Add NOPORTDOCS support to pkg-plist

2 files changed, 585 insertions, 586 deletions

diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 76fe2ff54f1e..001fe38a3ce2 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -41,7 +41,7 @@ do-install:
 		${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;)
 
 .if !defined(NOPORTDOCS)
-	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/java/${PKGNAME})
+	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/doc/${PKGNAME})
 .endif)
 
 post-install:
diff --git a/biology/biojava/pkg-plist b/biology/biojava/pkg-plist
index c0c4de8b8630..4075c88d44db 100644
--- a/biology/biojava/pkg-plist
+++ b/biology/biojava/pkg-plist
@@ -1,588 +1,587 @@
 share/java/classes/biojava.jar
 share/java/classes/xml.jar
-share/java/biojava-1.01/LICENSE
-share/java/biojava-1.01/README
-share/java/biojava-1.01/demos/acedb/AceTreeView.java
-share/java/biojava-1.01/demos/acedb/ServeAceAsCorba.java
-share/java/biojava-1.01/demos/acedb/AceClient.java
-share/java/biojava-1.01/demos/acedb/SequenceFetch.java
-share/java/biojava-1.01/demos/gff/GFFFilter.java
-share/java/biojava-1.01/demos/gff/EmblToGffFasta.java
-share/java/biojava-1.01/demos/gff/GFFToFeatures.java
-share/java/biojava-1.01/demos/gff/varC4-2.gff
-share/java/biojava-1.01/demos/gff/AL121903.embl
-share/java/biojava-1.01/demos/seq/db/AddFilesToIndex.java
-share/java/biojava-1.01/demos/seq/db/CreateIndex.java
-share/java/biojava-1.01/demos/seq/db/FetchSequence.java
-share/java/biojava-1.01/demos/seq/db/ListSeqsInIndex.java
-share/java/biojava-1.01/demos/seq/TestGenbank.java
-share/java/biojava-1.01/demos/seq/AL121903.genbank
-share/java/biojava-1.01/demos/seq/TestTranslation.java
-share/java/biojava-1.01/demos/seq/TestEmbl.java
-share/java/biojava-1.01/demos/seq/AL121903.embl
-share/java/biojava-1.01/demos/dist/TestDistribution.java
-share/java/biojava-1.01/demos/dp/PairwiseAlignment.java
-share/java/biojava-1.01/demos/dp/fake.fasta
-share/java/biojava-1.01/demos/dp/ViterbiAlign.java
-share/java/biojava-1.01/demos/dp/package.html
-share/java/biojava-1.01/demos/dp/SearchProfile.java
-share/java/biojava-1.01/demos/dp/fakepromoter.xml
-share/java/biojava-1.01/demos/dp/Dice.java
-share/java/biojava-1.01/demos/BioCorba/CorbaDBServer.java
-share/java/biojava-1.01/demos/BioCorba/ChrI.prom.fasta
-share/java/biojava-1.01/demos/BioCorba/CorbaDBClient.java
-share/java/biojava-1.01/demos/files/AL121903.embl
-share/java/biojava-1.01/demos/files/test.hmm
-share/java/biojava-1.01/demos/files/out.gff
-share/java/biojava-1.01/demos/files/AL121903.genbank
-share/java/biojava-1.01/demos/files/ChrI.prom.fasta
-share/java/biojava-1.01/demos/files/fakepromoter.xml
-share/java/biojava-1.01/demos/files/scoptest.fa
-share/java/biojava-1.01/demos/files/varC4-2.gff
-share/java/biojava-1.01/demos/files/varC4-2.dna
-share/java/biojava-1.01/demos/files/fake.fasta
-share/java/biojava-1.01/demos/symbol/TestAmbiguity.java
-share/java/biojava-1.01/demos/symbol/TestSimpleAlignment.java
-share/java/biojava-1.01/demos/symbol/Tools.java
-share/java/biojava-1.01/demos/symbol/TestOrderNSymbolList.java
-share/java/biojava-1.01/demos/symbol/TestGappedSymbolList.java
-share/java/biojava-1.01/demos/symbol/TestWindowedSymbolList.java
-share/java/biojava-1.01/demos/seqviewer/test.fa
-share/java/biojava-1.01/demos/seqviewer/EmblViewer.java
-share/java/biojava-1.01/demos/seqviewer/TestSequencePanel.java
-share/java/biojava-1.01/docs/api/GNOME/UnknownHolder.html
-share/java/biojava-1.01/docs/api/GNOME/package-tree.html
-share/java/biojava-1.01/docs/api/GNOME/package-frame.html
-share/java/biojava-1.01/docs/api/GNOME/_Unknown_Operations.html
-share/java/biojava-1.01/docs/api/GNOME/Unknown.html
-share/java/biojava-1.01/docs/api/GNOME/_Unknown_Tie.html
-share/java/biojava-1.01/docs/api/GNOME/_UnknownImplBase.html
-share/java/biojava-1.01/docs/api/GNOME/_UnknownStub.html
-share/java/biojava-1.01/docs/api/GNOME/UnknownHelper.html
-share/java/biojava-1.01/docs/api/GNOME/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/package-frame.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/SocketDriver.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/SocketResultSet.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticStringValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-frame.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceNode.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceObject.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceSet.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticDateValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticFloatValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticIntValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelInclude.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelNode.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelReference.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelType.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticReference.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/package-frame.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/AceAnnotation.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/AceSequence.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/AceSequenceDB.html
-share/java/biojava-1.01/docs/api/org/acedb/AceElement.html
-share/java/biojava-1.01/docs/api/org/acedb/AceNode.html
-share/java/biojava-1.01/docs/api/org/acedb/AceObject.html
-share/java/biojava-1.01/docs/api/org/acedb/AceSet.html
-share/java/biojava-1.01/docs/api/org/acedb/AceValue.html
