Systems Biology Markup Language (SBML)

Revision: 9463
          http://sbml.svn.sourceforge.net/sbml/?rev=9463&view=rev
Author:   ajouraku
Date:     2009-04-30 09:46:51 +0000 (Thu, 30 Apr 2009)

Log Message:
-----------
1. Added Makefile.in in win32/MSVC9 directory.
2. Updated configure scripts and Makefile.in for win32/MSVC9.

Modified Paths:
--------------
    branches/libsbml-4/configure
    branches/libsbml-4/configure.ac
    branches/libsbml-4/win32/Makefile.in

Added Paths:
-----------
    branches/libsbml-4/win32/MSVC9/Makefile.in

Modified: branches/libsbml-4/configure
===================================================================
--- branches/libsbml-4/configure	2009-04-30 08:36:56 UTC (rev 9462)
+++ branches/libsbml-4/configure	2009-04-30 09:46:51 UTC (rev 9463)
@@ -1,5 +1,5 @@
 #! /bin/sh
-# From configure.ac Revision: 9289 .
+# From configure.ac Revision: 9365 .
 # Guess values for system-dependent variables and create Makefiles.
 # Generated by GNU Autoconf 2.61 for libSBML 4.0.0-b1.
 #
@@ -26740,7 +26740,9 @@
 
 ac_config_files="$ac_config_files win32/MSVC8/Makefile"
 
+ac_config_files="$ac_config_files win32/MSVC9/Makefile"
 
+
 ac_config_files="$ac_config_files examples/c/Makefile"
 
 ac_config_files="$ac_config_files examples/c++/Makefile"
@@ -27356,6 +27358,7 @@
     "win32/Makefile") CONFIG_FILES="$CONFIG_FILES win32/Makefile" ;;
     "win32/MSVC7/Makefile") CONFIG_FILES="$CONFIG_FILES win32/MSVC7/Makefile" ;;
     "win32/MSVC8/Makefile") CONFIG_FILES="$CONFIG_FILES win32/MSVC8/Makefile" ;;
+    "win32/MSVC9/Makefile") CONFIG_FILES="$CONFIG_FILES win32/MSVC9/Makefile" ;;
     "examples/c/Makefile") CONFIG_FILES="$CONFIG_FILES examples/c/Makefile" ;;
     "examples/c++/Makefile") CONFIG_FILES="$CONFIG_FILES examples/c++/Makefile" ;;
     "examples/java/Makefile") CONFIG_FILES="$CONFIG_FILES examples/java/Makefile" ;;

Modified: branches/libsbml-4/configure.ac
===================================================================
--- branches/libsbml-4/configure.ac	2009-04-30 08:36:56 UTC (rev 9462)
+++ branches/libsbml-4/configure.ac	2009-04-30 09:46:51 UTC (rev 9463)
@@ -326,6 +326,7 @@
 AC_CONFIG_FILES([win32/Makefile])
 AC_CONFIG_FILES([win32/MSVC7/Makefile])
 AC_CONFIG_FILES([win32/MSVC8/Makefile])
+AC_CONFIG_FILES([win32/MSVC9/Makefile])
 
 AC_CONFIG_FILES([examples/c/Makefile])
 AC_CONFIG_FILES([examples/c++/Makefile])

Added: branches/libsbml-4/win32/MSVC9/Makefile.in
===================================================================
--- branches/libsbml-4/win32/MSVC9/Makefile.in	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/Makefile.in	2009-04-30 09:46:51 UTC (rev 9463)
@@ -0,0 +1,146 @@
+## @configure_input@
+##
+## Filename    : Makefile.in
+## Description : Makefile for win32/MSVC9 subdirectory
+## Author(s)   : SBML Team <sbml-team@...>
+## Organization: Caltech, USA, and University of Hertfordshire, UK
+## Created     : 2009-04-30
+## Revision    : $Id$
+## $HeadURL$
+##
+## Copyright 2009 California Institute of Technology and
+## Japan Science and Technology Corporation.
+##
+## This library is free software; you can redistribute it and/or modify it
+## under the terms of the GNU Lesser General Public License as published
+## by the Free Software Foundation; either version 2.1 of the License, or
+## any later version.
+##
+## This library is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+## MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
+## documentation provided hereunder is on an "as is" basis, and the
+## California Institute of Technology and Japan Science and Technology
+## Corporation have no obligations to provide maintenance, support,
+## updates, enhancements or modifications.  In no event shall the
+## California Institute of Technology or the Japan Science and Technology
+## Corporation be liable to any party for direct, indirect, special,
+## incidental or consequential damages, including lost profits, arising
+## out of the use of this software and its documentation, even if the
+## California Institute of Technology and/or Japan Science and Technology
+## Corporation have been advised of the possibility of such damage.  See
+## the GNU Lesser General Public License for more details.
+##
+## You should have received a copy of the GNU Lesser General Public License
+## along with this library; if not, write to the Free Software Foundation,
+## Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+##
+## The original code contained here was initially developed by:
+##
+##     Sarah Keating and Ben Bornstein
+##     SBML Team
+##     http://www.sbml.org
+##     mailto:sbml-team@...
+##
+## Contributor(s):
+##   Michael Hucka <mhucka@...> Wrote this Makefile.in.
+##
+
+# -----------------------------------------------------------------------------
+# Configuration variables
+# -----------------------------------------------------------------------------
+# Some of the following are substituted automatically by `configure'.  If
+# you are looking at "Makefile", do not edit these values; instead, run the
+# configure script at the top level of the src tree.  It will recreate
+# "Makefile".
+
+include @top_srcdir@...
+
+# `srcdir' points to the current directory, but should be set by configure.
+# `subdir' must be set manually to the relative dir under `srcdir'.  Don't 
+# set `subdir' to an absolute path, or some `make' actions will fail.
+
+srcdir  = @srcdir@
+thisdir = win32/MSVC9
+
+# This makefile only serves a role for `make dist'.
+
+distfiles = \
+  convertSBML.vcproj     \
+  echoSBML.vcproj        \
+  libsbml.sln            \
+  libsbml.vcproj         \
+  libsbml_expat.sln      \
+  libsbml_expat.vcproj   \
+  libsbml_xml.sln        \
+  libsbml_xml.vcproj     \
+  printSBML.vcproj       \
+  validateSBML.vcproj    \
+  Makefile.in
+
+
+# -----------------------------------------------------------------------------
+# Primary build actions
+# -----------------------------------------------------------------------------
+
+# At this time, this makefile currently does nothing except serve to set
+# variables for `make dist'.  Consequently, there is nothing here to build.
+
+all: 
+
+
+# -----------------------------------------------------------------------------
+# Checking.
+# -----------------------------------------------------------------------------
+
+check:
+
+
+# -----------------------------------------------------------------------------
+# Formatting documentation.
+# -----------------------------------------------------------------------------
+
+dvi:
+
+pdf:
+
+ps:
+
+info:
+
+html:
+
+
+# -----------------------------------------------------------------------------
+# Installation
+# -----------------------------------------------------------------------------
+
+# This library doesn't actually get installed.  The main libsbml library
+# (in ../src) slurps in the contents when it's built.
+
+install:
+
+uninstall:
+
+installcheck:
+
+
+# -----------------------------------------------------------------------------
+# Creating distribution (for libSBML maintainers only)
+# -----------------------------------------------------------------------------
+
+dist: dist-normal
+
+distcheck: distcheck-normal
+
+
+# -----------------------------------------------------------------------------
+# Miscellaneous
+# -----------------------------------------------------------------------------
+
+include @top_srcdir@...
+
+
+# -----------------------------------------------------------------------------
+# End.
+# -----------------------------------------------------------------------------

Modified: branches/libsbml-4/win32/Makefile.in
===================================================================
--- branches/libsbml-4/win32/Makefile.in	2009-04-30 08:36:56 UTC (rev 9462)
+++ branches/libsbml-4/win32/Makefile.in	2009-04-30 09:46:51 UTC (rev 9463)
@@ -63,7 +63,7 @@
 srcdir  = @srcdir@
 thisdir = win32
 
-subdirs = MSVC7 MSVC8
+subdirs = MSVC7 MSVC8 MSVC9
 
 # This makefile only serves a role for `make dist'.
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9462
          http://sbml.svn.sourceforge.net/sbml/?rev=9462&view=rev
Author:   ajouraku
Date:     2009-04-30 08:36:56 +0000 (Thu, 30 Apr 2009)

Log Message:
-----------
1. Added Makefile.in in win32/MSVC9 directory.
2. Updated configure scripts and Makefile.in for win32/MSVC9.

Modified Paths:
--------------
    trunk/libsbml/configure
    trunk/libsbml/configure.ac
    trunk/libsbml/win32/Makefile.in

Added Paths:
-----------
    trunk/libsbml/win32/MSVC9/Makefile.in

Modified: trunk/libsbml/configure
===================================================================
--- trunk/libsbml/configure	2009-04-29 21:47:21 UTC (rev 9461)
+++ trunk/libsbml/configure	2009-04-30 08:36:56 UTC (rev 9462)
@@ -1,5 +1,5 @@
 #! /bin/sh
-# From configure.ac Revision: 8979 .
+# From configure.ac Revision: 9224 .
 # Guess values for system-dependent variables and create Makefiles.
 # Generated by GNU Autoconf 2.61 for libSBML 3.3.2.
 #
@@ -11409,7 +11409,9 @@
 
 ac_config_files="$ac_config_files win32/MSVC8/Makefile"
 
+ac_config_files="$ac_config_files win32/MSVC9/Makefile"
 
+
 ac_config_files="$ac_config_files examples/c/Makefile"
 
 ac_config_files="$ac_config_files examples/c++/Makefile"
@@ -12023,6 +12025,7 @@
     "win32/Makefile") CONFIG_FILES="$CONFIG_FILES win32/Makefile" ;;
     "win32/MSVC7/Makefile") CONFIG_FILES="$CONFIG_FILES win32/MSVC7/Makefile" ;;
     "win32/MSVC8/Makefile") CONFIG_FILES="$CONFIG_FILES win32/MSVC8/Makefile" ;;
+    "win32/MSVC9/Makefile") CONFIG_FILES="$CONFIG_FILES win32/MSVC9/Makefile" ;;
     "examples/c/Makefile") CONFIG_FILES="$CONFIG_FILES examples/c/Makefile" ;;
     "examples/c++/Makefile") CONFIG_FILES="$CONFIG_FILES examples/c++/Makefile" ;;
     "examples/java/Makefile") CONFIG_FILES="$CONFIG_FILES examples/java/Makefile" ;;

Modified: trunk/libsbml/configure.ac
===================================================================
--- trunk/libsbml/configure.ac	2009-04-29 21:47:21 UTC (rev 9461)
+++ trunk/libsbml/configure.ac	2009-04-30 08:36:56 UTC (rev 9462)
@@ -321,6 +321,7 @@
 AC_CONFIG_FILES([win32/Makefile])
 AC_CONFIG_FILES([win32/MSVC7/Makefile])
 AC_CONFIG_FILES([win32/MSVC8/Makefile])
+AC_CONFIG_FILES([win32/MSVC9/Makefile])
 
 AC_CONFIG_FILES([examples/c/Makefile])
 AC_CONFIG_FILES([examples/c++/Makefile])

