LibSBML is an open-source programming library to help you read, write,

manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:		ports/135022
Submitted by:	Wen Heping <wenheping at gmail.com>

6 files changed, 343 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 1a9b5e34ef95..892e117aa36c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -41,6 +41,7 @@
     SUBDIR += lagan
     SUBDIR += lamarc
     SUBDIR += libgenome
+    SUBDIR += libsbml
     SUBDIR += linux-foldingathome
     SUBDIR += lsysexp
     SUBDIR += mafft
diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
new file mode 100644
index 000000000000..fa61cf8294e4
--- /dev/null
+++ b/biology/libsbml/Makefile
@@ -0,0 +1,56 @@
+# New ports collection makefile for:	libsbml
+# Date created:			29 May, 2009
+# Whom:				Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	libsbml
+PORTVERSION=	3.3.2
+CATEGORIES=	biology devel
+MASTER_SITES=	SF
+MASTER_SITE_SUBDIR=	sbml
+DISTNAME=	${PORTNAME}-${PORTVERSION}-src
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	An API Library for Working with SBML File
+
+LIB_DEPENDS=	xml2.5:${PORTSDIR}/textproc/libxml2
+
+OPTIONS=	PYTHON "Support for Python" off \
+		RUBY "Support for Ruby" off
+
+USE_GMAKE=	yes
+USE_ZIP=	yes
+GNU_CONFIGURE=	yes
+USE_LDCONFIG=	yes
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
+
+.include <bsd.port.pre.mk>
+.if defined(WITH_PYTHON)
+.include "../../Mk/bsd.python.mk"
+BUILD_DEPENDS+=		${LOCALBASE}/bin/python:${PORTSDIR}/lang/python
+CONFIGURE_ARGS+=	--with-python
+PLIST_SUB+=		WITH_PYTHON="" \
+			SBML_EGGINFO=${PORTNAME}-${PORTVERSION}-${PYTHON_VERSION:S/thon//}.egg-info
+.else
+PLIST_SUB+=		WITH_PYTHON="@comment "
+.endif
+
+.if defined(WITH_RUBY)
+.include "../../Mk/bsd.ruby.mk"
+BUILD_DEPENDS+=		${LOCALBASE}/bin/ruby:${PORTSDIR}/lang/ruby18
+CONFIGURE_ARGS+=	--with-ruby
+PLIST_SUB+=		WITH_RUBY=""
+.else
+PLIST_SUB+=		WITH_RUBY="@comment "
+.endif
+
+post-install:
+.if !defined(NOPORTEXAMPLES)
+	${MKDIR} ${EXAMPLESDIR}
+	cd ${WRKSRC}/examples \
+		&& ${FIND} . -type d -exec ${MKDIR} ${EXAMPLESDIR}/\{} \; \
+		&& ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${EXAMPLESDIR}/\{} \;
+.endif
+.include <bsd.port.post.mk>
diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo
new file mode 100644
index 000000000000..a54dd0635d09
--- /dev/null
+++ b/biology/libsbml/distinfo
@@ -0,0 +1,3 @@
+MD5 (libsbml-3.3.2-src.zip) = f8b3ff297848f8cf0918c065f8a65133
+SHA256 (libsbml-3.3.2-src.zip) = 5ebd8a57679fda954032e44111fdbcb8dc8598037354962d82a1742b621505d4
+SIZE (libsbml-3.3.2-src.zip) = 7076694
diff --git a/biology/libsbml/files/patch-Makefile.in b/biology/libsbml/files/patch-Makefile.in
new file mode 100644
index 000000000000..309111070348
--- /dev/null
+++ b/biology/libsbml/files/patch-Makefile.in
@@ -0,0 +1,34 @@
+--- Makefile.in.orig	2009-05-27 23:09:33.000000000 +0800
++++ Makefile.in	2009-05-27 23:33:47.000000000 +0800
+@@ -413,7 +413,7 @@
+ endif
+ 
+ install-pc: libsbml.pc
+-	$(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
++	$(INSTALL_SH) libsbml.pc -m 0644 "/usr/local/libdata/pkgconfig/libsbml.pc"
+ 
+ install-la: libsbml.la
+ ifeq "$(HOST_TYPE)" "cygwin"
+@@ -449,17 +449,17 @@
+ 	$(warning $(uninstall-warning-msg))
+ 
+ uninstall-libsbml-pc:
+-	@target="$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"; \
++	@target="/usr/local/libdata/pkgconfig/libsbml.pc"; \
+ 	if test -f $$target ; then \
+ 	  echo rm $$target; \
+ 	  rm $$target; \
+ 	fi; \
+-	if test -d "$(DESTDIR)$(LIBDIR)/pkgconfig"; then \
++	if test -d "/usr/local/libdata/pkgconfig"; then \
+ 	  if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
+-	    echo rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
+-	    rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
++	    echo rmdir "/usr/local/libdata/pkgconfig"; \
++	    rmdir "/usr/local/libdata/pkgconfig"; \
+ 	  else \
