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(-)biojava.new/Makefile (-53 / +26 lines)
Lines 2-68 Link Here
2 
# Date created:	15 September 2000
 2 
# Date created:	15 September 2000
3 
# Whom:		FreeBSD Bio porters (bio@freebsd.net)
 3 
# Whom:		FreeBSD Bio porters (bio@freebsd.net)
4 
#
 4 
#
5 
# $FreeBSD: ports/biology/biojava/Makefile,v 1.17 2008/12/08 06:43:45 linimon Exp $
 5 
# $FreeBSD: ports/biology/biojava/Makefile,v 1.16 2008/06/06 13:08:28 edwin Exp $
6 
#
 6 
#
7 

          7
          

        

        

          8
          
PORTNAME=	biojava

          8
          
PORTNAME=	biojava

        

          
            

              9
              
DISTVERSION=	1.5-beta2


              9
              
DISTVERSION=	1.7

            

            

              10
              
PORTREVISION=	2


              
              
            

        

          11
          
PORTEPOCH=	1

          10
          
PORTEPOCH=	1

        

        

          12
          
CATEGORIES=	biology java

          11
          
CATEGORIES=	biology java

        

          
            

              13
              
MASTER_SITES=	http://www.biojava.org/download/bj15b/all/:source	\


              12
              
MASTER_SITES=	http://www.biojava.org/download/bj17/all/

            

            

              14
              
		http://www.biojava.org/download/bj15b/bin/:bin


              13
              
DISTNAME=	${PORTNAME}-${DISTVERSION}-all

            

            

              15
              
DISTFILES=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:source	\


              14
              
EXTRACT_SUFX=	.jar

            

            

              16
              
		bytecode.jar:bin


              
              
            

            

              17
              
EXTRACT_ONLY=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}


            

        

          18
          

          15
          

        

          
            

              19
              
MAINTAINER=	ports@FreeBSD.org


              16
              
MAINTAINER=	wenheping@gmail.com

            

        

          20
          
COMMENT=	Open-source java tools for processing biological data

          17
          
COMMENT=	Open-source java tools for processing biological data

        

        

          21
          

          18
          

        

          
            

              22
              
BUILD_DEPENDS=	${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \


              19
              
EXTRACT_DEPENDS+=	jar:${PORTSDIR}/java/diablo-jdk16

            

            

              23
              
		${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \


              
              
            

            

              24
              
		${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \


            

            

              25
              
		${JAVALIBDIR}/commons-cli.jar:${PORTSDIR}/java/jakarta-commons-cli \


            

            

              26
              
		${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \


            

            

              27
              
		${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool \


            

            

              28
              
		${JAVALIBDIR}/commons-collections.jar:${PORTSDIR}/java/jakarta-commons-collections


            

            

              29
              
RUN_DEPENDS=	${JAVALIBDIR}/hsqldb.jar:${PORTSDIR}/databases/hsqldb \


            

            

              30
              
		${JAVALIBDIR}/xml-apis.jar:${PORTSDIR}/textproc/xerces-j \


            

            

              31
              
		${JAVALIBDIR}/jakarta-regexp.jar:${PORTSDIR}/java/jakarta-regexp \


            

            

              32
              
		${JAVALIBDIR}/commons-cli.jar:${PORTSDIR}/java/jakarta-commons-cli \


            

            

              33
              
		${JAVALIBDIR}/commons-dbcp.jar:${PORTSDIR}/java/jakarta-commons-dbcp \


            

            

              34
              
		${JAVALIBDIR}/commons-pool.jar:${PORTSDIR}/java/jakarta-commons-pool \


            

            

              35
              
		${JAVALIBDIR}/commons-collections.jar:${PORTSDIR}/java/jakarta-commons-collections


            

            

              36
              


            

            

              37
              
.if !defined(WITHOUT_TESTS)


            

            

