mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-23 00:43:28 +00:00
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>
This commit is contained in:
parent
7cf7e4315d
commit
043ce69d39
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=234730
@ -41,6 +41,7 @@
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SUBDIR += lagan
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SUBDIR += lamarc
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SUBDIR += libgenome
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SUBDIR += libsbml
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SUBDIR += linux-foldingathome
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SUBDIR += lsysexp
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SUBDIR += mafft
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|
56
biology/libsbml/Makefile
Normal file
56
biology/libsbml/Makefile
Normal file
@ -0,0 +1,56 @@
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# New ports collection makefile for: libsbml
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# Date created: 29 May, 2009
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# Whom: Wen Heping <wenheping@gmail.com>
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#
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# $FreeBSD$
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#
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PORTNAME= libsbml
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PORTVERSION= 3.3.2
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CATEGORIES= biology devel
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MASTER_SITES= SF
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MASTER_SITE_SUBDIR= sbml
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DISTNAME= ${PORTNAME}-${PORTVERSION}-src
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MAINTAINER= wenheping@gmail.com
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COMMENT= An API Library for Working with SBML File
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LIB_DEPENDS= xml2.5:${PORTSDIR}/textproc/libxml2
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OPTIONS= PYTHON "Support for Python" off \
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RUBY "Support for Ruby" off
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USE_GMAKE= yes
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USE_ZIP= yes
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GNU_CONFIGURE= yes
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USE_LDCONFIG= yes
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WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
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.include <bsd.port.pre.mk>
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.if defined(WITH_PYTHON)
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.include "../../Mk/bsd.python.mk"
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BUILD_DEPENDS+= ${LOCALBASE}/bin/python:${PORTSDIR}/lang/python
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CONFIGURE_ARGS+= --with-python
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PLIST_SUB+= WITH_PYTHON="" \
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SBML_EGGINFO=${PORTNAME}-${PORTVERSION}-${PYTHON_VERSION:S/thon//}.egg-info
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.else
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PLIST_SUB+= WITH_PYTHON="@comment "
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.endif
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.if defined(WITH_RUBY)
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.include "../../Mk/bsd.ruby.mk"
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BUILD_DEPENDS+= ${LOCALBASE}/bin/ruby:${PORTSDIR}/lang/ruby18
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CONFIGURE_ARGS+= --with-ruby
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PLIST_SUB+= WITH_RUBY=""
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.else
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PLIST_SUB+= WITH_RUBY="@comment "
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.endif
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post-install:
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.if !defined(NOPORTEXAMPLES)
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${MKDIR} ${EXAMPLESDIR}
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cd ${WRKSRC}/examples \
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&& ${FIND} . -type d -exec ${MKDIR} ${EXAMPLESDIR}/\{} \; \
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&& ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${EXAMPLESDIR}/\{} \;
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.endif
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.include <bsd.port.post.mk>
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3
biology/libsbml/distinfo
Normal file
3
biology/libsbml/distinfo
Normal file
@ -0,0 +1,3 @@
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MD5 (libsbml-3.3.2-src.zip) = f8b3ff297848f8cf0918c065f8a65133
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SHA256 (libsbml-3.3.2-src.zip) = 5ebd8a57679fda954032e44111fdbcb8dc8598037354962d82a1742b621505d4
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SIZE (libsbml-3.3.2-src.zip) = 7076694
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34
biology/libsbml/files/patch-Makefile.in
Normal file
34
biology/libsbml/files/patch-Makefile.in
Normal file
@ -0,0 +1,34 @@
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--- Makefile.in.orig 2009-05-27 23:09:33.000000000 +0800
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+++ Makefile.in 2009-05-27 23:33:47.000000000 +0800
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@@ -413,7 +413,7 @@
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endif
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install-pc: libsbml.pc
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- $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
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+ $(INSTALL_SH) libsbml.pc -m 0644 "/usr/local/libdata/pkgconfig/libsbml.pc"
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install-la: libsbml.la
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ifeq "$(HOST_TYPE)" "cygwin"
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@@ -449,17 +449,17 @@
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$(warning $(uninstall-warning-msg))
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uninstall-libsbml-pc:
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- @target="$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"; \
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+ @target="/usr/local/libdata/pkgconfig/libsbml.pc"; \
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if test -f $$target ; then \
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echo rm $$target; \
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rm $$target; \
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fi; \
