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From: <fbe...@us...> - 2014-01-30 17:46:46
|
Revision: 19576
http://sourceforge.net/p/sbml/code/19576
Author: fbergmann
Date: 2014-01-30 16:28:08 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
- added another check that will tell us about issues with dynamic linking on Windows
--> found missing declaration on the IdList class
Modified Paths:
--------------
trunk/libsbml/src/bindings/csharp/CMakeLists.txt
trunk/libsbml/src/sbml/util/IdList.h
Modified: trunk/libsbml/src/bindings/csharp/CMakeLists.txt
===================================================================
--- trunk/libsbml/src/bindings/csharp/CMakeLists.txt 2014-01-30 16:04:08 UTC (rev 19575)
+++ trunk/libsbml/src/bindings/csharp/CMakeLists.txt 2014-01-30 16:28:08 UTC (rev 19576)
@@ -317,7 +317,17 @@
# ${CMAKE_SOURCE_DIR}/src/sbml/test/test-data
# ${CMAKE_CURRENT_BINARY_DIR}/libsbmlcsP.dll
# )
+
+ # link again, this time against the dynamic librar, as this will reveal
+ # any potential link errors (this library will not be distributed)
+ #
+ add_library(binding_csharp_native_dll_link_check SHARED ${CMAKE_CURRENT_BINARY_DIR}/libsbml_wrap.cpp)
+ add_dependencies(binding_csharp_native_dll_link_check binding_csharp_swig)
+ set_target_properties (binding_csharp_native_dll_link_check PROPERTIES OUTPUT_NAME "DllLinkCheck")
+ target_link_libraries(binding_csharp_native_dll_link_check ${LIBSBML_LIBRARY})
+
+
endif()
endif()
Modified: trunk/libsbml/src/sbml/util/IdList.h
===================================================================
--- trunk/libsbml/src/sbml/util/IdList.h 2014-01-30 16:04:08 UTC (rev 19575)
+++ trunk/libsbml/src/sbml/util/IdList.h 2014-01-30 16:28:08 UTC (rev 19576)
@@ -37,10 +37,11 @@
#include <string>
#include <vector>
#include <sbml/common/libsbml-namespace.h>
+#include <sbml/common/extern.h>
LIBSBML_CPP_NAMESPACE_BEGIN
-class IdList
+class LIBSBML_EXTERN IdList
{
public:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fbe...@us...> - 2014-01-30 17:00:48
|
Revision: 19577
http://sourceforge.net/p/sbml/code/19577
Author: fbergmann
Date: 2014-01-30 17:00:44 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
- added option to create python source package to cmake, when WITH_CREATE_PYTHON_SOURCE is enabled the source archive is created
Modified Paths:
--------------
trunk/libsbml/src/bindings/python/CMakeLists.txt
Modified: trunk/libsbml/src/bindings/python/CMakeLists.txt
===================================================================
--- trunk/libsbml/src/bindings/python/CMakeLists.txt 2014-01-30 16:28:08 UTC (rev 19576)
+++ trunk/libsbml/src/bindings/python/CMakeLists.txt 2014-01-30 17:00:44 UTC (rev 19577)
@@ -221,6 +221,48 @@
INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/libsbml.py DESTINATION ${PYTHON_PACKAGE_INSTALL_DIR}/libsbml )
+option(WITH_CREATE_PYTHON_SOURCE "Generate Python Source Package." OFF)
+if (WITH_CREATE_PYTHON_SOURCE)
+
+SET(PYTHON_SOURCE_OUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/out)
+file(TO_NATIVE_PATH ${PYTHON_SOURCE_OUT_DIR} NATIVE_OUT)
+
+add_custom_command(
+ OUTPUT
+ ${PYTHON_SOURCE_OUT_DIR}/setup.py
+ COMMAND "${CMAKE_COMMAND}"
+ ARGS -E make_directory ${PYTHON_SOURCE_OUT_DIR}
+ COMMAND "${CMAKE_COMMAND}"
+ ARGS -DOUT_DIR=\"${NATIVE_OUT}\"
+ -DSRC_DIR=\"${CMAKE_SOURCE_DIR}/src\"
+ -DBIN_DIR=\"${CMAKE_BINARY_DIR}\"
+ -P "${CMAKE_SOURCE_DIR}/dev/utilities/python_package/create_package.cmake"
+
+ WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/dev/utilities/python_package/"
+ COMMENT "Configure Python source package"
+ )
+
+add_custom_target(binding_python_source_config ALL DEPENDS ${PYTHON_SOURCE_OUT_DIR}/setup.py)
+add_dependencies(binding_python_source_config binding_python_swig)
+
+add_custom_command(
+ OUTPUT ${PYTHON_SOURCE_OUT_DIR}/MANIFEST
+
+ COMMAND "${PYTHON_EXECUTABLE}"
+ ARGS setup.py
+ sdist
+
+ WORKING_DIRECTORY "${PYTHON_SOURCE_OUT_DIR}"
+ COMMENT "Create Python source package"
+ )
+
+add_custom_target(binding_python_source_package ALL DEPENDS ${PYTHON_SOURCE_OUT_DIR}/MANIFEST)
+add_dependencies(binding_python_source_package binding_python_source_config)
+
+
+endif(WITH_CREATE_PYTHON_SOURCE)
+
+
####################################################################
#
# testing
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|
|
From: <fbe...@us...> - 2014-01-30 16:04:11
|
Revision: 19575
http://sourceforge.net/p/sbml/code/19575
Author: fbergmann
Date: 2014-01-30 16:04:08 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
- mark SBMLVisitor as extern, so it will be exported across windows DLL boundaries
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBMLVisitor.h
Modified: trunk/libsbml/src/sbml/SBMLVisitor.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLVisitor.h 2014-01-30 09:46:25 UTC (rev 19574)
+++ trunk/libsbml/src/sbml/SBMLVisitor.h 2014-01-30 16:04:08 UTC (rev 19575)
@@ -52,8 +52,10 @@
#ifdef __cplusplus
+#include <sbml/common/extern.h>
#include <sbml/SBMLTypeCodes.h>
+
LIBSBML_CPP_NAMESPACE_BEGIN
/**
@@ -97,7 +99,7 @@
class ListOf;
-class SBMLVisitor
+class LIBSBML_EXTERN SBMLVisitor
{
public:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2014-01-30 10:26:04
|
Revision: 19572
http://sourceforge.net/p/sbml/code/19572
Author: sarahkeating
Date: 2014-01-30 09:31:05 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
tag the 5.9.2-experimental release
Added Paths:
-----------
tags/rel-5-9-2-experimental/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2014-01-30 09:46:29
|
Revision: 19574
http://sourceforge.net/p/sbml/code/19574
Author: sarahkeating
Date: 2014-01-30 09:46:25 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
Merged revision(s) 19571-19573 from trunk/libsbml:
update of version no following release
Modified Paths:
--------------
branches/libsbml-experimental/VERSION.txt
branches/libsbml-experimental/configure
branches/libsbml-experimental/src/sbml/common/libsbml-package.h
branches/libsbml-experimental/src/sbml/common/libsbml-version.h
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-30 09:44:13 UTC (rev 19573)
+++ branches/libsbml-experimental 2014-01-30 09:46:25 UTC (rev 19574)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19570
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19573
\ No newline at end of property
Modified: branches/libsbml-experimental/VERSION.txt
===================================================================
--- branches/libsbml-experimental/VERSION.txt 2014-01-30 09:44:13 UTC (rev 19573)
+++ branches/libsbml-experimental/VERSION.txt 2014-01-30 09:46:25 UTC (rev 19574)
@@ -1 +1 @@
-5.9.2
+5.9.3
Modified: branches/libsbml-experimental/configure
===================================================================
--- branches/libsbml-experimental/configure 2014-01-30 09:44:13 UTC (rev 19573)
+++ branches/libsbml-experimental/configure 2014-01-30 09:46:25 UTC (rev 19574)
@@ -1,7 +1,7 @@
#! /bin/sh
# From configure.ac Revision: 19183 .
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for libSBML 5.9.2.
+# Generated by GNU Autoconf 2.68 for libSBML 5.9.3.
#
# Report bugs to <lib...@ca...>.
#
@@ -715,8 +715,8 @@
# Identity of this package.
PACKAGE_NAME='libSBML'
PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.9.2'
-PACKAGE_STRING='libSBML 5.9.2'
+PACKAGE_VERSION='5.9.3'
+PACKAGE_STRING='libSBML 5.9.3'
PACKAGE_BUGREPORT='lib...@ca...'
PACKAGE_URL='http://sbml.org/Software/libSBML'
@@ -1566,7 +1566,7 @@
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures libSBML 5.9.2 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.9.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1631,7 +1631,7 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of libSBML 5.9.2:";;
+ short | recursive ) echo "Configuration of libSBML 5.9.3:";;
esac
cat <<\_ACEOF
@@ -1776,7 +1776,7 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-libSBML configure 5.9.2
+libSBML configure 5.9.3
generated by GNU Autoconf 2.68
Copyright (C) 2010 Free Software Foundation, Inc.
@@ -2495,7 +2495,7 @@
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by libSBML $as_me 5.9.2, which was
+It was created by libSBML $as_me 5.9.3, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -2885,7 +2885,7 @@
ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
-LIBSBML_VERSION_NUMERIC=50902
+LIBSBML_VERSION_NUMERIC=50903
@@ -2897,7 +2897,7 @@
-LIBSBML_REVISION_VERSION=2
+LIBSBML_REVISION_VERSION=3
@@ -27298,7 +27298,7 @@
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by libSBML $as_me 5.9.2, which was
+This file was extended by libSBML $as_me 5.9.3, which was
generated by GNU Autoconf 2.68. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -27361,7 +27361,7 @@
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-libSBML config.status 5.9.2
+libSBML config.status 5.9.3
configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
Modified: branches/libsbml-experimental/src/sbml/common/libsbml-package.h
===================================================================
--- branches/libsbml-experimental/src/sbml/common/libsbml-package.h 2014-01-30 09:44:13 UTC (rev 19573)
+++ branches/libsbml-experimental/src/sbml/common/libsbml-package.h 2014-01-30 09:46:25 UTC (rev 19574)
@@ -52,11 +52,11 @@
#define PACKAGE_NAME "libSBML"
/* Define to the full name and version of this package. */
-#define PACKAGE_STRING "libSBML 5.9.2"
+#define PACKAGE_STRING "libSBML 5.9.3"
/* Define to the one symbol short name of this package. */
#define PACKAGE_TARNAME "libsbml"
/* Define to the version of this package. */
-#define PACKAGE_VERSION "5.9.2"
+#define PACKAGE_VERSION "5.9.3"
Modified: branches/libsbml-experimental/src/sbml/common/libsbml-version.h
===================================================================
--- branches/libsbml-experimental/src/sbml/common/libsbml-version.h 2014-01-30 09:44:13 UTC (rev 19573)
+++ branches/libsbml-experimental/src/sbml/common/libsbml-version.h 2014-01-30 09:46:25 UTC (rev 19574)
@@ -37,7 +37,7 @@
*
* A version string of the form "1.2.3".
*/
-#define LIBSBML_DOTTED_VERSION "5.9.2"
+#define LIBSBML_DOTTED_VERSION "5.9.3"
/**
@@ -48,7 +48,7 @@
* libSBML is released, making it easy to use less-than and greater-than
* comparisons when testing versions numbers.
*/
-#define LIBSBML_VERSION 50902
+#define LIBSBML_VERSION 50903
/**
@@ -56,7 +56,7 @@
*
* The numeric version as a string: version 1.2.3 becomes "10203".
*/
-#define LIBSBML_VERSION_STRING "50902"
+#define LIBSBML_VERSION_STRING "50903"
LIBSBML_CPP_NAMESPACE_BEGIN
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2014-01-30 09:44:16
|
Revision: 19573
http://sourceforge.net/p/sbml/code/19573
Author: sarahkeating
Date: 2014-01-30 09:44:13 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
update the version number following the release
Modified Paths:
--------------
trunk/libsbml/VERSION.txt
trunk/libsbml/configure
trunk/libsbml/src/sbml/common/libsbml-package.h
trunk/libsbml/src/sbml/common/libsbml-version.h
Modified: trunk/libsbml/VERSION.txt
===================================================================
--- trunk/libsbml/VERSION.txt 2014-01-30 09:31:05 UTC (rev 19572)
+++ trunk/libsbml/VERSION.txt 2014-01-30 09:44:13 UTC (rev 19573)
@@ -1 +1 @@
-5.9.2
+5.9.3
Modified: trunk/libsbml/configure
===================================================================
--- trunk/libsbml/configure 2014-01-30 09:31:05 UTC (rev 19572)
+++ trunk/libsbml/configure 2014-01-30 09:44:13 UTC (rev 19573)
@@ -1,7 +1,7 @@
#! /bin/sh
# From configure.ac Revision: 19183 .
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for libSBML 5.9.2.
+# Generated by GNU Autoconf 2.68 for libSBML 5.9.3.
#
# Report bugs to <lib...@ca...>.
#
@@ -715,8 +715,8 @@
# Identity of this package.
PACKAGE_NAME='libSBML'
PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.9.2'
-PACKAGE_STRING='libSBML 5.9.2'
+PACKAGE_VERSION='5.9.3'
+PACKAGE_STRING='libSBML 5.9.3'
PACKAGE_BUGREPORT='lib...@ca...'
PACKAGE_URL='http://sbml.org/Software/libSBML'
@@ -1566,7 +1566,7 @@
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures libSBML 5.9.2 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.9.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1631,7 +1631,7 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of libSBML 5.9.2:";;
+ short | recursive ) echo "Configuration of libSBML 5.9.3:";;
esac
cat <<\_ACEOF
@@ -1776,7 +1776,7 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-libSBML configure 5.9.2
+libSBML configure 5.9.3
generated by GNU Autoconf 2.68
Copyright (C) 2010 Free Software Foundation, Inc.
@@ -2495,7 +2495,7 @@
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by libSBML $as_me 5.9.2, which was
+It was created by libSBML $as_me 5.9.3, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -2885,7 +2885,7 @@
ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
-LIBSBML_VERSION_NUMERIC=50902
+LIBSBML_VERSION_NUMERIC=50903
@@ -2897,7 +2897,7 @@
-LIBSBML_REVISION_VERSION=2
+LIBSBML_REVISION_VERSION=3
@@ -27298,7 +27298,7 @@
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by libSBML $as_me 5.9.2, which was
+This file was extended by libSBML $as_me 5.9.3, which was
generated by GNU Autoconf 2.68. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -27361,7 +27361,7 @@
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-libSBML config.status 5.9.2
+libSBML config.status 5.9.3
configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
Modified: trunk/libsbml/src/sbml/common/libsbml-package.h
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-package.h 2014-01-30 09:31:05 UTC (rev 19572)
+++ trunk/libsbml/src/sbml/common/libsbml-package.h 2014-01-30 09:44:13 UTC (rev 19573)
@@ -52,11 +52,11 @@
#define PACKAGE_NAME "libSBML"
/* Define to the full name and version of this package. */
-#define PACKAGE_STRING "libSBML 5.9.2"
+#define PACKAGE_STRING "libSBML 5.9.3"
/* Define to the one symbol short name of this package. */
#define PACKAGE_TARNAME "libsbml"
/* Define to the version of this package. */
-#define PACKAGE_VERSION "5.9.2"
+#define PACKAGE_VERSION "5.9.3"
Modified: trunk/libsbml/src/sbml/common/libsbml-version.h
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-version.h 2014-01-30 09:31:05 UTC (rev 19572)
+++ trunk/libsbml/src/sbml/common/libsbml-version.h 2014-01-30 09:44:13 UTC (rev 19573)
@@ -37,7 +37,7 @@
*
* A version string of the form "1.2.3".
*/
-#define LIBSBML_DOTTED_VERSION "5.9.2"
+#define LIBSBML_DOTTED_VERSION "5.9.3"
/**
@@ -48,7 +48,7 @@
* libSBML is released, making it easy to use less-than and greater-than
* comparisons when testing versions numbers.
*/
-#define LIBSBML_VERSION 50902
+#define LIBSBML_VERSION 50903
/**
@@ -56,7 +56,7 @@
*
* The numeric version as a string: version 1.2.3 becomes "10203".
*/
-#define LIBSBML_VERSION_STRING "50902"
+#define LIBSBML_VERSION_STRING "50903"
LIBSBML_CPP_NAMESPACE_BEGIN
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|
|
From: <sar...@us...> - 2014-01-30 09:24:50
|
Revision: 19571
http://sourceforge.net/p/sbml/code/19571
Author: sarahkeating
Date: 2014-01-30 09:24:46 +0000 (Thu, 30 Jan 2014)
Log Message:
-----------
Merged revision(s) 19564-19570 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/dev/packages/create_archives/create-zip-comp.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-fbc.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-qual.bat
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-28 08:13:31 UTC (rev 19570)
+++ branches/libsbml-experimental 2014-01-30 09:24:46 UTC (rev 19571)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19563
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19570
\ No newline at end of property
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-comp.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-comp.bat 2014-01-28 08:13:31 UTC (rev 19570)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-comp.bat 2014-01-30 09:24:46 UTC (rev 19571)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=comp
-set VERSION=libSBML-5.9.0-%PACKAGE_NAME%-src
+set VERSION=libSBML-5.9.2-%PACKAGE_NAME%-src
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-fbc.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-fbc.bat 2014-01-28 08:13:31 UTC (rev 19570)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-fbc.bat 2014-01-30 09:24:46 UTC (rev 19571)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=fbc
-set VERSION=libSBML-5.9.0-%PACKAGE_NAME%-src
+set VERSION=libSBML-5.9.2-%PACKAGE_NAME%-src
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-qual.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-qual.bat 2014-01-28 08:13:31 UTC (rev 19570)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-qual.bat 2014-01-30 09:24:46 UTC (rev 19571)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=qual
-set VERSION=libSBML-5.9.0-%PACKAGE_NAME%-src
+set VERSION=libSBML-5.9.2-%PACKAGE_NAME%-src
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
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|
|
From: <fbe...@us...> - 2014-01-28 08:13:33
|
Revision: 19570
http://sourceforge.net/p/sbml/code/19570
Author: fbergmann
Date: 2014-01-28 08:13:31 +0000 (Tue, 28 Jan 2014)
Log Message:
-----------
- updated version number
Modified Paths:
--------------
branches/libsbml-experimental/dev/packages/create_archives/create-zip-distrib.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-groups.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-multi.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-render.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-req.bat
branches/libsbml-experimental/dev/packages/create_archives/create-zip-spatial.bat
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-distrib.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-distrib.bat 2014-01-28 08:10:44 UTC (rev 19569)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-distrib.bat 2014-01-28 08:13:31 UTC (rev 19570)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=distrib
-set VERSION=%PACKAGE_NAME%-5.9.0-beta-1
+set VERSION=%PACKAGE_NAME%-5.9.2-beta-1
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-groups.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-groups.bat 2014-01-28 08:10:44 UTC (rev 19569)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-groups.bat 2014-01-28 08:13:31 UTC (rev 19570)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=groups
-set VERSION=%PACKAGE_NAME%-5.9.0-beta-1
+set VERSION=%PACKAGE_NAME%-5.9.2-beta-1
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-multi.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-multi.bat 2014-01-28 08:10:44 UTC (rev 19569)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-multi.bat 2014-01-28 08:13:31 UTC (rev 19570)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=multi
-set VERSION=%PACKAGE_NAME%-5.9.0-beta-1
+set VERSION=%PACKAGE_NAME%-5.9.2-beta-1
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-render.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-render.bat 2014-01-28 08:10:44 UTC (rev 19569)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-render.bat 2014-01-28 08:13:31 UTC (rev 19570)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=render
-set VERSION=%PACKAGE_NAME%-5.9.0-beta-1
+set VERSION=%PACKAGE_NAME%-5.9.2-beta-1
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-req.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-req.bat 2014-01-28 08:10:44 UTC (rev 19569)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-req.bat 2014-01-28 08:13:31 UTC (rev 19570)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=req
-set VERSION=%PACKAGE_NAME%-5.9.0-beta-1
+set VERSION=%PACKAGE_NAME%-5.9.2-beta-1
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: branches/libsbml-experimental/dev/packages/create_archives/create-zip-spatial.bat
===================================================================
--- branches/libsbml-experimental/dev/packages/create_archives/create-zip-spatial.bat 2014-01-28 08:10:44 UTC (rev 19569)
+++ branches/libsbml-experimental/dev/packages/create_archives/create-zip-spatial.bat 2014-01-28 08:13:31 UTC (rev 19570)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=spatial
-set VERSION=%PACKAGE_NAME%-5.9.0-beta-2
+set VERSION=%PACKAGE_NAME%-5.9.2-beta-1
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
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|
|
From: <fbe...@us...> - 2014-01-28 08:10:47
|
Revision: 19569
http://sourceforge.net/p/sbml/code/19569
Author: fbergmann
Date: 2014-01-28 08:10:44 +0000 (Tue, 28 Jan 2014)
Log Message:
-----------
- update version number
Modified Paths:
--------------
trunk/libsbml/dev/packages/create_archives/create-zip-comp.bat
trunk/libsbml/dev/packages/create_archives/create-zip-fbc.bat
trunk/libsbml/dev/packages/create_archives/create-zip-qual.bat
Modified: trunk/libsbml/dev/packages/create_archives/create-zip-comp.bat
===================================================================
--- trunk/libsbml/dev/packages/create_archives/create-zip-comp.bat 2014-01-27 13:45:02 UTC (rev 19568)
+++ trunk/libsbml/dev/packages/create_archives/create-zip-comp.bat 2014-01-28 08:10:44 UTC (rev 19569)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=comp
-set VERSION=libSBML-5.9.0-%PACKAGE_NAME%-src
+set VERSION=libSBML-5.9.2-%PACKAGE_NAME%-src
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: trunk/libsbml/dev/packages/create_archives/create-zip-fbc.bat
===================================================================
--- trunk/libsbml/dev/packages/create_archives/create-zip-fbc.bat 2014-01-27 13:45:02 UTC (rev 19568)
+++ trunk/libsbml/dev/packages/create_archives/create-zip-fbc.bat 2014-01-28 08:10:44 UTC (rev 19569)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=fbc
-set VERSION=libSBML-5.9.0-%PACKAGE_NAME%-src
+set VERSION=libSBML-5.9.2-%PACKAGE_NAME%-src
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
Modified: trunk/libsbml/dev/packages/create_archives/create-zip-qual.bat
===================================================================
--- trunk/libsbml/dev/packages/create_archives/create-zip-qual.bat 2014-01-27 13:45:02 UTC (rev 19568)
+++ trunk/libsbml/dev/packages/create_archives/create-zip-qual.bat 2014-01-28 08:10:44 UTC (rev 19569)
@@ -5,7 +5,7 @@
SET THIS_DIR=%~dp0
SET PACKAGE_NAME=qual
-set VERSION=libSBML-5.9.0-%PACKAGE_NAME%-src
+set VERSION=libSBML-5.9.2-%PACKAGE_NAME%-src
SET DIST_DIR=%~dp0\%VERSION%
SET PACKAGE_DIR=%~dp0\..\..\..\
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|
|
From: <sar...@us...> - 2014-01-27 13:45:06
|
Revision: 19568
http://sourceforge.net/p/sbml/code/19568
Author: sarahkeating
Date: 2014-01-27 13:45:02 +0000 (Mon, 27 Jan 2014)
Log Message:
-----------
so I now have an implementation of an AST vector class that works
Modified Paths:
--------------
branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp
branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h
branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp
branches/libsbml-ast-plugin/src/sbml/math/ASTNode.cpp
Modified: branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp 2014-01-27 10:10:50 UTC (rev 19567)
+++ branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp 2014-01-27 13:45:02 UTC (rev 19568)
@@ -203,33 +203,72 @@
bool
ASTBasePlugin::isSetMath() const
{
- return (mParent != NULL);
+ return false;
}
const ASTBase *
ASTBasePlugin::getMath() const
{
- return mParent;
+ return NULL;
}
-int
-ASTBasePlugin::setMath(ASTBase* math)
+void
+ASTBasePlugin::createMath(int type)
{
- connectToParent(math);
- return LIBSBML_OPERATION_SUCCESS;
+ // do nothing
}
int
-ASTBasePlugin::unsetMath()
-{
- delete mParent;
- mParent = NULL;
- return LIBSBML_OPERATION_SUCCESS;
+ASTBasePlugin::addChild(ASTBase * child)
+{
+ return LIBSBML_INVALID_OBJECT;
}
+
+ASTBase*
+ASTBasePlugin::getChild (unsigned int n) const
+{
+ return NULL;
+}
+
+
+unsigned int
+ASTBasePlugin::getNumChildren() const
+{
+ return 0;
+}
+
+
+int
+ASTBasePlugin::insertChild(unsigned int n, ASTBase* newChild)
+{
+ return LIBSBML_INVALID_OBJECT;
+}
+
+
+int
+ASTBasePlugin::prependChild(ASTBase* newChild)
+{
+ return LIBSBML_INVALID_OBJECT;
+}
+
+
+int
+ASTBasePlugin::removeChild(unsigned int n)
+{
+ return LIBSBML_INVALID_OBJECT;
+}
+
+
+int
+ASTBasePlugin::replaceChild(unsigned int n, ASTBase* newChild)
+{
+ return LIBSBML_INVALID_OBJECT;
+}
+
/*
* Enables/Disables the given package with child elements in this plugin
* object (if any).