              38
              
BUILD_DEPENDS+=	${JAVALIBDIR}/junit.jar:${PORTSDIR}/java/junit


            

            

              39
              
.endif


            

        

          40
          

          20
          

        

        

          41
          
USE_JAVA=	yes

          21
          
USE_JAVA=	yes

        

        

          42
          
JAVA_VERSION=	1.5+

          22
          
JAVA_VERSION=	1.5+

        

        

          43
          
USE_ANT=	yes

          23
          
USE_ANT=	yes

        

        

          44
          
MAKE_ENV=	CLASSPATH="${JAVALIBDIR}"

          24
          
MAKE_ENV=	CLASSPATH="${JAVALIBDIR}"

        

          
            

              45
              
ALL_TARGET=	compile-apps


              25
              
ALL_TARGET=	package-biojava

            

        

          46
          

          26
          

        

          
            

              47
              
PLIST_SUB+=	VER=${DISTVERSION}


              27
              
JARFILES=	biojava.jar bytecode.jar

            

            

              48
              


              
              
            

            

              49
              
JARFILES=	apps-${DISTVERSION}.jar biojava.jar bytecode.jar


            

        

          50
          
PORTDOCS=	biojava

          28
          
PORTDOCS=	biojava

        

          
            

              51
              
SAMPLES=	demos


              29
              
PORTEXAMPLES=	demos

            

            

              52
              
WRKSRC=${WRKDIR}


              30
              
EXTRACT_CMD=	jar -xvf ${_DISTDIR}/${DISTFILES}

            

            

              53
              


              31
              
WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}

            

            

              54
              
.if !defined(NOPORTDOCS)


              32
              

            

            

              55
              
ALL_TARGET+=	javadocs-biojava


              33
              
do-extract:

            

            

              56
              
.endif


              34
              
	@${RM} -rf ${WRKDIR}

            

            

              57
              
.if !defined(WITHOUT_SAMPLES)


              35
              
	@${MKDIR} ${WRKDIR}

            

            

              58
              
ALL_TARGET+=	compile-demos


              36
              
	@cd ${WRKDIR} && ${EXTRACT_CMD}

            

            

              59
              
PLIST_SUB+=	INSTEX=""


              
              
            

            

              60
              
.else


            

            

              61
              
PLIST_SUB+=	INSTEX="@comment "


            

            

              62
              
.endif


            

            

              63
              


            

            

              64
              
post-extract:


            

            

              65
              
	${CP} ${_DISTDIR}/bytecode.jar ${WRKSRC}


            

        

          66
          

          37
          

        

        

          67
          
.if !defined(WITHOUT_TESTS)

          38
          
.if !defined(WITHOUT_TESTS)

        

        

          68
          
regression-test:

          39
          
regression-test:

        

  

    
      
            Lines 70-76
          
      
      
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          70
          
		${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)

          41
          
		${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests)

        

        

          71
          
.endif

          42
          
.endif

        

        

          72
          

          43
          

        

            

              73
              
# from textproc/xerces-j

              
              
            

        

          74
          
do-install:

          44
          
do-install:

        

        

          75
          
	@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."

          45
          
	@${ECHO_MSG} -n ">> Installing JAR files in ${JAVAJARDIR}..."

        

        

          76
          
	@${MKDIR} ${JAVAJARDIR}

          46
          
	@${MKDIR} ${JAVAJARDIR}

        

  

    
      
            Lines 79-99
          
      
      
        Link Here
      
    
  

        

          79
          
	@${ECHO_MSG} -n " ${JARFILE}"

          49
          
	@${ECHO_MSG} -n " ${JARFILE}"

        

        

          80
          
.endfor

          50
          
.endfor

        

        

          81
          
	@${ECHO_MSG} " [ DONE ]"

          51
          
	@${ECHO_MSG} " [ DONE ]"

        

            

              
              
              52
              

            

        

          82
          
.if !defined(NOPORTDOCS)

          53
          
.if !defined(NOPORTDOCS)

        

        

          83
          
	@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."