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- if test -d "$(DESTDIR)$(LIBDIR)/pkgconfig"; then \
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+ if test -d "/usr/local/libdata/pkgconfig"; then \
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if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
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- echo rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
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- rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
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+ echo rmdir "/usr/local/libdata/pkgconfig"; \
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+ rmdir "/usr/local/libdata/pkgconfig"; \
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else \
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- echo "Directory $(DESTDIR)$(LIBDIR)/pkgconfig not empty; leaving it alone"; \
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+ echo "Directory /usr/local/libdata/pkgconfig not empty; leaving it alone"; \
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fi; \
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fi;
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11
biology/libsbml/pkg-descr
Normal file
11
biology/libsbml/pkg-descr
Normal file
@ -0,0 +1,11 @@
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LibSBML is an open-source programming library to help you read, write,
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manipulate, translate, and validate SBML files and data streams. It is
|
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not an application itself (though it does come with example programs),
|
||||
but rather a library you can embed in your own applications.
|
||||
|
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LibSBML understands all Levels and Versions of SBML, as well as the
|
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SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
|
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ISO C and C++ but can be used from all the languages listed in the
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right-hand box.
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WWW: http://www.sbml.org/
|
238
biology/libsbml/pkg-plist
Normal file
238
biology/libsbml/pkg-plist
Normal file
@ -0,0 +1,238 @@
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libdata/pkgconfig/libsbml.pc
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include/sbml/Compartment.h
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include/sbml/CompartmentType.h
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include/sbml/Constraint.h
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include/sbml/Delay.h
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include/sbml/Event.h
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include/sbml/EventAssignment.h
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include/sbml/FunctionDefinition.h
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include/sbml/InitialAssignment.h
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include/sbml/KineticLaw.h
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include/sbml/ListOf.h
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include/sbml/Model.h
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include/sbml/Parameter.h
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include/sbml/Reaction.h
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include/sbml/Rule.h
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include/sbml/SBMLDocument.h
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include/sbml/SBMLError.h
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include/sbml/SBMLErrorLog.h
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include/sbml/SBMLErrorTable.h
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include/sbml/SBMLReader.h
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include/sbml/SBMLTypeCodes.h
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include/sbml/SBMLTypes.h
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include/sbml/SBMLVisitor.h
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include/sbml/SBMLWriter.h
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include/sbml/SBO.h
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include/sbml/SBase.h
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include/sbml/Species.h
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include/sbml/SpeciesReference.h
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include/sbml/SpeciesType.h
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include/sbml/StoichiometryMath.h
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include/sbml/Trigger.h
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include/sbml/Unit.h
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include/sbml/UnitDefinition.h
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include/sbml/UnitKind.h
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include/sbml/annotation/CVTerm.h
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include/sbml/annotation/ModelHistory.h
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include/sbml/annotation/RDFAnnotation.h
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include/sbml/common/common.h
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include/sbml/common/extern.h
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include/sbml/common/libsbml-config-unix.h
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include/sbml/common/libsbml-config-win.h
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include/sbml/common/libsbml-config.h
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include/sbml/common/libsbml-version.h
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include/sbml/common/sbmlfwd.h
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include/sbml/compress/CompressCommon.h
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include/sbml/compress/InputDecompressor.h
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||||
include/sbml/compress/OutputCompressor.h
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include/sbml/compress/bzfstream.h
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include/sbml/compress/crypt.h
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include/sbml/compress/ioapi.h
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||||
include/sbml/compress/iowin32.h
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||||
include/sbml/compress/unzip.h
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include/sbml/compress/zfstream.h
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include/sbml/compress/zip.h
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||||
include/sbml/compress/zipfstream.h
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||||
include/sbml/math/ASTNode.h
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||||
include/sbml/math/FormulaFormatter.h