@@ -360,7 +399,8 @@
bool
-ASTBasePlugin::read(XMLInputStream& stream, const std::string& reqd_prefix)
+ASTBasePlugin::read(XMLInputStream& stream, const std::string& reqd_prefix,
+ const XMLToken currentElement)
{
return false;
}
Modified: branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h 2014-01-27 10:10:50 UTC (rev 19567)
+++ branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h 2014-01-27 13:45:02 UTC (rev 19568)
@@ -249,16 +249,30 @@
/** @endcond */
- bool isSetMath() const;
+ virtual bool isSetMath() const;
- const ASTBase * getMath() const;
+ virtual const ASTBase * getMath() const;
- int setMath(ASTBase* math);
+ virtual void createMath(int type);
- int unsetMath();
+ virtual int addChild(ASTBase * child);
+ virtual ASTBase* getChild (unsigned int n) const;
- virtual bool read(XMLInputStream& stream, const std::string& reqd_prefix="");
+ virtual unsigned int getNumChildren() const;
+
+ virtual int insertChild(unsigned int n, ASTBase* newChild);
+
+ virtual int prependChild(ASTBase* newChild);
+
+ virtual int removeChild(unsigned int n);
+
+ virtual int replaceChild(unsigned int n, ASTBase* newChild);
+
+
+
+ virtual bool read(XMLInputStream& stream, const std::string& reqd_prefix,
+ const XMLToken currentElement);
virtual void addExpectedAttributes(ExpectedAttributes& attributes,
XMLInputStream& stream, int type);
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp 2014-01-27 10:10:50 UTC (rev 19567)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp 2014-01-27 13:45:02 UTC (rev 19568)
@@ -189,12 +189,24 @@
mSemantics = new ASTSemanticsNode();
this->ASTBase::syncPluginsFrom(mSemantics);
}
- else
+ else if (type == AST_UNKNOWN)
{
- // the catch all - we dont know what type
- // so use the most generic
mNaryFunction = new ASTNaryFunctionNode(type);
this->ASTBase::syncPluginsFrom(mNaryFunction);
+ }
+ else
+ {
+ bool done = false;
+ unsigned int i = 0;
+ while (done == false && i < getNumPlugins())
+ {
+ if (getPlugin(i)->isFunctionNode(type) == true)
+ {
+ getPlugin(i)->createMath(type);
+ done = true;
+ }
+ i++;
+ }
mIsOther = true;
}
@@ -439,6 +451,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->addChild(child);
+ }
+ i++;
+ }
+
return LIBSBML_INVALID_OBJECT;
}
}
@@ -484,6 +506,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->getChild(n);
+ }
+ i++;
+ }
+
return NULL;
}
}
@@ -529,6 +561,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->getNumChildren();
+ }
+ i++;
+ }
+
return 0;
}
}
@@ -575,6 +617,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->removeChild(n);
+ }
+ i++;
+ }
+
return LIBSBML_OPERATION_FAILED;
}
}
@@ -621,6 +673,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->prependChild(newChild);
+ }
+ i++;
+ }
+
return LIBSBML_OPERATION_FAILED;
}
}
@@ -667,6 +729,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->replaceChild(n, newChild);
+ }
+ i++;
+ }
+
return LIBSBML_OPERATION_FAILED;
}
}
@@ -713,6 +785,16 @@
}
else
{
+ unsigned int i = 0;
+ while (i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ return getPlugin(i)->insertChild(n, newChild);
+ }
+ i++;
+ }
+
return LIBSBML_OPERATION_FAILED;
}
}
@@ -2331,8 +2413,17 @@
}
else if (mIsOther == true)
{
- // FIX ME
- //getPlugin("qual")->getMath()->write(stream);
+ bool done = false;
+ unsigned int i = 0;
+ while (done == false && i < getNumPlugins())
+ {
+ if (getPlugin(i)->isSetMath() == true)
+ {
+ getPlugin(i)->getMath()->write(stream);
+ done = true;
+ }
+ i++;
+ }
}
}
@@ -2397,13 +2488,13 @@
unsigned int i = 0;
while(read == false && i < getNumPlugins())
{
- read = getPlugin(i)->read(stream, reqd_prefix);
+ read = getPlugin(i)->read(stream, reqd_prefix, currentElement);
if (read == true)
{
reset();
setType(getPlugin(i)->getMath()->getType());
- this->ASTBase::syncMembersAndResetParentsFrom((ASTBase*)
- (getPlugin(i)->getMath()));
+ //this->ASTBase::syncMembersAndResetParentsFrom((ASTBase*)
+ // (getPlugin(i)->getMath()));
mIsOther = true;
}
}
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTNode.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTNode.cpp 2014-01-27 10:10:50 UTC (rev 19567)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTNode.cpp 2014-01-27 13:45:02 UTC (rev 19568)
@@ -92,7 +92,8 @@
for (unsigned int i = 0; i < ASTBase::getNumPlugins(); i++)
{
if (found == false
- && representsFunction(type, ASTBase::getPlugin(i)) == true)
+ && (representsFunction(type, ASTBase::getPlugin(i)) == true
+ || isTopLevelMathMLFunctionNodeTag(getNameFromType(type)) == true))
{
mFunction = new ASTFunction (type);
this->ASTBase::syncPluginsFrom(mFunction);
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|
|
From: <sar...@us...> - 2014-01-27 10:10:53
|
Revision: 19567
http://sourceforge.net/p/sbml/code/19567
Author: sarahkeating
Date: 2014-01-27 10:10:50 +0000 (Mon, 27 Jan 2014)
Log Message:
-----------
oops - took out a function that was meant to be there
Modified Paths:
--------------
branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp 2014-01-27 09:54:57 UTC (rev 19566)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp 2014-01-27 10:10:50 UTC (rev 19567)
@@ -2400,7 +2400,10 @@
read = getPlugin(i)->read(stream, reqd_prefix);
if (read == true)
{
+ reset();
setType(getPlugin(i)->getMath()->getType());
+ this->ASTBase::syncMembersAndResetParentsFrom((ASTBase*)
+ (getPlugin(i)->getMath()));
mIsOther = true;
}
}
@@ -2534,7 +2537,51 @@
"permitted MathML element.";
logError(stream, nextElement, DisallowedMathMLSymbol, message);
}
+
+ return read;
+}
+
+bool
+ASTFunction::readLambda(XMLInputStream& stream, const std::string& reqd_prefix,
+ const XMLToken currentElement)
+{
+ bool read = false;
+
+ stream.skipText();
+ const XMLToken nextElement = stream.peek();
+ const string& nextName = nextElement.getName();
+
+ unsigned int numChildren = determineNumChildren(stream, "lambda");
+ unsigned int numBvars = determineNumBvars(stream);
+
+ reset();
+
+ mLambda = new ASTLambdaFunctionNode();
+
+ mLambda->setNumBvars(numBvars);
+ mLambda->setExpectedNumChildren(numChildren);
+
+ // read attributes on this element here since we have already consumed
+ // the element
+ ExpectedAttributes expectedAttributes;
+ mLambda->addExpectedAttributes(expectedAttributes, stream);
+ read = mLambda->ASTBase::readAttributes(currentElement.getAttributes(),
+ expectedAttributes, stream, currentElement);
+ if (read == false)
+ {
+ mLambda = NULL;
+ }
+ else
+ {
+ read = mLambda->read(stream, reqd_prefix);
+ }
+
+ if (read == true && mLambda != NULL)
+ {
+ this->ASTBase::syncMembersAndResetParentsFrom(mLambda);
+ }
+
return read;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2014-01-27 09:54:59
|
Revision: 19566
http://sourceforge.net/p/sbml/code/19566
Author: sarahkeating
Date: 2014-01-27 09:54:57 +0000 (Mon, 27 Jan 2014)
Log Message:
-----------
some more refactoring of ASTFunction::read
Modified Paths:
--------------
branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp
branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.h
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp 2014-01-27 08:16:47 UTC (rev 19565)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.cpp 2014-01-27 09:54:57 UTC (rev 19566)
@@ -28,6 +28,7 @@
#include <sbml/math/ASTFunction.h>
#include <sbml/math/ASTNumber.h>
+#include <sbml/extension/ASTBasePlugin.h>
/** @cond doxygen-ignored */
@@ -35,6 +36,7 @@
/** @endcond */
+
LIBSBML_CPP_NAMESPACE_BEGIN
static unsigned int
@@ -2349,7 +2351,6 @@
ASTFunction::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
- bool done = false;
stream.skipText();
@@ -2369,83 +2370,107 @@
return read;
}
+ // create appropriate sub class
if (currentName == "apply")
{
- // this will not actually store the attributes for an apply element
- // but will log any unexpected attributes
- ExpectedAttributes expectedAttributes;
- addExpectedAttributes(expectedAttributes, stream);
- ASTBase::readAttributes(currentElement.getAttributes(), expectedAttributes,
- stream, currentElement);
-
- /* allow a <apply/> element */
- if (currentElement.isStart() && currentElement.isEnd())
- {
- return true;
- }
-
+ read = readApply(stream, reqd_prefix, currentElement);
}
-
- stream.skipText();
- const XMLToken nextElement = stream.peek();
- const string& nextName = nextElement.getName();
-
- unsigned int numChildren = 0;
-
- // create appropriate sub class
- if (currentName == "lambda")
+ else if (currentName == "lambda")
{
read = readLambda(stream, reqd_prefix, currentElement);
- done = true;
}
else if (currentName == "piecewise")
{
read = readPiecewise(stream, reqd_prefix, currentElement);
- done = true;
}
else if (representsQualifier(getTypeFromName(currentName)) == true)
{
read = readQualifier(stream, reqd_prefix, currentElement);
- done = true;
}
else if (currentName == "semantics")
{
read = readSemantics(stream, reqd_prefix, currentElement);
- done = true;
}
- else if (currentName == "apply" && nextName == "ci")
+ else
{
+ // we have a top level node that comes from a plugin
+ unsigned int i = 0;
+ while(read == false && i < getNumPlugins())
+ {
+ read = getPlugin(i)->read(stream, reqd_prefix);
+ if (read == true)
+ {
+ setType(getPlugin(i)->getMath()->getType());
+ mIsOther = true;
+ }
+ }
+ }
+
+ if (read == true)
+ {
+ stream.skipPastEnd(currentElement);
+ }
+
+ return read;
+}
+
+
+bool
+ASTFunction::readApply(XMLInputStream& stream, const std::string& reqd_prefix,
+ const XMLToken currentElement)
+{
+ bool read = false;
+
+ // this will not actually store the attributes for an apply element
+ // but will log any unexpected attributes
+ ExpectedAttributes expectedAttributes;
+ addExpectedAttributes(expectedAttributes, stream);
+ ASTBase::readAttributes(currentElement.getAttributes(), expectedAttributes,
+ stream, currentElement);
+
+ /* allow a <apply/> element */
+ if (currentElement.isStart() && currentElement.isEnd())
+ {
+ return true;
+ }
+
+ stream.skipText();
+ const XMLToken nextElement = stream.peek();
+ const string& nextName = nextElement.getName();
+
+ int type = ASTBase::getTypeFromName(nextName);
+ unsigned int numPlugins = ASTBase::getNumPlugins();
+
+ unsigned int i = 0;
+ bool done = false;
+
+ unsigned int numChildren = 0;
+
+ if (nextName == "ci")
+ {
read = readCiFunction(stream, reqd_prefix, currentElement);
done = true;
}
- else if (currentName == "apply" && nextName == "csymbol")
+ else if (nextName == "csymbol")
{
read = readCSymbol(stream, reqd_prefix, currentElement);
done = true;
}
-
- // before we allocate a function
- // check for completely invalid element
- if (done == false
- && isTopLevelMathMLNumberNodeTag(nextName) == true)
+ else
{
+ numChildren = determineNumChildren(stream);
+ }
+
+ if (done == false && isTopLevelMathMLNumberNodeTag(nextName) == true)
+ {
std::string message = "<" + nextName + "> cannot be used directly " +
- "following an <" + currentName + "> tag.";
+ "following an <apply> tag.";
logError(stream, nextElement, BadMathML, message);
done = true;
}
- int type = ASTBase::getTypeFromName(nextName);
- unsigned int numPlugins = ASTBase::getNumPlugins();
-
- unsigned int i = 0;
- if (done == false)
- {
- numChildren = determineNumChildren(stream);
- }
-
while (done == false && i <= numPlugins)
{
ASTBasePlugin* plugin = static_cast<ASTBasePlugin*>(getPlugin(i));
@@ -2501,19 +2526,6 @@
done = true;
}
}
- else
- {
- //std::string message = "The element <" + nextName + "> is not a " +
- // "permitted MathML element.";
- //logError(stream, nextElement, DisallowedMathMLSymbol, message);
-
- //read = getPlugin(0)->read(stream, reqd_prefix);
- //if (read == true)
- //{
- // setType(getPlugin(0)->getMath()->getType());
- // mIsOther = true;
- //}
- }
i++;
}
if (done == false)
@@ -2522,56 +2534,7 @@
"permitted MathML element.";
logError(stream, nextElement, DisallowedMathMLSymbol, message);
}
-
- if (read == true)
- {
- stream.skipPastEnd(currentElement);
- }
-
- return read;
-}
-
-bool
-ASTFunction::readLambda(XMLInputStream& stream, const std::string& reqd_prefix,
- const XMLToken currentElement)
-{
- bool read = false;
-
- stream.skipText();
- const XMLToken nextElement = stream.peek();
- const string& nextName = nextElement.getName();
-
- unsigned int numChildren = determineNumChildren(stream, "lambda");
- unsigned int numBvars = determineNumBvars(stream);
-
- reset();
-
- mLambda = new ASTLambdaFunctionNode();
-
- mLambda->setNumBvars(numBvars);
- mLambda->setExpectedNumChildren(numChildren);
-
- // read attributes on this element here since we have already consumed
- // the element
- ExpectedAttributes expectedAttributes;
- mLambda->addExpectedAttributes(expectedAttributes, stream);
- read = mLambda->ASTBase::readAttributes(currentElement.getAttributes(),
- expectedAttributes, stream, currentElement);
- if (read == false)
- {
- mLambda = NULL;
- }
- else
- {
- read = mLambda->read(stream, reqd_prefix);
- }
-
- if (read == true && mLambda != NULL)
- {
- this->ASTBase::syncMembersAndResetParentsFrom(mLambda);
- }
-
return read;
}
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.h
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.h 2014-01-27 08:16:47 UTC (rev 19565)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTFunction.h 2014-01-27 09:54:57 UTC (rev 19566)
@@ -245,6 +245,9 @@
void reset();
+ bool readApply(XMLInputStream& stream, const std::string& reqd_prefix,
+ const XMLToken currentElement);
+
bool readLambda(XMLInputStream& stream, const std::string& reqd_prefix,
const XMLToken currentElement);
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|
|
From: <sar...@us...> - 2014-01-27 08:16:50
|
Revision: 19565
http://sourceforge.net/p/sbml/code/19565
Author: sarahkeating
Date: 2014-01-27 08:16:47 +0000 (Mon, 27 Jan 2014)
Log Message:
-----------
need to pass tracking the potential top level tags to plugins as vector in arrays is a tag with no apply
Modified Paths:
--------------
branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp
branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h
branches/libsbml-ast-plugin/src/sbml/math/ASTBase.cpp
branches/libsbml-ast-plugin/src/sbml/math/ASTBase.h
branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.cpp
branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.h
Modified: branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp 2014-01-25 10:19:12 UTC (rev 19564)
+++ branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.cpp 2014-01-27 08:16:47 UTC (rev 19565)
@@ -392,14 +392,14 @@
}
bool
-ASTBasePlugin::isNumberNode() const
+ASTBasePlugin::isNumberNode(int type) const
{
return false;
}
bool
-ASTBasePlugin::isFunctionNode() const
+ASTBasePlugin::isFunctionNode(int type) const
{
return false;
}
@@ -496,6 +496,20 @@
}
+bool
+ASTBasePlugin::isTopLevelMathMLFunctionNodeTag(const std::string& name) const
+{
+ return false;
+}
+
+
+bool
+ASTBasePlugin::isTopLevelMathMLNumberNodeTag(const std::string& name) const
+{
+ return false;
+}
+
+
int
ASTBasePlugin::getTypeFromName(const std::string& name) const
{
Modified: branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h 2014-01-25 10:19:12 UTC (rev 19564)
+++ branches/libsbml-ast-plugin/src/sbml/extension/ASTBasePlugin.h 2014-01-27 08:16:47 UTC (rev 19565)
@@ -271,8 +271,8 @@
virtual void writeXMLNS(XMLOutputStream& stream) const;
- virtual bool isNumberNode() const;
- virtual bool isFunctionNode() const;
+ virtual bool isNumberNode(int type) const;
+ virtual bool isFunctionNode(int type) const;
virtual bool isLogical(int type) const;
virtual bool isConstantNumber(int type) const;
@@ -289,6 +289,10 @@
virtual bool representsBinaryFunction(int type) const;
virtual bool representsNaryFunction(int type) const;
+ virtual bool isTopLevelMathMLFunctionNodeTag(const std::string& name) const;
+
+ virtual bool isTopLevelMathMLNumberNodeTag(const std::string& name) const;
+
virtual int getTypeFromName(const std::string& name) const;
virtual const char * getNameFromType(int type) const;
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTBase.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTBase.cpp 2014-01-25 10:19:12 UTC (rev 19564)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTBase.cpp 2014-01-27 08:16:47 UTC (rev 19565)
@@ -894,7 +894,7 @@
while(isNumberNode == false && i < getNumPlugins())
{
const ASTBasePlugin* plugin = static_cast<const ASTBasePlugin*>(getPlugin(i));
- if (plugin->isNumberNode() == true)
+ if (plugin->isNumberNode(getType()) == true)
{
isNumberNode = true;
}
@@ -929,7 +929,7 @@
while(isFunctionNode == false && i < getNumPlugins())
{
const ASTBasePlugin* plugin = static_cast<const ASTBasePlugin*>(getPlugin(i));
- if (plugin->isFunctionNode() == true)
+ if (plugin->isFunctionNode(getType()) == true)
{
isFunctionNode = true;
}
@@ -941,6 +941,60 @@
}
+bool
+ASTBase::isTopLevelMathMLFunctionNodeTag(const std::string& name) const
+{
+ bool isNode = false;
+
+ if ( isCoreTopLevelMathMLFunctionNodeTag(name))
+ {
+ isNode = true;
+ }
+ else if (getNumPlugins() > 0)
+ {
+ unsigned int i = 0;
+ while(isNode == false && i < getNumPlugins())
+ {
+ const ASTBasePlugin* plugin = static_cast<const ASTBasePlugin*>(getPlugin(i));
+ if (plugin->isTopLevelMathMLFunctionNodeTag(name) == true)
+ {
+ isNode = true;
+ }
+ i++;
+ }
+ }
+
+ return isNode;
+}
+
+
+bool
+ASTBase::isTopLevelMathMLNumberNodeTag(const std::string& name) const
+{
+ bool isNode = false;
+
+ if ( isCoreTopLevelMathMLNumberNodeTag(name))
+ {
+ isNode = true;
+ }
+ else if (getNumPlugins() > 0)
+ {
+ unsigned int i = 0;
+ while(isNode == false && i < getNumPlugins())
+ {
+ const ASTBasePlugin* plugin = static_cast<const ASTBasePlugin*>(getPlugin(i));
+ if (plugin->isTopLevelMathMLNumberNodeTag(name) == true)
+ {
+ isNode = true;
+ }
+ i++;
+ }
+ }
+
+ return isNode;
+}
+
+
int
ASTBase::setUserData(void *userData)
{
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTBase.h
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTBase.h 2014-01-25 10:19:12 UTC (rev 19564)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTBase.h 2014-01-27 08:16:47 UTC (rev 19565)
@@ -152,12 +152,15 @@
bool isNumberNode() const;
bool isFunctionNode() const;
+ bool isTopLevelMathMLFunctionNodeTag(const std::string& name) const;
+ bool isTopLevelMathMLNumberNodeTag(const std::string& name) const;
+
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.cpp
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.cpp 2014-01-25 10:19:12 UTC (rev 19564)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.cpp 2014-01-27 08:16:47 UTC (rev 19565)
@@ -426,7 +426,7 @@
bool
-isTopLevelMathMLNodeTag(const std::string& name)
+isCoreTopLevelMathMLFunctionNodeTag(const std::string& name)
{
if (&name == NULL)
{
@@ -434,36 +434,6 @@
}
if ( name == "apply"
- || name == "cn"
- || name == "ci"
- || name == "csymbol"
- || name == "true"
- || name == "false"
- || name == "notanumber"
- || name == "pi"
- || name == "infinity"
- || name == "exponentiale"
- || name == "semantics"
- || name == "piecewise")
- {
- return true;
- }
- else
- {
- return false;
- }
-}
-
-
-bool
-isTopLevelMathMLFunctionNodeTag(const std::string& name)
-{
- if (&name == NULL)
- {
- return false;
- }
-
- if ( name == "apply"
|| name == "lambda"
|| name == "semantics"
|| name == "piecewise")
@@ -482,7 +452,7 @@
bool
-isTopLevelMathMLNumberNodeTag(const std::string& name)
+isCoreTopLevelMathMLNumberNodeTag(const std::string& name)
{
if (&name == NULL)
{
@@ -565,8 +535,9 @@
if (type < AST_UNKNOWN)
{
bool found = false;
+ static const int size = sizeof(MATHML_ELEMENTS) / sizeof(MATHML_ELEMENTS[0]);
unsigned int i;
- for (i = 0; i < 69, found == false; i++)
+ for (i = 0; i < size, found == false; i++)
{
if (type == MATHML_TYPES[i])
found = true;
Modified: branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.h
===================================================================
--- branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.h 2014-01-25 10:19:12 UTC (rev 19564)
+++ branches/libsbml-ast-plugin/src/sbml/math/ASTTypes.h 2014-01-27 08:16:47 UTC (rev 19565)
@@ -168,14 +168,11 @@
const std::string getNameFromCoreType(int type);
LIBSBML_EXTERN
-bool isTopLevelMathMLNodeTag(const std::string& name);
+bool isCoreTopLevelMathMLFunctionNodeTag(const std::string& name);
LIBSBML_EXTERN
-bool isTopLevelMathMLFunctionNodeTag(const std::string& name);
+bool isCoreTopLevelMathMLNumberNodeTag(const std::string& name);
-LIBSBML_EXTERN
-bool isTopLevelMathMLNumberNodeTag(const std::string& name);
-
LIBSBML_CPP_NAMESPACE_END
#endif /* cplusplus */
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|
|
From: <sar...@us...> - 2014-01-25 10:19:15
|
Revision: 19564
http://sourceforge.net/p/sbml/code/19564
Author: sarahkeating
Date: 2014-01-25 10:19:12 +0000 (Sat, 25 Jan 2014)
Log Message:
-----------
Merged revision(s) 19562-19563 from trunk/libsbml:
Added Paths:
-----------
branches/libsbml-experimental/examples/perl/reanameSId.pl
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-24 16:02:23 UTC (rev 19563)
+++ branches/libsbml-experimental 2014-01-25 10:19:12 UTC (rev 19564)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19561
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19563
\ No newline at end of property
Copied: branches/libsbml-experimental/examples/perl/reanameSId.pl (from rev 19563, trunk/libsbml/examples/perl/reanameSId.pl)
===================================================================
--- branches/libsbml-experimental/examples/perl/reanameSId.pl (rev 0)
+++ branches/libsbml-experimental/examples/perl/reanameSId.pl 2014-01-25 10:19:12 UTC (rev 19564)
@@ -0,0 +1,62 @@
+#!/usr/bin/env perl
+# -*-Perl-*-
+##
+## \file reanameSId.pl
+## \brief renames a specified SId to the new identifier
+## \author Frank T. Bergmann
+##
+## This file is part of libSBML. Please visit http://sbml.org for more
+## information about SBML, and the latest version of libSBML.
