.acd
>+%%DATADIR%%/acd/descseq.acd
>+%%DATADIR%%/acd/diffseq.acd
>+%%DATADIR%%/acd/digest.acd
>+%%DATADIR%%/acd/distmat.acd
>+%%DATADIR%%/acd/dotmatcher.acd
>+%%DATADIR%%/acd/dotpath.acd
>+%%DATADIR%%/acd/dottup.acd
>+%%DATADIR%%/acd/dreg.acd
>+%%DATADIR%%/acd/einverted.acd
>+%%DATADIR%%/acd/embossdata.acd
>+%%DATADIR%%/acd/iep.acd
>+%%DATADIR%%/acd/embossversion.acd
>+%%DATADIR%%/acd/emma.acd
>+%%DATADIR%%/acd/emowse.acd
>+%%DATADIR%%/acd/entrails.acd
>+%%DATADIR%%/acd/entret.acd
>+%%DATADIR%%/acd/epestfind.acd
>+%%DATADIR%%/acd/eprimer3.acd
>+%%DATADIR%%/acd/equicktandem.acd
>+%%DATADIR%%/acd/est2genome.acd
>+%%DATADIR%%/acd/etandem.acd
>+%%DATADIR%%/acd/extractfeat.acd
>+%%DATADIR%%/acd/extractseq.acd
>+%%DATADIR%%/acd/findkm.acd
>+%%DATADIR%%/acd/freak.acd
>+%%DATADIR%%/acd/fuzznuc.acd
>+%%DATADIR%%/acd/fuzzpro.acd
>+%%DATADIR%%/acd/fuzztran.acd
>+%%DATADIR%%/acd/garnier.acd
>+%%DATADIR%%/acd/geecee.acd
>+%%DATADIR%%/acd/getorf.acd
>+%%DATADIR%%/acd/giep.acd
>+%%DATADIR%%/acd/helixturnhelix.acd
>+%%DATADIR%%/acd/hmoment.acd
>+%%DATADIR%%/acd/histogramtest.acd
>+%%DATADIR%%/acd/infoalign.acd
>+%%DATADIR%%/acd/infoseq.acd
>+%%DATADIR%%/acd/intconv.acd
>+%%DATADIR%%/acd/isochore.acd
>+%%DATADIR%%/acd/kmrsplitter.acd
>+%%DATADIR%%/acd/kmrunion.acd
>+%%DATADIR%%/acd/lindna.acd
>+%%DATADIR%%/acd/listor.acd
>+%%DATADIR%%/acd/marscan.acd
>+%%DATADIR%%/acd/maskfeat.acd
>+%%DATADIR%%/acd/maskseq.acd
>+%%DATADIR%%/acd/matcher.acd
>+%%DATADIR%%/acd/megamerger.acd
>+%%DATADIR%%/acd/merger.acd
>+%%DATADIR%%/acd/msbar.acd
>+%%DATADIR%%/acd/mwcontam.acd
>+%%DATADIR%%/acd/mwfilter.acd
>+%%DATADIR%%/data/AAINDEX/dummyfile
>+%%DATADIR%%/data/CODONS/Cut.index
>+%%DATADIR%%/data/CODONS/Eacica.cut
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>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/SequenceFilter.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Favorites.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultList.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java
>+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
>+%%DATADIR%%/jemboss/resources/jemboss.properties
>+%%DATADIR%%/jemboss/resources/readme.html
>+%%DATADIR%%/jemboss/resources/readmeAlign.html
>+%%DATADIR%%/jemboss/resources/readmeDNADraw.html
>+%%DATADIR%%/jemboss/resources/results.html
>+%%DATADIR%%/jemboss/resources/version
>+%%DATADIR%%/jemboss/resources/filemgr.html
>+%%DATADIR%%/jemboss/resources/seqList.html
>+%%DATADIR%%/jemboss/utils/install-jemboss-server.sh
>+%%DATADIR%%/jemboss/utils/keys.sh
>+%%DATADIR%%/jemboss/utils/makeJar.csh
>+%%DATADIR%%/jemboss/utils/makeJNLP.sh
>+%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
>+%%DATADIR%%/jemboss/utils/template.html