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include/sbml/math/FormulaParser.h
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include/sbml/math/FormulaTokenizer.h
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include/sbml/math/MathML.h
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include/sbml/units/FormulaUnitsData.h
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include/sbml/units/UnitFormulaFormatter.h
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include/sbml/units/UnitKindList.h
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include/sbml/util/List.h
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include/sbml/util/Stack.h
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include/sbml/util/StringBuffer.h
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||||
include/sbml/util/memory.h
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include/sbml/util/util.h
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include/sbml/validator/ConsistencyValidator.h
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include/sbml/validator/ConstraintMacros.h
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||||
include/sbml/validator/IdentifierConsistencyValidator.h
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||||
include/sbml/validator/InternalConsistencyValidator.h
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||||
include/sbml/validator/L1CompatibilityValidator.h
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||||
include/sbml/validator/L2v1CompatibilityValidator.h
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||||
include/sbml/validator/L2v2CompatibilityValidator.h
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||||
include/sbml/validator/L2v3CompatibilityValidator.h
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include/sbml/validator/L2v4CompatibilityValidator.h
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||||
include/sbml/validator/MathMLConsistencyValidator.h
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||||
include/sbml/validator/ModelingPracticeValidator.h
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||||
include/sbml/validator/OverdeterminedValidator.h
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||||
include/sbml/validator/SBOConsistencyValidator.h
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include/sbml/validator/UnitConsistencyValidator.h
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include/sbml/validator/VConstraint.h
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include/sbml/validator/Validator.h
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include/sbml/validator/constraints/IdBase.h
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include/sbml/validator/constraints/IdList.h
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||||
include/sbml/validator/constraints/MathMLBase.h
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||||
include/sbml/validator/constraints/OverDeterminedCheck.h
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||||
include/sbml/validator/constraints/UniqueIdBase.h
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||||
include/sbml/validator/constraints/UniqueMetaId.h
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||||
include/sbml/validator/constraints/UnitsBase.h
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||||
include/sbml/xml/LibXMLAttributes.h
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||||
include/sbml/xml/LibXMLHandler.h
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include/sbml/xml/LibXMLNamespaces.h
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||||
include/sbml/xml/LibXMLParser.h
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||||
include/sbml/xml/LibXMLTranscode.h
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||||
include/sbml/xml/XMLAttributes.h
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||||
include/sbml/xml/XMLBuffer.h
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||||
include/sbml/xml/XMLError.h
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||||
include/sbml/xml/XMLErrorLog.h
|
||||
include/sbml/xml/XMLExtern.h
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||||
include/sbml/xml/XMLFileBuffer.h
|
||||
include/sbml/xml/XMLHandler.h
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||||
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
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||||
include/sbml/xml/XMLTriple.h
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||||
lib/libsbml.3.3.2.so
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||||
lib/libsbml.so
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||||
lib/libsbml.a
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@dirrm include/sbml/annotation
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@dirrm include/sbml/common
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@dirrm include/sbml/compress
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@dirrm include/sbml/math
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||||
@dirrm include/sbml/units
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@dirrm include/sbml/util
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||||
@dirrm include/sbml/validator/constraints
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@dirrm include/sbml/validator
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||||
@dirrm include/sbml/xml
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@dirrm include/sbml/
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%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
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||||
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
|
||||
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.pyc
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||||
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth
|
||||
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/%%SBML_EGGINFO%%
|
||||
%%WITH_PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml
|
||||
%%WITH_RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so
|
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile.in
|
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%%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
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||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp
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||||
%%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
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||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp
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||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp
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||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
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||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile.in
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||||
%%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%%
|
Loading…
Reference in New Issue
Block a user