          54
          
	@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."

        

        

          84
          
	@${MKDIR} ${DOCSDIR}

          55
          
	@${MKDIR} ${DOCSDIR}

        

        

          85
          
	@${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR}

          56
          
	@${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR}

        

        

          86
          
	@${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}

          57
          
	@${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}

        

          
            

              87
              
	@cd ${WRKSRC}/ant-build/docs && \


              58
              
	@cd ${WRKSRC}/doc && \

            

        

          88
          
		${FIND} ${PORTDOCS} -type d -exec ${MKDIR} "${DOCSDIR}/{}" \; && \

          59
          
		${FIND} ${PORTDOCS} -type d -exec ${MKDIR} "${DOCSDIR}/{}" \; && \

        

        

          89
          
		${FIND} ${PORTDOCS} -not -type d -exec ${INSTALL_DATA} "{}" "${DOCSDIR}/{}" \;

          60
          
		${FIND} ${PORTDOCS} -not -type d -exec ${INSTALL_DATA} "{}" "${DOCSDIR}/{}" \;

        

        

          90
          
	@${ECHO_MSG} " [ DONE ]"

          61
          
	@${ECHO_MSG} " [ DONE ]"

        

        

          91
          
.endif

          62
          
.endif

        

          
            

              92
              
.if !defined(WITHOUT_SAMPLES)


              63
              

            

            

              93
              
	@${ECHO_MSG} -n ">> Installing demos in ${EXAMPLESDIR}..."


              64
              
.if !defined(NOPORTEXAMPLES)

            

            

              94
              
	cd ${WRKSRC} && \


              65
              
	@${ECHO_MSG} -n ">> Installing examples in ${EXAMPLESDIR}..."

            

            

              95
              
		${FIND} ${SAMPLES} -type d -exec ${MKDIR} "${EXAMPLESDIR}/{}" \; && \


              66
              
	@${MKDIR} ${EXAMPLESDIR}

            

            

              96
              
		${FIND} ${SAMPLES} -not -type d -exec ${INSTALL_DATA} "{}" "${EXAMPLESDIR}/{}" \;


              67
              
	cd ${WRKSRC}/doc && \

            

            

              
              

              68
              
		${FIND} ${PORTEXAMPLES} -type d -exec ${MKDIR} "${EXAMPLESDIR}/{}" \; && \

            

            


              69
              
		${FIND} ${PORTEXAMPLES} -not -type d -exec ${INSTALL_DATA} "{}" "${EXAMPLESDIR}/{}" \;

            

        

          97
          
	@${ECHO_MSG} " [ DONE ]"

          70
          
	@${ECHO_MSG} " [ DONE ]"

        

        

          98
          
.endif

          71
          
.endif

        

        

          99
          

          72
          

        



(-)biojava.new/distinfo
      (-6 / +3 lines)




  

    
      
            Lines 1-6
          
      
      
        Link Here
      
    
  

          
            

              1
              
MD5 (biojava-1.5-beta2.tar.gz) = 904e9a5600102a9a5238b87868e3f09f


              1
              
MD5 (biojava-1.7-all.jar) = aedb49b6600430bc2b80090536c6ebff

            

            

              2
              
SHA256 (biojava-1.5-beta2.tar.gz) = f2912bc90d4b9c01ac24e9db9718203af01b098538020989d4519cfabd901208


              2
              
SHA256 (biojava-1.7-all.jar) = 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f

            

            

              3
              
SIZE (biojava-1.5-beta2.tar.gz) = 28767548


              3
              
SIZE (biojava-1.7-all.jar) = 28062592

            

            

              4
              
MD5 (bytecode.jar) = 332e0b06b485645802067c92f1055e37


              
              
            

            

              5
              
SHA256 (bytecode.jar) = 745bf5899361565f1a3572f19d4ae9c99354856d8a9f29bf52908650c0e9e48f