Added: trunk/libsbml/win32/MSVC9/Makefile.in
===================================================================
--- trunk/libsbml/win32/MSVC9/Makefile.in	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/Makefile.in	2009-04-30 08:36:56 UTC (rev 9462)
@@ -0,0 +1,146 @@
+## @configure_input@
+##
+## Filename    : Makefile.in
+## Description : Makefile for win32/MSVC9 subdirectory
+## Author(s)   : SBML Team <sbml-team@...>
+## Organization: Caltech, USA, and University of Hertfordshire, UK
+## Created     : 2009-04-30
+## Revision    : $Id$
+## $HeadURL$
+##
+## Copyright 2009 California Institute of Technology and
+## Japan Science and Technology Corporation.
+##
+## This library is free software; you can redistribute it and/or modify it
+## under the terms of the GNU Lesser General Public License as published
+## by the Free Software Foundation; either version 2.1 of the License, or
+## any later version.
+##
+## This library is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+## MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
+## documentation provided hereunder is on an "as is" basis, and the
+## California Institute of Technology and Japan Science and Technology
+## Corporation have no obligations to provide maintenance, support,
+## updates, enhancements or modifications.  In no event shall the
+## California Institute of Technology or the Japan Science and Technology
+## Corporation be liable to any party for direct, indirect, special,
+## incidental or consequential damages, including lost profits, arising
+## out of the use of this software and its documentation, even if the
+## California Institute of Technology and/or Japan Science and Technology
+## Corporation have been advised of the possibility of such damage.  See
+## the GNU Lesser General Public License for more details.
+##
+## You should have received a copy of the GNU Lesser General Public License
+## along with this library; if not, write to the Free Software Foundation,
+## Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+##
+## The original code contained here was initially developed by:
+##
+##     Sarah Keating and Ben Bornstein
+##     SBML Team
+##     http://www.sbml.org
+##     mailto:sbml-team@...
+##
+## Contributor(s):
+##   Michael Hucka <mhucka@...> Wrote this Makefile.in.
+##
+
+# -----------------------------------------------------------------------------
+# Configuration variables
+# -----------------------------------------------------------------------------
+# Some of the following are substituted automatically by `configure'.  If
+# you are looking at "Makefile", do not edit these values; instead, run the
+# configure script at the top level of the src tree.  It will recreate
+# "Makefile".
+
+include @top_srcdir@...
+
+# `srcdir' points to the current directory, but should be set by configure.
+# `subdir' must be set manually to the relative dir under `srcdir'.  Don't 
+# set `subdir' to an absolute path, or some `make' actions will fail.
+
+srcdir  = @srcdir@
+thisdir = win32/MSVC9
+
+# This makefile only serves a role for `make dist'.
+
+distfiles = \
+  convertSBML.vcproj     \
+  echoSBML.vcproj        \
+  libsbml.sln            \
+  libsbml.vcproj         \
+  libsbml_expat.sln      \
+  libsbml_expat.vcproj   \
+  libsbml_xml.sln        \
+  libsbml_xml.vcproj     \
+  printSBML.vcproj       \
+  validateSBML.vcproj    \
+  Makefile.in
+
+
+# -----------------------------------------------------------------------------
+# Primary build actions
+# -----------------------------------------------------------------------------
+
+# At this time, this makefile currently does nothing except serve to set
+# variables for `make dist'.  Consequently, there is nothing here to build.
+
+all: 
+
+
+# -----------------------------------------------------------------------------
+# Checking.
+# -----------------------------------------------------------------------------
+
+check:
+
+
+# -----------------------------------------------------------------------------
+# Formatting documentation.
+# -----------------------------------------------------------------------------
+
+dvi:
+
+pdf:
+
+ps:
+
+info:
+
+html:
+
+
+# -----------------------------------------------------------------------------
+# Installation
+# -----------------------------------------------------------------------------
+
+# This library doesn't actually get installed.  The main libsbml library
+# (in ../src) slurps in the contents when it's built.
+
+install:
+
+uninstall:
+
+installcheck:
+
+
+# -----------------------------------------------------------------------------
+# Creating distribution (for libSBML maintainers only)
+# -----------------------------------------------------------------------------
+
+dist: dist-normal
+
+distcheck: distcheck-normal
+
+
+# -----------------------------------------------------------------------------
+# Miscellaneous
+# -----------------------------------------------------------------------------
+
+include @top_srcdir@...
+
+
+# -----------------------------------------------------------------------------
+# End.
+# -----------------------------------------------------------------------------

Modified: trunk/libsbml/win32/Makefile.in
===================================================================
--- trunk/libsbml/win32/Makefile.in	2009-04-29 21:47:21 UTC (rev 9461)
+++ trunk/libsbml/win32/Makefile.in	2009-04-30 08:36:56 UTC (rev 9462)
@@ -63,7 +63,7 @@
 srcdir  = @srcdir@
 thisdir = win32
 
-subdirs = MSVC7 MSVC8
+subdirs = MSVC7 MSVC8 MSVC9
 
 # This makefile only serves a role for `make dist'.
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9461
          http://sbml.svn.sourceforge.net/sbml/?rev=9461&view=rev
Author:   sarahkeating
Date:     2009-04-29 21:47:21 +0000 (Wed, 29 Apr 2009)

Log Message:
-----------
corrected data identified as incorrect during hackathon
NOTE: these results have been verified with Copasi and iBioSim

Modified Paths:
--------------
    trunk/test-suite/cases/semantic/00250/00250-plot.jpg
    trunk/test-suite/cases/semantic/00250/00250-results.csv
    trunk/test-suite/cases/semantic/00385/00385-model.m
    trunk/test-suite/cases/semantic/00385/00385-plot.jpg
    trunk/test-suite/cases/semantic/00385/00385-results.csv
    trunk/test-suite/cases/semantic/00385/00385-sbml-l2v1.xml
    trunk/test-suite/cases/semantic/00385/00385-sbml-l2v2.xml
    trunk/test-suite/cases/semantic/00385/00385-sbml-l2v3.xml
    trunk/test-suite/cases/semantic/00385/00385-sbml-l2v4.xml
    trunk/test-suite/cases/semantic/00506/00506-plot.jpg
    trunk/test-suite/cases/semantic/00506/00506-results.csv

Modified: trunk/test-suite/cases/semantic/00250/00250-plot.jpg
===================================================================
(Binary files differ)

Modified: trunk/test-suite/cases/semantic/00250/00250-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00250/00250-results.csv	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00250/00250-results.csv	2009-04-29 21:47:21 UTC (rev 9461)
@@ -1,52 +1,52 @@
 time,S1,S2,S3,S4,S5
 0,1e-006,1.5e-006,2e-006,5e-007,1e-006
-0.04,7.194336174896538e-007,1.219433617489654e-006,2.280566382510345e-006,7.805663825103458e-007,1e-006
-0.08,5.576290276379696e-007,1.05762902763797e-006,2.442370972362029e-006,9.423709723620301e-007,1e-006
-0.12,4.560430924373447e-007,9.560430924373452e-007,2.543956907562655e-006,1.043956907562655e-006,1e-006
-0.16,3.888279905729221e-007,8.888279905729226e-007,2.611172009427077e-006,1.111172009427077e-006,1e-006
-0.2,3.427975564961449e-007,8.427975564961451e-007,2.657202443503854e-006,1.157202443503855e-006,1e-006
-0.24,3.105273199947131e-007,8.105273199947134e-007,2.689472680005285e-006,1.189472680005287e-006,1e-006
-0.28,2.87530371760306e-007,7.875303717603063e-007,2.712469628239692e-006,1.212469628239694e-006,1e-006
-0.32,2.709500177200908e-007,7.70950017720091e-007,2.729049982279907e-006,1.229049982279909e-006,1e-006
-0.36,2.588953139295691e-007,7.588953139295694e-007,2.741104686070429e-006,1.241104686070431e-006,1e-006
-0.4,2.500774801619746e-007,7.50077480161975e-007,2.749922519838024e-006,1.249922519838025e-006,1e-006
-0.44,2.43598616399667e-007,7.435986163996674e-007,2.756401383600331e-006,1.256401383600333e-006,1e-006
-0.48,2.388227280456654e-007,7.388227280456659e-007,2.761177271954333e-006,1.261177271954334e-006,1e-006
-0.52,2.352937046490826e-007,7.352937046490831e-007,2.764706295350916e-006,1.264706295350917e-006,1e-006
-0.56,2.326813823093608e-007,7.326813823093612e-007,2.767318617690638e-006,1.267318617690639e-006,1e-006
-0.6,2.307450908271132e-007,7.307450908271136e-007,2.769254909172885e-006,1.269254909172887e-006,1e-006
-0.64,2.293084847435279e-007,7.293084847435284e-007,2.77069151525647e-006,1.270691515256472e-006,1e-006
-0.68,2.282418418188597e-007,7.282418418188602e-007,2.771758158181139e-006,1.27175815818114e-006,1e-006
-0.72,2.274494628579585e-007,7.274494628579589e-007,2.77255053714204e-006,1.272550537142041e-006,1e-006
-0.76,2.268605900139941e-007,7.268605900139944e-007,2.773139409986004e-006,1.273139409986006e-006,1e-006
-0.8,2.264228284488332e-007,7.264228284488336e-007,2.773577171551166e-006,1.273577171551166e-006,1e-006
-0.84,2.260973298664715e-007,7.26097329866472e-007,2.773902670133527e-006,1.273902670133528e-006,1e-006
-0.88,2.258552647728578e-007,7.258552647728583e-007,2.774144735227141e-006,1.274144735227142e-006,1e-006
-0.92,2.256752249907657e-007,7.256752249907662e-007,2.774324775009233e-006,1.274324775009234e-006,1e-006
-0.96,2.255413053211286e-007,7.255413053211291e-007,2.77445869467887e-006,1.274458694678871e-006,1e-006
-1,2.254416845871725e-007,7.25441684587173e-007,2.774558315412826e-006,1.274558315412827e-006,1e-006
-1.04,2.253675746344876e-007,7.253675746344881e-007,2.774632425365511e-006,1.274632425365512e-006,1e-006
-1.08,2.253124409252195e-007,7.2531244092522e-007,2.774687559074779e-006,1.27468755907478e-006,1e-006
-1.12,2.252714236956562e-007,7.252714236956567e-007,2.774728576304342e-006,1.274728576304343e-006,1e-006
-1.16,2.25240907201625e-007,7.252409072016256e-007,2.774759092798373e-006,1.274759092798375e-006,1e-006
-1.2,2.252182022279686e-007,7.252182022279692e-007,2.77478179777203e-006,1.274781797772031e-006,1e-006
-1.24,2.252013103943606e-007,7.252013103943612e-007,2.774798689605638e-006,1.274798689605639e-006,1e-006
-1.28,2.251887431063613e-007,7.251887431063618e-007,2.774811256893637e-006,1.274811256893638e-006,1e-006
-1.32,2.25179391563439e-007,7.251793915634396e-007,2.774820608436559e-006,1.274820608436561e-006,1e-006
-1.36,2.251724352899928e-007,7.251724352899934e-007,2.774827564710006e-006,1.274827564710007e-006,1e-006
-1.4,2.251672584646061e-007,7.251672584646067e-007,2.774832741535392e-006,1.274832741535394e-006,1e-006
-1.44,2.251634076536546e-007,7.251634076536551e-007,2.774836592346344e-006,1.274836592346345e-006,1e-006
-1.48,2.251605418848323e-007,7.251605418848328e-007,2.774839458115166e-006,1.274839458115167e-006,1e-006
-1.52,2.251584103940354e-007,7.25158410394036e-007,2.774841589605963e-006,1.274841589605964e-006,1e-006
-1.56,2.251568235892699e-007,7.251568235892705e-007,2.774843176410729e-006,1.27484317641073e-006,1e-006
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Modified: trunk/test-suite/cases/semantic/00385/00385-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00385/00385-model.m	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00385/00385-model.m	2009-04-29 21:47:21 UTC (rev 9461)
@@ -56,6 +56,6 @@
 addReaction[ S3 -> S1 + S2, reversible -> False,
 	     kineticLaw -> k2 * S3 * S4 * C ];
 addEvent[ trigger -> S2 < S4, eventAssignment -> S1->2/10^3 ];
-addEvent[ trigger -> S3 > 2/(10^15), eventAssignment -> S3->1/10^3 ];
+addEvent[ trigger -> S3 > 2/(10^3), eventAssignment -> S3->1/10^3 ];
 
 makemodel[]

Modified: trunk/test-suite/cases/semantic/00385/00385-plot.jpg
===================================================================
(Binary files differ)

Modified: trunk/test-suite/cases/semantic/00385/00385-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00385/00385-results.csv	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00385/00385-results.csv	2009-04-29 21:47:21 UTC (rev 9461)
@@ -1,52 +1,52 @@
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+2.4,0.001427666078042398,0.0004276660655812159,0.001672333921400586,0.001
+2.45,0.001425753598566461,0.000425753586105278,0.001674246400876524,0.001
+2.5,0.001423991567758559,0.0004239915552973764,0.001676008431684426,0.001
\ No newline at end of file

Modified: trunk/test-suite/cases/semantic/00385/00385-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00385/00385-sbml-l2v1.xml	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00385/00385-sbml-l2v1.xml	2009-04-29 21:47:21 UTC (rev 9461)
@@ -73,7 +73,7 @@
         <listOfEventAssignments>
           <eventAssignment variable="S1">
             <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="rational"> 1 <sep/> 500 </cn>
+              <cn> 0.002 </cn>
             </math>
           </eventAssignment>
         </listOfEventAssignments>
@@ -84,7 +84,7 @@
             <apply>
               <gt/>
               <ci> S3 </ci>
-              <cn type="rational"> 1 <sep/> 1 </cn>
+              <cn> 0.002 </cn>
             </apply>
           </math>
         </trigger>

Modified: trunk/test-suite/cases/semantic/00385/00385-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00385/00385-sbml-l2v2.xml	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00385/00385-sbml-l2v2.xml	2009-04-29 21:47:21 UTC (rev 9461)
@@ -73,7 +73,7 @@
         <listOfEventAssignments>
           <eventAssignment variable="S1">
             <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="rational"> 1 <sep/> 500 </cn>
+              <cn> 0.002 </cn>
             </math>
           </eventAssignment>
         </listOfEventAssignments>
@@ -84,7 +84,7 @@
             <apply>
               <gt/>
               <ci> S3 </ci>
-              <cn type="rational"> 1 <sep/> 1 </cn>
+              <cn> 0.002 </cn>
             </apply>
           </math>
         </trigger>

Modified: trunk/test-suite/cases/semantic/00385/00385-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00385/00385-sbml-l2v3.xml	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00385/00385-sbml-l2v3.xml	2009-04-29 21:47:21 UTC (rev 9461)
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 21-February-2009 10:28:18.9440038 -->
+<!-- Generated 8-April-2009 03:43:36.7500000 -->
 <!-- Generated by MathSBML 2.7.5 [2-May-2008] -->
 <!-- Generated using Mathematica Version 5.2 for Microsoft Windows (June 20, 2005) -->
 <sbml xmlns="http://www.sbml.org/sbml/level2/version3"
@@ -133,7 +133,7 @@
     <listOfEventAssignments>
      <eventAssignment variable="S1">
       <math xmlns="http://www.w3.org/1998/Math/MathML">
-       <cn type="rational">1<sep/>500</cn>
+       <cn>0.002</cn>
       </math>
      </eventAssignment>
     </listOfEventAssignments>
@@ -145,7 +145,7 @@
       <apply>
        <gt/>
        <ci>S3</ci>
-       <cn type="rational">1<sep/>500000000000000</cn>
+       <cn>0.002</cn>
       </apply>
      </math>
     </trigger>

