Fix install and packaging list.

Reported by:	kris

3 files changed, 67 insertions, 59 deletions

diff --git a/biology/libgenome/Makefile b/biology/libgenome/Makefile
index 2695838321e7..5a7678f9c668 100644
--- a/biology/libgenome/Makefile
+++ b/biology/libgenome/Makefile
@@ -13,6 +13,7 @@ MASTER_SITES=	http://www.libgenome.org/releases/
 DISTNAME=	libGenome-${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
+COMMENT=	Toolkit for developing bioinformatic related software in C++
 
 USE_REINPLACE=	yes
 USE_LIBTOOL=	yes
@@ -26,7 +27,7 @@ post-install:
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/html/*.css ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/doc/html/*.gif ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/doc/html/*.png ${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/html/*.html ${DOCSDIR}
 .endif
 
diff --git a/biology/libgenome/pkg-comment b/biology/libgenome/pkg-comment
deleted file mode 100644
index 86930ba80fb8..000000000000
--- a/biology/libgenome/pkg-comment
+++ /dev/null
@@ -1 +0,0 @@
-Toolkit for developing bioinformatic related software in C++
diff --git a/biology/libgenome/pkg-plist b/biology/libgenome/pkg-plist
index 52a30fa1df8d..93021fedefa5 100644
--- a/biology/libgenome/pkg-plist
+++ b/biology/libgenome/pkg-plist
@@ -49,121 +49,129 @@ lib/libGenome.so
 lib/libGenome.so.0
 %%PORTDOCS%%share/doc/libgenome/GNPREC_8H-source.html
 %%PORTDOCS%%share/doc/libgenome/GNPREC_8H.html
-%%PORTDOCS%%share/doc/libgenome/TestRevComp_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/TestRevComp_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/TestgpSeqConverter_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/TestgpSeqConverter_8cpp.html
 %%PORTDOCS%%share/doc/libgenome/annotated.html
+%%PORTDOCS%%share/doc/libgenome/classArray-members.html
+%%PORTDOCS%%share/doc/libgenome/classArray.html
 %%PORTDOCS%%share/doc/libgenome/classes.html
 %%PORTDOCS%%share/doc/libgenome/classgnABISource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnABISource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnABISource.html
+%%PORTDOCS%%share/doc/libgenome/classgnABISource.png
 %%PORTDOCS%%share/doc/libgenome/classgnBaseFeature-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnBaseFeature.gif
 %%PORTDOCS%%share/doc/libgenome/classgnBaseFeature.html
+%%PORTDOCS%%share/doc/libgenome/classgnBaseFeature.png
 %%PORTDOCS%%share/doc/libgenome/classgnBaseFilter-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnBaseFilter.gif
 %%PORTDOCS%%share/doc/libgenome/classgnBaseFilter.html
+%%PORTDOCS%%share/doc/libgenome/classgnBaseFilter.png
 %%PORTDOCS%%share/doc/libgenome/classgnBaseHeader-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnBaseHeader.gif
 %%PORTDOCS%%share/doc/libgenome/classgnBaseHeader.html
+%%PORTDOCS%%share/doc/libgenome/classgnBaseHeader.png
 %%PORTDOCS%%share/doc/libgenome/classgnBaseQualifier-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnBaseQualifier.gif
 %%PORTDOCS%%share/doc/libgenome/classgnBaseQualifier.html
+%%PORTDOCS%%share/doc/libgenome/classgnBaseQualifier.png
 %%PORTDOCS%%share/doc/libgenome/classgnBaseSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnBaseSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnBaseSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnBaseSource.png
 %%PORTDOCS%%share/doc/libgenome/classgnBaseSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnBaseSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnBaseSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnBaseSpec.png
 %%PORTDOCS%%share/doc/libgenome/classgnClone-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnClone.gif
 %%PORTDOCS%%share/doc/libgenome/classgnClone.html