-share/java/biojava-1.01/docs/api/org/acedb/Connection.html
-share/java/biojava-1.01/docs/api/org/acedb/Database.html
-share/java/biojava-1.01/docs/api/org/acedb/DateValue.html
-share/java/biojava-1.01/docs/api/org/acedb/Driver.html
-share/java/biojava-1.01/docs/api/org/acedb/FloatValue.html
-share/java/biojava-1.01/docs/api/org/acedb/IntValue.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelInclude.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelNode.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelReference.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelType.html
-share/java/biojava-1.01/docs/api/org/acedb/Reference.html
-share/java/biojava-1.01/docs/api/org/acedb/StringValue.html
-share/java/biojava-1.01/docs/api/org/acedb/Ace.html
-share/java/biojava-1.01/docs/api/org/acedb/AcePerlParser.html
-share/java/biojava-1.01/docs/api/org/acedb/AceURL.html
-share/java/biojava-1.01/docs/api/org/acedb/AceUtils.html
-share/java/biojava-1.01/docs/api/org/acedb/Handler.html
-share/java/biojava-1.01/docs/api/org/acedb/AceException.html
-share/java/biojava-1.01/docs/api/org/acedb/AceURLException.html
-share/java/biojava-1.01/docs/api/org/acedb/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/AceError.html
-share/java/biojava-1.01/docs/api/org/acedb/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/package-frame.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcess.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-tree.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-frame.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeq_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeq_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDB_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_Seq_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDB_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeature_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeq.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeq.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDB.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIterator.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/Seq.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDB.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeature.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIterator.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeq_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeqImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeqStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeq_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDB_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDBImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDBStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIteratorImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIteratorStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_Seq_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDB_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDBImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDBStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeature_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIteratorImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIteratorStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeqHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeqHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStreamHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStreamHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSet.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRangeHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRangeHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/primaryidListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/primaryidListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDBHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDBHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIteratorHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIteratorHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLargeHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLargeHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDBHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDBHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIteratorHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIteratorHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqType.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqTypeHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqTypeHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/stringListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/stringListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcessHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcessHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStream.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRange.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLarge.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-summary.html
-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/IgnoreRecordException.html
-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/package-tree.html
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-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFDocumentHandler.html
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-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFEntrySet.html
-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html
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