+##
+
+use LibSBML;
+no strict;
+
+if ($#ARGV != 3) {
+ print "usage: reanameSId <input-filename> <output-filename> <oldId> <newId>\n";
+ print " renames an id in the model\n";
+ exit 1;
+}
+
+print("Using LibSBML : ");
+print(LibSBML::getLibSBMLDottedVersion());
+print("\n");
+
+if (!LibSBML::SyntaxChecker::isValidInternalSId($ARGV[3])) {
+ print("The newId is not a valid SId\n");
+ exit 3;
+}
+
+$d = LibSBML::readSBML($ARGV[0]);
+$errors = $d->getNumErrors($LibSBML::LIBSBML_SEV_ERROR);
+
+if ($errors > 0) {
+ print("Read Error(s):\n");
+ $d->printErrors();
+ print("Correct the above and re-run.\n");
+ exit $errors;
+}
+
+# find elements for old id
+$element = $d->getElementBySId($ARGV[2]);
+if (!defined($element))
+{
+ print("Found no element with the old SId ");
+ exit 2;
+}
+
+# found element --> renaming
+$element->setId($ARGV[3]);
+
+# update all references to this element
+$allElements = $d->getListOfAllElements();
+for ($i = 0; $i < $allElements->getSize(); $i++) {
+ $current = $allElements->get($i);
+ bless $current, 'LibSBML::SBase';
+ $current->renameSIdRefs($ARGV[2], $ARGV[3]);
+}
+
+LibSBML::writeSBML($d, $ARGV[1]);
+
+exit $errors;
+
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|
|
From: <fbe...@us...> - 2014-01-24 16:02:26
|
Revision: 19563
http://sourceforge.net/p/sbml/code/19563
Author: fbergmann
Date: 2014-01-24 16:02:23 +0000 (Fri, 24 Jan 2014)
Log Message:
-----------
- ported example for renaming SIds to perl
Added Paths:
-----------
trunk/libsbml/examples/perl/reanameSId.pl
Added: trunk/libsbml/examples/perl/reanameSId.pl
===================================================================
--- trunk/libsbml/examples/perl/reanameSId.pl (rev 0)
+++ trunk/libsbml/examples/perl/reanameSId.pl 2014-01-24 16:02:23 UTC (rev 19563)
@@ -0,0 +1,62 @@
+#!/usr/bin/env perl
+# -*-Perl-*-
+##
+## \file reanameSId.pl
+## \brief renames a specified SId to the new identifier
+## \author Frank T. Bergmann
+##
+## This file is part of libSBML. Please visit http://sbml.org for more
+## information about SBML, and the latest version of libSBML.
+##
+
+use LibSBML;
+no strict;
+
+if ($#ARGV != 3) {
+ print "usage: reanameSId <input-filename> <output-filename> <oldId> <newId>\n";
+ print " renames an id in the model\n";
+ exit 1;
+}
+
+print("Using LibSBML : ");
+print(LibSBML::getLibSBMLDottedVersion());
+print("\n");
+
+if (!LibSBML::SyntaxChecker::isValidInternalSId($ARGV[3])) {
+ print("The newId is not a valid SId\n");
+ exit 3;
+}
+
+$d = LibSBML::readSBML($ARGV[0]);
+$errors = $d->getNumErrors($LibSBML::LIBSBML_SEV_ERROR);
+
+if ($errors > 0) {
+ print("Read Error(s):\n");
+ $d->printErrors();
+ print("Correct the above and re-run.\n");
+ exit $errors;
+}
+
+# find elements for old id
+$element = $d->getElementBySId($ARGV[2]);
+if (!defined($element))
+{
+ print("Found no element with the old SId ");
+ exit 2;
+}
+
+# found element --> renaming
+$element->setId($ARGV[3]);
+
+# update all references to this element
+$allElements = $d->getListOfAllElements();
+for ($i = 0; $i < $allElements->getSize(); $i++) {
+ $current = $allElements->get($i);
+ bless $current, 'LibSBML::SBase';
+ $current->renameSIdRefs($ARGV[2], $ARGV[3]);
+}
+
+LibSBML::writeSBML($d, $ARGV[1]);
+
+exit $errors;
+
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|
|
From: <sar...@us...> - 2014-01-24 09:19:56
|
Revision: 19562
http://sourceforge.net/p/sbml/code/19562
Author: sarahkeating
Date: 2014-01-24 09:19:52 +0000 (Fri, 24 Jan 2014)
Log Message:
-----------
Merged revision(s) 19559-19561 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/NEWS.txt
branches/libsbml-experimental/docs/src/libsbml-example-c.txt
branches/libsbml-experimental/src/sbml/Compartment.h
branches/libsbml-experimental/src/sbml/Event.h
branches/libsbml-experimental/src/sbml/SBMLDocument.cpp
branches/libsbml-experimental/src/sbml/SBMLDocument.h
branches/libsbml-experimental/src/sbml/SBMLReader.h
branches/libsbml-experimental/src/sbml/SBase.cpp
branches/libsbml-experimental/src/sbml/SBase.h
branches/libsbml-experimental/src/sbml/xml/XMLAttributes.cpp
branches/libsbml-experimental/src/sbml/xml/XMLAttributes.h
branches/libsbml-experimental/src/sbml/xml/XMLToken.cpp
branches/libsbml-experimental/src/sbml/xml/XMLToken.h
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental 2014-01-24 09:19:52 UTC (rev 19562)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19558
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19561
\ No newline at end of property
Modified: branches/libsbml-experimental/NEWS.txt
===================================================================
--- branches/libsbml-experimental/NEWS.txt 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/NEWS.txt 2014-01-24 09:19:52 UTC (rev 19562)
@@ -37,6 +37,16 @@
- A new version of the SBMLTransforms::evaluateASTNode function
is available; allowing the user to pass a map of ids and values
to the function rather than needing a whole model.
+
+ - Two new functions are available to allow users to determine
+ the compiled dependencies for the given instance of libSBML.
+ int isLibSBMLCompiledWith(const char* option) will take the name
+ of a dependency library e.g. 'expat' as argument and return a
+ positive integer this library was used to compile libSBML, 0
+ otherwise.
+ const char* getLibSBMLDependencyVersionOf(const char* option)
+ takes the name of the library and returns the version number
+ of this library.
* Bug fixes
Modified: branches/libsbml-experimental/docs/src/libsbml-example-c.txt
===================================================================
--- branches/libsbml-experimental/docs/src/libsbml-example-c.txt 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/docs/src/libsbml-example-c.txt 2014-01-24 09:19:52 UTC (rev 19562)
@@ -158,9 +158,9 @@
@subsection creator Function for creating the model
-We begin this function by creating an @link SBMLDocument SBMLDocument
-@endlink object, creating a @link Model Model @endlink object within
-the document object, and setting the @link Model Model @endlink
+We begin this function by creating an @link SBMLDocument_t SBMLDocument_t
+@endlink object, creating a @link Model_t Model_t @endlink object within
+the document object, and setting the @link Model_t Model_t @endlink
object's identifier.
@verbatim
@@ -185,8 +185,8 @@
the quantities used in the model. The libSBML API for unit
definitions mirrors the SBML object model, which means there is an
object class for UnitDefinition and an object class for the Unit
-objects that can be placed inside a @link UnitDefinition
-UnitDefinition @endlink object to compose whatever unit is desired.
+objects that can be placed inside a @link UnitDefinition_t
+UnitDefinition_t @endlink object to compose whatever unit is desired.
The resulting code for creating units is a little bit tedious because
there is a lot to set up, but on the other hand, it is quite
straightforward and hopefully easy to follow:
@@ -236,11 +236,11 @@
Before going on, we digress to explain one libSBML API idiom
illustrated in the code above and in the rest of the program below.
LibSBML provides two main mechanisms for creating objects: class
-constructors (e.g., @link Unit::Unit() Unit() @endlink), and
+constructors (e.g., @link Unit_create() Unit_create() @endlink), and
<code>create<span class="placeholder"><i>Object</i></span>()</code>
-methods provided by certain object classes such as @link Model Model
+methods provided by certain object classes such as @link Model_t Model_t
@endlink, where <span class="placeholder"><i>Object</i></span> is
-another object class such as @link UnitDefinition UnitDefinition
+another object class such as @link UnitDefinition_t UnitDefinition_t
@endlink. The multiple mechanisms are provided by libSBML for
flexibility and to support different use-cases, but they also have
different implications for the overall model structure.
@@ -251,7 +251,7 @@
instance and immediately link it into the parent, as well as return a
pointer to the object created. By contrast, the other main way of
creating an object involves first using the class constructor (e.g.,
-@link Unit::Unit() Unit() @endlink) to create an object instance, and
+@link Unit_create() Unit_create() @endlink) to create an object instance, and
then calling an <code>add<span
class="placeholder"><i>Object</i></span>(...)</code> method to add the
instance to another object. However, the <code>add<span
Modified: branches/libsbml-experimental/src/sbml/Compartment.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Compartment.h 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/src/sbml/Compartment.h 2014-01-24 09:19:52 UTC (rev 19562)
@@ -2496,8 +2496,10 @@
/**
- * @return item in this ListOfCompartment with the given @p id or a null pointer if no such
+ * @return item in the @p lo ListOfCompartments with the given @p sid or a null pointer if no such
* item exists.
+ *
+ * @memberof ListOfCompartments_t
*/
LIBSBML_EXTERN
Compartment_t *
@@ -2505,9 +2507,11 @@
/**
- * Removes item in this ListOf items with the given @p id or a null pointer if no such
+ * Removes item in the @p lo ListOfCompartments with the given @p sid or a null pointer if no such
* item exists. The caller owns the returned item and is responsible for
* deleting it.
+ *
+ * @memberof ListOfCompartments_t
*/
LIBSBML_EXTERN
Compartment_t *
Modified: branches/libsbml-experimental/src/sbml/Event.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Event.h 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/src/sbml/Event.h 2014-01-24 09:19:52 UTC (rev 19562)
@@ -2168,7 +2168,7 @@
* @return item in this ListOfEvent with the given @p id or @c NULL if no such
* item exists.
*
- * @memberof Event_t
+ * @memberof ListOfEvents_t
*/
LIBSBML_EXTERN
Event_t *
@@ -2180,7 +2180,7 @@
* item exists. The caller owns the returned item and is responsible for
* deleting it.
*
- * @memberof Event_t
+ * @memberof ListOfEvents_t
*/
LIBSBML_EXTERN
Event_t *
Modified: branches/libsbml-experimental/src/sbml/SBMLDocument.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/SBMLDocument.cpp 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/src/sbml/SBMLDocument.cpp 2014-01-24 09:19:52 UTC (rev 19562)
@@ -1850,14 +1850,6 @@
-/**
- * Creates a new, empty SBMLDocument_t structure.
- *
- * The SBML Level and Version attributes default to the most recent SBML
- * specification (at the time this libSBML was released).
- *
- * @return the SBMLDocument_t structure created
- */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_create ()
@@ -1874,19 +1866,6 @@
}
-/**
- * Creates a new, empty SBMLDocument_t structure with given values for the
- * SBML Level and Version.
- *
- * If not specified, the SBML Level and Version attributes default to the
- * most recent SBML specification (at the time this libSBML was
- * released).
- *
- * @param level an integer for the SBML Level
- * @param version an integer for the Version within the SBML Level
- *
- * @return the SBMLDocument_t structure created
- */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_createWithLevelAndVersion (unsigned int level, unsigned int version)
@@ -1919,11 +1898,6 @@
}
-/**
- * Frees the given SBMLDocument_t structure.
- *
- * @param d the SBMLDocument_t structure
- */
LIBSBML_EXTERN
void
SBMLDocument_free (SBMLDocument_t *d)
@@ -1934,13 +1908,6 @@
}
-/**
- * Creates and returns a deep copy of the given SBMLDocument_t structure
- *
- * @param d the SBMLDocument_t structure
- *
- * @return a (deep) copy of the SBMLDocument_t structure
- */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_clone (const SBMLDocument_t *d)
@@ -1949,13 +1916,6 @@
}
-/**
- * Returns the SBML Level of the given SBMLDocument_t structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the SBML Level number
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getLevel (const SBMLDocument_t *d)
@@ -1964,14 +1924,6 @@
}
-/**
- * Returns the Version within the SBML Level of the given SBMLDocument_t
- * structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the version number
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getVersion (const SBMLDocument_t *d)
@@ -1980,13 +1932,6 @@
}
-/**
- * Returns the Model object stored in this SBMLDocument_t structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the Model contained in this SBMLDocument_t structure.
- */
LIBSBML_EXTERN
Model_t *
SBMLDocument_getModel (SBMLDocument_t *d)
@@ -1995,28 +1940,6 @@
}
-/**
- * Removes any FunctionDefinitions from the document and expands
- * any instances of their use within >math< elements.
- *
- * For example a Model contains a FunctionDefinition with id f
- * representing the math expression: f(x, y) = x * y.
- * The math element of the KineticLaw uses f(s, p).
- * The outcome of the function is that the math of the KineticLaw
- * now represents the math expression: s * p and the model no longer
- * contains any FunctionDefinitions.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return true (non-zero) if the transformation was successful,
- * false (0) otherwise.
- *
- * @note This function will check the consistency of a model
- * before attemptimg the transformation. In the case of a model
- * with invalid SBML the transformation will not be done and the
- * function will return @c false.
- *
- */
LIBSBML_EXTERN
int
SBMLDocument_expandFunctionDefintions (SBMLDocument_t *d)
@@ -2026,33 +1949,6 @@
}
-/**
- * Removes any InitialAssignments from the document and replaces
- * the appropriate values.
- *
- * For example a Model contains a InitialAssignment with symbol k
- * where k is the id of a Parameter.
- * The outcome of the function is that the value attribute of
- * the Parameter is the value calculated using the math expression
- * of the InitialAssignment and the corresponding InitialAssignment
- * has been removed from the Model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return true (non-zero) if the transformation was successful,
- * false (0) otherwise.
- *
- *
- * @note This function will check the consistency of a model
- * before attemptimg the transformation. In the case of a model
- * with invalid SBML the transformation will not be done and the
- * function will return @c false. As part of the process the
- * function will check that it has values for any components
- * referred to by the math elements of InitialAssignments. In
- * the case where not all values have been declared the particular
- * InitialAssignment will not be removed and the function will
- * return @c false.
- */
LIBSBML_EXTERN
int
SBMLDocument_expandInitialAssignments (SBMLDocument_t *d)
@@ -2062,46 +1958,6 @@
}
-/**
- * Sets the SBML Level and Version of this SBMLDocument, attempting to
- * convert the model as needed.
- *
- * This method is used to convert models between Levels and Versions of
- * SBML. Generally, models can be converted upward without difficulty
- * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
- * Level 2 to the latest version of Level 2). Sometimes models can be
- * translated downward as well, if they do not use constructs specific to
- * more advanced Levels of SBML.
- *
- * Callers can also check compatibility directly using the methods
- * checkL1Compatibility(), checkL2v1Compatibility(), and
- * checkL2v2Compatibility().
- *
- * The valid combinations as of this release of libSBML are the
- * following:
- *
- * @li Level 1 Version 1
- * @li Level 1 Version 2
- * @li Level 2 Version 1
- * @li Level 2 Version 2
- * @li Level 2 Version 3
- * @li Level 2 Version 4
- *
- * @param d the SBMLDocument_t structure
- *
- * @param level the desired SBML Level
- *
- * @param version the desired Version within the SBML Level
- *
- * @note Calling this method will not @em necessarily lead to successful
- * conversion. If the conversion fails, it will be logged in the error
- * list associated with this SBMLDocument_t structure. Callers should
- * consult getNumErrors() to find out if the conversion succeeded without
- * problems. For conversions from Level 2 to Level 1, callers can also
- * check the Level of the model after calling this method to find out
- * whether it is Level 1. (If the conversion to Level 1 failed, the Level
- * of this model will be left unchanged.)
- */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersion ( SBMLDocument_t *d
@@ -2113,57 +1969,6 @@
}
-/**
- * Sets the SBML Level and Version of this SBMLDocument, attempting to
- * convert the model as needed.
- *
- * This method is used to convert models between Levels and Versions of
- * SBML. Generally, models can be converted upward without difficulty
- * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
- * Level 2 to the latest version of Level 2). Sometimes models can be
- * translated downward as well, if they do not use constructs specific to
- * more advanced Levels of SBML.