            

            

              6
              
SIZE (bytecode.jar) = 93463


            



(-)biojava.new/files/patch-build.xml
      (-11 lines)




  

    
      
            Lines 1-11
          
      
      
        Link Here
      
    
  

            

              1
              
--- build.xml.orig	Fri Dec 29 14:12:28 2006

              
              
            

            

              2
              
+++ build.xml	Wed Mar 21 16:14:38 2007

            

            

              3
              
@@ -49,7 +49,7 @@

            

            

              4
              
 

            

            

              5
              
     <property name="build.compiler" value="javac1.4" />

            

            

              6
              
 

            

            

              7
              
-    <property name="classpath" value="bytecode.jar:commons-cli.jar:commons-dbcp-1.1.jar:commons-pool-1.1.jar:hsqldb.jar" />

            

            

              8
              
+    <property name="classpath" value="bytecode.jar:commons-cli.jar:commons-dbcp.jar:commons-pool.jar:hsqldb.jar" />

            

            

              9
              
 

            

            

              10
              
     <property name="ant-tasks.path" value="ant-lib/sablecc.jar:ant-lib/anttask.jar" />

            

            

              11
              
 

            



(-)biojava.new/pkg-plist
      (-213 / +2 lines)




  

    
      
            Lines 1-215
          
      
      
        Link Here
      
    
  

            

              1
              
%%PORTDOCS%%%%DOCSDIR%%/LICENSE

              
              
            

            

              2
              
%%PORTDOCS%%%%DOCSDIR%%/README

            

            

              3
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/CircLocTest/CircularLocationTester.java

            

            

              4
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/CircLocTest/TestFrame.java

            

            

              5
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ListChangeTypes.java

            

            

              6
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/RFetch.java

            

            

              7
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/annodb/CreateIndexDB.java

            

            

              8
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/DummyFromGFF.java

            

            

              9
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/LargeSequenceTest.java

            

            

              10
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqDumper.java

            

            

              11
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqEMBL.java

            

            

              12
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SeqGFF.java

            

            

              13
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/SequenceTest.java

            

            

              14
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/biosql/UploadFlat.java

            

            

              15
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/blastxml/BlastParser.java

            

            

              16
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/blastxml/input.xml

            

            

              17
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDAS.java

            

            

              18
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDASG.java

            

            

              19
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDASH.java

            

            

              20
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/das/TestDSN.java

            

            

              21
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestDistribution.java

            

            

              22
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestOrderNAlphabet.java

            

            

              23
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/TestOrderNDistribution.java

            

            

              24
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dist/Tools.java

            

            

              25
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/Dice.java

            

            

              26
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/PairwiseAlignment.java

            

            

              27
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/PatternFinder.java

            

            

              28
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/SearchProfile.java

            

            

              29
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/ViterbiAlign.java

            

            

              30
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/fake.fasta

            

            

              31
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/fakepromoter.xml

            

            

              32
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/dp/package.html

            

            

              33
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Blast2HTML.java

            

            

              34
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/BlastLike2XML.java

            

            

              35
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Fasta2XML.java

            

            

              36
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/Pdb2XML.java

            

            

              37
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/TutorialEx1.java

            

            

              38
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/TutorialEx1Handler.java

            

            

              39
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets/copyall.xsl

            

            

              40
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets/hitlisthtml.xsl

            

            

              41
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ACTN_HUMAN.uniprot

            

            

              42
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AF438419.embl

            

            

              43
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AL121903.embl

            

            

              44
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/AL121903.genbank

            

            

              45
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ChrI.prom.fasta

            

            

              46
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/GCG/blast.report

            

            

              47
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/NP_001307.gp

            

            

              48
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/clustal/keratin.aln

            

            

              49
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fake.fasta

            

            

              50
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fakepromoter.xml

            

            

              51
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_demo.db

            

            