Modified: trunk/test-suite/cases/semantic/00385/00385-sbml-l2v4.xml
===================================================================
--- trunk/test-suite/cases/semantic/00385/00385-sbml-l2v4.xml	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00385/00385-sbml-l2v4.xml	2009-04-29 21:47:21 UTC (rev 9461)
@@ -73,7 +73,7 @@
         <listOfEventAssignments>
           <eventAssignment variable="S1">
             <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="rational"> 1 <sep/> 500 </cn>
+              <cn> 0.002 </cn>
             </math>
           </eventAssignment>
         </listOfEventAssignments>
@@ -84,7 +84,7 @@
             <apply>
               <gt/>
               <ci> S3 </ci>
-              <cn type="rational"> 1 <sep/> 1 </cn>
+              <cn> 0.002 </cn>
             </apply>
           </math>
         </trigger>

Modified: trunk/test-suite/cases/semantic/00506/00506-plot.jpg
===================================================================
(Binary files differ)

Modified: trunk/test-suite/cases/semantic/00506/00506-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00506/00506-results.csv	2009-04-27 22:27:36 UTC (rev 9460)
+++ trunk/test-suite/cases/semantic/00506/00506-results.csv	2009-04-29 21:47:21 UTC (rev 9461)
@@ -1,52 +1,52 @@
-time,case00506`S1,case00506`S2,case00506`S3,case00506`S4
+time,S1,S2,S3,S4
 0,0.0025,0.02,0.01,0.01
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-1.2,0.004942068795272475,0.02244206879527246,0.007557931204727527,0.01
-1.6,0.005585995597429867,0.02308599559742985,0.006914004402570134,0.01
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-5.2,0.008992702058400026,0.02649270205840001,0.003507297941599975,0.01
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-8.4,0.01012159946930747,0.02762159946930746,0.002378400530692526,0.01
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+20,0.01208003969858138,0.0295800396985814,0.0004199603014186159,0.01


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9460
          http://sbml.svn.sourceforge.net/sbml/?rev=9460&view=rev
Author:   sarahkeating
Date:     2009-04-27 22:27:36 +0000 (Mon, 27 Apr 2009)

Log Message:
-----------
added MSVC9 files
NOTE: these are not yet added to the make scripts 

Added Paths:
-----------
    trunk/libsbml/win32/MSVC9/
    trunk/libsbml/win32/MSVC9/convertSBML.vcproj
    trunk/libsbml/win32/MSVC9/echoSBML.vcproj
    trunk/libsbml/win32/MSVC9/libsbml.sln
    trunk/libsbml/win32/MSVC9/libsbml.vcproj
    trunk/libsbml/win32/MSVC9/libsbml_expat.sln
    trunk/libsbml/win32/MSVC9/libsbml_expat.vcproj
    trunk/libsbml/win32/MSVC9/libsbml_xml.sln
    trunk/libsbml/win32/MSVC9/libsbml_xml.vcproj
    trunk/libsbml/win32/MSVC9/printSBML.vcproj
    trunk/libsbml/win32/MSVC9/validateSBML.vcproj

Added: trunk/libsbml/win32/MSVC9/convertSBML.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC9/convertSBML.vcproj	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/convertSBML.vcproj	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,223 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="convertSBML"
+	ProjectGUID="{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	RootNamespace="convertSBML"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\bin"
+			IntermediateDirectory=".\convertSBML___Win32_Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/printSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\convertSBML___Win32_Debug/convertSBML.pch"
+				AssemblerListingLocation=".\convertSBML___Win32_Debug/"
+				ObjectFile=".\convertSBML___Win32_Debug/"
+				ProgramDataBaseFileName=".\convertSBML___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbmlD.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/convertSBMLD.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/convertSBMLD.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\convertSBML___Win32_Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/printSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\convertSBML___Win32_Release/convertSBML.pch"
+				AssemblerListingLocation=".\convertSBML___Win32_Release/"
+				ObjectFile=".\convertSBML___Win32_Release/"
+				ProgramDataBaseFileName=".\convertSBML___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbml.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/convertSBML.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/convertSBML.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="..\..\examples\c++\convertSBML.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="..\..\examples\util.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: trunk/libsbml/win32/MSVC9/echoSBML.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC9/echoSBML.vcproj	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/echoSBML.vcproj	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,226 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="echoSBML"
+	ProjectGUID="{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	RootNamespace="echoSBML"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\bin"
+			IntermediateDirectory=".\echoSBML___Win32_Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/echoSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\echoSBML___Win32_Debug/echoSBML.pch"
+				AssemblerListingLocation=".\echoSBML___Win32_Debug/"
+				ObjectFile=".\echoSBML___Win32_Debug/"
+				ProgramDataBaseFileName=".\echoSBML___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbmlD.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/echoSBMLD.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/echoSBMLD.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\bin"
+			IntermediateDirectory=".\echoSBML___Win32_Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/echoSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\echoSBML___Win32_Release/echoSBML.pch"
+				AssemblerListingLocation=".\echoSBML___Win32_Release/"
+				ObjectFile=".\echoSBML___Win32_Release/"
+				ProgramDataBaseFileName=".\echoSBML___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbml.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/echoSBML.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/echoSBML.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="..\..\examples\c++\echoSBML.cpp">
+			</File>
+			<File
+				RelativePath="..\..\examples\c++\util.c">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="..\..\examples\util.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: trunk/libsbml/win32/MSVC9/libsbml.sln
===================================================================
--- trunk/libsbml/win32/MSVC9/libsbml.sln	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/libsbml.sln	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,47 @@
+
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libsbml", "libsbml.vcproj", "{713656C6-8BBB-40DC-9B5C-F13443DBE12C}"
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "convertSBML", "convertSBML.vcproj", "{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C} = {713656C6-8BBB-40DC-9B5C-F13443DBE12C}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "echoSBML", "echoSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C} = {713656C6-8BBB-40DC-9B5C-F13443DBE12C}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "validateSBML", "validateSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C} = {713656C6-8BBB-40DC-9B5C-F13443DBE12C}
+	EndProjectSection
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Debug|Win32.Build.0 = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Release|Win32.ActiveCfg = Release|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Release|Win32.Build.0 = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.Build.0 = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.ActiveCfg = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Added: trunk/libsbml/win32/MSVC9/libsbml.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC9/libsbml.vcproj	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/libsbml.vcproj	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,1483 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="libsbml"
+	ProjectGUID="{713656C6-8BBB-40DC-9B5C-F13443DBE12C}"
+	RootNamespace="libsbml"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_XERCES;USE_ZLIB;USE_BZ2;USE_LAYOUT"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Debug/libsbml.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalOptions="/NODEFAULTLIB:MSVCRT"
+				AdditionalDependencies="../bin/xerces-c_2D.lib ../bin/zlib.lib ../bin/bzip2.lib"
+				OutputFile="../bin/libsbmlD.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				IgnoreAllDefaultLibraries="false"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/libsbmlD.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbmlD.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				ExcludedFromBuild="false"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;USE_XERCES;LIBLAX_EXPORTS;USE_ZLIB;USE_BZ2;USE_LAYOUT"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Release/libsbml.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/xerces-c_2.lib ../bin/zlib.lib ../bin/bzip2.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/libsbml.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/libsbml.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbml.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheckWarnings.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentRuleOrdering.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\ASTNode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\BoundingBox.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\bzfstream.cpp"
+				>
+			</File>
+                        <File
+                                RelativePath="..\..\src\compress\zipfstream.cpp"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\ioapi.c"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\iowin32.c"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\zip.c"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\unzip.c"
+                                >
+                        </File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CiElementMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Compartment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CompartmentGlyph.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CompartmentOutsideCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\CompartmentType.cpp"
+				>
+			</File>
+                        <File
+                                RelativePath="..\..\src\compress\CompressCommon.cpp"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\InputDecompressor.cpp"
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+			<File
+				RelativePath="..\..\src\validator\constraints\LambdaMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Layout.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\LayoutAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\layoutfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LayoutUtilities.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-config-win.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-package.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LineSegment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\List.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\ListOf.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterShadowsIdInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LogicalArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\MathML.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\MathMLConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\memory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Model.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\ModelHistory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ModelingPracticeValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumberArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericReturnMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverDeterminedCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\OverdeterminedValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Parameter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PieceBooleanMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PiecewiseValueMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Point.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PowerUnitsCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\RDFAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Reaction.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\ReactionGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Rule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLDocument.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorTable.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\sbmlfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLReader.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLTypeCodes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLVisitor.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLWriter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBO.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\SBOConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Species.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\SpeciesReactionOrRule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesReference.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceRole.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesType.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\Stack.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\StoichiometryMath.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\StoichiometryMathVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\StringMap.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\TextGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Trigger.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsForUnitDefinitions.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInKineticLaw.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueMetaId.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSpeciesTypesInCompartment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSymbolsInInitialAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInInitialAssignmentsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Unit.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\UnitConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitDefinition.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitFormulaFormatter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitKind.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitKindList.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UnitsBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\util.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\Validator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\VConstraint.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesNamespaces.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesTranscode.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLExtern.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLFileBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLInputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLMemoryBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNamespaces.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNode.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLOutputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLToken.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTokenizer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTriple.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\zfstream.h"
+				>
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+			>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: trunk/libsbml/win32/MSVC9/libsbml_expat.sln
===================================================================
--- trunk/libsbml/win32/MSVC9/libsbml_expat.sln	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/libsbml_expat.sln	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,47 @@
+
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "convertSBML", "convertSBML.vcproj", "{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB} = {F1E45E77-55AC-43D6-974F-0987F5D0EFAB}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "echoSBML", "echoSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB} = {F1E45E77-55AC-43D6-974F-0987F5D0EFAB}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "validateSBML", "validateSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB} = {F1E45E77-55AC-43D6-974F-0987F5D0EFAB}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libsbml", "libsbml_expat.vcproj", "{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.Build.0 = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.ActiveCfg = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Debug|Win32.Build.0 = Debug|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Release|Win32.ActiveCfg = Release|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Added: trunk/libsbml/win32/MSVC9/libsbml_expat.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC9/libsbml_expat.vcproj	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/libsbml_expat.vcproj	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,1455 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="libsbml"
+	ProjectGUID="{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}"
+	RootNamespace="libsbml"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml_expat.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="USE_EXPAT;USE_ZLIB;USE_BZ2;WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_LAYOUT"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Debug/libsbml_expat.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalOptions="/NODEFAULTLIB:MSVCRT"
+				AdditionalDependencies="../bin/libexpat.lib ../bin/zlib.lib ../bin/bzip2.lib"
+				OutputFile="../bin/libsbmlD.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				IgnoreAllDefaultLibraries="false"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/libsbmlD.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbmlD.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				ExcludedFromBuild="false"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml_expat.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="USE_EXPAT;USE_ZLIB;USE_BZ2;WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_LAYOUT"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Release/libsbml_expat.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
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+				RelativePath="..\..\src\xml\ExpatAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\ExpatHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\ExpatParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ExponentUnitsCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\extern.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaFormatter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaTokenizer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\FormulaUnitsData.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionApplyMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\FunctionDefinition.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\GraphicalObject.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\IdentifierConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdList.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\InitialAssignment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\InternalConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\KineticLaw.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\KineticLawVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L1CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v1CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v2CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v3CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v4CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LambdaMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Layout.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\LayoutAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\layoutfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LayoutUtilities.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-config-win.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-package.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LineSegment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\List.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\ListOf.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterShadowsIdInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LogicalArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\MathML.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\MathMLConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\memory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Model.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\ModelHistory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ModelingPracticeValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumberArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericReturnMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverDeterminedCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\OverdeterminedValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Parameter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PieceBooleanMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PiecewiseValueMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Point.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PowerUnitsCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\RDFAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Reaction.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\ReactionGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Rule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLDocument.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorTable.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\sbmlfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLReader.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLTypeCodes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLVisitor.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLWriter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBO.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\SBOConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Species.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\SpeciesReactionOrRule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesReference.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceRole.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesType.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\Stack.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\StoichiometryMath.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\StoichiometryMathVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\StringMap.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\TextGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Trigger.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsForUnitDefinitions.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInKineticLaw.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueMetaId.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSpeciesTypesInCompartment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSymbolsInInitialAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInInitialAssignmentsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Unit.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\UnitConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitDefinition.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitFormulaFormatter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitKind.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitKindList.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UnitsBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\util.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\Validator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\VConstraint.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLExtern.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLFileBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLInputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLMemoryBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNamespaces.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNode.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLOutputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLToken.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTokenizer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTriple.h"
+				>
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+			>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: trunk/libsbml/win32/MSVC9/libsbml_xml.sln
===================================================================
--- trunk/libsbml/win32/MSVC9/libsbml_xml.sln	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/libsbml_xml.sln	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,47 @@
+
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "convertSBML", "convertSBML.vcproj", "{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D} = {713656C6-8BBB-40DC-9B5C-F13443DBF23D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "echoSBML", "echoSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D} = {713656C6-8BBB-40DC-9B5C-F13443DBF23D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "validateSBML", "validateSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D} = {713656C6-8BBB-40DC-9B5C-F13443DBF23D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libsbml", "libsbml_xml.vcproj", "{713656C6-8BBB-40DC-9B5C-F13443DBF23D}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.Build.0 = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.ActiveCfg = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Debug|Win32.Build.0 = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Release|Win32.ActiveCfg = Release|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Added: trunk/libsbml/win32/MSVC9/libsbml_xml.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC9/libsbml_xml.vcproj	                        (rev 0)
+++ trunk/libsbml/win32/MSVC9/libsbml_xml.vcproj	2009-04-27 22:27:36 UTC (rev 9460)
@@ -0,0 +1,1471 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="libsbml"
+	ProjectGUID="{713656C6-8BBB-40DC-9B5C-F13443DBF23D}"
+	RootNamespace="libsbml"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_LIBXML;USE_ZLIB;USE_BZ2;USE_LAYOUT"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Debug/libsbml.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalOptions="/NODEFAULTLIB:MSVCRT"
+				AdditionalDependencies="../bin/libxml2.lib ../bin/iconv.lib ../bin/zlib.lib ../bin/bzip2.lib"
+				OutputFile="../bin/libsbmlD.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				IgnoreAllDefaultLibraries="false"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/libsbmlD.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbmlD.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				ExcludedFromBuild="false"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;USE_LIBXML;USE_ZLIB;USE_BZ2;LIBLAX_EXPORTS;USE_LAYOUT"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Release/libsbml.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libxml2.lib ../bin/iconv.lib ../bin/zlib.lib ../bin/bzip2.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/libsbml.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/libsbml.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbml.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheckWarnings.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentRuleOrdering.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\ASTNode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\BoundingBox.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\bzfstream.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CiElementMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Compartment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CompartmentGlyph.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CompartmentOutsideCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\CompartmentType.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\CompressCommon.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Constraint.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CubicBezier.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Curve.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\CVTerm.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Delay.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Dimensions.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\EqualityArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Event.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\EventAssignment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ExponentUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaFormatter.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaParser.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaTokenizer.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\FormulaUnitsData.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionApplyMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\FunctionDefinition.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\GraphicalObject.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdBase.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdentifierConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\IdentifierConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdList.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\InitialAssignment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\InputDecompressor.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\InternalConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\InternalConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\ioapi.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\iowin32.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\KineticLaw.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\KineticLawVars.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L1CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L1CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v1CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v1CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v2CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v2CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v3CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v3CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v4CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v4CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LambdaMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Layout.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\LayoutAnnotation.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LayoutUtilities.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-version.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLAttributes.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLHandler.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLNamespaces.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLParser.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLTranscode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LineSegment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\List.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\ListOf.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterShadowsIdInModel.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LogicalArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\MathML.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLBase.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\MathMLConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\memory.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Model.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\ModelHistory.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ModelingPracticeConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ModelingPracticeValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumberArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericReturnMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\OutputCompressor.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverDeterminedCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverdeterminedConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\OverdeterminedValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Parameter.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PieceBooleanMathCheck.cpp"
+				>