+%%PORTDOCS%%share/doc/libgenome/classgnClone.png
 %%PORTDOCS%%share/doc/libgenome/classgnCompare-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnCompare.gif
 %%PORTDOCS%%share/doc/libgenome/classgnCompare.html
+%%PORTDOCS%%share/doc/libgenome/classgnCompare.png
 %%PORTDOCS%%share/doc/libgenome/classgnContigSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnContigSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnContigSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnContigSpec.png
 %%PORTDOCS%%share/doc/libgenome/classgnDNASequence-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnDNASequence.gif
 %%PORTDOCS%%share/doc/libgenome/classgnDNASequence.html
+%%PORTDOCS%%share/doc/libgenome/classgnDNASequence.png
 %%PORTDOCS%%share/doc/libgenome/classgnDNXSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnDNXSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnDNXSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnDNXSource.png
 %%PORTDOCS%%share/doc/libgenome/classgnDataBaseSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnDataBaseSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnDataBaseSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnDataBaseSource.png
+%%PORTDOCS%%share/doc/libgenome/classgnException-members.html
+%%PORTDOCS%%share/doc/libgenome/classgnException.html
+%%PORTDOCS%%share/doc/libgenome/classgnExceptionCode-members.html
+%%PORTDOCS%%share/doc/libgenome/classgnExceptionCode.html
 %%PORTDOCS%%share/doc/libgenome/classgnFASSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnFASSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnFASSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnFASSource.png
+%%PORTDOCS%%share/doc/libgenome/classgnFastTranslator-members.html
+%%PORTDOCS%%share/doc/libgenome/classgnFastTranslator.html
+%%PORTDOCS%%share/doc/libgenome/classgnFastTranslator.png
 %%PORTDOCS%%share/doc/libgenome/classgnFeature-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnFeature.gif
 %%PORTDOCS%%share/doc/libgenome/classgnFeature.html
+%%PORTDOCS%%share/doc/libgenome/classgnFeature.png
 %%PORTDOCS%%share/doc/libgenome/classgnFileContig-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnFileContig.gif
 %%PORTDOCS%%share/doc/libgenome/classgnFileContig.html
+%%PORTDOCS%%share/doc/libgenome/classgnFileContig.png
 %%PORTDOCS%%share/doc/libgenome/classgnFileSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnFileSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnFileSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnFileSource.png
 %%PORTDOCS%%share/doc/libgenome/classgnFilter-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnFilter.gif
 %%PORTDOCS%%share/doc/libgenome/classgnFilter.html
+%%PORTDOCS%%share/doc/libgenome/classgnFilter.png
 %%PORTDOCS%%share/doc/libgenome/classgnFragmentSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnFragmentSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnFragmentSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnFragmentSpec.png
 %%PORTDOCS%%share/doc/libgenome/classgnGBKSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnGBKSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnGBKSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnGBKSource.png
 %%PORTDOCS%%share/doc/libgenome/classgnGenomeSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnGenomeSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnGenomeSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnGenomeSpec.png
 %%PORTDOCS%%share/doc/libgenome/classgnLocation-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnLocation.gif
 %%PORTDOCS%%share/doc/libgenome/classgnLocation.html
+%%PORTDOCS%%share/doc/libgenome/classgnLocation.png