- *
- * Callers can also check compatibility directly using the methods
- * checkL1Compatibility(), checkL2v1Compatibility(), and
- * checkL2v2Compatibility().
- *
- * The valid combinations as of this release of libSBML are the
- * following:
- *
- * @li Level 1 Version 1
- * @li Level 1 Version 2
- * @li Level 2 Version 1
- * @li Level 2 Version 2
- * @li Level 2 Version 3
- * @li Level 2 Version 4
- *
- * @param d the SBMLDocument_t structure
- *
- * @param level the desired SBML Level
- *
- * @param version the desired Version within the SBML Level
- *
- * @note Calling this method will not @em necessarily lead to successful
- * conversion. If the conversion fails, it will be logged in the error
- * list associated with this SBMLDocument_t structure. Callers should
- * consult getNumErrors() to find out if the conversion succeeded without
- * problems. For conversions from Level 2 to Level 1, callers can also
- * check the Level of the model after calling this method to find out
- * whether it is Level 1. (If the conversion to Level 1 failed, the Level
- * of this model will be left unchanged.)
- *
- *
- * Strict conversion applies the additional criteria that both the source
- * and the target model must be consistent SBML. Users can control the
- * consistency checks that are applied using the
- * SBMLDocument::setConsistencyChecks function. If either the source
- * or the potential target model have validation errors, the conversion
- * is not performed. When a strict conversion is successful, the
- * underlying SBML object model is altered to reflect the new level
- * and version. Thus information that cannot be converted (e.g. sboTerms)
- * will be lost.
- */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionStrict ( SBMLDocument_t *d
@@ -2175,46 +1980,6 @@
}
-/**
- * Sets the SBML Level and Version of this SBMLDocument, attempting to
- * convert the model as needed.
- *
- * This method is used to convert models between Levels and Versions of
- * SBML. Generally, models can be converted upward without difficulty
- * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
- * Level 2 to the latest version of Level 2). Sometimes models can be
- * translated downward as well, if they do not use constructs specific to
- * more advanced Levels of SBML.
- *
- * Callers can also check compatibility directly using the methods
- * checkL1Compatibility(), checkL2v1Compatibility(), and
- * checkL2v2Compatibility().
- *
- * The valid combinations as of this release of libSBML are the
- * following:
- *
- * @li Level 1 Version 1
- * @li Level 1 Version 2
- * @li Level 2 Version 1
- * @li Level 2 Version 2
- * @li Level 2 Version 3
- * @li Level 2 Version 4
- *
- * @param d the SBMLDocument_t structure
- *
- * @param level the desired SBML Level
- *
- * @param version the desired Version within the SBML Level
- *
- * @note Calling this method will not @em necessarily lead to successful
- * conversion. If the conversion fails, it will be logged in the error
- * list associated with this SBMLDocument_t structure. Callers should
- * consult getNumErrors() to find out if the conversion succeeded without
- * problems. For conversions from Level 2 to Level 1, callers can also
- * check the Level of the model after calling this method to find out
- * whether it is Level 1. (If the conversion to Level 1 failed, the Level
- * of this model will be left unchanged.)
- */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionNonStrict ( SBMLDocument_t *d
@@ -2226,22 +1991,6 @@
}
-/**
- * Sets the model contained in the given SBMLDocument_t structure to a copy
- * of the given Model_t structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @param m the new Model_t structure to use.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif@~ The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_LEVEL_MISMATCH
- * @li LIBSBML_VERSION_MISMATCH
- */
LIBSBML_EXTERN
int
SBMLDocument_setModel (SBMLDocument_t *d, const Model_t *m)
@@ -2250,14 +1999,6 @@
}
-/**
- * Creates a new Model_t structure inside the given SBMLDocument_t
- * structure and returns a pointer to it.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the Model_t structure created
- */
LIBSBML_EXTERN
Model_t *
SBMLDocument_createModel (SBMLDocument_t *d)
@@ -2280,56 +2021,6 @@
}
-/**
- * Allows particular validators to be turned on or off prior to
- * calling checkConsistency.
- *
- * The second argument (@p category) to this method indicates which
- * category of consistency/error checks are being turned on or off, and
- * the second argument (a boolean) indicates whether to turn on (value of
- * @c true) or off (value of @c false) that particula category of checks.
- * The possible categories are represented as values of the enumeration
- * SBMLErrorCategory_t. The following are the possible choices in libSBML
- * version 3.0.2:
- *
- * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
- *
- * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
- * example of inconsistency would be using a species identifier in a
- * reaction rate formula without first having declared the species.
- *
- * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
- *
- * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
- *
- * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
- *
- * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
- * equations implied by a model is mathematically overdetermined.
- *
- * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
- * model construction.
- *
- * By default, all validation checks are applied to the model in an
- * SBMLDocument object @em unless setConsistencyChecks() is called to
- * indicate that only a subset should be applied.
- *
- * @param d the SBMLDocument_t structure
- *
- * @param category a value drawn from SBMLErrorCategory_t indicating the
- * consistency checking/validation to be turned on or off
- *
- * @param apply a boolean indicating whether the checks indicated by @p
- * category should be applied or not.
- *
- * @note The default (i.e., performing all checks) applies to each new
- * SBMLDocument object created. This means that each time a model is
- * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
- * the global functions readSBML() and readSBMLFromString(), a new
- * SBMLDocument is created and for that document all checks are enabled.
- *
- * @see SBMLDocument_checkConsistency()
- */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecks(SBMLDocument_t * d,
@@ -2341,56 +2032,6 @@
}
-/**
- * Allows particular validators to be turned on or off prior to
- * calling setLevelAndVersion.
- *
- * The second argument (@p category) to this method indicates which
- * category of consistency/error checks are being turned on or off, and
- * the second argument (a boolean) indicates whether to turn on (value of
- * @c true) or off (value of @c false) that particula category of checks.
- * The possible categories are represented as values of the enumeration
- * SBMLErrorCategory_t. The following are the possible choices in libSBML
- * version 3.0.2:
- *
- * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
- *
- * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
- * example of inconsistency would be using a species identifier in a
- * reaction rate formula without first having declared the species.
- *
- * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
- *
- * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
- *
- * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
- *
- * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
- * equations implied by a model is mathematically overdetermined.
- *
- * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
- * model construction.
- *
- * By default, all validation checks are applied to the model in an
- * SBMLDocument object @em unless setConsistencyChecks() is called to
- * indicate that only a subset should be applied.
- *
- * @param d the SBMLDocument_t structure
- *
- * @param category a value drawn from SBMLErrorCategory_t indicating the
- * consistency checking/validation to be turned on or off
- *
- * @param apply a boolean indicating whether the checks indicated by @p
- * category should be applied or not.
- *
- * @note The default (i.e., performing all checks) applies to each new
- * SBMLDocument object created. This means that each time a model is
- * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
- * the global functions readSBML() and readSBMLFromString(), a new
- * SBMLDocument is created and for that document all checks are enabled.
- *
- * @see SBMLDocument_setLevelAndVersionStrict()
- */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecksForConversion(SBMLDocument_t * d,
@@ -2402,20 +2043,6 @@
}
-/**
- * Performs a set of consistency and validation checks on the given SBML
- * document.
- *
- * If this method returns a nonzero value (meaning, one or more
- * consistency checks have failed for SBML document), the failures may be
- * due to warnings @em or errors. Callers should inspect the severity
- * flag in the individual SBMLError objects returned by getError() to
- * determine the nature of the failures.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkConsistency (SBMLDocument_t *d)
@@ -2424,18 +2051,6 @@
}
-/**
- * Performs consistency checking on libSBML's internal representation of
- * an SBML Model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- *
- * @note The consistency checks performed by this function are limited
- * to inconsistencies that are not caught by other consistency checks.
- * @see setConsistencyChecks()
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkInternalConsistency (SBMLDocument_t *d)
@@ -2444,18 +2059,6 @@
}
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 1 and can be converted to
- * Level 1.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL1Compatibility (SBMLDocument_t *d)
@@ -2464,18 +2067,6 @@
}
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 1 and can be
- * converted to Level 2 Version 1.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v1Compatibility (SBMLDocument_t *d)
@@ -2485,18 +2076,6 @@
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 2 and can be
- * converted to Level 2 Version 2.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v2Compatibility (SBMLDocument_t *d)
@@ -2506,18 +2085,6 @@
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 3 and can be
- * converted to Level 2 Version 3.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v3Compatibility (SBMLDocument_t *d)
@@ -2526,18 +2093,6 @@
}
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 4 and can be
- * converted to Level 2 Version 4.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v4Compatibility (SBMLDocument_t *d)
@@ -2546,27 +2101,6 @@
}
-/**
- * Returns the nth error or warning encountered during parsing,
- * consistency checking, or attempted translation of this model.
- *
- * Callers can use method XMLError_getSeverity() on the result to assess
- * the severity of the problem. The severity levels range from
- * informationl messages to fatal errors.
- *
- * @return the error or warning indexed by integer @p n, or return @c NULL
- * if n > (SBMLDocument_getNumErrors() - 1).
- *
- * @param d the SBMLDocument_t structure
- *
- * @param n the index of the error sought.
- *
- * @see SBMLDocument_getNumErrors(), SBMLDocument_setLevelAndVersion(),
- * SBMLDocument_checkConsistency(), SBMLDocument_checkL1Compatibility(),
- * SBMLDocument_checkL2v1Compatibility()
- * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
- * SBMLReader_readSBMLFromString().
- */
LIBSBML_EXTERN
const SBMLError_t *
SBMLDocument_getError (SBMLDocument_t *d, unsigned int n)
@@ -2575,20 +2109,6 @@
}
-/**
- * Returns the number of errors or warnings encountered during parsing,
- * consistency checking, or attempted translation of this model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of errors or warnings encountered
- *
- * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
- * SBMLDocument_checkL1Compatibility(),
- * SBMLDocument_checkL2v1Compatibility()
- * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
- * SBMLReader_readSBMLFromString().
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrors (const SBMLDocument_t *d)
@@ -2596,20 +2116,6 @@
return (d != NULL) ? d->getNumErrors() : SBML_INT_MAX;
}
-/**
- * Returns the number of errors or warnings encountered during parsing,
- * consistency checking, or attempted translation of this model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of errors or warnings encountered
- *
- * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
- * SBMLDocument_checkL1Compatibility(),
- * SBMLDocument_checkL2v1Compatibility()
- * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
- * SBMLReader_readSBMLFromString().
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrorsWithSeverity (const SBMLDocument_t *d, unsigned int severity)
@@ -2618,23 +2124,6 @@
}
-/**
- * Prints to the given output stream all the errors or warnings
- * encountered during parsing, consistency checking, or attempted
- * translation of this model.
- *
- * If no errors have occurred, i.e., SBMLDocument_getNumErrors() == 0, no
- * output will be sent to the stream.
- *
- * The format of the output is:
- *
- * N error(s):
- * line NNN: (id) message
- *
- * @param d the SBMLDocument_t structure
- *
- * @param stream the output stream where the messages should be printed
- */
LIBSBML_EXTERN
void
SBMLDocument_printErrors (SBMLDocument_t *d, FILE *stream)
@@ -2652,10 +2141,6 @@
}
-/**
- * @return the most recent SBML specification level (at the time this
- * libSBML was released).
- */
unsigned int
SBMLDocument_getDefaultLevel ()
{
@@ -2663,24 +2148,12 @@
}
-/**
- * @return the most recent SBML specification version (at the time this
- * libSBML was released).
- */
unsigned int
SBMLDocument_getDefaultVersion ()
{
return SBMLDocument::getDefaultVersion();
}
-/**
- * Returns a list of XMLNamespaces_t associated with the XML content
- * of this SBML document.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return pointer to the XMLNamespaces_t structure associated with this SBML object
- */
LIBSBML_EXTERN
const XMLNamespaces_t *
SBMLDocument_getNamespaces(SBMLDocument_t *d)
@@ -2740,22 +2213,6 @@
return (d != NULL) ? static_cast<int>(d->isSetPackageRequired(package)) : 0;
}
-/**
- * Converts this document using the converter that best matches
- * the given conversion properties.
- *
- * @param d the SBMLDocument_t structure
- * @param props the conversion properties to use
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif@~ The possible values
- * returned by this function are:
- * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
- * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
- * @li @link OperationReturnValues_t#LIBSBML_CONV_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
- * @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
- */
LIBSBML_EXTERN
int
SBMLDocument_convert(SBMLDocument_t *d, const ConversionProperties_t* props)
Modified: branches/libsbml-experimental/src/sbml/SBMLDocument.h
===================================================================
--- branches/libsbml-experimental/src/sbml/SBMLDocument.h 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/src/sbml/SBMLDocument.h 2014-01-24 09:19:52 UTC (rev 19562)
@@ -1630,16 +1630,36 @@
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
-/* ----------------------------------------------------------------------------
- * See the .cpp file for the documentation of the following functions.
- * --------------------------------------------------------------------------*/
-
-
+/**
+ * Creates a new, empty SBMLDocument_t structure.
+ *
+ * The SBML Level and Version attributes default to the most recent SBML
+ * specification (at the time this libSBML was released).
+ *
+ * @return the SBMLDocument_t structure created
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_create (void);
+/**
+ * Creates a new, empty SBMLDocument_t structure with given values for the
+ * SBML Level and Version.
+ *
+ * If not specified, the SBML Level and Version attributes default to the
+ * most recent SBML specification (at the time this libSBML was
+ * released).
+ *
+ * @param level an integer for the SBML Level
+ * @param version an integer for the Version within the SBML Level
+ *
+ * @return the SBMLDocument_t structure created
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_createWithLevelAndVersion (unsigned int level, unsigned int version);
@@ -1650,41 +1670,180 @@
SBMLDocument_createWithSBMLNamespaces (SBMLNamespaces_t *sbmlns);
+/**
+ * Frees the given SBMLDocument_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_free (SBMLDocument_t *d);
+/**
+ * Creates and returns a deep copy of the given SBMLDocument_t structure
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return a (deep) copy of the SBMLDocument_t structure
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_clone (const SBMLDocument_t *d);
+/**
+ * Returns the SBML Level of the given SBMLDocument_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the SBML Level number
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getLevel (const SBMLDocument_t *d);
+/**
+ * Returns the Version within the SBML Level of the given SBMLDocument_t
+ * structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the version number
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getVersion (const SBMLDocument_t *d);
+/**
+ * Returns the Model object stored in this SBMLDocument_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the Model contained in this SBMLDocument_t structure.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
Model_t *
SBMLDocument_getModel (SBMLDocument_t *d);
+/**
+ * Removes any FunctionDefinitions from the document and expands
+ * any instances of their use within >math< elements.
+ *
+ * For example a Model contains a FunctionDefinition with id f
+ * representing the math expression: f(x, y) = x * y.
+ * The math element of the KineticLaw uses f(s, p).
+ * The outcome of the function is that the math of the KineticLaw
+ * now represents the math expression: s * p and the model no longer
+ * contains any FunctionDefinitions.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return true (non-zero) if the transformation was successful,
+ * false (0) otherwise.
+ *
+ * @note This function will check the consistency of a model
+ * before attemptimg the transformation. In the case of a model
+ * with invalid SBML the transformation will not be done and the
+ * function will return @c false.
+ *
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_expandFunctionDefintions (SBMLDocument_t *d);
+/**
+ * Removes any InitialAssignments from the document and replaces
+ * the appropriate values.
+ *
+ * For example a Model contains a InitialAssignment with symbol k
+ * where k is the id of a Parameter.
+ * The outcome of the function is that the value attribute of
+ * the Parameter is the value calculated using the math expression
+ * of the InitialAssignment and the corresponding InitialAssignment
+ * has been removed from the Model.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return true (non-zero) if the transformation was successful,
+ * false (0) otherwise.
+ *
+ *
+ * @note This function will check the consistency of a model
+ * before attemptimg the transformation. In the case of a model
+ * with invalid SBML the transformation will not be done and the
+ * function will return @c false. As part of the process the
+ * function will check that it has values for any components
+ * referred to by the math elements of InitialAssignments. In
+ * the case where not all values have been declared the particular
+ * InitialAssignment will not be removed and the function will
+ * return @c false.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_expandInitialAssignments (SBMLDocument_t *d);
+/**
+ * Sets the SBML Level and Version of this SBMLDocument, attempting to
+ * convert the model as needed.
+ *
+ * This method is used to convert models between Levels and Versions of
+ * SBML. Generally, models can be converted upward without difficulty
+ * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
+ * Level 2 to the latest version of Level 2). Sometimes models can be
+ * translated downward as well, if they do not use constructs specific to
+ * more advanced Levels of SBML.
+ *
+ * Callers can also check compatibility directly using the methods
+ * checkL1Compatibility(), checkL2v1Compatibility(), and
+ * checkL2v2Compatibility().
+ *
+ * The valid combinations as of this release of libSBML are the
+ * following:
+ *
+ * @li Level 1 Version 1
+ * @li Level 1 Version 2
+ * @li Level 2 Version 1
+ * @li Level 2 Version 2
+ * @li Level 2 Version 3
+ * @li Level 2 Version 4
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param level the desired SBML Level
+ *
+ * @param version the desired Version within the SBML Level
+ *
+ * @note Calling this method will not @em necessarily lead to successful
+ * conversion. If the conversion fails, it will be logged in the error
+ * list associated with this SBMLDocument_t structure. Callers should
+ * consult getNumErrors() to find out if the conversion succeeded without
+ * problems. For conversions from Level 2 to Level 1, callers can also
+ * check the Level of the model after calling this method to find out
+ * whether it is Level 1. (If the conversion to Level 1 failed, the Level
+ * of this model will be left unchanged.)
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersion ( SBMLDocument_t *d
@@ -1692,6 +1851,59 @@
, unsigned int version );
+/**
+ * Sets the SBML Level and Version of this SBMLDocument, attempting to
+ * convert the model as needed.
+ *
+ * This method is used to convert models between Levels and Versions of
+ * SBML. Generally, models can be converted upward without difficulty
+ * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
+ * Level 2 to the latest version of Level 2). Sometimes models can be
+ * translated downward as well, if they do not use constructs specific to
+ * more advanced Levels of SBML.
+ *
+ * Callers can also check compatibility directly using the methods
+ * checkL1Compatibility(), checkL2v1Compatibility(), and
+ * checkL2v2Compatibility().
+ *
+ * The valid combinations as of this release of libSBML are the
+ * following:
+ *
+ * @li Level 1 Version 1
+ * @li Level 1 Version 2
+ * @li Level 2 Version 1
+ * @li Level 2 Version 2
+ * @li Level 2 Version 3
+ * @li Level 2 Version 4
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param level the desired SBML Level
+ *
+ * @param version the desired Version within the SBML Level
+ *
+ * @note Calling this method will not @em necessarily lead to successful
+ * conversion. If the conversion fails, it will be logged in the error
+ * list associated with this SBMLDocument_t structure. Callers should
+ * consult getNumErrors() to find out if the conversion succeeded without
+ * problems. For conversions from Level 2 to Level 1, callers can also
+ * check the Level of the model after calling this method to find out
+ * whether it is Level 1. (If the conversion to Level 1 failed, the Level
+ * of this model will be left unchanged.)
+ *
+ *
+ * Strict conversion applies the additional criteria that both the source
+ * and the target model must be consistent SBML. Users can control the
+ * consistency checks that are applied using the
+ * SBMLDocument::setConsistencyChecks function. If either the source
+ * or the potential target model have validation errors, the conversion
+ * is not performed. When a strict conversion is successful, the
+ * underlying SBML object model is altered to reflect the new level
+ * and version. Thus information that cannot be converted (e.g. sboTerms)
+ * will be lost.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionStrict ( SBMLDocument_t *d
@@ -1699,6 +1911,48 @@
, unsigned int version );
+/**
+ * Sets the SBML Level and Version of this SBMLDocument, attempting to
+ * convert the model as needed.
+ *
+ * This method is used to convert models between Levels and Versions of
+ * SBML. Generally, models can be converted upward without difficulty
+ * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
+ * Level 2 to the latest version of Level 2). Sometimes models can be
+ * translated downward as well, if they do not use constructs specific to
+ * more advanced Levels of SBML.
+ *
+ * Callers can also check compatibility directly using the methods
+ * checkL1Compatibility(), checkL2v1Compatibility(), and
+ * checkL2v2Compatibility().
+ *
+ * The valid combinations as of this release of libSBML are the
+ * following:
+ *
+ * @li Level 1 Version 1
+ * @li Level 1 Version 2
+ * @li Level 2 Version 1
+ * @li Level 2 Version 2
+ * @li Level 2 Version 3
+ * @li Level 2 Version 4
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param level the desired SBML Level
+ *
+ * @param version the desired Version within the SBML Level
+ *
+ * @note Calling this method will not @em necessarily lead to successful
+ * conversion. If the conversion fails, it will be logged in the error
+ * list associated with this SBMLDocument_t structure. Callers should
+ * consult getNumErrors() to find out if the conversion succeeded without
+ * problems. For conversions from Level 2 to Level 1, callers can also
+ * check the Level of the model after calling this method to find out
+ * whether it is Level 1. (If the conversion to Level 1 failed, the Level
+ * of this model will be left unchanged.)
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionNonStrict ( SBMLDocument_t *d
@@ -1706,11 +1960,39 @@
, unsigned int version );
+/**
+ * Sets the model contained in the given SBMLDocument_t structure to a copy
+ * of the given Model_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param m the new Model_t structure to use.
+ *
+ * @return integer value indicating success/failure of the
+ * function. @if clike The value is drawn from the
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
+ * returned by this function are:
+ * @li LIBSBML_OPERATION_SUCCESS
+ * @li LIBSBML_LEVEL_MISMATCH
+ * @li LIBSBML_VERSION_MISMATCH
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setModel (SBMLDocument_t *d, const Model_t *m);
+/**
+ * Creates a new Model_t structure inside the given SBMLDocument_t
+ * structure and returns a pointer to it.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the Model_t structure created
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
Model_t *
SBMLDocument_createModel (SBMLDocument_t *d);
@@ -1723,18 +2005,138 @@
char*
SBMLDocument_getLocationURI(SBMLDocument_t *d);
+/**
+ * Allows particular validators to be turned on or off prior to
+ * calling checkConsistency.