@@ Diff output truncated at 100000 characters. @@

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9459
          http://sbml.svn.sourceforge.net/sbml/?rev=9459&view=rev
Author:   sarahkeating
Date:     2009-04-27 22:25:27 +0000 (Mon, 27 Apr 2009)

Log Message:
-----------
added MSVC9 files
NOTE: these are not yet added to the make scripts 

Added Paths:
-----------
    branches/libsbml-4/win32/MSVC9/
    branches/libsbml-4/win32/MSVC9/convertSBML.vcproj
    branches/libsbml-4/win32/MSVC9/echoSBML.vcproj
    branches/libsbml-4/win32/MSVC9/libsbml.sln
    branches/libsbml-4/win32/MSVC9/libsbml.vcproj
    branches/libsbml-4/win32/MSVC9/libsbml_expat.sln
    branches/libsbml-4/win32/MSVC9/libsbml_expat.vcproj
    branches/libsbml-4/win32/MSVC9/libsbml_xml.sln
    branches/libsbml-4/win32/MSVC9/libsbml_xml.vcproj
    branches/libsbml-4/win32/MSVC9/printSBML.vcproj
    branches/libsbml-4/win32/MSVC9/validateSBML.vcproj

Added: branches/libsbml-4/win32/MSVC9/convertSBML.vcproj
===================================================================
--- branches/libsbml-4/win32/MSVC9/convertSBML.vcproj	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/convertSBML.vcproj	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,223 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="convertSBML"
+	ProjectGUID="{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	RootNamespace="convertSBML"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\bin"
+			IntermediateDirectory=".\convertSBML___Win32_Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/printSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\convertSBML___Win32_Debug/convertSBML.pch"
+				AssemblerListingLocation=".\convertSBML___Win32_Debug/"
+				ObjectFile=".\convertSBML___Win32_Debug/"
+				ProgramDataBaseFileName=".\convertSBML___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbmlD.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/convertSBMLD.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/convertSBMLD.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\convertSBML___Win32_Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/printSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\convertSBML___Win32_Release/convertSBML.pch"
+				AssemblerListingLocation=".\convertSBML___Win32_Release/"
+				ObjectFile=".\convertSBML___Win32_Release/"
+				ProgramDataBaseFileName=".\convertSBML___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbml.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/convertSBML.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/convertSBML.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="..\..\examples\c++\convertSBML.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="..\..\examples\util.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: branches/libsbml-4/win32/MSVC9/echoSBML.vcproj
===================================================================
--- branches/libsbml-4/win32/MSVC9/echoSBML.vcproj	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/echoSBML.vcproj	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,226 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="echoSBML"
+	ProjectGUID="{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	RootNamespace="echoSBML"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\bin"
+			IntermediateDirectory=".\echoSBML___Win32_Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/echoSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\echoSBML___Win32_Debug/echoSBML.pch"
+				AssemblerListingLocation=".\echoSBML___Win32_Debug/"
+				ObjectFile=".\echoSBML___Win32_Debug/"
+				ProgramDataBaseFileName=".\echoSBML___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbmlD.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/echoSBMLD.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/echoSBMLD.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\bin"
+			IntermediateDirectory=".\echoSBML___Win32_Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2">
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\bin/echoSBML.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\echoSBML___Win32_Release/echoSBML.pch"
+				AssemblerListingLocation=".\echoSBML___Win32_Release/"
+				ObjectFile=".\echoSBML___Win32_Release/"
+				ProgramDataBaseFileName=".\echoSBML___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				CompileAs="2"/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libsbml.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/echoSBML.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/echoSBML.pdb"
+				SubSystem="1"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="..\..\examples\c++\echoSBML.cpp">
+			</File>
+			<File
+				RelativePath="..\..\examples\c++\util.c">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="..\..\examples\util.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: branches/libsbml-4/win32/MSVC9/libsbml.sln
===================================================================
--- branches/libsbml-4/win32/MSVC9/libsbml.sln	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/libsbml.sln	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,47 @@
+
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libsbml", "libsbml.vcproj", "{713656C6-8BBB-40DC-9B5C-F13443DBE12C}"
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "convertSBML", "convertSBML.vcproj", "{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C} = {713656C6-8BBB-40DC-9B5C-F13443DBE12C}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "echoSBML", "echoSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C} = {713656C6-8BBB-40DC-9B5C-F13443DBE12C}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "validateSBML", "validateSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C} = {713656C6-8BBB-40DC-9B5C-F13443DBE12C}
+	EndProjectSection
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Debug|Win32.Build.0 = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Release|Win32.ActiveCfg = Release|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBE12C}.Release|Win32.Build.0 = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.Build.0 = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.ActiveCfg = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Added: branches/libsbml-4/win32/MSVC9/libsbml.vcproj
===================================================================
--- branches/libsbml-4/win32/MSVC9/libsbml.vcproj	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/libsbml.vcproj	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,1483 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="libsbml"
+	ProjectGUID="{713656C6-8BBB-40DC-9B5C-F13443DBE12C}"
+	RootNamespace="libsbml"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_XERCES;USE_ZLIB;USE_BZ2;USE_LAYOUT"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Debug/libsbml.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalOptions="/NODEFAULTLIB:MSVCRT"
+				AdditionalDependencies="../bin/xerces-c_2D.lib ../bin/zlib.lib ../bin/bzip2.lib"
+				OutputFile="../bin/libsbmlD.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				IgnoreAllDefaultLibraries="false"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/libsbmlD.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbmlD.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				ExcludedFromBuild="false"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;USE_XERCES;LIBLAX_EXPORTS;USE_ZLIB;USE_BZ2;USE_LAYOUT"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Release/libsbml.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/xerces-c_2.lib ../bin/zlib.lib ../bin/bzip2.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/libsbml.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/libsbml.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbml.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheckWarnings.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentRuleOrdering.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\ASTNode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\BoundingBox.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\bzfstream.cpp"
+				>
+			</File>
+                        <File
+                                RelativePath="..\..\src\compress\zipfstream.cpp"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\ioapi.c"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\iowin32.c"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\zip.c"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\unzip.c"
+                                >
+                        </File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CiElementMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Compartment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CompartmentGlyph.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CompartmentOutsideCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\CompartmentType.cpp"
+				>
+			</File>
+                        <File
+                                RelativePath="..\..\src\compress\CompressCommon.cpp"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\InputDecompressor.cpp"
+                                >
+                        </File>
+                        <File
+                                RelativePath="..\..\src\compress\OutputCompressor.cpp"
+                                >
+                        </File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Constraint.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CubicBezier.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Curve.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\CVTerm.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Delay.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Dimensions.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\EqualityArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Event.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\EventAssignment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ExponentUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaFormatter.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaParser.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaTokenizer.c"
+				>
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+			</File>
+			<File
+				RelativePath="..\..\src\util\memory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Model.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\ModelHistory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ModelingPracticeValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumberArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericReturnMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverDeterminedCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\OverdeterminedValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Parameter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PieceBooleanMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PiecewiseValueMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Point.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PowerUnitsCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\RDFAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Reaction.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\ReactionGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Rule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLDocument.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorTable.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\sbmlfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLReader.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLTypeCodes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLVisitor.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLWriter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBO.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\SBOConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Species.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\SpeciesReactionOrRule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesReference.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceRole.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesType.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\Stack.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\StoichiometryMath.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\StoichiometryMathVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\StringMap.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\TextGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Trigger.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsForUnitDefinitions.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInKineticLaw.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueMetaId.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSpeciesTypesInCompartment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSymbolsInInitialAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInInitialAssignmentsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Unit.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\UnitConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitDefinition.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitFormulaFormatter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitKind.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitKindList.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UnitsBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\util.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\Validator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\VConstraint.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesNamespaces.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XercesTranscode.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLExtern.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLFileBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLInputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLMemoryBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNamespaces.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNode.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLOutputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLToken.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTokenizer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTriple.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\zfstream.h"
+				>
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+			>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: branches/libsbml-4/win32/MSVC9/libsbml_expat.sln
===================================================================
--- branches/libsbml-4/win32/MSVC9/libsbml_expat.sln	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/libsbml_expat.sln	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,47 @@
+
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "convertSBML", "convertSBML.vcproj", "{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB} = {F1E45E77-55AC-43D6-974F-0987F5D0EFAB}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "echoSBML", "echoSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB} = {F1E45E77-55AC-43D6-974F-0987F5D0EFAB}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "validateSBML", "validateSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB} = {F1E45E77-55AC-43D6-974F-0987F5D0EFAB}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libsbml", "libsbml_expat.vcproj", "{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.Build.0 = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.ActiveCfg = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Debug|Win32.Build.0 = Debug|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Release|Win32.ActiveCfg = Release|Win32
+		{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Added: branches/libsbml-4/win32/MSVC9/libsbml_expat.vcproj
===================================================================
--- branches/libsbml-4/win32/MSVC9/libsbml_expat.vcproj	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/libsbml_expat.vcproj	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,1455 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="libsbml"
+	ProjectGUID="{F1E45E77-55AC-43D6-974F-0987F5D0EFAB}"
+	RootNamespace="libsbml"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml_expat.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="USE_EXPAT;USE_ZLIB;USE_BZ2;WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_LAYOUT"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Debug/libsbml_expat.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalOptions="/NODEFAULTLIB:MSVCRT"
+				AdditionalDependencies="../bin/libexpat.lib ../bin/zlib.lib ../bin/bzip2.lib"
+				OutputFile="../bin/libsbmlD.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				IgnoreAllDefaultLibraries="false"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/libsbmlD.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbmlD.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				ExcludedFromBuild="false"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml_expat.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="USE_EXPAT;USE_ZLIB;USE_BZ2;WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_LAYOUT"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Release/libsbml_expat.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libexpat.lib ../bin/zlib.lib ../bin/bzip2.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/libsbml.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/libsbml.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbml.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheckWarnings.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentRuleOrdering.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\ASTNode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\BoundingBox.cpp"
+				>
+			</File>
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+				RelativePath="..\..\src\validator\IdentifierConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdList.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\InitialAssignment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\InternalConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\KineticLaw.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\KineticLawVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L1CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v1CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v2CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v3CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v4CompatibilityValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LambdaMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Layout.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\LayoutAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\layoutfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LayoutUtilities.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-config-win.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-package.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LineSegment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\List.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\ListOf.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterShadowsIdInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LogicalArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\MathML.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\MathMLConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\memory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Model.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\ModelHistory.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ModelingPracticeValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumberArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericArgsMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericReturnMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverDeterminedCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\OverdeterminedValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Parameter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PieceBooleanMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PiecewiseValueMathCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Point.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\PowerUnitsCheck.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\RDFAnnotation.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Reaction.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\ReactionGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Rule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLDocument.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLErrorTable.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\sbmlfwd.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLReader.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLTypeCodes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLVisitor.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBMLWriter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SBO.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\SBOConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Species.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\SpeciesReactionOrRule.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesReference.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\SpeciesReferenceRole.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\SpeciesType.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\Stack.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\StoichiometryMath.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\StoichiometryMathVars.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\StringMap.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\TextGlyph.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Trigger.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsForUnitDefinitions.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInKineticLaw.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueIdsInModel.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueMetaId.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSpeciesTypesInCompartment.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueSymbolsInInitialAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventAssignments.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInEventsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInInitialAssignmentsAndRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UniqueVarsInRules.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Unit.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\UnitConsistencyValidator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitDefinition.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitFormulaFormatter.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\UnitKind.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\UnitKindList.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\UnitsBase.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\util.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\Validator.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\VConstraint.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLAttributes.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLError.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLErrorLog.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLExtern.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLFileBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLHandler.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLInputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLMemoryBuffer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNamespaces.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLNode.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLOutputStream.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLParser.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLToken.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTokenizer.h"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\XMLTriple.h"
+				>
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+			>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Added: branches/libsbml-4/win32/MSVC9/libsbml_xml.sln
===================================================================
--- branches/libsbml-4/win32/MSVC9/libsbml_xml.sln	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/libsbml_xml.sln	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,47 @@
+
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "convertSBML", "convertSBML.vcproj", "{1574F9F3-425F-4726-A338-C6EBB3076BAF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D} = {713656C6-8BBB-40DC-9B5C-F13443DBF23D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "echoSBML", "echoSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D} = {713656C6-8BBB-40DC-9B5C-F13443DBF23D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "validateSBML", "validateSBML.vcproj", "{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}"
+	ProjectSection(ProjectDependencies) = postProject
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D} = {713656C6-8BBB-40DC-9B5C-F13443DBF23D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libsbml", "libsbml_xml.vcproj", "{713656C6-8BBB-40DC-9B5C-F13443DBF23D}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Debug|Win32.Build.0 = Debug|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.ActiveCfg = Release|Win32
+		{1574F9F3-425F-4726-A338-C6EBB3076BAF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC4FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Debug|Win32.Build.0 = Debug|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.ActiveCfg = Release|Win32
+		{BEE99AD9-8649-48CA-A095-9A80AC0FDFDF}.Release|Win32.Build.0 = Release|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Debug|Win32.Build.0 = Debug|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Release|Win32.ActiveCfg = Release|Win32
+		{713656C6-8BBB-40DC-9B5C-F13443DBF23D}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Added: branches/libsbml-4/win32/MSVC9/libsbml_xml.vcproj
===================================================================
--- branches/libsbml-4/win32/MSVC9/libsbml_xml.vcproj	                        (rev 0)
+++ branches/libsbml-4/win32/MSVC9/libsbml_xml.vcproj	2009-04-27 22:25:27 UTC (rev 9459)
@@ -0,0 +1,1471 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="9.00"
+	Name="libsbml"
+	ProjectGUID="{713656C6-8BBB-40DC-9B5C-F13443DBF23D}"
+	RootNamespace="libsbml"
+	TargetFrameworkVersion="131072"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;LIBLAX_EXPORTS;USE_LIBXML;USE_ZLIB;USE_BZ2;USE_LAYOUT"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Debug/libsbml.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="4"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalOptions="/NODEFAULTLIB:MSVCRT"
+				AdditionalDependencies="../bin/libxml2.lib ../bin/iconv.lib ../bin/zlib.lib ../bin/bzip2.lib"
+				OutputFile="../bin/libsbmlD.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				IgnoreAllDefaultLibraries="false"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile=".\bin/libsbmlD.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbmlD.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				ExcludedFromBuild="false"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory="..\bin"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC71.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			CharacterSet="2"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+				CommandLine="..\createIncludeFromMSVC.bat"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName=".\bin/libsbml.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="0"
+				AdditionalIncludeDirectories="../../include;../include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBSBML_EXPORTS;USE_LIBXML;USE_ZLIB;USE_BZ2;LIBLAX_EXPORTS;USE_LAYOUT"
+				StringPooling="false"
+				ExceptionHandling="1"
+				BasicRuntimeChecks="0"
+				RuntimeLibrary="2"
+				BufferSecurityCheck="false"
+				EnableFunctionLevelLinking="false"
+				RuntimeTypeInfo="true"
+				UsePrecompiledHeader="0"
+				PrecompiledHeaderFile=".\Release/libsbml.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="2057"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="../bin/libxml2.lib ../bin/iconv.lib ../bin/zlib.lib ../bin/bzip2.lib odbc32.lib odbccp32.lib"
+				OutputFile="../bin/libsbml.dll"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile=".\bin/libsbml.pdb"
+				RandomizedBaseAddress="1"
+				DataExecutionPrevention="0"
+				ImportLibrary="../bin/libsbml.lib"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ArgumentsUnitsCheckWarnings.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\AssignmentRuleOrdering.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\ASTNode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\BoundingBox.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\bzfstream.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CiElementMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Compartment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CompartmentGlyph.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\CompartmentOutsideCycles.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\CompartmentType.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\CompressCommon.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Constraint.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\CubicBezier.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Curve.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\CVTerm.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Delay.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Dimensions.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\EqualityArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Event.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\EventAssignment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ExponentUnitsCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaFormatter.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaParser.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\FormulaTokenizer.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\units\FormulaUnitsData.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionApplyMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\FunctionDefinition.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\GraphicalObject.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdBase.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdentifierConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\IdentifierConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\IdList.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\InitialAssignment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\InputDecompressor.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\InternalConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\InternalConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\ioapi.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\iowin32.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\KineticLaw.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\KineticLawVars.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L1CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L1CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v1CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v1CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v2CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v2CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v3CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v3CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\L2v4CompatibilityConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\L2v4CompatibilityValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LambdaMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\Layout.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\LayoutAnnotation.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LayoutUtilities.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\common\libsbml-version.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLAttributes.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLHandler.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLNamespaces.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLParser.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\xml\LibXMLTranscode.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\layout\LineSegment.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\List.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\ListOf.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LocalParameterShadowsIdInModel.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\LogicalArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\math\MathML.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLBase.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\MathMLConsistencyConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\MathMLConsistencyValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\util\memory.c"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\sbml\Model.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\annotation\ModelHistory.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\ModelingPracticeConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\ModelingPracticeValidator.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumberArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericArgsMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\NumericReturnMathCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\compress\OutputCompressor.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverDeterminedCheck.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\constraints\OverdeterminedConstraints.cpp"
+				>
+			</File>
+			<File
+				RelativePath="..\..\src\validator\OverdeterminedValidator.cpp"
+				>
+			</File>
+			<File