+-	    echo "Directory $(DESTDIR)$(LIBDIR)/pkgconfig not empty; leaving it alone"; \
++	    echo "Directory /usr/local/libdata/pkgconfig not empty; leaving it alone"; \
+ 	  fi; \
+ 	fi;
+ 
diff --git a/biology/libsbml/pkg-descr b/biology/libsbml/pkg-descr
new file mode 100644
index 000000000000..b013d3cc7730
--- /dev/null
+++ b/biology/libsbml/pkg-descr
@@ -0,0 +1,11 @@
+LibSBML is an open-source programming library to help you read, write,
+manipulate, translate, and validate SBML files and data streams. It is
+not an application itself (though it does come with example programs),
+but rather a library you can embed in your own applications.
+
+LibSBML understands all Levels and Versions of SBML, as well as the
+SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
+ISO C and C++ but can be used from all the languages listed in the
+right-hand box.
+
+WWW: http://www.sbml.org/
diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist
new file mode 100644
index 000000000000..5a337b1f66fb
--- /dev/null
+++ b/biology/libsbml/pkg-plist
@@ -0,0 +1,238 @@
+libdata/pkgconfig/libsbml.pc
+include/sbml/Compartment.h
+include/sbml/CompartmentType.h
+include/sbml/Constraint.h
+include/sbml/Delay.h
+include/sbml/Event.h
+include/sbml/EventAssignment.h
+include/sbml/FunctionDefinition.h
+include/sbml/InitialAssignment.h
+include/sbml/KineticLaw.h
+include/sbml/ListOf.h
+include/sbml/Model.h
+include/sbml/Parameter.h
+include/sbml/Reaction.h
+include/sbml/Rule.h
+include/sbml/SBMLDocument.h
+include/sbml/SBMLError.h
+include/sbml/SBMLErrorLog.h
+include/sbml/SBMLErrorTable.h
+include/sbml/SBMLReader.h
+include/sbml/SBMLTypeCodes.h
+include/sbml/SBMLTypes.h
+include/sbml/SBMLVisitor.h
+include/sbml/SBMLWriter.h
+include/sbml/SBO.h
+include/sbml/SBase.h
+include/sbml/Species.h
+include/sbml/SpeciesReference.h
+include/sbml/SpeciesType.h
+include/sbml/StoichiometryMath.h
+include/sbml/Trigger.h
+include/sbml/Unit.h
+include/sbml/UnitDefinition.h
+include/sbml/UnitKind.h
+include/sbml/annotation/CVTerm.h
+include/sbml/annotation/ModelHistory.h
+include/sbml/annotation/RDFAnnotation.h
+include/sbml/common/common.h
+include/sbml/common/extern.h
+include/sbml/common/libsbml-config-unix.h
+include/sbml/common/libsbml-config-win.h
+include/sbml/common/libsbml-config.h
+include/sbml/common/libsbml-version.h
+include/sbml/common/sbmlfwd.h
+include/sbml/compress/CompressCommon.h
+include/sbml/compress/InputDecompressor.h
+include/sbml/compress/OutputCompressor.h
+include/sbml/compress/bzfstream.h
+include/sbml/compress/crypt.h
+include/sbml/compress/ioapi.h
+include/sbml/compress/iowin32.h
+include/sbml/compress/unzip.h
+include/sbml/compress/zfstream.h
+include/sbml/compress/zip.h
+include/sbml/compress/zipfstream.h
+include/sbml/math/ASTNode.h
+include/sbml/math/FormulaFormatter.h
+include/sbml/math/FormulaParser.h
+include/sbml/math/FormulaTokenizer.h
+include/sbml/math/MathML.h
+include/sbml/units/FormulaUnitsData.h
+include/sbml/units/UnitFormulaFormatter.h
+include/sbml/units/UnitKindList.h
+include/sbml/util/List.h
+include/sbml/util/Stack.h
+include/sbml/util/StringBuffer.h
+include/sbml/util/memory.h
+include/sbml/util/util.h
+include/sbml/validator/ConsistencyValidator.h
+include/sbml/validator/ConstraintMacros.h
+include/sbml/validator/IdentifierConsistencyValidator.h
+include/sbml/validator/InternalConsistencyValidator.h
+include/sbml/validator/L1CompatibilityValidator.h
+include/sbml/validator/L2v1CompatibilityValidator.h
+include/sbml/validator/L2v2CompatibilityValidator.h
+include/sbml/validator/L2v3CompatibilityValidator.h
+include/sbml/validator/L2v4CompatibilityValidator.h
+include/sbml/validator/MathMLConsistencyValidator.h
+include/sbml/validator/ModelingPracticeValidator.h
+include/sbml/validator/OverdeterminedValidator.h
+include/sbml/validator/SBOConsistencyValidator.h
+include/sbml/validator/UnitConsistencyValidator.h
+include/sbml/validator/VConstraint.h
+include/sbml/validator/Validator.h