+ *
+ * The second argument (@p category) to this method indicates which
+ * category of consistency/error checks are being turned on or off, and
+ * the second argument (a boolean) indicates whether to turn on (value of
+ * @c true) or off (value of @c false) that particula category of checks.
+ * The possible categories are represented as values of the enumeration
+ * SBMLErrorCategory_t. The following are the possible choices in libSBML
+ * version 3.0.2:
+ *
+ * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
+ *
+ * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
+ * example of inconsistency would be using a species identifier in a
+ * reaction rate formula without first having declared the species.
+ *
+ * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
+ *
+ * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
+ *
+ * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
+ *
+ * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
+ * equations implied by a model is mathematically overdetermined.
+ *
+ * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
+ * model construction.
+ *
+ * By default, all validation checks are applied to the model in an
+ * SBMLDocument object @em unless setConsistencyChecks() is called to
+ * indicate that only a subset should be applied.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param category a value drawn from SBMLErrorCategory_t indicating the
+ * consistency checking/validation to be turned on or off
+ *
+ * @param apply a boolean indicating whether the checks indicated by @p
+ * category should be applied or not.
+ *
+ * @note The default (i.e., performing all checks) applies to each new
+ * SBMLDocument object created. This means that each time a model is
+ * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
+ * the global functions readSBML() and readSBMLFromString(), a new
+ * SBMLDocument is created and for that document all checks are enabled.
+ *
+ * @see SBMLDocument_checkConsistency()
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecks(SBMLDocument_t *d,
- int validator,
- int apply);
+ SBMLErrorCategory_t category,
+ int apply);
+/**
+ * Allows particular validators to be turned on or off prior to
+ * calling setLevelAndVersion.
+ *
+ * The second argument (@p category) to this method indicates which
+ * category of consistency/error checks are being turned on or off, and
+ * the second argument (a boolean) indicates whether to turn on (value of
+ * @c true) or off (value of @c false) that particula category of checks.
+ * The possible categories are represented as values of the enumeration
+ * SBMLErrorCategory_t. The following are the possible choices in libSBML
+ * version 3.0.2:
+ *
+ * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
+ *
+ * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
+ * example of inconsistency would be using a species identifier in a
+ * reaction rate formula without first having declared the species.
+ *
+ * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
+ *
+ * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
+ *
+ * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
+ *
+ * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
+ * equations implied by a model is mathematically overdetermined.
+ *
+ * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
+ * model construction.
+ *
+ * By default, all validation checks are applied to the model in an
+ * SBMLDocument object @em unless setConsistencyChecks() is called to
+ * indicate that only a subset should be applied.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param category a value drawn from SBMLErrorCategory_t indicating the
+ * consistency checking/validation to be turned on or off
+ *
+ * @param apply a boolean indicating whether the checks indicated by @p
+ * category should be applied or not.
+ *
+ * @note The default (i.e., performing all checks) applies to each new
+ * SBMLDocument object created. This means that each time a model is
+ * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
+ * the global functions readSBML() and readSBMLFromString(), a new
+ * SBMLDocument is created and for that document all checks are enabled.
+ *
+ * @see SBMLDocument_setLevelAndVersionStrict()
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecksForConversion(SBMLDocument_t *d,
int validator,
int apply);
+/**
+ * Performs a set of consistency and validation checks on the given SBML
+ * document.
+ *
+ * If this method returns a nonzero value (meaning, one or more
+ * consistency checks have failed for SBML document), the failures may be
+ * due to warnings @em or errors. Callers should inspect the severity
+ * flag in the individual SBMLError objects returned by getError() to
+ * determine the nature of the failures.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkConsistency (SBMLDocument_t *d);
@@ -1745,64 +2147,246 @@
SBMLDocument_validateSBML (SBMLDocument_t *d);
+/**
+ * Performs consistency checking on libSBML's internal representation of
+ * an SBML Model.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @note The consistency checks performed by this function are limited
+ * to inconsistencies that are not caught by other consistency checks.
+ * @see setConsistencyChecks()
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkInternalConsistency (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 1 and can be converted to
+ * Level 1.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL1Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 1 and can be
+ * converted to Level 2 Version 1.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v1Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 2 and can be
+ * converted to Level 2 Version 2.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v2Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 3 and can be
+ * converted to Level 2 Version 3.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v3Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 4 and can be
+ * converted to Level 2 Version 4.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v4Compatibility (SBMLDocument_t *d);
+/**
+ * Returns the nth error or warning encountered during parsing,
+ * consistency checking, or attempted translation of this model.
+ *
+ * Callers can use method XMLError_getSeverity() on the result to assess
+ * the severity of the problem. The severity levels range from
+ * informationl messages to fatal errors.
+ *
+ * @return the error or warning indexed by integer @p n, or return @c NULL
+ * if n > (SBMLDocument_getNumErrors() - 1).
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param n the index of the error sought.
+ *
+ * @see SBMLDocument_getNumErrors(), SBMLDocument_setLevelAndVersion(),
+ * SBMLDocument_checkConsistency(), SBMLDocument_checkL1Compatibility(),
+ * SBMLDocument_checkL2v1Compatibility()
+ * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
+ * SBMLReader_readSBMLFromString().
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
const SBMLError_t *
SBMLDocument_getError (SBMLDocument_t *d, unsigned int n);
+/**
+ * Returns the number of errors or warnings encountered during parsing,
+ * consistency checking, or attempted translation of this model.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of errors or warnings encountered
+ *
+ * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
+ * SBMLDocument_checkL1Compatibility(),
+ * SBMLDocument_checkL2v1Compatibility()
+ * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
+ * SBMLReader_readSBMLFromString().
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrors (const SBMLDocument_t *d);
+/**
+ * Returns the number of errors or warnings encountered during parsing,
+ * consistency checking, or attempted translation of this model.
+ *
+ * @param d the SBMLDocument_t structure
+ * @param severity the severity requested
+ *
+ * @return the number of errors or warnings encountered with the given severity
+ * level
+ *
+ * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
+ * SBMLDocument_checkL1Compatibility(),
+ * SBMLDocument_checkL2v1Compatibility()
+ * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
+ * SBMLReader_readSBMLFromString().
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrorsWithSeverity (const SBMLDocument_t *d, unsigned int severity);
+/**
+ * Prints to the given output stream all the errors or warnings
+ * encountered during parsing, consistency checking, or attempted
+ * translation of this model.
+ *
+ * If no errors have occurred, i.e., SBMLDocument_getNumErrors() == 0, no
+ * output will be sent to the stream.
+ *
+ * The format of the output is:
+ *
+ * N error(s):
+ * line NNN: (id) message
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param stream the output stream where the messages should be printed
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_printErrors (SBMLDocument_t *d, FILE *stream);
+/**
+ * @return the most recent SBML specification level (at the time this
+ * libSBML was released).
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getDefaultLevel ();
+/**
+ * @return the most recent SBML specification version (at the time this
+ * libSBML was released).
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getDefaultVersion ();
+/**
+ * Returns a list of XMLNamespaces_t associated with the XML content
+ * of this SBML document.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return pointer to the XMLNamespaces_t structure associated with this SBML object
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
const XMLNamespaces_t *
SBMLDocument_getNamespaces(SBMLDocument_t *d);
@@ -1839,6 +2423,24 @@
int
SBMLDocument_isSetPackageRequired (SBMLDocument_t *d, const char * package);
+/**
+ * Converts this document using the converter that best matches
+ * the given conversion properties.
+ *
+ * @param d the SBMLDocument_t structure
+ * @param props the conversion properties to use
+ *
+ * @return integer value indicating success/failure of the
+ * function. @if clike The value is drawn from the
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
+ * returned by this function are:
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_CONV_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_convert(SBMLDocument_t *d, const ConversionProperties_t* props);
Modified: branches/libsbml-experimental/src/sbml/SBMLReader.h
===================================================================
--- branches/libsbml-experimental/src/sbml/SBMLReader.h 2014-01-24 08:44:43 UTC (rev 19561)
+++ branches/libsbml-experimental/src/sbml/SBMLReader.h 2014-01-24 09:19:52 UTC (rev 19562)
@@ -466,6 +466,8 @@
/**
* Creates a new SBMLReader and returns it. By default XML Schema
* validation is off.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLReader_t *
@@ -473,6 +475,8 @@
/**
* Frees the given SBMLReader.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
void
@@ -508,6 +512,8 @@
* @return a pointer to the SBMLDocument read.
*
* @copydetails doc_note_sbmlreader_error_handling
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLDocument_t *
@@ -531,6 +537,8 @@
* checking code.
*
* @return a pointer to the SBMLDocument read.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLDocument_t *
@@ -539,9 +547,11 @@
/**
* Predicate returning @c non-zero or @c zero depending on whether
- * underlying libSBML is linked with..
+ * underlying libSBML is linked with zlib or not.
*
* @return @c non-zero if libSBML is linked with zlib, @c zero otherwise.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
int
@@ -553,12 +563,16 @@
* libSBML is linked with bzip2.
*
* @return @c non-zero if libSBML is linked with bzip2, @c zero otherwise.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
int
SBMLReader_hasBzip2 ();
-#endif /* !SWIG */
+#endif /* !SWIG *
+ * @memberof SBMLReader_t
+ */
/**
@@ -571,6 +585,8 @@
* S...
[truncated message content] |
|
From: <sar...@us...> - 2014-01-24 08:44:46
|
Revision: 19561
http://sourceforge.net/p/sbml/code/19561
Author: sarahkeating
Date: 2014-01-24 08:44:43 +0000 (Fri, 24 Jan 2014)
Log Message:
-----------
updating NEWS
Modified Paths:
--------------
trunk/libsbml/NEWS.txt
Modified: trunk/libsbml/NEWS.txt
===================================================================
--- trunk/libsbml/NEWS.txt 2014-01-23 21:04:01 UTC (rev 19560)
+++ trunk/libsbml/NEWS.txt 2014-01-24 08:44:43 UTC (rev 19561)
@@ -37,6 +37,16 @@
- A new version of the SBMLTransforms::evaluateASTNode function
is available; allowing the user to pass a map of ids and values
to the function rather than needing a whole model.
+
+ - Two new functions are available to allow users to determine
+ the compiled dependencies for the given instance of libSBML.
+ int isLibSBMLCompiledWith(const char* option) will take the name
+ of a dependency library e.g. 'expat' as argument and return a
+ positive integer this library was used to compile libSBML, 0
+ otherwise.
+ const char* getLibSBMLDependencyVersionOf(const char* option)
+ takes the name of the library and returns the version number
+ of this library.
* Bug fixes
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2014-01-23 21:04:05
|
Revision: 19560
http://sourceforge.net/p/sbml/code/19560
Author: luciansmith
Date: 2014-01-23 21:04:01 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
Further updates for the docs, moving things from .cpp files to .h files, focusing on those files that were generating warnings in the C documentation generation.
(Note: the libsbml-example-c.txt file is not yet actually C code, but now at least links to C functions.)
Modified Paths:
--------------
trunk/libsbml/docs/src/libsbml-example-c.txt
trunk/libsbml/src/sbml/Compartment.h
trunk/libsbml/src/sbml/Event.h
trunk/libsbml/src/sbml/SBMLDocument.cpp
trunk/libsbml/src/sbml/SBMLDocument.h
trunk/libsbml/src/sbml/SBMLReader.h
trunk/libsbml/src/sbml/SBase.cpp
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/xml/XMLAttributes.cpp
trunk/libsbml/src/sbml/xml/XMLAttributes.h
trunk/libsbml/src/sbml/xml/XMLToken.cpp
trunk/libsbml/src/sbml/xml/XMLToken.h
Modified: trunk/libsbml/docs/src/libsbml-example-c.txt
===================================================================
--- trunk/libsbml/docs/src/libsbml-example-c.txt 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/docs/src/libsbml-example-c.txt 2014-01-23 21:04:01 UTC (rev 19560)
@@ -158,9 +158,9 @@
@subsection creator Function for creating the model
-We begin this function by creating an @link SBMLDocument SBMLDocument
-@endlink object, creating a @link Model Model @endlink object within
-the document object, and setting the @link Model Model @endlink
+We begin this function by creating an @link SBMLDocument_t SBMLDocument_t
+@endlink object, creating a @link Model_t Model_t @endlink object within
+the document object, and setting the @link Model_t Model_t @endlink
object's identifier.
@verbatim
@@ -185,8 +185,8 @@
the quantities used in the model. The libSBML API for unit
definitions mirrors the SBML object model, which means there is an
object class for UnitDefinition and an object class for the Unit
-objects that can be placed inside a @link UnitDefinition
-UnitDefinition @endlink object to compose whatever unit is desired.
+objects that can be placed inside a @link UnitDefinition_t
+UnitDefinition_t @endlink object to compose whatever unit is desired.
The resulting code for creating units is a little bit tedious because
there is a lot to set up, but on the other hand, it is quite
straightforward and hopefully easy to follow:
@@ -236,11 +236,11 @@
Before going on, we digress to explain one libSBML API idiom
illustrated in the code above and in the rest of the program below.
LibSBML provides two main mechanisms for creating objects: class
-constructors (e.g., @link Unit::Unit() Unit() @endlink), and
+constructors (e.g., @link Unit_create() Unit_create() @endlink), and
<code>create<span class="placeholder"><i>Object</i></span>()</code>
-methods provided by certain object classes such as @link Model Model
+methods provided by certain object classes such as @link Model_t Model_t
@endlink, where <span class="placeholder"><i>Object</i></span> is
-another object class such as @link UnitDefinition UnitDefinition
+another object class such as @link UnitDefinition_t UnitDefinition_t
@endlink. The multiple mechanisms are provided by libSBML for
flexibility and to support different use-cases, but they also have
different implications for the overall model structure.
@@ -251,7 +251,7 @@
instance and immediately link it into the parent, as well as return a
pointer to the object created. By contrast, the other main way of
creating an object involves first using the class constructor (e.g.,
-@link Unit::Unit() Unit() @endlink) to create an object instance, and
+@link Unit_create() Unit_create() @endlink) to create an object instance, and
then calling an <code>add<span
class="placeholder"><i>Object</i></span>(...)</code> method to add the
instance to another object. However, the <code>add<span
Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/src/sbml/Compartment.h 2014-01-23 21:04:01 UTC (rev 19560)
@@ -2496,8 +2496,10 @@
/**
- * @return item in this ListOfCompartment with the given @p id or a null pointer if no such
+ * @return item in the @p lo ListOfCompartments with the given @p sid or a null pointer if no such
* item exists.
+ *
+ * @memberof ListOfCompartments_t
*/
LIBSBML_EXTERN
Compartment_t *
@@ -2505,9 +2507,11 @@
/**
- * Removes item in this ListOf items with the given @p id or a null pointer if no such
+ * Removes item in the @p lo ListOfCompartments with the given @p sid or a null pointer if no such
* item exists. The caller owns the returned item and is responsible for
* deleting it.
+ *
+ * @memberof ListOfCompartments_t
*/
LIBSBML_EXTERN
Compartment_t *
Modified: trunk/libsbml/src/sbml/Event.h
===================================================================
--- trunk/libsbml/src/sbml/Event.h 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/src/sbml/Event.h 2014-01-23 21:04:01 UTC (rev 19560)
@@ -2168,7 +2168,7 @@
* @return item in this ListOfEvent with the given @p id or @c NULL if no such
* item exists.
*
- * @memberof Event_t
+ * @memberof ListOfEvents_t
*/
LIBSBML_EXTERN
Event_t *
@@ -2180,7 +2180,7 @@
* item exists. The caller owns the returned item and is responsible for
* deleting it.
*
- * @memberof Event_t
+ * @memberof ListOfEvents_t
*/
LIBSBML_EXTERN
Event_t *
Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp 2014-01-23 21:04:01 UTC (rev 19560)
@@ -1850,14 +1850,6 @@
-/**
- * Creates a new, empty SBMLDocument_t structure.
- *
- * The SBML Level and Version attributes default to the most recent SBML
- * specification (at the time this libSBML was released).
- *
- * @return the SBMLDocument_t structure created
- */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_create ()
@@ -1874,19 +1866,6 @@
}
-/**
- * Creates a new, empty SBMLDocument_t structure with given values for the
- * SBML Level and Version.
- *
- * If not specified, the SBML Level and Version attributes default to the
- * most recent SBML specification (at the time this libSBML was
- * released).
- *
- * @param level an integer for the SBML Level
- * @param version an integer for the Version within the SBML Level
- *
- * @return the SBMLDocument_t structure created
- */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_createWithLevelAndVersion (unsigned int level, unsigned int version)
@@ -1919,11 +1898,6 @@
}
-/**
- * Frees the given SBMLDocument_t structure.
- *
- * @param d the SBMLDocument_t structure
- */
LIBSBML_EXTERN
void
SBMLDocument_free (SBMLDocument_t *d)
@@ -1934,13 +1908,6 @@
}
-/**
- * Creates and returns a deep copy of the given SBMLDocument_t structure
- *
- * @param d the SBMLDocument_t structure
- *
- * @return a (deep) copy of the SBMLDocument_t structure
- */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_clone (const SBMLDocument_t *d)
@@ -1949,13 +1916,6 @@
}
-/**
- * Returns the SBML Level of the given SBMLDocument_t structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the SBML Level number
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getLevel (const SBMLDocument_t *d)
@@ -1964,14 +1924,6 @@
}
-/**
- * Returns the Version within the SBML Level of the given SBMLDocument_t
- * structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the version number
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getVersion (const SBMLDocument_t *d)
@@ -1980,13 +1932,6 @@
}
-/**
- * Returns the Model object stored in this SBMLDocument_t structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the Model contained in this SBMLDocument_t structure.
- */
LIBSBML_EXTERN
Model_t *
SBMLDocument_getModel (SBMLDocument_t *d)
@@ -1995,28 +1940,6 @@
}
-/**
- * Removes any FunctionDefinitions from the document and expands
- * any instances of their use within >math< elements.
- *
- * For example a Model contains a FunctionDefinition with id f
- * representing the math expression: f(x, y) = x * y.
- * The math element of the KineticLaw uses f(s, p).
- * The outcome of the function is that the math of the KineticLaw
- * now represents the math expression: s * p and the model no longer
- * contains any FunctionDefinitions.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return true (non-zero) if the transformation was successful,
- * false (0) otherwise.
- *
- * @note This function will check the consistency of a model
- * before attemptimg the transformation. In the case of a model
- * with invalid SBML the transformation will not be done and the
- * function will return @c false.
- *
- */
LIBSBML_EXTERN
int
SBMLDocument_expandFunctionDefintions (SBMLDocument_t *d)
@@ -2026,33 +1949,6 @@
}
-/**
- * Removes any InitialAssignments from the document and replaces
- * the appropriate values.
- *
- * For example a Model contains a InitialAssignment with symbol k
- * where k is the id of a Parameter.
- * The outcome of the function is that the value attribute of
- * the Parameter is the value calculated using the math expression
- * of the InitialAssignment and the corresponding InitialAssignment
- * has been removed from the Model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return true (non-zero) if the transformation was successful,
- * false (0) otherwise.
- *
- *
- * @note This function will check the consistency of a model
- * before attemptimg the transformation. In the case of a model
- * with invalid SBML the transformation will not be done and the
- * function will return @c false. As part of the process the
- * function will check that it has values for any components
- * referred to by the math elements of InitialAssignments. In
- * the case where not all values have been declared the particular
- * InitialAssignment will not be removed and the function will
- * return @c false.
- */
LIBSBML_EXTERN
int
SBMLDocument_expandInitialAssignments (SBMLDocument_t *d)
@@ -2062,46 +1958,6 @@
}
-/**
- * Sets the SBML Level and Version of this SBMLDocument, attempting to
- * convert the model as needed.
- *
- * This method is used to convert models between Levels and Versions of
- * SBML. Generally, models can be converted upward without difficulty
- * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
- * Level 2 to the latest version of Level 2). Sometimes models can be
- * translated downward as well, if they do not use constructs specific to
- * more advanced Levels of SBML.
- *
- * Callers can also check compatibility directly using the methods
- * checkL1Compatibility(), checkL2v1Compatibility(), and
- * checkL2v2Compatibility().
- *
- * The valid combinations as of this release of libSBML are the
- * following:
- *
- * @li Level 1 Version 1
- * @li Level 1 Version 2
- * @li Level 2 Version 1
- * @li Level 2 Version 2
- * @li Level 2 Version 3
- * @li Level 2 Version 4
- *
- * @param d the SBMLDocument_t structure
- *
- * @param level the desired SBML Level
- *
- * @param version the desired Version within the SBML Level
- *
- * @note Calling this method will not @em necessarily lead to successful
- * conversion. If the conversion fails, it will be logged in the error
- * list associated with this SBMLDocument_t structure. Callers should
- * consult getNumErrors() to find out if the conversion succeeded without
- * problems. For conversions from Level 2 to Level 1, callers can also
- * check the Level of the model after calling this method to find out
- * whether it is Level 1. (If the conversion to Level 1 failed, the Level
- * of this model will be left unchanged.)
- */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersion ( SBMLDocument_t *d
@@ -2113,57 +1969,6 @@
}
-/**
- * Sets the SBML Level and Version of this SBMLDocument, attempting to
- * convert the model as needed.
- *
- * This method is used to convert models between Levels and Versions of
- * SBML. Generally, models can be converted upward without difficulty
- * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
- * Level 2 to the latest version of Level 2). Sometimes models can be
- * translated downward as well, if they do not use constructs specific to
- * more advanced Levels of SBML.
- *
- * Callers can also check compatibility directly using the methods
- * checkL1Compatibility(), checkL2v1Compatibility(), and
- * checkL2v2Compatibility().