@@ Diff output truncated at 100000 characters. @@

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9443
          http://sbml.svn.sourceforge.net/sbml/?rev=9443&view=rev
Author:   sarahkeating
Date:     2009-04-16 18:33:10 +0000 (Thu, 16 Apr 2009)

Log Message:
-----------
added a "empty string" member variable to facilitate the getId/getName functions on SBase for classes that dont have an id or name

Modified Paths:
--------------
    branches/libsbml-4/src/sbml/SBase.cpp
    branches/libsbml-4/src/sbml/SBase.h

Modified: branches/libsbml-4/src/sbml/SBase.cpp
===================================================================
--- branches/libsbml-4/src/sbml/SBase.cpp	2009-04-16 16:48:09 UTC (rev 9442)
+++ branches/libsbml-4/src/sbml/SBase.cpp	2009-04-16 18:33:10 UTC (rev 9443)
@@ -151,6 +151,7 @@
  , mParentSBMLObject (0)
  , mCVTerms   ( 0 )
  , mHasBeenDeleted (false)
+ , mEmptyString ("")
 {
 }
 /** @endcond doxygen-libsbml-internal */
@@ -174,6 +175,7 @@
  , mParentSBMLObject (0)
  , mCVTerms   ( 0 )
  , mHasBeenDeleted (false)
+ , mEmptyString ("")
 {
 }
 /** @endcond doxygen-libsbml-internal */
@@ -420,11 +422,11 @@
 #endif  /* USE_LAYOUT */
 
   default:
-    return "";
+    return mEmptyString;
     break;
   }
 
-  return "";
+  return mEmptyString;
 }
 
 
@@ -495,11 +497,11 @@
     #endif  /* USE_LAYOUT */
 
       default:
-        return "";
+        return mEmptyString;
         break;
     }
 
-    return "";
+    return mEmptyString;
   }
   else
   {
@@ -554,11 +556,11 @@
       break;
 
     default:
-      return "";
+      return mEmptyString;
       break;
     }
 
-    return "";
+    return mEmptyString;
   }
 }
 

Modified: branches/libsbml-4/src/sbml/SBase.h
===================================================================
--- branches/libsbml-4/src/sbml/SBase.h	2009-04-16 16:48:09 UTC (rev 9442)
+++ branches/libsbml-4/src/sbml/SBase.h	2009-04-16 18:33:10 UTC (rev 9443)
@@ -1739,6 +1739,8 @@
    */
   bool mHasBeenDeleted;
 
+  std::string mEmptyString;
+
   /** @endcond doxygen-libsbml-internal */
 
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9457
          http://sbml.svn.sourceforge.net/sbml/?rev=9457&view=rev
Author:   sarahkeating
Date:     2009-04-27 21:54:13 +0000 (Mon, 27 Apr 2009)

Log Message:
-----------
Tracker issue #2714870
If the sbo term is not set then getSBOTermID should return an empty string

Modified Paths:
--------------
    trunk/libsbml/src/sbml/SBase.cpp

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2009-04-27 21:46:57 UTC (rev 9456)
+++ trunk/libsbml/src/sbml/SBase.cpp	2009-04-27 21:54:13 UTC (rev 9457)
@@ -491,10 +491,7 @@
 std::string
 SBase::getSBOTermID () const
 {
-  //if (mSBOTerm == -1)
-  //  return NULL;
-  //else
-    return SBO::intToString(mSBOTerm);
+  return SBO::intToString(mSBOTerm);
 }
 
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9444
          http://sbml.svn.sourceforge.net/sbml/?rev=9444&view=rev
Author:   sarahkeating
Date:     2009-04-17 00:21:57 +0000 (Fri, 17 Apr 2009)

Log Message:
-----------
added createTrigger, createDelay and createStoichiometryMath functions to both libsbml-3 and libsbml-4. These functions were really "missing" from teh API but adding them allows complete creation of a model using ONLY create functions and not constructors.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/Event.cpp
    trunk/libsbml/src/sbml/Event.h
    trunk/libsbml/src/sbml/Model.cpp
    trunk/libsbml/src/sbml/Model.h
    trunk/libsbml/src/sbml/SpeciesReference.cpp
    trunk/libsbml/src/sbml/SpeciesReference.h
    trunk/libsbml/src/sbml/test/TestAncestor.cpp

Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/Event.cpp	2009-04-17 00:21:57 UTC (rev 9444)
@@ -383,6 +383,40 @@
 
 
 /*
+ * Creates a new Trigger, adds it to this Event
+ * and returns it.
+ */
+Trigger*
+Event::createTrigger ()
+{
+  delete mTrigger;
+  mTrigger = new Trigger;
+
+  mTrigger->setSBMLDocument(mSBML);
+  mTrigger->setParentSBMLObject(this);
+
+  return mTrigger;
+}
+
+
+/*
+ * Creates a new Delay, adds it to this Event
+ * and returns it.
+ */
+Delay*
+Event::createDelay ()
+{
+  delete mDelay;
+  mDelay = new Delay;
+
+  mDelay->setSBMLDocument(mSBML);
+  mDelay->setParentSBMLObject(this);
+
+  return mDelay;
+}
+
+
+/*
  * @return the list of EventAssignments for this Event.
  */
 const ListOfEventAssignments*
@@ -1344,6 +1378,36 @@
 
 
 /**
+ * Creates a new, empty Trigger_t structure, adds it to this
+ * Event, and returns the Trigger_t.
+ *
+ * @param e the Event_t structure to which the trigger should be
+ * added
+ */
+LIBSBML_EXTERN
+Trigger_t *
+Event_createTrigger (Event_t *e)
+{
+  return e->createTrigger();
+}
+
+
+/**
+ * Creates a new, empty Delay_t structure, adds it to this
+ * Event, and returns the Delay_t.
+ *
+ * @param e the Event_t structure to which the delay should be
+ * added
+ */
+LIBSBML_EXTERN
+Delay_t *
+Event_createDelay (Event_t *e)
+{
+  return e->createDelay();
+}
+
+
+/**
  * Get the list of EventAssignment_t structures from this Event_t
  * structure.
  *