+include/sbml/validator/constraints/IdBase.h
+include/sbml/validator/constraints/IdList.h
+include/sbml/validator/constraints/MathMLBase.h
+include/sbml/validator/constraints/OverDeterminedCheck.h
+include/sbml/validator/constraints/UniqueIdBase.h
+include/sbml/validator/constraints/UniqueMetaId.h
+include/sbml/validator/constraints/UnitsBase.h
+include/sbml/xml/LibXMLAttributes.h
+include/sbml/xml/LibXMLHandler.h
+include/sbml/xml/LibXMLNamespaces.h
+include/sbml/xml/LibXMLParser.h
+include/sbml/xml/LibXMLTranscode.h
+include/sbml/xml/XMLAttributes.h
+include/sbml/xml/XMLBuffer.h
+include/sbml/xml/XMLError.h
+include/sbml/xml/XMLErrorLog.h
+include/sbml/xml/XMLExtern.h
+include/sbml/xml/XMLFileBuffer.h
+include/sbml/xml/XMLHandler.h
+include/sbml/xml/XMLInputStream.h
+include/sbml/xml/XMLMemoryBuffer.h
+include/sbml/xml/XMLNamespaces.h
+include/sbml/xml/XMLNode.h
+include/sbml/xml/XMLOutputStream.h
+include/sbml/xml/XMLParser.h
+include/sbml/xml/XMLToken.h
+include/sbml/xml/XMLTokenizer.h
+include/sbml/xml/XMLTriple.h
+lib/libsbml.3.3.2.so
+lib/libsbml.so
+lib/libsbml.a
+@dirrm include/sbml/annotation
+@dirrm include/sbml/common
+@dirrm include/sbml/compress
+@dirrm include/sbml/math
+@dirrm include/sbml/units
+@dirrm include/sbml/util
+@dirrm include/sbml/validator/constraints
+@dirrm include/sbml/validator
+@dirrm include/sbml/xml
+@dirrm include/sbml/
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.pyc
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth
+%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/%%SBML_EGGINFO%%
+%%WITH_PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml
+%%WITH_RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCVTerms.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/appendAnnotation.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCVTerms.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addModelHistory.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/appendAnnotation.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/convertSBML.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/echoSBML.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateMath.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printAnnotation.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printMath.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printNotes.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printSBML.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printUnits.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/readSBML.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/translateMath.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.java
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example2.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example3.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/layout2svg.xsl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactions.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printMath.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/algebraicrules.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/assignmentrules.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/boundarycondition.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/delay.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/dimerization.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/enzymekinetics.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/events.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/functiondef.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/multicomp.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/overdetermined.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/twodimensional.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/units.xml
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-2
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%