- *
- * The valid combinations as of this release of libSBML are the
- * following:
- *
- * @li Level 1 Version 1
- * @li Level 1 Version 2
- * @li Level 2 Version 1
- * @li Level 2 Version 2
- * @li Level 2 Version 3
- * @li Level 2 Version 4
- *
- * @param d the SBMLDocument_t structure
- *
- * @param level the desired SBML Level
- *
- * @param version the desired Version within the SBML Level
- *
- * @note Calling this method will not @em necessarily lead to successful
- * conversion. If the conversion fails, it will be logged in the error
- * list associated with this SBMLDocument_t structure. Callers should
- * consult getNumErrors() to find out if the conversion succeeded without
- * problems. For conversions from Level 2 to Level 1, callers can also
- * check the Level of the model after calling this method to find out
- * whether it is Level 1. (If the conversion to Level 1 failed, the Level
- * of this model will be left unchanged.)
- *
- *
- * Strict conversion applies the additional criteria that both the source
- * and the target model must be consistent SBML. Users can control the
- * consistency checks that are applied using the
- * SBMLDocument::setConsistencyChecks function. If either the source
- * or the potential target model have validation errors, the conversion
- * is not performed. When a strict conversion is successful, the
- * underlying SBML object model is altered to reflect the new level
- * and version. Thus information that cannot be converted (e.g. sboTerms)
- * will be lost.
- */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionStrict ( SBMLDocument_t *d
@@ -2175,46 +1980,6 @@
}
-/**
- * Sets the SBML Level and Version of this SBMLDocument, attempting to
- * convert the model as needed.
- *
- * This method is used to convert models between Levels and Versions of
- * SBML. Generally, models can be converted upward without difficulty
- * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
- * Level 2 to the latest version of Level 2). Sometimes models can be
- * translated downward as well, if they do not use constructs specific to
- * more advanced Levels of SBML.
- *
- * Callers can also check compatibility directly using the methods
- * checkL1Compatibility(), checkL2v1Compatibility(), and
- * checkL2v2Compatibility().
- *
- * The valid combinations as of this release of libSBML are the
- * following:
- *
- * @li Level 1 Version 1
- * @li Level 1 Version 2
- * @li Level 2 Version 1
- * @li Level 2 Version 2
- * @li Level 2 Version 3
- * @li Level 2 Version 4
- *
- * @param d the SBMLDocument_t structure
- *
- * @param level the desired SBML Level
- *
- * @param version the desired Version within the SBML Level
- *
- * @note Calling this method will not @em necessarily lead to successful
- * conversion. If the conversion fails, it will be logged in the error
- * list associated with this SBMLDocument_t structure. Callers should
- * consult getNumErrors() to find out if the conversion succeeded without
- * problems. For conversions from Level 2 to Level 1, callers can also
- * check the Level of the model after calling this method to find out
- * whether it is Level 1. (If the conversion to Level 1 failed, the Level
- * of this model will be left unchanged.)
- */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionNonStrict ( SBMLDocument_t *d
@@ -2226,22 +1991,6 @@
}
-/**
- * Sets the model contained in the given SBMLDocument_t structure to a copy
- * of the given Model_t structure.
- *
- * @param d the SBMLDocument_t structure
- *
- * @param m the new Model_t structure to use.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif@~ The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_LEVEL_MISMATCH
- * @li LIBSBML_VERSION_MISMATCH
- */
LIBSBML_EXTERN
int
SBMLDocument_setModel (SBMLDocument_t *d, const Model_t *m)
@@ -2250,14 +1999,6 @@
}
-/**
- * Creates a new Model_t structure inside the given SBMLDocument_t
- * structure and returns a pointer to it.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the Model_t structure created
- */
LIBSBML_EXTERN
Model_t *
SBMLDocument_createModel (SBMLDocument_t *d)
@@ -2280,56 +2021,6 @@
}
-/**
- * Allows particular validators to be turned on or off prior to
- * calling checkConsistency.
- *
- * The second argument (@p category) to this method indicates which
- * category of consistency/error checks are being turned on or off, and
- * the second argument (a boolean) indicates whether to turn on (value of
- * @c true) or off (value of @c false) that particula category of checks.
- * The possible categories are represented as values of the enumeration
- * SBMLErrorCategory_t. The following are the possible choices in libSBML
- * version 3.0.2:
- *
- * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
- *
- * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
- * example of inconsistency would be using a species identifier in a
- * reaction rate formula without first having declared the species.
- *
- * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
- *
- * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
- *
- * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
- *
- * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
- * equations implied by a model is mathematically overdetermined.
- *
- * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
- * model construction.
- *
- * By default, all validation checks are applied to the model in an
- * SBMLDocument object @em unless setConsistencyChecks() is called to
- * indicate that only a subset should be applied.
- *
- * @param d the SBMLDocument_t structure
- *
- * @param category a value drawn from SBMLErrorCategory_t indicating the
- * consistency checking/validation to be turned on or off
- *
- * @param apply a boolean indicating whether the checks indicated by @p
- * category should be applied or not.
- *
- * @note The default (i.e., performing all checks) applies to each new
- * SBMLDocument object created. This means that each time a model is
- * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
- * the global functions readSBML() and readSBMLFromString(), a new
- * SBMLDocument is created and for that document all checks are enabled.
- *
- * @see SBMLDocument_checkConsistency()
- */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecks(SBMLDocument_t * d,
@@ -2341,56 +2032,6 @@
}
-/**
- * Allows particular validators to be turned on or off prior to
- * calling setLevelAndVersion.
- *
- * The second argument (@p category) to this method indicates which
- * category of consistency/error checks are being turned on or off, and
- * the second argument (a boolean) indicates whether to turn on (value of
- * @c true) or off (value of @c false) that particula category of checks.
- * The possible categories are represented as values of the enumeration
- * SBMLErrorCategory_t. The following are the possible choices in libSBML
- * version 3.0.2:
- *
- * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
- *
- * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
- * example of inconsistency would be using a species identifier in a
- * reaction rate formula without first having declared the species.
- *
- * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
- *
- * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
- *
- * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
- *
- * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
- * equations implied by a model is mathematically overdetermined.
- *
- * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
- * model construction.
- *
- * By default, all validation checks are applied to the model in an
- * SBMLDocument object @em unless setConsistencyChecks() is called to
- * indicate that only a subset should be applied.
- *
- * @param d the SBMLDocument_t structure
- *
- * @param category a value drawn from SBMLErrorCategory_t indicating the
- * consistency checking/validation to be turned on or off
- *
- * @param apply a boolean indicating whether the checks indicated by @p
- * category should be applied or not.
- *
- * @note The default (i.e., performing all checks) applies to each new
- * SBMLDocument object created. This means that each time a model is
- * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
- * the global functions readSBML() and readSBMLFromString(), a new
- * SBMLDocument is created and for that document all checks are enabled.
- *
- * @see SBMLDocument_setLevelAndVersionStrict()
- */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecksForConversion(SBMLDocument_t * d,
@@ -2402,20 +2043,6 @@
}
-/**
- * Performs a set of consistency and validation checks on the given SBML
- * document.
- *
- * If this method returns a nonzero value (meaning, one or more
- * consistency checks have failed for SBML document), the failures may be
- * due to warnings @em or errors. Callers should inspect the severity
- * flag in the individual SBMLError objects returned by getError() to
- * determine the nature of the failures.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkConsistency (SBMLDocument_t *d)
@@ -2424,18 +2051,6 @@
}
-/**
- * Performs consistency checking on libSBML's internal representation of
- * an SBML Model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- *
- * @note The consistency checks performed by this function are limited
- * to inconsistencies that are not caught by other consistency checks.
- * @see setConsistencyChecks()
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkInternalConsistency (SBMLDocument_t *d)
@@ -2444,18 +2059,6 @@
}
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 1 and can be converted to
- * Level 1.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL1Compatibility (SBMLDocument_t *d)
@@ -2464,18 +2067,6 @@
}
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 1 and can be
- * converted to Level 2 Version 1.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v1Compatibility (SBMLDocument_t *d)
@@ -2485,18 +2076,6 @@
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 2 and can be
- * converted to Level 2 Version 2.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v2Compatibility (SBMLDocument_t *d)
@@ -2506,18 +2085,6 @@
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 3 and can be
- * converted to Level 2 Version 3.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v3Compatibility (SBMLDocument_t *d)
@@ -2526,18 +2093,6 @@
}
-/**
- * Performs a set of consistency checks on the document to establish
- * whether it is compatible with SBML Level 2 Version 4 and can be
- * converted to Level 2 Version 4.
- *
- * Callers should query the results of the consistency check by calling
- * getError().
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of failed checks (errors) encountered.
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v4Compatibility (SBMLDocument_t *d)
@@ -2546,27 +2101,6 @@
}
-/**
- * Returns the nth error or warning encountered during parsing,
- * consistency checking, or attempted translation of this model.
- *
- * Callers can use method XMLError_getSeverity() on the result to assess
- * the severity of the problem. The severity levels range from
- * informationl messages to fatal errors.
- *
- * @return the error or warning indexed by integer @p n, or return @c NULL
- * if n > (SBMLDocument_getNumErrors() - 1).
- *
- * @param d the SBMLDocument_t structure
- *
- * @param n the index of the error sought.
- *
- * @see SBMLDocument_getNumErrors(), SBMLDocument_setLevelAndVersion(),
- * SBMLDocument_checkConsistency(), SBMLDocument_checkL1Compatibility(),
- * SBMLDocument_checkL2v1Compatibility()
- * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
- * SBMLReader_readSBMLFromString().
- */
LIBSBML_EXTERN
const SBMLError_t *
SBMLDocument_getError (SBMLDocument_t *d, unsigned int n)
@@ -2575,20 +2109,6 @@
}
-/**
- * Returns the number of errors or warnings encountered during parsing,
- * consistency checking, or attempted translation of this model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of errors or warnings encountered
- *
- * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
- * SBMLDocument_checkL1Compatibility(),
- * SBMLDocument_checkL2v1Compatibility()
- * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
- * SBMLReader_readSBMLFromString().
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrors (const SBMLDocument_t *d)
@@ -2596,20 +2116,6 @@
return (d != NULL) ? d->getNumErrors() : SBML_INT_MAX;
}
-/**
- * Returns the number of errors or warnings encountered during parsing,
- * consistency checking, or attempted translation of this model.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return the number of errors or warnings encountered
- *
- * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
- * SBMLDocument_checkL1Compatibility(),
- * SBMLDocument_checkL2v1Compatibility()
- * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
- * SBMLReader_readSBMLFromString().
- */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrorsWithSeverity (const SBMLDocument_t *d, unsigned int severity)
@@ -2618,23 +2124,6 @@
}
-/**
- * Prints to the given output stream all the errors or warnings
- * encountered during parsing, consistency checking, or attempted
- * translation of this model.
- *
- * If no errors have occurred, i.e., SBMLDocument_getNumErrors() == 0, no
- * output will be sent to the stream.
- *
- * The format of the output is:
- *
- * N error(s):
- * line NNN: (id) message
- *
- * @param d the SBMLDocument_t structure
- *
- * @param stream the output stream where the messages should be printed
- */
LIBSBML_EXTERN
void
SBMLDocument_printErrors (SBMLDocument_t *d, FILE *stream)
@@ -2652,10 +2141,6 @@
}
-/**
- * @return the most recent SBML specification level (at the time this
- * libSBML was released).
- */
unsigned int
SBMLDocument_getDefaultLevel ()
{
@@ -2663,24 +2148,12 @@
}
-/**
- * @return the most recent SBML specification version (at the time this
- * libSBML was released).
- */
unsigned int
SBMLDocument_getDefaultVersion ()
{
return SBMLDocument::getDefaultVersion();
}
-/**
- * Returns a list of XMLNamespaces_t associated with the XML content
- * of this SBML document.
- *
- * @param d the SBMLDocument_t structure
- *
- * @return pointer to the XMLNamespaces_t structure associated with this SBML object
- */
LIBSBML_EXTERN
const XMLNamespaces_t *
SBMLDocument_getNamespaces(SBMLDocument_t *d)
@@ -2740,22 +2213,6 @@
return (d != NULL) ? static_cast<int>(d->isSetPackageRequired(package)) : 0;
}
-/**
- * Converts this document using the converter that best matches
- * the given conversion properties.
- *
- * @param d the SBMLDocument_t structure
- * @param props the conversion properties to use
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif@~ The possible values
- * returned by this function are:
- * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
- * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
- * @li @link OperationReturnValues_t#LIBSBML_CONV_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
- * @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
- */
LIBSBML_EXTERN
int
SBMLDocument_convert(SBMLDocument_t *d, const ConversionProperties_t* props)
Modified: trunk/libsbml/src/sbml/SBMLDocument.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.h 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/src/sbml/SBMLDocument.h 2014-01-23 21:04:01 UTC (rev 19560)
@@ -1630,16 +1630,36 @@
LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS
-/* ----------------------------------------------------------------------------
- * See the .cpp file for the documentation of the following functions.
- * --------------------------------------------------------------------------*/
-
-
+/**
+ * Creates a new, empty SBMLDocument_t structure.
+ *
+ * The SBML Level and Version attributes default to the most recent SBML
+ * specification (at the time this libSBML was released).
+ *
+ * @return the SBMLDocument_t structure created
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_create (void);
+/**
+ * Creates a new, empty SBMLDocument_t structure with given values for the
+ * SBML Level and Version.
+ *
+ * If not specified, the SBML Level and Version attributes default to the
+ * most recent SBML specification (at the time this libSBML was
+ * released).
+ *
+ * @param level an integer for the SBML Level
+ * @param version an integer for the Version within the SBML Level
+ *
+ * @return the SBMLDocument_t structure created
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_createWithLevelAndVersion (unsigned int level, unsigned int version);
@@ -1650,41 +1670,180 @@
SBMLDocument_createWithSBMLNamespaces (SBMLNamespaces_t *sbmlns);
+/**
+ * Frees the given SBMLDocument_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_free (SBMLDocument_t *d);
+/**
+ * Creates and returns a deep copy of the given SBMLDocument_t structure
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return a (deep) copy of the SBMLDocument_t structure
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
SBMLDocument_t *
SBMLDocument_clone (const SBMLDocument_t *d);
+/**
+ * Returns the SBML Level of the given SBMLDocument_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the SBML Level number
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getLevel (const SBMLDocument_t *d);
+/**
+ * Returns the Version within the SBML Level of the given SBMLDocument_t
+ * structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the version number
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getVersion (const SBMLDocument_t *d);
+/**
+ * Returns the Model object stored in this SBMLDocument_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the Model contained in this SBMLDocument_t structure.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
Model_t *
SBMLDocument_getModel (SBMLDocument_t *d);
+/**
+ * Removes any FunctionDefinitions from the document and expands
+ * any instances of their use within >math< elements.
+ *
+ * For example a Model contains a FunctionDefinition with id f
+ * representing the math expression: f(x, y) = x * y.
+ * The math element of the KineticLaw uses f(s, p).
+ * The outcome of the function is that the math of the KineticLaw
+ * now represents the math expression: s * p and the model no longer
+ * contains any FunctionDefinitions.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return true (non-zero) if the transformation was successful,
+ * false (0) otherwise.
+ *
+ * @note This function will check the consistency of a model
+ * before attemptimg the transformation. In the case of a model
+ * with invalid SBML the transformation will not be done and the
+ * function will return @c false.
+ *
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_expandFunctionDefintions (SBMLDocument_t *d);
+/**
+ * Removes any InitialAssignments from the document and replaces
+ * the appropriate values.
+ *
+ * For example a Model contains a InitialAssignment with symbol k
+ * where k is the id of a Parameter.
+ * The outcome of the function is that the value attribute of
+ * the Parameter is the value calculated using the math expression
+ * of the InitialAssignment and the corresponding InitialAssignment
+ * has been removed from the Model.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return true (non-zero) if the transformation was successful,
+ * false (0) otherwise.
+ *
+ *
+ * @note This function will check the consistency of a model
+ * before attemptimg the transformation. In the case of a model
+ * with invalid SBML the transformation will not be done and the
+ * function will return @c false. As part of the process the
+ * function will check that it has values for any components
+ * referred to by the math elements of InitialAssignments. In
+ * the case where not all values have been declared the particular
+ * InitialAssignment will not be removed and the function will
+ * return @c false.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_expandInitialAssignments (SBMLDocument_t *d);
+/**
+ * Sets the SBML Level and Version of this SBMLDocument, attempting to
+ * convert the model as needed.
+ *
+ * This method is used to convert models between Levels and Versions of
+ * SBML. Generally, models can be converted upward without difficulty
+ * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
+ * Level 2 to the latest version of Level 2). Sometimes models can be
+ * translated downward as well, if they do not use constructs specific to
+ * more advanced Levels of SBML.
+ *
+ * Callers can also check compatibility directly using the methods
+ * checkL1Compatibility(), checkL2v1Compatibility(), and
+ * checkL2v2Compatibility().
+ *
+ * The valid combinations as of this release of libSBML are the
+ * following:
+ *
+ * @li Level 1 Version 1
+ * @li Level 1 Version 2
+ * @li Level 2 Version 1
+ * @li Level 2 Version 2
+ * @li Level 2 Version 3
+ * @li Level 2 Version 4
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param level the desired SBML Level
+ *
+ * @param version the desired Version within the SBML Level
+ *
+ * @note Calling this method will not @em necessarily lead to successful
+ * conversion. If the conversion fails, it will be logged in the error
+ * list associated with this SBMLDocument_t structure. Callers should
+ * consult getNumErrors() to find out if the conversion succeeded without
+ * problems. For conversions from Level 2 to Level 1, callers can also
+ * check the Level of the model after calling this method to find out
+ * whether it is Level 1. (If the conversion to Level 1 failed, the Level
+ * of this model will be left unchanged.)
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersion ( SBMLDocument_t *d
@@ -1692,6 +1851,59 @@
, unsigned int version );
+/**
+ * Sets the SBML Level and Version of this SBMLDocument, attempting to
+ * convert the model as needed.
+ *
+ * This method is used to convert models between Levels and Versions of
+ * SBML. Generally, models can be converted upward without difficulty
+ * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
+ * Level 2 to the latest version of Level 2). Sometimes models can be
+ * translated downward as well, if they do not use constructs specific to
+ * more advanced Levels of SBML.
+ *
+ * Callers can also check compatibility directly using the methods
+ * checkL1Compatibility(), checkL2v1Compatibility(), and
+ * checkL2v2Compatibility().
+ *
+ * The valid combinations as of this release of libSBML are the
+ * following:
+ *
+ * @li Level 1 Version 1
+ * @li Level 1 Version 2
+ * @li Level 2 Version 1
+ * @li Level 2 Version 2
+ * @li Level 2 Version 3
+ * @li Level 2 Version 4
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param level the desired SBML Level
+ *
+ * @param version the desired Version within the SBML Level
+ *
+ * @note Calling this method will not @em necessarily lead to successful
+ * conversion. If the conversion fails, it will be logged in the error
+ * list associated with this SBMLDocument_t structure. Callers should
+ * consult getNumErrors() to find out if the conversion succeeded without
+ * problems. For conversions from Level 2 to Level 1, callers can also
+ * check the Level of the model after calling this method to find out
+ * whether it is Level 1. (If the conversion to Level 1 failed, the Level
+ * of this model will be left unchanged.)
+ *
+ *
+ * Strict conversion applies the additional criteria that both the source
+ * and the target model must be consistent SBML. Users can control the
+ * consistency checks that are applied using the
+ * SBMLDocument::setConsistencyChecks function. If either the source
+ * or the potential target model have validation errors, the conversion
+ * is not performed. When a strict conversion is successful, the
+ * underlying SBML object model is altered to reflect the new level
+ * and version. Thus information that cannot be converted (e.g. sboTerms)
+ * will be lost.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionStrict ( SBMLDocument_t *d
@@ -1699,6 +1911,48 @@
, unsigned int version );
+/**
+ * Sets the SBML Level and Version of this SBMLDocument, attempting to
+ * convert the model as needed.
+ *
+ * This method is used to convert models between Levels and Versions of
+ * SBML. Generally, models can be converted upward without difficulty
+ * (e.g., from SBML Level 1 to Level 2, or from an earlier version of
+ * Level 2 to the latest version of Level 2). Sometimes models can be
+ * translated downward as well, if they do not use constructs specific to
+ * more advanced Levels of SBML.
+ *
+ * Callers can also check compatibility directly using the methods
+ * checkL1Compatibility(), checkL2v1Compatibility(), and
+ * checkL2v2Compatibility().
+ *
+ * The valid combinations as of this release of libSBML are the
+ * following:
+ *
+ * @li Level 1 Version 1
+ * @li Level 1 Version 2
+ * @li Level 2 Version 1
+ * @li Level 2 Version 2
+ * @li Level 2 Version 3
+ * @li Level 2 Version 4
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param level the desired SBML Level
+ *
+ * @param version the desired Version within the SBML Level
+ *
+ * @note Calling this method will not @em necessarily lead to successful
+ * conversion. If the conversion fails, it will be logged in the error
+ * list associated with this SBMLDocument_t structure. Callers should
+ * consult getNumErrors() to find out if the conversion succeeded without
+ * problems. For conversions from Level 2 to Level 1, callers can also
+ * check the Level of the model after calling this method to find out
+ * whether it is Level 1. (If the conversion to Level 1 failed, the Level
+ * of this model will be left unchanged.)
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setLevelAndVersionNonStrict ( SBMLDocument_t *d
@@ -1706,11 +1960,39 @@
, unsigned int version );
+/**
+ * Sets the model contained in the given SBMLDocument_t structure to a copy
+ * of the given Model_t structure.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param m the new Model_t structure to use.