 %%PORTDOCS%%share/doc/libgenome/classgnMultiSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnMultiSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnMultiSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnMultiSpec.png
+%%PORTDOCS%%share/doc/libgenome/classgnPosSpecificTranslator-members.html
+%%PORTDOCS%%share/doc/libgenome/classgnPosSpecificTranslator.html
+%%PORTDOCS%%share/doc/libgenome/classgnPosSpecificTranslator.png
 %%PORTDOCS%%share/doc/libgenome/classgnProteinSequence-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnProteinSequence.gif
 %%PORTDOCS%%share/doc/libgenome/classgnProteinSequence.html
+%%PORTDOCS%%share/doc/libgenome/classgnProteinSequence.png
 %%PORTDOCS%%share/doc/libgenome/classgnRAWSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnRAWSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnRAWSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnRAWSource.png
 %%PORTDOCS%%share/doc/libgenome/classgnRNASequence-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnRNASequence.gif
 %%PORTDOCS%%share/doc/libgenome/classgnRNASequence.html
+%%PORTDOCS%%share/doc/libgenome/classgnRNASequence.png
 %%PORTDOCS%%share/doc/libgenome/classgnSEQSource-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnSEQSource.gif
 %%PORTDOCS%%share/doc/libgenome/classgnSEQSource.html
+%%PORTDOCS%%share/doc/libgenome/classgnSEQSource.png
 %%PORTDOCS%%share/doc/libgenome/classgnSequence-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnSequence.gif
 %%PORTDOCS%%share/doc/libgenome/classgnSequence.html
+%%PORTDOCS%%share/doc/libgenome/classgnSequence.png
 %%PORTDOCS%%share/doc/libgenome/classgnSourceFactory-members.html
 %%PORTDOCS%%share/doc/libgenome/classgnSourceFactory.html
 %%PORTDOCS%%share/doc/libgenome/classgnSourceHeader-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnSourceHeader.gif
 %%PORTDOCS%%share/doc/libgenome/classgnSourceHeader.html
+%%PORTDOCS%%share/doc/libgenome/classgnSourceHeader.png
 %%PORTDOCS%%share/doc/libgenome/classgnSourceQualifier-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnSourceQualifier.gif
 %%PORTDOCS%%share/doc/libgenome/classgnSourceQualifier.html
+%%PORTDOCS%%share/doc/libgenome/classgnSourceQualifier.png
 %%PORTDOCS%%share/doc/libgenome/classgnSourceSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnSourceSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnSourceSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnSourceSpec.png
 %%PORTDOCS%%share/doc/libgenome/classgnStringHeader-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnStringHeader.gif
 %%PORTDOCS%%share/doc/libgenome/classgnStringHeader.html
+%%PORTDOCS%%share/doc/libgenome/classgnStringHeader.png
 %%PORTDOCS%%share/doc/libgenome/classgnStringQualifier-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnStringQualifier.gif
 %%PORTDOCS%%share/doc/libgenome/classgnStringQualifier.html
+%%PORTDOCS%%share/doc/libgenome/classgnStringQualifier.png
 %%PORTDOCS%%share/doc/libgenome/classgnStringSpec-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnStringSpec.gif
 %%PORTDOCS%%share/doc/libgenome/classgnStringSpec.html
+%%PORTDOCS%%share/doc/libgenome/classgnStringSpec.png
 %%PORTDOCS%%share/doc/libgenome/classgnTranslator-members.html
-%%PORTDOCS%%share/doc/libgenome/classgnTranslator.gif
 %%PORTDOCS%%share/doc/libgenome/classgnTranslator.html
+%%PORTDOCS%%share/doc/libgenome/classgnTranslator.png
 %%PORTDOCS%%share/doc/libgenome/doxygen.css
-%%PORTDOCS%%share/doc/libgenome/doxygen.gif
+%%PORTDOCS%%share/doc/libgenome/doxygen.png
 %%PORTDOCS%%share/doc/libgenome/files.html
 %%PORTDOCS%%share/doc/libgenome/functions.html
 %%PORTDOCS%%share/doc/libgenome/globals.html
@@ -207,10 +215,22 @@ lib/libGenome.so.0
 %%PORTDOCS%%share/doc/libgenome/gnDebug_8h.html