              52
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_demo.m10

            

            

              53
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/fp_queries.db

            

            

              54
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/hmmer/plus_tot.out

            

            

              55
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/Massive.out

            

            

              56
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/ReadMe

            

            

              57
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastn.out

            

            

              58
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastp.out

            

            

              59
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/blastx.out

            

            

              60
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/shortBlastn.out

            

            

              61
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/tblastn.out

            

            

              62
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/tblastx.out

            

            

              63
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/ncbiblast/unsuppVersionBlastn.out

            

            

              64
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/out.gff

            

            

              65
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/12E8.pdb

            

            

              66
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/hgh_ori.pdb

            

            

              67
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/hmga_1.pdb

            

            

              68
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/pdb/tnf.pdb

            

            

              69
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/scoptest.fa

            

            

              70
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/test.hmm

            

            

              71
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/varC4-2.dna

            

            

              72
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/varC4-2.gff

            

            

              73
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastn.out

            

            

              74
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastp.out

            

            

              75
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/blastx.out

            

            

              76
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastn.out

            

            

              77
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastp.out

            

            

              78
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_blastx.out

            

            

              79
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/sh_tblastx.out

            

            

              80
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/tblastn.out

            

            

              81
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/files/wublast/tblastx.out

            

            

              82
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/AE002734.game

            

            

              83
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/README.txt

            

            

              84
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/SeqIOTatler.java

            

            

              85
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/game/TestGAME.java

            

            

              86
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/AL121903.embl

            

            

              87
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/EmblToGffFasta.java

            

            

              88
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFCompare.java

            

            

              89
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFFilter.java

            

            

              90
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFMask.java

            

            

              91
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GFFToFeatures.java

            

            

              92
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/GenbankToGffFasta.java

            

            

              93
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/SwissprotToGffFasta.java

            

            

              94
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/XFF2GFF.java

            

            

              95
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/gff/varC4-2.gff

            

            

              96
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateFAIndex.java

            

            

              97
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateIndex.java

            

            

              98
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/CreateSPIndex.java

            

            

              99
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ListIDs.java

            

            

              100
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ReadRaw.java

            

            

              101
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/indexing/ReadRawSecondary.java

            

            

              102
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/nativeapps/BlastLike2XML.java

            

            

              103
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/nativeapps/Pdb2XML.java

            

            

              104
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/process/ProcessToolsTest.java

            

            

              105
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/prot/TestDigestIO.java

            

            

              106
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/search/IndexFastaDB.java

            

            

              107
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/AL121903.embl

            

            

              108
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/AL121903.genbank

            

            

              109
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/FetchSeq.java

            

            

              110
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/GCContent.java

            

            

              111
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/MotifFinder2.java

            

            

              112
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/ReverseComplement.java

            

            

              113
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/SimpleAssemblyTest.java

            

            

              114
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestEmbl.java

            

            

              115
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestEmbl2.java

            

            

              116
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestGenbank.java

            

            

              117
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestRefSeqPrt.java

            

            

              118
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestSubSequence.java

            

            

              119
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestSwissprot.java

            

            

              120
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/TestTranslation.java

            

            

              121
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/UniProtDemo.java

            

            

              122
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/AddFilesToIndex.java

            

            

              123
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/CreateIndex.java

            

            

              124
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/FetchSequence.java

            

            

              125
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/db/ListSeqsInIndex.java

            

            

              126
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seq/utrs.fa

            

            

              127
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/BeadDemo.java

            

            

              128
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/CircularEmblViewer.java

            

            

              129
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/EmblViewer.java

            

            

              130
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/EmblViewer2.java

            

            

              131
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/FastBeadDemo.java

            

            

              132
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/GappedViewer.java

            

            

              133
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/TraceViewer.java

            

            

              134
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/seqviewer/test.fa

            

            

              135
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTable.java

            

            

              136
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTableCompact.java

            

            