+ *
+ * @return integer value indicating success/failure of the
+ * function. @if clike The value is drawn from the
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
+ * returned by this function are:
+ * @li LIBSBML_OPERATION_SUCCESS
+ * @li LIBSBML_LEVEL_MISMATCH
+ * @li LIBSBML_VERSION_MISMATCH
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_setModel (SBMLDocument_t *d, const Model_t *m);
+/**
+ * Creates a new Model_t structure inside the given SBMLDocument_t
+ * structure and returns a pointer to it.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the Model_t structure created
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
Model_t *
SBMLDocument_createModel (SBMLDocument_t *d);
@@ -1723,18 +2005,138 @@
char*
SBMLDocument_getLocationURI(SBMLDocument_t *d);
+/**
+ * Allows particular validators to be turned on or off prior to
+ * calling checkConsistency.
+ *
+ * The second argument (@p category) to this method indicates which
+ * category of consistency/error checks are being turned on or off, and
+ * the second argument (a boolean) indicates whether to turn on (value of
+ * @c true) or off (value of @c false) that particula category of checks.
+ * The possible categories are represented as values of the enumeration
+ * SBMLErrorCategory_t. The following are the possible choices in libSBML
+ * version 3.0.2:
+ *
+ * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
+ *
+ * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
+ * example of inconsistency would be using a species identifier in a
+ * reaction rate formula without first having declared the species.
+ *
+ * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
+ *
+ * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
+ *
+ * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
+ *
+ * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
+ * equations implied by a model is mathematically overdetermined.
+ *
+ * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
+ * model construction.
+ *
+ * By default, all validation checks are applied to the model in an
+ * SBMLDocument object @em unless setConsistencyChecks() is called to
+ * indicate that only a subset should be applied.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param category a value drawn from SBMLErrorCategory_t indicating the
+ * consistency checking/validation to be turned on or off
+ *
+ * @param apply a boolean indicating whether the checks indicated by @p
+ * category should be applied or not.
+ *
+ * @note The default (i.e., performing all checks) applies to each new
+ * SBMLDocument object created. This means that each time a model is
+ * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
+ * the global functions readSBML() and readSBMLFromString(), a new
+ * SBMLDocument is created and for that document all checks are enabled.
+ *
+ * @see SBMLDocument_checkConsistency()
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecks(SBMLDocument_t *d,
- int validator,
- int apply);
+ SBMLErrorCategory_t category,
+ int apply);
+/**
+ * Allows particular validators to be turned on or off prior to
+ * calling setLevelAndVersion.
+ *
+ * The second argument (@p category) to this method indicates which
+ * category of consistency/error checks are being turned on or off, and
+ * the second argument (a boolean) indicates whether to turn on (value of
+ * @c true) or off (value of @c false) that particula category of checks.
+ * The possible categories are represented as values of the enumeration
+ * SBMLErrorCategory_t. The following are the possible choices in libSBML
+ * version 3.0.2:
+ *
+ * @li LIBSBML_CAT_GENERAL_CONSISTENCY: General overall SBML consistency.
+ *
+ * @li LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Consistency of identifiers. An
+ * example of inconsistency would be using a species identifier in a
+ * reaction rate formula without first having declared the species.
+ *
+ * @li LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of units of measure.
+ *
+ * @li LIBSBML_CAT_MATHML_CONSISTENCY: Consistency of MathML constructs.
+ *
+ * @li LIBSBML_CAT_SBO_CONSISTENCY: Consistency of SBO identifiers.
+ *
+ * @li LIBSBML_CAT_OVERDETERMINED_MODEL: Checking whether the system of
+ * equations implied by a model is mathematically overdetermined.
+ *
+ * @li LIBSBML_CAT_MODELING_PRACTICE: General good practice in
+ * model construction.
+ *
+ * By default, all validation checks are applied to the model in an
+ * SBMLDocument object @em unless setConsistencyChecks() is called to
+ * indicate that only a subset should be applied.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param category a value drawn from SBMLErrorCategory_t indicating the
+ * consistency checking/validation to be turned on or off
+ *
+ * @param apply a boolean indicating whether the checks indicated by @p
+ * category should be applied or not.
+ *
+ * @note The default (i.e., performing all checks) applies to each new
+ * SBMLDocument object created. This means that each time a model is
+ * read using SBMLReader::readSBML(), SBMLReader::readSBMLFromString, or
+ * the global functions readSBML() and readSBMLFromString(), a new
+ * SBMLDocument is created and for that document all checks are enabled.
+ *
+ * @see SBMLDocument_setLevelAndVersionStrict()
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_setConsistencyChecksForConversion(SBMLDocument_t *d,
int validator,
int apply);
+/**
+ * Performs a set of consistency and validation checks on the given SBML
+ * document.
+ *
+ * If this method returns a nonzero value (meaning, one or more
+ * consistency checks have failed for SBML document), the failures may be
+ * due to warnings @em or errors. Callers should inspect the severity
+ * flag in the individual SBMLError objects returned by getError() to
+ * determine the nature of the failures.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkConsistency (SBMLDocument_t *d);
@@ -1745,64 +2147,246 @@
SBMLDocument_validateSBML (SBMLDocument_t *d);
+/**
+ * Performs consistency checking on libSBML's internal representation of
+ * an SBML Model.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @note The consistency checks performed by this function are limited
+ * to inconsistencies that are not caught by other consistency checks.
+ * @see setConsistencyChecks()
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkInternalConsistency (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 1 and can be converted to
+ * Level 1.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL1Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 1 and can be
+ * converted to Level 2 Version 1.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v1Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 2 and can be
+ * converted to Level 2 Version 2.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v2Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 3 and can be
+ * converted to Level 2 Version 3.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v3Compatibility (SBMLDocument_t *d);
+/**
+ * Performs a set of consistency checks on the document to establish
+ * whether it is compatible with SBML Level 2 Version 4 and can be
+ * converted to Level 2 Version 4.
+ *
+ * Callers should query the results of the consistency check by calling
+ * getError().
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of failed checks (errors) encountered.
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_checkL2v4Compatibility (SBMLDocument_t *d);
+/**
+ * Returns the nth error or warning encountered during parsing,
+ * consistency checking, or attempted translation of this model.
+ *
+ * Callers can use method XMLError_getSeverity() on the result to assess
+ * the severity of the problem. The severity levels range from
+ * informationl messages to fatal errors.
+ *
+ * @return the error or warning indexed by integer @p n, or return @c NULL
+ * if n > (SBMLDocument_getNumErrors() - 1).
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param n the index of the error sought.
+ *
+ * @see SBMLDocument_getNumErrors(), SBMLDocument_setLevelAndVersion(),
+ * SBMLDocument_checkConsistency(), SBMLDocument_checkL1Compatibility(),
+ * SBMLDocument_checkL2v1Compatibility()
+ * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
+ * SBMLReader_readSBMLFromString().
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
const SBMLError_t *
SBMLDocument_getError (SBMLDocument_t *d, unsigned int n);
+/**
+ * Returns the number of errors or warnings encountered during parsing,
+ * consistency checking, or attempted translation of this model.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return the number of errors or warnings encountered
+ *
+ * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
+ * SBMLDocument_checkL1Compatibility(),
+ * SBMLDocument_checkL2v1Compatibility()
+ * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
+ * SBMLReader_readSBMLFromString().
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrors (const SBMLDocument_t *d);
+/**
+ * Returns the number of errors or warnings encountered during parsing,
+ * consistency checking, or attempted translation of this model.
+ *
+ * @param d the SBMLDocument_t structure
+ * @param severity the severity requested
+ *
+ * @return the number of errors or warnings encountered with the given severity
+ * level
+ *
+ * @see SBMLDocument_setLevelAndVersion(), SBMLDocument_checkConsistency(),
+ * SBMLDocument_checkL1Compatibility(),
+ * SBMLDocument_checkL2v1Compatibility()
+ * SBMLDocument_checkL2v2Compatibility(), SBMLReader_readSBML(),
+ * SBMLReader_readSBMLFromString().
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getNumErrorsWithSeverity (const SBMLDocument_t *d, unsigned int severity);
+/**
+ * Prints to the given output stream all the errors or warnings
+ * encountered during parsing, consistency checking, or attempted
+ * translation of this model.
+ *
+ * If no errors have occurred, i.e., SBMLDocument_getNumErrors() == 0, no
+ * output will be sent to the stream.
+ *
+ * The format of the output is:
+ *
+ * N error(s):
+ * line NNN: (id) message
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @param stream the output stream where the messages should be printed
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
void
SBMLDocument_printErrors (SBMLDocument_t *d, FILE *stream);
+/**
+ * @return the most recent SBML specification level (at the time this
+ * libSBML was released).
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getDefaultLevel ();
+/**
+ * @return the most recent SBML specification version (at the time this
+ * libSBML was released).
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
unsigned int
SBMLDocument_getDefaultVersion ();
+/**
+ * Returns a list of XMLNamespaces_t associated with the XML content
+ * of this SBML document.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return pointer to the XMLNamespaces_t structure associated with this SBML object
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
const XMLNamespaces_t *
SBMLDocument_getNamespaces(SBMLDocument_t *d);
@@ -1839,6 +2423,24 @@
int
SBMLDocument_isSetPackageRequired (SBMLDocument_t *d, const char * package);
+/**
+ * Converts this document using the converter that best matches
+ * the given conversion properties.
+ *
+ * @param d the SBMLDocument_t structure
+ * @param props the conversion properties to use
+ *
+ * @return integer value indicating success/failure of the
+ * function. @if clike The value is drawn from the
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
+ * returned by this function are:
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_CONV_CONVERSION_NOT_AVAILABLE LIBSBML_CONV_CONVERSION_NOT_AVAILABLE @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
+ *
+ * @memberof SBMLDocument_t
+ */
LIBSBML_EXTERN
int
SBMLDocument_convert(SBMLDocument_t *d, const ConversionProperties_t* props);
Modified: trunk/libsbml/src/sbml/SBMLReader.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLReader.h 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/src/sbml/SBMLReader.h 2014-01-23 21:04:01 UTC (rev 19560)
@@ -466,6 +466,8 @@
/**
* Creates a new SBMLReader and returns it. By default XML Schema
* validation is off.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLReader_t *
@@ -473,6 +475,8 @@
/**
* Frees the given SBMLReader.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
void
@@ -508,6 +512,8 @@
* @return a pointer to the SBMLDocument read.
*
* @copydetails doc_note_sbmlreader_error_handling
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLDocument_t *
@@ -531,6 +537,8 @@
* checking code.
*
* @return a pointer to the SBMLDocument read.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLDocument_t *
@@ -539,9 +547,11 @@
/**
* Predicate returning @c non-zero or @c zero depending on whether
- * underlying libSBML is linked with..
+ * underlying libSBML is linked with zlib or not.
*
* @return @c non-zero if libSBML is linked with zlib, @c zero otherwise.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
int
@@ -553,12 +563,16 @@
* libSBML is linked with bzip2.
*
* @return @c non-zero if libSBML is linked with bzip2, @c zero otherwise.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
int
SBMLReader_hasBzip2 ();
-#endif /* !SWIG */
+#endif /* !SWIG *
+ * @memberof SBMLReader_t
+ */
/**
@@ -571,6 +585,8 @@
* SBMLDocument for more information about the error reporting mechanism.
*
* @return a pointer to the SBMLDocument read.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLDocument_t *
@@ -599,6 +615,8 @@
* SBMLDocument for more information about the error reporting mechanism.
*
* @return a pointer to the SBMLDocument read.
+ *
+ * @memberof SBMLReader_t
*/
LIBSBML_EXTERN
SBMLDocument_t *
Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp 2014-01-23 17:58:03 UTC (rev 19559)
+++ trunk/libsbml/src/sbml/SBase.cpp 2014-01-23 21:04:01 UTC (rev 19560)
@@ -6350,26 +6350,6 @@
/** @cond doxygenCOnly */
-/**
- * Adds a copy of the given CVTerm to this SBML object.
- *
- * @param sb the object to add the CVTerm to
- * @param term the CVTerm_t to assign
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif@~ The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_OPERATION_FAILED
- * @li LIBSBML_UNEXPECTED_ATTRIBUTE
- * @li LIBSBML_INVALID_OBJECT
- *
- * @note The annotation constructed from a CVTerm uses the metaid
- * of the object to identify it. Adding a CVTerm to an object
- * where the 'metaId' attribute has not been set will fail with the
- * return value LIBSBML_UNEXPECTED_ATTRIBUTE.
- */
LIBSBML_EXTERN
int
SBase_addCVTerm(SBase_t *sb, CVTerm_t *term)
@@ -6378,27 +6358,6 @@
}
-/**
- * Adds a copy of the given CVTerm to this SBML object creating
- * a new bBag element with the same identifier.
- *
- * @param sb the object to add the CVTerm to
- * @param term the CVTerm_t to assign
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif@~ The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_OPERATION_FAILED
- * @li LIBSBML_UNEXPECTED_ATTRIBUTE
- * @li LIBSBML_INVALID_OBJECT
- *
- * @note The annotation constructed from a CVTerm uses the metaid
- * of the object to identify it. Adding a CVTerm to an object
- * where the 'metaId' attribute has not been set will fail with the
- * return value LIBSBML_UNEXPECTED_ATTRIBUTE.
- */
LIBSBML_EXTERN
int
SBase_addCVTermNewBag(SBase_t *sb, CVTerm_t *term)
@@ -6407,14 +6366,6 @@
}
-/**
- * Retu...
[truncated message content] |
|
From: <sar...@us...> - 2014-01-23 17:58:06
|
Revision: 19559
http://sourceforge.net/p/sbml/code/19559
Author: sarahkeating
Date: 2014-01-23 17:58:03 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
Merged revision(s) 19557-19558 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/CMakeLists.txt
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-23 15:57:35 UTC (rev 19558)
+++ branches/libsbml-experimental 2014-01-23 17:58:03 UTC (rev 19559)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19556
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19558
\ No newline at end of property
Modified: branches/libsbml-experimental/CMakeLists.txt
===================================================================
--- branches/libsbml-experimental/CMakeLists.txt 2014-01-23 15:57:35 UTC (rev 19558)
+++ branches/libsbml-experimental/CMakeLists.txt 2014-01-23 17:58:03 UTC (rev 19559)
@@ -280,16 +280,17 @@
if(WITH_EXPAT)
find_library(LIBEXPAT_LIBRARY
NAMES libexpat.lib expat
- PATHS /usr/lib /usr/local/lib
- ${LIBSBML_DEPENDENCY_DIR}/lib
+ PATHS ${LIBSBML_DEPENDENCY_DIR}/lib
+ /usr/lib /usr/local/lib
+ /usr/lib/i386-linux-gnu
DOC "The file name of the Expat library."
)
find_path(LIBEXPAT_INCLUDE_DIR
NAMES expat.h
- PATHS /usr/include /usr/local/include
- ${CMAKE_OSX_SYSROOT}/usr/include
- ${LIBSBML_DEPENDENCY_DIR}/include
+ PATHS ${LIBSBML_DEPENDENCY_DIR}/include
+ /usr/include /usr/local/include
+ ${CMAKE_OSX_SYSROOT}/usr/include
DOC "The directory containing the Expat include files."
)
@@ -320,11 +321,12 @@
find_path(LIBXML_INCLUDE_DIR
NAMES libxml/parser.h
- PATHS /usr/include /usr/local/include
+ PATHS ${LIBSBML_DEPENDENCY_DIR}/include
+ /usr/include /usr/local/include
/usr/include/libxml2
${CMAKE_OSX_SYSROOT}/usr/include/libxml2
/usr/local/include/libxml2
- ${LIBSBML_DEPENDENCY_DIR}/include
+
DOC "The directory containing the libxml2 include files."
)
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|
|
From: <fbe...@us...> - 2014-01-23 15:57:38
|
Revision: 19558
http://sourceforge.net/p/sbml/code/19558
Author: fbergmann
Date: 2014-01-23 15:57:35 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
- make it easier to find the system expat on ubuntu
Modified Paths:
--------------
trunk/libsbml/CMakeLists.txt
Modified: trunk/libsbml/CMakeLists.txt
===================================================================
--- trunk/libsbml/CMakeLists.txt 2014-01-23 15:41:56 UTC (rev 19557)
+++ trunk/libsbml/CMakeLists.txt 2014-01-23 15:57:35 UTC (rev 19558)
@@ -280,16 +280,17 @@
if(WITH_EXPAT)
find_library(LIBEXPAT_LIBRARY
NAMES libexpat.lib expat
- PATHS /usr/lib /usr/local/lib
- ${LIBSBML_DEPENDENCY_DIR}/lib
+ PATHS ${LIBSBML_DEPENDENCY_DIR}/lib
+ /usr/lib /usr/local/lib
+ /usr/lib/i386-linux-gnu
DOC "The file name of the Expat library."
)
find_path(LIBEXPAT_INCLUDE_DIR
NAMES expat.h
- PATHS /usr/include /usr/local/include
- ${CMAKE_OSX_SYSROOT}/usr/include
- ${LIBSBML_DEPENDENCY_DIR}/include
+ PATHS ${LIBSBML_DEPENDENCY_DIR}/include
+ /usr/include /usr/local/include
+ ${CMAKE_OSX_SYSROOT}/usr/include
DOC "The directory containing the Expat include files."
)
@@ -320,11 +321,12 @@
find_path(LIBXML_INCLUDE_DIR
NAMES libxml/parser.h
- PATHS /usr/include /usr/local/include
+ PATHS ${LIBSBML_DEPENDENCY_DIR}/include
+ /usr/include /usr/local/include
/usr/include/libxml2
${CMAKE_OSX_SYSROOT}/usr/include/libxml2
/usr/local/include/libxml2
- ${LIBSBML_DEPENDENCY_DIR}/include
+
DOC "The directory containing the libxml2 include files."