Modified: trunk/libsbml/src/sbml/Event.h
===================================================================
--- trunk/libsbml/src/sbml/Event.h	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/Event.h	2009-04-17 00:21:57 UTC (rev 9444)
@@ -523,6 +523,28 @@
 
 
   /**
+   * Creates a new, empty Trigger, adds it to this Event and 
+   * returns the Trigger.
+   *
+   * @return the newly created Trigger object instance
+   *
+   * @see addEvent()
+   */
+  Trigger* createTrigger ();
+
+
+  /**
+   * Creates a new, empty Delay, adds it to this Event and 
+   * returns the Delay.
+   *
+   * @return the newly created Delay object instance
+   *
+   * @see addEvent()
+   */
+  Delay* createDelay ();
+
+
+  /**
    * Returns the list of event assignments for this Event.
    * 
    * @return the list of EventAssignments for this Event.
@@ -1045,6 +1067,16 @@
 
 
 LIBSBML_EXTERN
+Trigger_t *
+Event_createTrigger (Event_t *e);
+
+
+LIBSBML_EXTERN
+Delay_t *
+Event_createDelay (Event_t *e);
+
+
+LIBSBML_EXTERN
 ListOf_t *
 Event_getListOfEventAssignments (Event_t *e);
 

Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/Model.cpp	2009-04-17 00:21:57 UTC (rev 9444)
@@ -876,6 +876,36 @@
 
 
 /*
+ * Creates a new Trigger inside this Model and returns a pointer to
+ * it.  The Trigger is added to the the last Event created.
+ *
+ * If an Event does not exist for this model, a new Trigger is not
+ * created and NULL is returned.
+ */
+Trigger*
+Model::createTrigger ()
+{
+  unsigned int size = getNumEvents();
+  return (size > 0) ? getEvent(size - 1)->createTrigger() : 0;
+}
+
+
+/*
+ * Creates a new Delay inside this Model and returns a pointer to
+ * it.  The Delay is added to the the last Event created.
+ *
+ * If an Event does not exist for this model, a new Delay is not
+ * created and NULL is returned.
+ */
+Delay*
+Model::createDelay ()
+{
+  unsigned int size = getNumEvents();
+  return (size > 0) ? getEvent(size - 1)->createDelay() : 0;
+}
+
+
+/*
  * Sets the annotation of this SBML object to a copy of annotation.
  */
 void
@@ -3961,6 +3991,52 @@
 
 
 /**
+ * Creates a new Trigger_t structure inside the last Event_t
+ * structure created in the given Model_t structure, and returns a pointer
+ * to it.
+ *
+ * The mechanism by which the last Event_t structure was created is not
+ * significant.  It could have been created in a variety of ways, for
+ * example by using Model_createEvent().  If an Event_t structure does not
+ * exist, a new Trigger_t structure is @em not created and NULL is
+ * returned instead.
+ *
+ * @param m the Model_t structure
+ *
+ * @return the new Trigger_t structure
+ */
+LIBSBML_EXTERN
+Trigger_t *
+Model_createTrigger (Model_t *m)
+{
+  return m->createTrigger();
+}
+
+
+/**
+ * Creates a new Delay_t structure inside the last Event_t
+ * structure created in the given Model_t structure, and returns a pointer
+ * to it.
+ *
+ * The mechanism by which the last Event_t structure was created is not
+ * significant.  It could have been created in a variety of ways, for
+ * example by using Model_createEvent().  If an Event_t structure does not
+ * exist, a new Delay_t structure is @em not created and NULL is
+ * returned instead.
+ *
+ * @param m the Model_t structure
+ *
+ * @return the new Delay_t structure
+ */
+LIBSBML_EXTERN
+Delay_t *
+Model_createDelay (Model_t *m)
+{
+  return m->createDelay();
+}
+
+
+/**
  * Get the list of FunctionDefinition_t structures contained in the given
  * Model_t structure.
  *

Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/Model.h	2009-04-17 00:21:57 UTC (rev 9444)
@@ -842,6 +842,36 @@
 
 
   /**
+   * Creates a new Trigger inside the last Event object created in
+   * this Model, and returns a pointer to it.
+   *
+   * The mechanism by which the last Event object in this model was created
+   * is not significant.  It could have been created in a variety of ways,
+   * for example by using createEvent().  If no Event object exists in this
+   * Model object, a new Trigger is @em not created and NULL is
+   * returned instead.
+   *
+   * @return the Trigger object created
+   */
+  Trigger* createTrigger ();
+
+
+  /**
+   * Creates a new Delay inside the last Event object created in
+   * this Model, and returns a pointer to it.
+   *
+   * The mechanism by which the last Event object in this model was created
+   * is not significant.  It could have been created in a variety of ways,
+   * for example by using createEvent().  If no Event object exists in this
+   * Model object, a new Delay is @em not created and NULL is
+   * returned instead.
+   *
+   * @return the Delay object created
+   */
+  Delay* createDelay ();
+
+
+  /**
    * Sets the value of the "annotation" subelement of this SBML object to a
    * copy of @p annotation.
    *
@@ -2227,6 +2257,16 @@
 
 
 LIBSBML_EXTERN
+Trigger_t *
+Model_createTrigger (Model_t *m);
+
+
+LIBSBML_EXTERN
+Delay_t *
+Model_createDelay (Model_t *m);
+
+
+LIBSBML_EXTERN
 ListOf_t *
 Model_getListOfFunctionDefinitions (Model_t *m);
 

Modified: trunk/libsbml/src/sbml/SpeciesReference.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesReference.cpp	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/SpeciesReference.cpp	2009-04-17 00:21:57 UTC (rev 9444)
@@ -514,9 +514,23 @@
 }
 
 
+/*
+ * Creates a new StoichiometryMath, adds it to this SpeciesReference
+ * and returns it.
+ */
+StoichiometryMath*
+SpeciesReference::createStoichiometryMath ()
+{
+  delete mStoichiometryMath;
+  mStoichiometryMath = new StoichiometryMath;
 
+  mStoichiometryMath->setSBMLDocument(mSBML);
+  mStoichiometryMath->setParentSBMLObject(this);
 
+  return mStoichiometryMath;
+}
 
+
 /*
  * @return the SBMLTypeCode_t of this SBML object or SBML_UNKNOWN
  * (default).
@@ -1940,4 +1954,20 @@
   sr->unsetName();
 }
 
+
+/**
+ * Creates a new, empty StoichiometryMath_t structure, adds it to this
+ * SpeciesReference, and returns the StoichiometryMath_t.
+ *
+ * @param e the SpeciesReference_t structure to which the StoichiometryMath should be
+ * added
+ */
+LIBSBML_EXTERN
+StoichiometryMath_t *
+SpeciesReference_createStoichiometryMath (SpeciesReference_t *sr)
+{
+  return static_cast<SpeciesReference*>(sr)->createStoichiometryMath();
+}
+
+
 /** @endcond doxygen-c-only */

Modified: trunk/libsbml/src/sbml/SpeciesReference.h
===================================================================
--- trunk/libsbml/src/sbml/SpeciesReference.h	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/SpeciesReference.h	2009-04-17 00:21:57 UTC (rev 9444)
@@ -760,6 +760,18 @@
 
 
   /**
+   * Creates a new, empty StoichiometryMath, adds it to this SpeciesReference
+   * and returns the StoichiometryMath.
+   *
+   * @return the newly created StoichiometryMath object instance
+   *
+   * @see addReactant()
+   * @see addProduct()
+   */
+  StoichiometryMath* createStoichiometryMath ();
+
+
+  /**
    * Sets the value of the "annotation" subelement of this SBML object to a
    * copy of @p annotation.
    *
@@ -1451,6 +1463,10 @@
 SpeciesReference_unsetName (SpeciesReference_t *sr);
 
 
+LIBSBML_EXTERN
+StoichiometryMath_t *
+SpeciesReference_createStoichiometryMath (SpeciesReference_t *sr);
+
 END_C_DECLS
 
 

Modified: trunk/libsbml/src/sbml/test/TestAncestor.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestAncestor.cpp	2009-04-16 18:33:10 UTC (rev 9443)
+++ trunk/libsbml/src/sbml/test/TestAncestor.cpp	2009-04-17 00:21:57 UTC (rev 9444)
@@ -585,6 +585,47 @@
 END_TEST
 
 
+START_TEST ( test_Delay_ancestor_create )
+{
+  Event *e = new Event();
+
+  Delay *ea = e->createDelay();
+
+  fail_unless(ea->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(ea->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(ea->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+
+  Delay *obj = e->getDelay();
+
+  fail_unless(obj->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(obj->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(obj->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+}
+END_TEST
+
+
+START_TEST ( test_Delay_ancestor_create_model )
+{
+  Model *m = new Model();
+  Event *e = m->createEvent();
+
+  Delay *ea = m->createDelay();
+
+  fail_unless(ea->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(ea->getAncestorOfType(SBML_MODEL)    == m);
+  fail_unless(ea->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(ea->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+
+  Delay *obj = e->getDelay();
+
+  fail_unless(obj->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(obj->getAncestorOfType(SBML_MODEL)    == m);
+  fail_unless(obj->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(obj->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+}
+END_TEST
+
+
 START_TEST ( test_Event_ancestor_create )
 {
   Model *m = new Model();
@@ -1116,6 +1157,66 @@
 END_TEST
 
 
+START_TEST ( test_StoichiometryMath_ancestor_create )
+{
+  SpeciesReference *sr = new SpeciesReference();
+  StoichiometryMath *sm = sr->createStoichiometryMath();
+
+  fail_unless(sm->getAncestorOfType(SBML_SPECIES_REFERENCE) == sr);
+  fail_unless(sm->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(sm->getAncestorOfType(SBML_COMPARTMENT) == NULL);
+
+  StoichiometryMath *obj = sr->getStoichiometryMath();
+
+  fail_unless(obj->getAncestorOfType(SBML_SPECIES_REFERENCE) == sr);
+  fail_unless(obj->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(obj->getAncestorOfType(SBML_COMPARTMENT) == NULL);
+
+}
+END_TEST
+
+
+START_TEST ( test_Trigger_ancestor_create )
+{
+  Event *e = new Event();
+
+  Trigger *ea = e->createTrigger();
+
+  fail_unless(ea->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(ea->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(ea->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+
+  Trigger *obj = e->getTrigger();
+
+  fail_unless(obj->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(obj->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(obj->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+}
+END_TEST
+
+
+START_TEST ( test_Trigger_ancestor_create_model )
+{
+  Model *m = new Model();
+  Event *e = m->createEvent();
+
+  Trigger *ea = m->createTrigger();
+
+  fail_unless(ea->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(ea->getAncestorOfType(SBML_MODEL)    == m);
+  fail_unless(ea->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(ea->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+
+  Trigger *obj = e->getTrigger();
+
+  fail_unless(obj->getAncestorOfType(SBML_EVENT)    == e);
+  fail_unless(obj->getAncestorOfType(SBML_MODEL)    == m);
+  fail_unless(obj->getAncestorOfType(SBML_DOCUMENT) == NULL);
+  fail_unless(obj->getAncestorOfType(SBML_COMPARTMENT)    == NULL);
+}
+END_TEST
+
+
 START_TEST ( test_Unit_ancestor_create )
 {
   UnitDefinition* ud = new UnitDefinition();
@@ -1225,6 +1326,8 @@
   tcase_add_test( tcase, test_Compartment_ancestor_create );
   tcase_add_test( tcase, test_CompartmentType_ancestor_create );
   tcase_add_test( tcase, test_Constraint_ancestor_create );
+  tcase_add_test( tcase, test_Delay_ancestor_create );
+  tcase_add_test( tcase, test_Delay_ancestor_create_model );
   tcase_add_test( tcase, test_Event_ancestor_create );
   tcase_add_test( tcase, test_EventAssignment_ancestor_create );
   tcase_add_test( tcase, test_EventAssignment_ancestor_create_model );
@@ -1248,6 +1351,9 @@
   tcase_add_test( tcase, test_SpeciesReference_Modifier_ancestor_create );
   tcase_add_test( tcase, test_SpeciesReference_Modifier_ancestor_create_model );
   tcase_add_test( tcase, test_SpeciesType_ancestor_create );
+  tcase_add_test( tcase, test_StoichiometryMath_ancestor_create );
+  tcase_add_test( tcase, test_Trigger_ancestor_create );
+  tcase_add_test( tcase, test_Trigger_ancestor_create_model );
   tcase_add_test( tcase, test_Unit_ancestor_create );
   tcase_add_test( tcase, test_Unit_ancestor_create_model );
   tcase_add_test( tcase, test_UnitDefinition_ancestor_create );


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Revision: 9455
          http://sbml.svn.sourceforge.net/sbml/?rev=9455&view=rev
Author:   mhucka
Date:     2009-04-25 02:54:17 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
Old graphics files, no longer current.

Removed Paths:
-------------
    trunk/project/graphics/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9454
          http://sbml.svn.sourceforge.net/sbml/?rev=9454&view=rev
Author:   mhucka
Date:     2009-04-25 02:53:08 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
The CD ROMs are ancient and only interesting for historical purposes.