 %%PORTDOCS%%share/doc/libgenome/gnDefs_8h-source.html
 %%PORTDOCS%%share/doc/libgenome/gnDefs_8h.html
+%%PORTDOCS%%share/doc/libgenome/gnExceptionCode_8cpp-source.html
+%%PORTDOCS%%share/doc/libgenome/gnExceptionCode_8cpp.html
+%%PORTDOCS%%share/doc/libgenome/gnExceptionCode_8h-source.html
+%%PORTDOCS%%share/doc/libgenome/gnExceptionCode_8h.html
+%%PORTDOCS%%share/doc/libgenome/gnException_8cpp-source.html
+%%PORTDOCS%%share/doc/libgenome/gnException_8cpp.html
+%%PORTDOCS%%share/doc/libgenome/gnException_8h-source.html
+%%PORTDOCS%%share/doc/libgenome/gnException_8h.html
 %%PORTDOCS%%share/doc/libgenome/gnFASSource_8cpp-source.html
 %%PORTDOCS%%share/doc/libgenome/gnFASSource_8cpp.html
 %%PORTDOCS%%share/doc/libgenome/gnFASSource_8h-source.html
 %%PORTDOCS%%share/doc/libgenome/gnFASSource_8h.html
+%%PORTDOCS%%share/doc/libgenome/gnFastTranslator_8cpp-source.html
+%%PORTDOCS%%share/doc/libgenome/gnFastTranslator_8cpp.html
+%%PORTDOCS%%share/doc/libgenome/gnFastTranslator_8h-source.html
+%%PORTDOCS%%share/doc/libgenome/gnFastTranslator_8h.html
 %%PORTDOCS%%share/doc/libgenome/gnFeature_8cpp-source.html
 %%PORTDOCS%%share/doc/libgenome/gnFeature_8cpp.html
 %%PORTDOCS%%share/doc/libgenome/gnFeature_8h-source.html
@@ -247,6 +267,10 @@ lib/libGenome.so.0
 %%PORTDOCS%%share/doc/libgenome/gnMultiSpec_8cpp.html
 %%PORTDOCS%%share/doc/libgenome/gnMultiSpec_8h-source.html
 %%PORTDOCS%%share/doc/libgenome/gnMultiSpec_8h.html
+%%PORTDOCS%%share/doc/libgenome/gnPosSpecificTranslator_8cpp-source.html
+%%PORTDOCS%%share/doc/libgenome/gnPosSpecificTranslator_8cpp.html
+%%PORTDOCS%%share/doc/libgenome/gnPosSpecificTranslator_8h-source.html
+%%PORTDOCS%%share/doc/libgenome/gnPosSpecificTranslator_8h.html
 %%PORTDOCS%%share/doc/libgenome/gnProteinSequence_8h-source.html
 %%PORTDOCS%%share/doc/libgenome/gnProteinSequence_8h.html
 %%PORTDOCS%%share/doc/libgenome/gnRAWSource_8cpp-source.html
@@ -259,10 +283,6 @@ lib/libGenome.so.0
 %%PORTDOCS%%share/doc/libgenome/gnSEQSource_8cpp.html
 %%PORTDOCS%%share/doc/libgenome/gnSEQSource_8h-source.html
 %%PORTDOCS%%share/doc/libgenome/gnSEQSource_8h.html
-%%PORTDOCS%%share/doc/libgenome/gnSKYSource_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/gnSKYSource_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/gnSKYSource_8h-source.html
-%%PORTDOCS%%share/doc/libgenome/gnSKYSource_8h.html
 %%PORTDOCS%%share/doc/libgenome/gnSeqStringTest_8cpp-source.html
 %%PORTDOCS%%share/doc/libgenome/gnSeqStringTest_8cpp.html
 %%PORTDOCS%%share/doc/libgenome/gnSequence_8cpp-source.html
@@ -319,19 +339,7 @@ lib/libGenome.so.0
 %%PORTDOCS%%share/doc/libgenome/gn__cw__dlld_8h.html
 %%PORTDOCS%%share/doc/libgenome/hierarchy.html
 %%PORTDOCS%%share/doc/libgenome/index.html
-%%PORTDOCS%%share/doc/libgenome/namespace__std.html
 %%PORTDOCS%%share/doc/libgenome/namespaces.html
-%%PORTDOCS%%share/doc/libgenome/test-o-matic_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/test-o-matic_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/testSourceFactory_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/testSourceFactory_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/testSourceSeq_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/testSourceSeq_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/testSource_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/testSource_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/testTests_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/testTests_8cpp.html
-%%PORTDOCS%%share/doc/libgenome/testgpSequence_8cpp-source.html
-%%PORTDOCS%%share/doc/libgenome/testgpSequence_8cpp.html
+%%PORTDOCS%%share/doc/libgenome/namespacestd.html
 %%PORTDOCS%%@dirrm share/doc/libgenome
 @dirrm include/gn