)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2014-01-23 15:41:59
|
Revision: 19557
http://sourceforge.net/p/sbml/code/19557
Author: sarahkeating
Date: 2014-01-23 15:41:56 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
Merged revision(s) 19555-19556 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/common/libsbml-version.cpp
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-23 15:39:47 UTC (rev 19556)
+++ branches/libsbml-experimental 2014-01-23 15:41:56 UTC (rev 19557)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19554
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19556
\ No newline at end of property
Modified: branches/libsbml-experimental/src/sbml/common/libsbml-version.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/common/libsbml-version.cpp 2014-01-23 15:39:47 UTC (rev 19556)
+++ branches/libsbml-experimental/src/sbml/common/libsbml-version.cpp 2014-01-23 15:41:56 UTC (rev 19557)
@@ -33,7 +33,8 @@
#include <expat.h>
#endif
-#ifdef USE_XERCESC
+#ifdef USE_XERCES
+#include <xercesc/util/XercesDefs.hpp>
#include <xercesc/util/XercesVersion.hpp>
#endif
@@ -133,8 +134,12 @@
strcmp(option, "xercesc") == 0)
{
#ifdef USE_XERCES
- return XERCES_FULLVERSIONNUM;
+#ifdef _XERCES_VERSION
+ return _XERCES_VERSION;
#else
+ return 1;
+#endif
+#else
return 0;
#endif
}
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|
|
From: <fbe...@us...> - 2014-01-23 15:39:51
|
Revision: 19556
http://sourceforge.net/p/sbml/code/19556
Author: fbergmann
Date: 2014-01-23 15:39:47 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
- correct xerces version gathering
Modified Paths:
--------------
trunk/libsbml/src/sbml/common/libsbml-version.cpp
Modified: trunk/libsbml/src/sbml/common/libsbml-version.cpp
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-version.cpp 2014-01-23 15:15:58 UTC (rev 19555)
+++ trunk/libsbml/src/sbml/common/libsbml-version.cpp 2014-01-23 15:39:47 UTC (rev 19556)
@@ -33,7 +33,8 @@
#include <expat.h>
#endif
-#ifdef USE_XERCESC
+#ifdef USE_XERCES
+#include <xercesc/util/XercesDefs.hpp>
#include <xercesc/util/XercesVersion.hpp>
#endif
@@ -133,8 +134,12 @@
strcmp(option, "xercesc") == 0)
{
#ifdef USE_XERCES
- return XERCES_FULLVERSIONNUM;
+#ifdef _XERCES_VERSION
+ return _XERCES_VERSION;
#else
+ return 1;
+#endif
+#else
return 0;
#endif
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2014-01-23 15:16:02
|
Revision: 19555
http://sourceforge.net/p/sbml/code/19555
Author: sarahkeating
Date: 2014-01-23 15:15:58 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
Merged revision(s) 19552-19554 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/examples/comp-package.cmake
branches/libsbml-experimental/examples/fbc-package.cmake
branches/libsbml-experimental/examples/layout-package.cmake
branches/libsbml-experimental/examples/qual-package.cmake
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-01-23 15:12:21 UTC (rev 19554)
+++ branches/libsbml-experimental 2014-01-23 15:15:58 UTC (rev 19555)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -1,4 +1,4 ##
/branches/L3Parser:15528-15625,15656-15673
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19551
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19554
\ No newline at end of property
Modified: branches/libsbml-experimental/examples/comp-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/comp-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
+++ branches/libsbml-experimental/examples/comp-package.cmake 2014-01-23 15:15:58 UTC (rev 19555)
@@ -37,16 +37,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/comp/*.rb"
+ file(GLOB ruby_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/comp/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/comp/README.txt")
- install(FILES ${perl_comp_samples} DESTINATION ${MISC_PREFIX}examples/ruby/comp)
+ install(FILES ${ruby_comp_samples} DESTINATION ${MISC_PREFIX}examples/ruby/comp)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/comp/*.R"
+ file(GLOB r_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/comp/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/comp/README.txt")
- install(FILES ${python_comp_samples} DESTINATION ${MISC_PREFIX}examples/r/comp)
+ install(FILES ${r_comp_samples} DESTINATION ${MISC_PREFIX}examples/r/comp)
endif()
endif(ENABLE_COMP)
Modified: branches/libsbml-experimental/examples/fbc-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/fbc-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
+++ branches/libsbml-experimental/examples/fbc-package.cmake 2014-01-23 15:15:58 UTC (rev 19555)
@@ -37,16 +37,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/fbc/*.rb"
+ file(GLOB ruby_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/fbc/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/fbc/README.txt")
- install(FILES ${perl_fbc_samples} DESTINATION ${MISC_PREFIX}examples/ruby/fbc)
+ install(FILES ${ruby_fbc_samples} DESTINATION ${MISC_PREFIX}examples/ruby/fbc)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/fbc/*.R"
+ file(GLOB r_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/fbc/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/fbc/README.txt")
- install(FILES ${python_fbc_samples} DESTINATION ${MISC_PREFIX}examples/r/fbc)
+ install(FILES ${r_fbc_samples} DESTINATION ${MISC_PREFIX}examples/r/fbc)
endif()
endif(ENABLE_FBC)
Modified: branches/libsbml-experimental/examples/layout-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/layout-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
+++ branches/libsbml-experimental/examples/layout-package.cmake 2014-01-23 15:15:58 UTC (rev 19555)
@@ -38,16 +38,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/layout/*.rb"
+ file(GLOB ruby_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/layout/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/layout/README.txt")
- install(FILES ${perl_layout_samples} DESTINATION ${MISC_PREFIX}examples/ruby/layout)
+ install(FILES ${ruby_layout_samples} DESTINATION ${MISC_PREFIX}examples/ruby/layout)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/layout/*.R"
+ file(GLOB r_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/layout/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/layout/README.txt")
- install(FILES ${python_layout_samples} DESTINATION ${MISC_PREFIX}examples/r/layout)
+ install(FILES ${r_layout_samples} DESTINATION ${MISC_PREFIX}examples/r/layout)
endif()
endif(ENABLE_LAYOUT)
Modified: branches/libsbml-experimental/examples/qual-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/qual-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
+++ branches/libsbml-experimental/examples/qual-package.cmake 2014-01-23 15:15:58 UTC (rev 19555)
@@ -36,16 +36,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/qual/*.rb"
+ file(GLOB ruby_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/qual/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/qual/README.txt")
- install(FILES ${perl_qual_samples} DESTINATION ${MISC_PREFIX}examples/ruby/qual)
+ install(FILES ${ruby_qual_samples} DESTINATION ${MISC_PREFIX}examples/ruby/qual)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/qual/*.R"
+ file(GLOB r_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/qual/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/qual/README.txt")
- install(FILES ${python_qual_samples} DESTINATION ${MISC_PREFIX}examples/r/qual)
+ install(FILES ${r_qual_samples} DESTINATION ${MISC_PREFIX}examples/r/qual)
endif()
endif(ENABLE_QUAL)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fbe...@us...> - 2014-01-23 15:12:23
|
Revision: 19554
http://sourceforge.net/p/sbml/code/19554
Author: fbergmann
Date: 2014-01-23 15:12:21 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
- fix typo
Modified Paths:
--------------
trunk/libsbml/examples/comp-package.cmake
trunk/libsbml/examples/fbc-package.cmake
trunk/libsbml/examples/layout-package.cmake
trunk/libsbml/examples/qual-package.cmake
Modified: trunk/libsbml/examples/comp-package.cmake
===================================================================
--- trunk/libsbml/examples/comp-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
+++ trunk/libsbml/examples/comp-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
@@ -37,16 +37,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/comp/*.rb"
+ file(GLOB ruby_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/comp/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/comp/README.txt")
- install(FILES ${perl_comp_samples} DESTINATION ${MISC_PREFIX}examples/ruby/comp)
+ install(FILES ${ruby_comp_samples} DESTINATION ${MISC_PREFIX}examples/ruby/comp)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/comp/*.R"
+ file(GLOB r_comp_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/comp/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/comp/README.txt")
- install(FILES ${python_comp_samples} DESTINATION ${MISC_PREFIX}examples/r/comp)
+ install(FILES ${r_comp_samples} DESTINATION ${MISC_PREFIX}examples/r/comp)
endif()
endif(ENABLE_COMP)
Modified: trunk/libsbml/examples/fbc-package.cmake
===================================================================
--- trunk/libsbml/examples/fbc-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
+++ trunk/libsbml/examples/fbc-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
@@ -37,16 +37,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/fbc/*.rb"
+ file(GLOB ruby_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/fbc/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/fbc/README.txt")
- install(FILES ${perl_fbc_samples} DESTINATION ${MISC_PREFIX}examples/ruby/fbc)
+ install(FILES ${ruby_fbc_samples} DESTINATION ${MISC_PREFIX}examples/ruby/fbc)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/fbc/*.R"
+ file(GLOB r_fbc_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/fbc/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/fbc/README.txt")
- install(FILES ${python_fbc_samples} DESTINATION ${MISC_PREFIX}examples/r/fbc)
+ install(FILES ${r_fbc_samples} DESTINATION ${MISC_PREFIX}examples/r/fbc)
endif()
endif(ENABLE_FBC)
Modified: trunk/libsbml/examples/layout-package.cmake
===================================================================
--- trunk/libsbml/examples/layout-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
+++ trunk/libsbml/examples/layout-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
@@ -38,16 +38,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/layout/*.rb"
+ file(GLOB ruby_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/layout/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/layout/README.txt")
- install(FILES ${perl_layout_samples} DESTINATION ${MISC_PREFIX}examples/ruby/layout)
+ install(FILES ${ruby_layout_samples} DESTINATION ${MISC_PREFIX}examples/ruby/layout)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/layout/*.R"
+ file(GLOB r_layout_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/layout/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/layout/README.txt")
- install(FILES ${python_layout_samples} DESTINATION ${MISC_PREFIX}examples/r/layout)
+ install(FILES ${r_layout_samples} DESTINATION ${MISC_PREFIX}examples/r/layout)
endif()
endif(ENABLE_LAYOUT)
Modified: trunk/libsbml/examples/qual-package.cmake
===================================================================
--- trunk/libsbml/examples/qual-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
+++ trunk/libsbml/examples/qual-package.cmake 2014-01-23 15:12:21 UTC (rev 19554)
@@ -36,16 +36,16 @@
if(WITH_RUBY)
# install ruby examples
- file(GLOB perl_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/qual/*.rb"
+ file(GLOB ruby_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/qual/*.rb"
"${CMAKE_CURRENT_SOURCE_DIR}/ruby/qual/README.txt")
- install(FILES ${perl_qual_samples} DESTINATION ${MISC_PREFIX}examples/ruby/qual)
+ install(FILES ${ruby_qual_samples} DESTINATION ${MISC_PREFIX}examples/ruby/qual)
endif()
if (WITH_R)
# install r examples
- file(GLOB python_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/qual/*.R"
+ file(GLOB r_qual_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/qual/*.R"
"${CMAKE_CURRENT_SOURCE_DIR}/r/qual/README.txt")
- install(FILES ${python_qual_samples} DESTINATION ${MISC_PREFIX}examples/r/qual)
+ install(FILES ${r_qual_samples} DESTINATION ${MISC_PREFIX}examples/r/qual)
endif()
endif(ENABLE_QUAL)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fbe...@us...> - 2014-01-23 15:11:11
|
Revision: 19553
http://sourceforge.net/p/sbml/code/19553
Author: fbergmann
Date: 2014-01-23 15:11:08 +0000 (Thu, 23 Jan 2014)
Log Message:
-----------
- copy examples of experimental packages
Modified Paths:
--------------
branches/libsbml-experimental/examples/arrays-package.cmake
branches/libsbml-experimental/examples/distrib-package.cmake
branches/libsbml-experimental/examples/groups-package.cmake
branches/libsbml-experimental/examples/multi-package.cmake
branches/libsbml-experimental/examples/render-package.cmake
branches/libsbml-experimental/examples/req-package.cmake
branches/libsbml-experimental/examples/spatial-package.cmake
Modified: branches/libsbml-experimental/examples/arrays-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/arrays-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/arrays-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -11,11 +11,52 @@
# add_subdirectory(c/arrays)
# add_subdirectory(c++/arrays)
- if(WITH_CSHARP)
- add_subdirectory(csharp/arrays)
- endif(WITH_CSHARP)
+ if(WITH_CSHARP)
+ add_subdirectory(csharp/arrays)
+ endif(WITH_CSHARP)
+
+ if(WITH_JAVA)
+ add_subdirectory(java/arrays)
+ endif(WITH_JAVA)
+
+ file(GLOB c_arrays_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/arrays/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/arrays/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/arrays/README.txt")
+ install(FILES ${c_arrays_samples} DESTINATION ${MISC_PREFIX}examples/c/arrays)
- if(WITH_JAVA)
- add_subdirectory(java/arrays)
- endif(WITH_JAVA)
+ file(GLOB cpp_arrays_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/arrays/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/arrays/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/arrays/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/arrays/README.txt")
+ install(FILES ${cpp_arrays_samples} DESTINATION ${MISC_PREFIX}examples/c++/arrays)
+
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_arrays_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/arrays/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/arrays/README.txt")
+ install(FILES ${perl_arrays_samples} DESTINATION ${MISC_PREFIX}examples/perl/arrays)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_arrays_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/arrays/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/arrays/README.txt")
+ install(FILES ${python_arrays_samples} DESTINATION ${MISC_PREFIX}examples/python/arrays)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_arrays_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/arrays/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/arrays/README.txt")
+ install(FILES ${ruby_arrays_samples} DESTINATION ${MISC_PREFIX}examples/ruby/arrays)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_arrays_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/arrays/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/arrays/README.txt")
+ install(FILES ${r_arrays_samples} DESTINATION ${MISC_PREFIX}examples/r/arrays)
+ endif()
+
endif(ENABLE_ARRAYS)
Modified: branches/libsbml-experimental/examples/distrib-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/distrib-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/distrib-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -8,14 +8,56 @@
#
if (ENABLE_DISTRIB)
-# add_subdirectory(c/distrib)
-# add_subdirectory(c++/distrib)
+# add_subdirectory(c/distrib)
+add_subdirectory(c++/distrib)
- if(WITH_CSHARP)
-# add_subdirectory(csharp/distrib)
- endif(WITH_CSHARP)
+ if(WITH_CSHARP)
+# add_subdirectory(csharp/distrib)
+ endif(WITH_CSHARP)
- if(WITH_JAVA)
-# add_subdirectory(java/distrib)
- endif(WITH_JAVA)
+ if(WITH_JAVA)
+# add_subdirectory(java/distrib)
+ endif(WITH_JAVA)
+
+ file(GLOB c_distrib_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/distrib/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/distrib/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/distrib/README.txt")
+ install(FILES ${c_distrib_samples} DESTINATION ${MISC_PREFIX}examples/c/distrib)
+
+ file(GLOB cpp_distrib_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/distrib/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/distrib/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/distrib/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/distrib/README.txt")
+ install(FILES ${cpp_distrib_samples} DESTINATION ${MISC_PREFIX}examples/c++/distrib)
+
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_distrib_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/distrib/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/distrib/README.txt")
+ install(FILES ${perl_distrib_samples} DESTINATION ${MISC_PREFIX}examples/perl/distrib)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_distrib_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/distrib/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/distrib/README.txt")
+ install(FILES ${python_distrib_samples} DESTINATION ${MISC_PREFIX}examples/python/distrib)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_distrib_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/distrib/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/distrib/README.txt")
+ install(FILES ${ruby_distrib_samples} DESTINATION ${MISC_PREFIX}examples/ruby/distrib)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_distrib_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/distrib/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/distrib/README.txt")
+ install(FILES ${r_distrib_samples} DESTINATION ${MISC_PREFIX}examples/r/distrib)
+ endif()
+
+
endif(ENABLE_DISTRIB)
Modified: branches/libsbml-experimental/examples/groups-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/groups-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/groups-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -9,13 +9,55 @@
if (ENABLE_GROUPS)
# add_subdirectory(c/groups)
- add_subdirectory(c++/groups)
+ add_subdirectory(c++/groups)
+
+ if(WITH_CSHARP)
+ add_subdirectory(csharp/groups)
+ endif(WITH_CSHARP)
+
+ if(WITH_JAVA)
+ add_subdirectory(java/groups)
+ endif(WITH_JAVA)
+
+
+ file(GLOB c_groups_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/groups/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/groups/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/groups/README.txt")
+ install(FILES ${c_groups_samples} DESTINATION ${MISC_PREFIX}examples/c/groups)
- if(WITH_CSHARP)
- add_subdirectory(csharp/groups)
- endif(WITH_CSHARP)
+ file(GLOB cpp_groups_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/groups/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/groups/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/groups/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/groups/README.txt")
+ install(FILES ${cpp_groups_samples} DESTINATION ${MISC_PREFIX}examples/c++/groups)
- if(WITH_JAVA)
- add_subdirectory(java/groups)
- endif(WITH_JAVA)
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_groups_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/groups/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/groups/README.txt")
+ install(FILES ${perl_groups_samples} DESTINATION ${MISC_PREFIX}examples/perl/groups)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_groups_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/groups/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/groups/README.txt")
+ install(FILES ${python_groups_samples} DESTINATION ${MISC_PREFIX}examples/python/groups)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_groups_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/groups/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/groups/README.txt")
+ install(FILES ${ruby_groups_samples} DESTINATION ${MISC_PREFIX}examples/ruby/groups)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_groups_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/groups/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/groups/README.txt")
+ install(FILES ${r_groups_samples} DESTINATION ${MISC_PREFIX}examples/r/groups)
+ endif()
+
endif(ENABLE_GROUPS)
Modified: branches/libsbml-experimental/examples/multi-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/multi-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/multi-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -8,14 +8,55 @@
#
if (ENABLE_MULTI)
- # add_subdirectory(c/fbc)
- add_subdirectory(c++/multi)
+ # add_subdirectory(c/fbc)
+ add_subdirectory(c++/multi)
+
+ if(WITH_CSHARP)
+ # add_subdirectory(csharp/fbc)
+ endif(WITH_CSHARP)
+
+ if(WITH_JAVA)
+ # add_subdirectory(java/fbc)
+ endif(WITH_JAVA)
+
+ file(GLOB c_multi_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/multi/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/multi/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/multi/README.txt")
+ install(FILES ${c_multi_samples} DESTINATION ${MISC_PREFIX}examples/c/multi)
- if(WITH_CSHARP)
- # add_subdirectory(csharp/fbc)
- endif(WITH_CSHARP)
+ file(GLOB cpp_multi_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/multi/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/multi/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/multi/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/multi/README.txt")
+ install(FILES ${cpp_multi_samples} DESTINATION ${MISC_PREFIX}examples/c++/multi)
- if(WITH_JAVA)
- # add_subdirectory(java/fbc)
- endif(WITH_JAVA)
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_multi_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/multi/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/multi/README.txt")
+ install(FILES ${perl_multi_samples} DESTINATION ${MISC_PREFIX}examples/perl/multi)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_multi_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/multi/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/multi/README.txt")
+ install(FILES ${python_multi_samples} DESTINATION ${MISC_PREFIX}examples/python/multi)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_multi_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/multi/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/multi/README.txt")
+ install(FILES ${ruby_multi_samples} DESTINATION ${MISC_PREFIX}examples/ruby/multi)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_multi_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/multi/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/multi/README.txt")
+ install(FILES ${r_multi_samples} DESTINATION ${MISC_PREFIX}examples/r/multi)
+ endif()
+
endif(ENABLE_MULTI)
Modified: branches/libsbml-experimental/examples/render-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/render-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/render-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -9,13 +9,54 @@
if (ENABLE_RENDER)
# add_subdirectory(c/render)
- add_subdirectory(c++/render)
+ add_subdirectory(c++/render)
-# if(WITH_CSHARP)
-# add_subdirectory(csharp/render)
-# endif(WITH_CSHARP)
+# if(WITH_CSHARP)
+# add_subdirectory(csharp/render)
+# endif(WITH_CSHARP)
- if(WITH_JAVA)
- add_subdirectory(java/render)
- endif(WITH_JAVA)
+ if(WITH_JAVA)
+ add_subdirectory(java/render)
+ endif(WITH_JAVA)
+
+ file(GLOB c_render_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/render/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/render/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/render/README.txt")
+ install(FILES ${c_render_samples} DESTINATION ${MISC_PREFIX}examples/c/render)
+
+ file(GLOB cpp_render_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/render/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/render/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/render/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/render/README.txt")
+ install(FILES ${cpp_render_samples} DESTINATION ${MISC_PREFIX}examples/c++/render)
+
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_render_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/render/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/render/README.txt")
+ install(FILES ${perl_render_samples} DESTINATION ${MISC_PREFIX}examples/perl/render)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_render_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/render/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/render/README.txt")
+ install(FILES ${python_render_samples} DESTINATION ${MISC_PREFIX}examples/python/render)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_render_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/render/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/render/README.txt")
+ install(FILES ${ruby_render_samples} DESTINATION ${MISC_PREFIX}examples/ruby/render)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_render_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/render/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/render/README.txt")
+ install(FILES ${r_render_samples} DESTINATION ${MISC_PREFIX}examples/r/render)
+ endif()
+
endif(ENABLE_RENDER)
Modified: branches/libsbml-experimental/examples/req-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/req-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/req-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -8,14 +8,56 @@
#
if (ENABLE_REQUIREDELEMENTS)
-# add_subdirectory(c/req)
- add_subdirectory(c++/req)
+# add_subdirectory(c/req)
+ add_subdirectory(c++/req)
- if(WITH_CSHARP)
-# add_subdirectory(csharp/req)
- endif(WITH_CSHARP)
+ if(WITH_CSHARP)
+# add_subdirectory(csharp/req)
+ endif(WITH_CSHARP)
- if(WITH_JAVA)
-# add_subdirectory(java/req)
- endif(WITH_JAVA)
+ if(WITH_JAVA)
+# add_subdirectory(java/req)
+ endif(WITH_JAVA)
+
+ file(GLOB c_req_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/req/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/req/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/req/README.txt")
+ install(FILES ${c_req_samples} DESTINATION ${MISC_PREFIX}examples/c/req)
+
+ file(GLOB cpp_req_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/req/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/req/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/req/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/req/README.txt")
+ install(FILES ${cpp_req_samples} DESTINATION ${MISC_PREFIX}examples/c++/req)
+
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_req_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/req/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/req/README.txt")
+ install(FILES ${perl_req_samples} DESTINATION ${MISC_PREFIX}examples/perl/req)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_req_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/req/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/req/README.txt")
+ install(FILES ${python_req_samples} DESTINATION ${MISC_PREFIX}examples/python/req)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_req_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/req/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/req/README.txt")
+ install(FILES ${ruby_req_samples} DESTINATION ${MISC_PREFIX}examples/ruby/req)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_req_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/req/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/req/README.txt")
+ install(FILES ${r_req_samples} DESTINATION ${MISC_PREFIX}examples/r/req)
+ endif()
+
+
endif(ENABLE_REQUIREDELEMENTS)
Modified: branches/libsbml-experimental/examples/spatial-package.cmake
===================================================================
--- branches/libsbml-experimental/examples/spatial-package.cmake 2014-01-23 14:32:33 UTC (rev 19552)
+++ branches/libsbml-experimental/examples/spatial-package.cmake 2014-01-23 15:11:08 UTC (rev 19553)
@@ -8,14 +8,55 @@
#
if (ENABLE_SPATIAL)
-# add_subdirectory(c/spatial)
- add_subdirectory(c++/spatial)
+# add_subdirectory(c/spatial)
+ add_subdirectory(c++/spatial)
+
+ if(WITH_CSHARP)
+# add_subdirectory(csharp/spatial)
+ endif(WITH_CSHARP)
+
+ if(WITH_JAVA)
+# add_subdirectory(java/spatial)
+ endif(WITH_JAVA)
+
+ file(GLOB c_spatial_samples "${CMAKE_CURRENT_SOURCE_DIR}/c/spatial/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/spatial/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c/spatial/README.txt")
+ install(FILES ${c_spatial_samples} DESTINATION ${MISC_PREFIX}examples/c/spatial)
- if(WITH_CSHARP)
-# add_subdirectory(csharp/spatial)
- endif(WITH_CSHARP)
+ file(GLOB cpp_spatial_samples "${CMAKE_CURRENT_SOURCE_DIR}/c++/spatial/*.c"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/spatial/*.cpp"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/spatial/*.h"
+ "${CMAKE_CURRENT_SOURCE_DIR}/c++/spatial/README.txt")
+ install(FILES ${cpp_spatial_samples} DESTINATION ${MISC_PREFIX}examples/c++/spatial)
- if(WITH_JAVA)
-# add_subdirectory(java/spatial)
- endif(WITH_JAVA)
+ if(WITH_PERL)
+ # install perl examples
+ file(GLOB perl_spatial_samples "${CMAKE_CURRENT_SOURCE_DIR}/perl/spatial/*.pl"
+ "${CMAKE_CURRENT_SOURCE_DIR}/perl/spatial/README.txt")
+ install(FILES ${perl_spatial_samples} DESTINATION ${MISC_PREFIX}examples/perl/spatial)
+ endif()
+
+ if (WITH_PYTHON)
+ # install python examples
+ file(GLOB python_spatial_samples "${CMAKE_CURRENT_SOURCE_DIR}/python/spatial/*.py"
+ "${CMAKE_CURRENT_SOURCE_DIR}/python/spatial/README.txt")
+ install(FILES ${python_spatial_samples} DESTINATION ${MISC_PREFIX}examples/python/spatial)
+ endif()
+
+
+ if(WITH_RUBY)
+ # install ruby examples
+ file(GLOB ruby_spatial_samples "${CMAKE_CURRENT_SOURCE_DIR}/ruby/spatial/*.rb"
+ "${CMAKE_CURRENT_SOURCE_DIR}/ruby/spatial/README.txt")
+ install(FILES ${ruby_spatial_samples} DESTINATION ${MISC_PREFIX}examples/ruby/spatial)
+ endif()
+
+ if (WITH_R)
+ # install r examples
+ file(GLOB r_spatial_samples "${CMAKE_CURRENT_SOURCE_DIR}/r/spatial/*.R"
+ "${CMAKE_CURRENT_SOURCE_DIR}/r/spatial/README.txt")
+ install(FILES ${r_spatial_samples} DESTINATION ${MISC_PREFIX}examples/r/spatial)
+ endif()
+
endif(ENABLE_SPATIAL)
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