Removed Paths:
-------------
    trunk/project/cd-roms/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9453
          http://sbml.svn.sourceforge.net/sbml/?rev=9453&view=rev
Author:   mhucka
Date:     2009-04-25 02:51:36 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
Old experimental work by Andrew; let's archive it.

Removed Paths:
-------------
    trunk/project/experimental/


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Revision: 9452
          http://sbml.svn.sourceforge.net/sbml/?rev=9452&view=rev
Author:   mhucka
Date:     2009-04-25 02:50:58 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
This is a truly old SBML process description and not really
relevant anymore, except for historical interests.

Removed Paths:
-------------
    trunk/project/sbml-forum/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9451
          http://sbml.svn.sourceforge.net/sbml/?rev=9451&view=rev
Author:   mhucka
Date:     2009-04-25 02:50:17 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
These are not truly specifications and are not being
used anymore anyway.

Removed Paths:
-------------
    trunk/specifications/notation/
    trunk/specifications/parameter-sets/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9450
          http://sbml.svn.sourceforge.net/sbml/?rev=9450&view=rev
Author:   mhucka
Date:     2009-04-25 02:48:49 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
This is no longer the source for the SBML FAQ.  The
current FAQ is kept online on the website, using the wiki system.

Removed Paths:
-------------
    trunk/specifications/sbml-faq/


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Revision: 9449
          http://sbml.svn.sourceforge.net/sbml/?rev=9449&view=rev
Author:   mhucka
Date:     2009-04-25 02:47:57 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
A place for old stuff.

Added Paths:
-----------
    trunk/project/old/


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Revision: 9448
          http://sbml.svn.sourceforge.net/sbml/?rev=9448&view=rev
Author:   mhucka
Date:     2009-04-19 21:03:28 +0000 (Sun, 19 Apr 2009)

Log Message:
-----------
Let's list the inherited methods in the class descriptions.

Modified Paths:
--------------
    branches/libsbml-4/docs/src/doxygen-config-common.txt

Modified: branches/libsbml-4/docs/src/doxygen-config-common.txt
===================================================================
--- branches/libsbml-4/docs/src/doxygen-config-common.txt	2009-04-19 21:02:22 UTC (rev 9447)
+++ branches/libsbml-4/docs/src/doxygen-config-common.txt	2009-04-19 21:03:28 UTC (rev 9448)
@@ -68,7 +68,7 @@
 # ordinary class members. Constructors, destructors and assignment operators of 
 # the base classes will not be shown.
 
-INLINE_INHERITED_MEMB  = NO
+INLINE_INHERITED_MEMB  = YES
 
 # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
 # path before files name in the file list and in the header files. If set 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9447
          http://sbml.svn.sourceforge.net/sbml/?rev=9447&view=rev
Author:   mhucka
Date:     2009-04-19 21:02:22 +0000 (Sun, 19 Apr 2009)

Log Message:
-----------
Let's list the inherited methods in the class descriptions.

Modified Paths:
--------------
    trunk/libsbml/docs/src/doxygen-config-common.txt

Modified: trunk/libsbml/docs/src/doxygen-config-common.txt
===================================================================
--- trunk/libsbml/docs/src/doxygen-config-common.txt	2009-04-17 00:23:37 UTC (rev 9446)
+++ trunk/libsbml/docs/src/doxygen-config-common.txt	2009-04-19 21:02:22 UTC (rev 9447)
@@ -68,7 +68,7 @@
 # ordinary class members. Constructors, destructors and assignment operators of 
 # the base classes will not be shown.
 
-INLINE_INHERITED_MEMB  = NO
+INLINE_INHERITED_MEMB  = YES
 
 # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
 # path before files name in the file list and in the header files. If set 


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Revision: 9446
          http://sbml.svn.sourceforge.net/sbml/?rev=9446&view=rev
Author:   sarahkeating
Date:     2009-04-17 00:23:37 +0000 (Fri, 17 Apr 2009)

Log Message:
-----------
caught missing assignment to NULL

Modified Paths:
--------------
    branches/libsbml-4/src/sbml/Reaction.cpp

Modified: branches/libsbml-4/src/sbml/Reaction.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Reaction.cpp	2009-04-17 00:22:47 UTC (rev 9445)
+++ branches/libsbml-4/src/sbml/Reaction.cpp	2009-04-17 00:23:37 UTC (rev 9446)
@@ -805,6 +805,7 @@
 Reaction::createKineticLaw ()
 {
   delete mKineticLaw;
+  mKineticLaw = 0;
 
   try
   {


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Revision: 9442
          http://sbml.svn.sourceforge.net/sbml/?rev=9442&view=rev
Author:   sarahkeating
Date:     2009-04-16 16:48:09 +0000 (Thu, 16 Apr 2009)

Log Message:
-----------
assignment operator should check for self-assignment

Modified Paths:
--------------
    branches/libsbml-4/src/annotation/CVTerm.cpp
    branches/libsbml-4/src/annotation/ModelHistory.cpp
    branches/libsbml-4/src/sbml/Compartment.cpp
    branches/libsbml-4/src/sbml/CompartmentType.cpp
    branches/libsbml-4/src/sbml/Constraint.cpp
    branches/libsbml-4/src/sbml/Delay.cpp
    branches/libsbml-4/src/sbml/Event.cpp
    branches/libsbml-4/src/sbml/EventAssignment.cpp
    branches/libsbml-4/src/sbml/FunctionDefinition.cpp
    branches/libsbml-4/src/sbml/InitialAssignment.cpp
    branches/libsbml-4/src/sbml/KineticLaw.cpp
    branches/libsbml-4/src/sbml/ListOf.cpp
    branches/libsbml-4/src/sbml/Model.cpp
    branches/libsbml-4/src/sbml/Parameter.cpp
    branches/libsbml-4/src/sbml/Reaction.cpp
    branches/libsbml-4/src/sbml/Rule.cpp
    branches/libsbml-4/src/sbml/SBase.cpp
    branches/libsbml-4/src/sbml/Species.cpp
    branches/libsbml-4/src/sbml/SpeciesReference.cpp
    branches/libsbml-4/src/sbml/SpeciesType.cpp
    branches/libsbml-4/src/sbml/StoichiometryMath.cpp
    branches/libsbml-4/src/sbml/Trigger.cpp
    branches/libsbml-4/src/sbml/Unit.cpp
    branches/libsbml-4/src/sbml/UnitDefinition.cpp
    branches/libsbml-4/src/sbml/layout/BoundingBox.cpp
    branches/libsbml-4/src/sbml/layout/CompartmentGlyph.cpp
    branches/libsbml-4/src/sbml/layout/CubicBezier.cpp
    branches/libsbml-4/src/sbml/layout/Curve.cpp
    branches/libsbml-4/src/sbml/layout/Dimensions.cpp
    branches/libsbml-4/src/sbml/layout/GraphicalObject.cpp
    branches/libsbml-4/src/sbml/layout/Layout.cpp
    branches/libsbml-4/src/sbml/layout/LineSegment.cpp
    branches/libsbml-4/src/sbml/layout/Point.cpp
    branches/libsbml-4/src/sbml/layout/ReactionGlyph.cpp
    branches/libsbml-4/src/sbml/layout/SpeciesGlyph.cpp
    branches/libsbml-4/src/sbml/layout/SpeciesReferenceGlyph.cpp
    branches/libsbml-4/src/sbml/layout/TextGlyph.cpp
    branches/libsbml-4/src/xml/XMLAttributes.cpp
    branches/libsbml-4/src/xml/XMLNamespaces.cpp
    branches/libsbml-4/src/xml/XMLNode.cpp
    branches/libsbml-4/src/xml/XMLToken.cpp
    branches/libsbml-4/src/xml/XMLTriple.cpp

Modified: branches/libsbml-4/src/annotation/CVTerm.cpp
===================================================================
--- branches/libsbml-4/src/annotation/CVTerm.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/annotation/CVTerm.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -157,11 +157,15 @@
 CVTerm& 
 CVTerm::operator=(const CVTerm& rhs)
 {
-  mQualifier       = rhs.mQualifier;
-  mModelQualifier  = rhs.mModelQualifier;
-  mBiolQualifier   = rhs.mBiolQualifier;
+  if(&rhs!=this)
+  {
+    mQualifier       = rhs.mQualifier;
+    mModelQualifier  = rhs.mModelQualifier;
+    mBiolQualifier   = rhs.mBiolQualifier;
 
-  mResources=new XMLAttributes(*rhs.mResources);
+    mResources=new XMLAttributes(*rhs.mResources);
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/annotation/ModelHistory.cpp
===================================================================
--- branches/libsbml-4/src/annotation/ModelHistory.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/annotation/ModelHistory.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -90,18 +90,22 @@
   */
 Date& Date::operator=(const Date& orig)
 {
-  mYear   = orig.mYear;
-  mMonth  = orig.mMonth;
-  mDay    = orig.mDay;
-  mHour   = orig.mHour;  
-  mMinute = orig.mMinute;
-  mSecond = orig.mSecond;
-  
-  mSignOffset     = orig.mSignOffset;
-  mHoursOffset    = orig.mHoursOffset;
-  mMinutesOffset  = orig.mMinutesOffset;;
+  if(&orig!=this)
+  {
+    mYear   = orig.mYear;
+    mMonth  = orig.mMonth;
+    mDay    = orig.mDay;
+    mHour   = orig.mHour;  
+    mMinute = orig.mMinute;
+    mSecond = orig.mSecond;
+    
+    mSignOffset     = orig.mSignOffset;
+    mHoursOffset    = orig.mHoursOffset;
+    mMinutesOffset  = orig.mMinutesOffset;;
 
-  mDate = orig.mDate;
+    mDate = orig.mDate;
+  }
+
   return *this;
 }
 
@@ -676,10 +680,14 @@
   */
 ModelCreator& ModelCreator::operator=(const ModelCreator& orig)
 {
-  mFamilyName   = orig.mFamilyName;
-  mGivenName    = orig.mGivenName;
-  mEmail        = orig.mEmail;
-  mOrganization = orig.mOrganization;
+  if(&orig!=this)
+  {
+    mFamilyName   = orig.mFamilyName;
+    mGivenName    = orig.mGivenName;
+    mEmail        = orig.mEmail;
+    mOrganization = orig.mOrganization;
+  }
+
   return *this;
 }
 
@@ -946,18 +954,21 @@
 ModelHistory& 
 ModelHistory::operator=(const ModelHistory& orig)
 {
-  unsigned int i;
-  for (i = 0; i < orig.mCreators->getSize(); i++)
+  if(&orig!=this)
   {
-    addCreator(static_cast<ModelCreator*>(orig.mCreators->get(i)));
+    unsigned int i;
+    for (i = 0; i < orig.mCreators->getSize(); i++)
+    {
+      addCreator(static_cast<ModelCreator*>(orig.mCreators->get(i)));
+    }
+
+    for (i = 0; i < orig.mModifiedDates->getSize(); i++)
+    {
+      addModifiedDate(static_cast<Date*>(orig.mModifiedDates->get(i)));
+    }
+    if (orig.mCreatedDate) setCreatedDate(orig.mCreatedDate);
   }
 
-  for (i = 0; i < orig.mModifiedDates->getSize(); i++)
-  {
-    addModifiedDate(static_cast<Date*>(orig.mModifiedDates->get(i)));
-  }
-  if (orig.mCreatedDate) setCreatedDate(orig.mCreatedDate);
-//  if (orig.mModifiedDate)setModifiedDate(orig.mModifiedDate);
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Compartment.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Compartment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Compartment.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -101,16 +101,20 @@
  */
 Compartment& Compartment::operator=(const Compartment& rhs)
 {
-  this->SBase::operator =(rhs);
-  mSpatialDimensions= rhs.mSpatialDimensions  ;
-  mSize             = rhs.mSize      ;
-  mConstant         = rhs.mConstant     ;
-  mIsSetSize        = rhs.mIsSetSize    ;
-  mCompartmentType  = rhs.mCompartmentType;
-  mUnits            = rhs.mUnits ;
-  mOutside          = rhs.mOutside ;
-  mId = rhs.mId;
-  mName = rhs.mName;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mSpatialDimensions= rhs.mSpatialDimensions  ;
+    mSize             = rhs.mSize      ;
+    mConstant         = rhs.mConstant     ;
+    mIsSetSize        = rhs.mIsSetSize    ;
+    mCompartmentType  = rhs.mCompartmentType;
+    mUnits            = rhs.mUnits ;
+    mOutside          = rhs.mOutside ;
+    mId = rhs.mId;
+    mName = rhs.mName;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/CompartmentType.cpp
===================================================================
--- branches/libsbml-4/src/sbml/CompartmentType.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/CompartmentType.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -89,9 +89,13 @@
  */
 CompartmentType& CompartmentType::operator=(const CompartmentType& rhs)
 {
-  this->SBase::operator =(rhs);
-  mId = rhs.mId;
-  mName = rhs.mName;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mId = rhs.mId;
+    mName = rhs.mName;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Constraint.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Constraint.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Constraint.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -102,14 +102,17 @@
  */
 Constraint& Constraint::operator=(const Constraint& rhs)
 {
-  this->SBase::operator =(rhs);
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
 