              137
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateDNAFastaHashTableLarge.java

            

            

              138
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateEmblHashTable.java

            

            

              139
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/CreateEmblHashTableLarge.java

            

            

              140
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/ResultPrinter.java

            

            

              141
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHA.java

            

            

              142
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHALarge.java

            

            

              143
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHASeq.java

            

            

              144
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssaha/SSAHASeqLarge.java

            

            

              145
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/AlignmentBuilder.java

            

            

              146
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/CountHits.java

            

            

              147
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/CountSubHits.java

            

            

              148
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/Echoer.java

            

            

              149
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/FilterByValue.java

            

            

              150
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ListQueries.java

            

            

              151
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ListSubjects.java

            

            

              152
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/ProcessBlastReport.java

            

            

              153
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/PropertyEchoer.java

            

            

              154
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/SubHitBuilder.java

            

            

              155
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/ssbind/SubHitFilter.java

            

            

              156
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/MatrixValue.java

            

            

              157
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/PatternDemo.java

            

            

              158
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestAlphabetIndexers.java

            

            

              159
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestAmbiguity.java

            

            

              160
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestGappedSymbolList.java

            

            

              161
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestIndexedIntegers.java

            

            

              162
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestLocation.java

            

            

              163
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestOrderNSymbolList.java

            

            

              164
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestSimpleAlignment.java

            

            

              165
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/TestWindowedSymbolList.java

            

            

              166
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/Tools.java

            

            

              167
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/symbol/WindowCount.java

            

            

              168
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Grep.java

            

            

              169
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Index.java

            

            

              170
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/Parse.java

            

            

              171
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/ParseEmbl.java

            

            

              172
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/ParseSwissprot.java

            

            

              173
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/tagvalue/PrintFormat.java

            

            

              174
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/CreateUnigeneFlat.java

            

            

              175
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/ParseLibInfo.java

            

            

              176
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/ParseUnigene.java

            

            

              177
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/unigene/SearchUnigeneFlat.java

            

            

              178
              
%%INSTEX%%%%EXAMPLESDIR%%/demos/xff/TestXFFStreaming.java

            

            

              179
              
%%JAVAJARDIR%%/apps-%%VER%%.jar

            

        

          180
          
%%JAVAJARDIR%%/biojava.jar

          1
          
%%JAVAJARDIR%%/biojava.jar

        

        

          181
          
%%JAVAJARDIR%%/bytecode.jar

          2
          
%%JAVAJARDIR%%/bytecode.jar

        

          
            

              182
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/xff


              3
              
%%PORTDOCS%%%%DOCSDIR%%/LICENSE

            

            

              183
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/unigene


              4
              
%%PORTDOCS%%%%DOCSDIR%%/README

            

            

              184
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/tagvalue


              
              
            

            

              185
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/symbol


            

            

              186
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/ssbind


            

            

              187
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/ssaha


            

            

              188
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seqviewer


            

            

              189
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seq/db


            

            

              190
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/seq


            

            

              191
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/search


            

            

              192
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/prot


            

            

              193
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/process


            

            

              194
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/nativeapps


            

            

              195
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/indexing


            

            

              196
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/gff


            

            

              197
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/game


            

            

              198
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/wublast


            

            

              199
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/pdb


            

            

              200
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/ncbiblast


            

            

              201
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/hmmer


            

            

              202
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/clustal


            

            

              203
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files/GCG


            

            

              204
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/files


            

            

              205
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/eventbasedparsing/stylesheets


            

            

              206
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/eventbasedparsing


            

            

              207
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/dp


            

            

              208
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/dist


            

            

              209
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/das


            

            

              210
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/blastxml


            

            

              211
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/biosql


            

            

              212
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/annodb


            

            

              213
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos/CircLocTest


            

            

              214
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%/demos


            

            

              215
              
%%INSTEX%%@dirrm %%EXAMPLESDIR%%


            






  

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