>+%%DATADIR%%/jemboss/utils/README
>+%%DATADIR%%/jemboss/LICENSE
>+%%DATADIR%%/jemboss/readme.html
>+%%DATADIR%%/jemboss/runJemboss.sh
>+%%DATADIR%%/jemboss/README
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
> %%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
> %%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
> %%PORTDOCS%%@dirrm %%DOCSDIR%%
>-@dirrm %%DATADIR%%/test/wormpep
>-@dirrm %%DATADIR%%/test/swnew
>-@dirrm %%DATADIR%%/test/swiss
>-@dirrm %%DATADIR%%/test/pir
>+@dirrm %%DATADIR%%/acd
>+@dirrm %%DATADIR%%/data/AAINDEX
>+@dirrm %%DATADIR%%/data/CODONS
>+@dirrm %%DATADIR%%/data/REBASE
>+@dirrm %%DATADIR%%/data/PRINTS
>+@dirrm %%DATADIR%%/data/PROSITE
>+@dirrmtry %%DATADIR%%/data
>+@dirrm %%DATADIR%%/test/data
>+@dirrm %%DATADIR%%/test/embl
> @dirrm %%DATADIR%%/test/genbank
> @dirrm %%DATADIR%%/test/gb
>-@dirrm %%DATADIR%%/test/embl
>-@dirrm %%DATADIR%%/test/data
>+@dirrm %%DATADIR%%/test/pir
>+@dirrm %%DATADIR%%/test/swiss
>+@dirrm %%DATADIR%%/test/swnew
>+@dirrm %%DATADIR%%/test/wormpep
> @dirrm %%DATADIR%%/test
>-@dirrm %%DATADIR%%/jemboss/utils
>-@dirrm %%DATADIR%%/jemboss/resources
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
>-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
>-@dirrm %%DATADIR%%/jemboss/org/emboss
>-@dirrm %%DATADIR%%/jemboss/org
>-@dirrm %%DATADIR%%/jemboss/lib/axis
>-@dirrm %%DATADIR%%/jemboss/lib
>-@dirrm %%DATADIR%%/jemboss/images
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
>-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
> @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
> @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
>+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
> @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss
> @dirrm %%DATADIR%%/jemboss/api/org/emboss
> @dirrm %%DATADIR%%/jemboss/api/org
> @dirrm %%DATADIR%%/jemboss/api
>+@dirrm %%DATADIR%%/jemboss/images
>+@dirrm %%DATADIR%%/jemboss/lib/axis
>+@dirrm %%DATADIR%%/jemboss/lib
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
>+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
>+@dirrm %%DATADIR%%/jemboss/org/emboss
>+@dirrm %%DATADIR%%/jemboss/org
>+@dirrm %%DATADIR%%/jemboss/resources
>+@dirrm %%DATADIR%%/jemboss/utils
> @dirrm %%DATADIR%%/jemboss
>-@dirrm %%DATADIR%%/data/REBASE
>-@dirrm %%DATADIR%%/data/PROSITE
>-@dirrm %%DATADIR%%/data/PRINTS
>-@dirrm %%DATADIR%%/data/CODONS
>-@dirrm %%DATADIR%%/data/AAINDEX
>-@dirrm %%DATADIR%%/data
>-@dirrm %%DATADIR%%/acd
>-@dirrm %%DATADIR%%
>+@dirrmtry %%DATADIR%%
>+@dirrmtry bin
>+@dirrmtry include
>+@dirrmtry lib
>+@dirrmtry share/doc
>+@dirrmtry share
>+

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Attachments on bug 93053: 62217 | 62218 | 62219 | 62220 | 62221