-  if (rhs.mMath)    
-  {
-    mMath    = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    if (rhs.mMath)    
+    {
+      mMath    = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
+    if (rhs.mMessage) mMessage = new XMLNode(*rhs.mMessage);
   }
-  if (rhs.mMessage) mMessage = new XMLNode(*rhs.mMessage);
 
   return *this;
 }

Modified: branches/libsbml-4/src/sbml/Delay.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Delay.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Delay.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -101,13 +101,17 @@
  */
 Delay& Delay::operator=(const Delay& rhs)
 {
-  this->SBase::operator =(rhs);
-  this->mInternalId = rhs.mInternalId;
-  if (rhs.mMath) 
+  if(&rhs!=this)
   {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    this->mInternalId = rhs.mInternalId;
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Event.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Event.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Event.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -123,30 +123,33 @@
  */
 Event& Event::operator=(const Event& rhs)
 {
-  this->SBase::operator =(rhs);
- 
-  mId = rhs.mId;
-  mName = rhs.mName;
-  mTimeUnits        = rhs.mTimeUnits        ;
-  mUseValuesFromTriggerTime = rhs.mUseValuesFromTriggerTime;
-  mInternalIdOnly   = rhs.mInternalIdOnly   ;
-  mEventAssignments = rhs.mEventAssignments ;
-
-  if (rhs.getNumEventAssignments() > 0)
+  if(&rhs!=this)
   {
-    mEventAssignments.setParentSBMLObject(this);
-  }
- 
-  if (rhs.mTrigger) 
-  {
-    mTrigger = new Trigger(*rhs.getTrigger());
-    mTrigger->setParentSBMLObject(this);
-  }
+    this->SBase::operator =(rhs);
+   
+    mId = rhs.mId;
+    mName = rhs.mName;
+    mTimeUnits        = rhs.mTimeUnits        ;
+    mUseValuesFromTriggerTime = rhs.mUseValuesFromTriggerTime;
+    mInternalIdOnly   = rhs.mInternalIdOnly   ;
+    mEventAssignments = rhs.mEventAssignments ;
 
-  if (rhs.mDelay) 
-  {
-    mDelay = new Delay(*rhs.getDelay());
-    mDelay->setParentSBMLObject(this);
+    if (rhs.getNumEventAssignments() > 0)
+    {
+      mEventAssignments.setParentSBMLObject(this);
+    }
+   
+    if (rhs.mTrigger) 
+    {
+      mTrigger = new Trigger(*rhs.getTrigger());
+      mTrigger->setParentSBMLObject(this);
+    }
+
+    if (rhs.mDelay) 
+    {
+      mDelay = new Delay(*rhs.getDelay());
+      mDelay->setParentSBMLObject(this);
+    }
   }
 
   return *this;

Modified: branches/libsbml-4/src/sbml/EventAssignment.cpp
===================================================================
--- branches/libsbml-4/src/sbml/EventAssignment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/EventAssignment.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -99,14 +99,18 @@
  */
 EventAssignment& EventAssignment::operator=(const EventAssignment& rhs)
 {
-  this->SBase::operator =(rhs);
-  this->mVariable = rhs.mVariable;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    this->mVariable = rhs.mVariable;
 
-  if (rhs.mMath) 
-  {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/FunctionDefinition.cpp
===================================================================
--- branches/libsbml-4/src/sbml/FunctionDefinition.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/FunctionDefinition.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -103,14 +103,18 @@
  */
 FunctionDefinition& FunctionDefinition::operator=(const FunctionDefinition& rhs)
 {
-  this->SBase::operator =(rhs);
-  mId = rhs.mId;
-  mName = rhs.mName;
-  if (rhs.mMath) 
+  if(&rhs!=this)
   {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    mId = rhs.mId;
+    mName = rhs.mName;
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/InitialAssignment.cpp
===================================================================
--- branches/libsbml-4/src/sbml/InitialAssignment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/InitialAssignment.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -98,13 +98,17 @@
  */
 InitialAssignment& InitialAssignment::operator=(const InitialAssignment& rhs)
 {
-  this->SBase::operator =(rhs);
-  this->mSymbol = rhs.mSymbol;
-  if (rhs.mMath) 
+  if(&rhs!=this)
   {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    this->mSymbol = rhs.mSymbol;
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/KineticLaw.cpp
===================================================================
--- branches/libsbml-4/src/sbml/KineticLaw.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/KineticLaw.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -116,23 +116,27 @@
  */
 KineticLaw& KineticLaw::operator=(const KineticLaw& rhs)
 {
-  this->SBase::operator =(rhs);
-  mFormula        = rhs.mFormula        ;
-  mTimeUnits      = rhs.mTimeUnits      ;
-  mSubstanceUnits = rhs.mSubstanceUnits ;
-  mParameters     = rhs.mParameters     ;
-  mInternalId     = rhs.mInternalId     ;
-  
-  if (rhs.getNumParameters() > 0)
+  if(&rhs!=this)
   {
-    mParameters.setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    mFormula        = rhs.mFormula        ;
+    mTimeUnits      = rhs.mTimeUnits      ;
+    mSubstanceUnits = rhs.mSubstanceUnits ;
+    mParameters     = rhs.mParameters     ;
+    mInternalId     = rhs.mInternalId     ;
+    
+    if (rhs.getNumParameters() > 0)
+    {
+      mParameters.setParentSBMLObject(this);
+    }
+    
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
-  
-  if (rhs.mMath) 
-  {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
-  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/ListOf.cpp
===================================================================
--- branches/libsbml-4/src/sbml/ListOf.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/ListOf.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -85,11 +85,15 @@
  */
 ListOf& ListOf::operator=(const ListOf& rhs)
 {
-  this->SBase::operator =(rhs);
-  // Deletes existing items
-  for_each( mItems.begin(), mItems.end(), Delete() );
-  mItems.resize( rhs.size() );
-  transform( rhs.mItems.begin(), rhs.mItems.end(), mItems.begin(), Clone() );
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    // Deletes existing items
+    for_each( mItems.begin(), mItems.end(), Delete() );
+    mItems.resize( rhs.size() );
+    transform( rhs.mItems.begin(), rhs.mItems.end(), mItems.begin(), Clone() );
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Model.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Model.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Model.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -194,98 +194,101 @@
  */
 Model& Model::operator=(const Model& rhs)
 {
-  this->SBase::operator = (rhs);
-  mId = rhs.mId;
-  mName = rhs.mName;
-  mFunctionDefinitions  = rhs.mFunctionDefinitions;
-  mUnitDefinitions      = rhs.mUnitDefinitions;
-  mCompartmentTypes     = rhs.mCompartmentTypes;
-  mSpeciesTypes         = rhs.mSpeciesTypes;
-  mCompartments         = rhs.mCompartments;
-  mSpecies              = rhs.mSpecies;
-  mParameters           = rhs.mParameters;
-  mInitialAssignments   = rhs.mInitialAssignments;
-  mRules                = rhs.mRules;
-  mConstraints          = rhs.mConstraints;
-  mReactions            = rhs.mReactions;
-  mEvents               = rhs.mEvents;
-#ifdef USE_LAYOUT
-  mLayouts              = rhs.mLayouts;
-#endif
+  if(&rhs!=this)
+  {
+    this->SBase::operator = (rhs);
+    mId = rhs.mId;
+    mName = rhs.mName;
+    mFunctionDefinitions  = rhs.mFunctionDefinitions;
+    mUnitDefinitions      = rhs.mUnitDefinitions;
+    mCompartmentTypes     = rhs.mCompartmentTypes;
+    mSpeciesTypes         = rhs.mSpeciesTypes;
+    mCompartments         = rhs.mCompartments;
+    mSpecies              = rhs.mSpecies;
+    mParameters           = rhs.mParameters;
+    mInitialAssignments   = rhs.mInitialAssignments;
+    mRules                = rhs.mRules;
+    mConstraints          = rhs.mConstraints;
+    mReactions            = rhs.mReactions;
+    mEvents               = rhs.mEvents;
+  #ifdef USE_LAYOUT
+    mLayouts              = rhs.mLayouts;
+  #endif
 
 
-  if (rhs.getNumFunctionDefinitions() > 0)
-  {
-    mFunctionDefinitions.setParentSBMLObject(this);
-  }
-  if (rhs.getNumUnitDefinitions() > 0)
-  {
-    mUnitDefinitions.setParentSBMLObject(this);
-  }
-  if (rhs.getNumCompartmentTypes() > 0)
-  {
-    mCompartmentTypes.setParentSBMLObject(this);
-  }
-  if (rhs.getNumSpeciesTypes() > 0)
-  {
-    mSpeciesTypes.setParentSBMLObject(this);
-  }
-  if (rhs.getNumCompartments() > 0)
-  {
-    mCompartments.setParentSBMLObject(this);
-  }
-  if (rhs.getNumSpecies() > 0)
-  {
-    mSpecies.setParentSBMLObject(this);
-  }
-  if (rhs.getNumParameters() > 0)
-  {
-    mParameters.setParentSBMLObject(this);
-  }
-  if (rhs.getNumInitialAssignments() > 0)
-  {
-    mInitialAssignments.setParentSBMLObject(this);
-  }
-  if (rhs.getNumRules() > 0)
-  {
-    mRules.setParentSBMLObject(this);
-  }
-  if (rhs.getNumConstraints() > 0)
-  {
-    mConstraints.setParentSBMLObject(this);
-  }
-  if (rhs.getNumReactions() > 0)
-  {
-    mReactions.setParentSBMLObject(this);
-  }
-  if (rhs.getNumEvents() > 0)
-  {
-    mEvents.setParentSBMLObject(this);
-  }
+    if (rhs.getNumFunctionDefinitions() > 0)
+    {
+      mFunctionDefinitions.setParentSBMLObject(this);
+    }
+    if (rhs.getNumUnitDefinitions() > 0)
+    {
+      mUnitDefinitions.setParentSBMLObject(this);
+    }
+    if (rhs.getNumCompartmentTypes() > 0)
+    {
+      mCompartmentTypes.setParentSBMLObject(this);
+    }
+    if (rhs.getNumSpeciesTypes() > 0)
+    {
+      mSpeciesTypes.setParentSBMLObject(this);
+    }
+    if (rhs.getNumCompartments() > 0)
+    {
+      mCompartments.setParentSBMLObject(this);
+    }
+    if (rhs.getNumSpecies() > 0)
+    {
+      mSpecies.setParentSBMLObject(this);
+    }
+    if (rhs.getNumParameters() > 0)
+    {
+      mParameters.setParentSBMLObject(this);
+    }
+    if (rhs.getNumInitialAssignments() > 0)
+    {
+      mInitialAssignments.setParentSBMLObject(this);
+    }
+    if (rhs.getNumRules() > 0)
+    {
+      mRules.setParentSBMLObject(this);
+    }
+    if (rhs.getNumConstraints() > 0)
+    {
+      mConstraints.setParentSBMLObject(this);
+    }
+    if (rhs.getNumReactions() > 0)
+    {
+      mReactions.setParentSBMLObject(this);
+    }
+    if (rhs.getNumEvents() > 0)
+    {
+      mEvents.setParentSBMLObject(this);
+    }
 
-  if (rhs.mHistory)
-  {
-    this->mHistory = rhs.mHistory->clone();
-  }
-  else
-  {
-    this->mHistory = 0;
-  }
-  if(rhs.mFormulaUnitsData)
-  {
-    this->mFormulaUnitsData  = new List();
-    unsigned int i,iMax = rhs.mFormulaUnitsData->getSize();
-    for(i = 0; i < iMax; ++i)
+    if (rhs.mHistory)
     {
-      this->mFormulaUnitsData
-        ->add(static_cast<FormulaUnitsData*>
-                                 (rhs.mFormulaUnitsData->get(i))->clone());
+      this->mHistory = rhs.mHistory->clone();
     }
+    else
+    {
+      this->mHistory = 0;
+    }
+    if(rhs.mFormulaUnitsData)
+    {
+      this->mFormulaUnitsData  = new List();
+      unsigned int i,iMax = rhs.mFormulaUnitsData->getSize();
+      for(i = 0; i < iMax; ++i)
+      {
+        this->mFormulaUnitsData
+          ->add(static_cast<FormulaUnitsData*>
+                                   (rhs.mFormulaUnitsData->get(i))->clone());
+      }
+    }
+    else
+    {
+      this->mFormulaUnitsData = 0;
+    }
   }
-  else
-  {
-    this->mFormulaUnitsData = 0;
-  }
 
   return *this;
 }

Modified: branches/libsbml-4/src/sbml/Parameter.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Parameter.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Parameter.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -99,13 +99,17 @@
  */
 Parameter& Parameter::operator=(const Parameter& rhs)
 {
-  this->SBase::operator =(rhs);
-     mValue      = rhs.mValue    ;
-     mUnits      = rhs.mUnits    ;
-     mConstant   = rhs.mConstant ;
-     mIsSetValue = rhs.mIsSetValue;
-  mId = rhs.mId;
-  mName = rhs.mName;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mValue      = rhs.mValue    ;
+    mUnits      = rhs.mUnits    ;
+    mConstant   = rhs.mConstant ;
+    mIsSetValue = rhs.mIsSetValue;
+    mId = rhs.mId;
+    mName = rhs.mName;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Reaction.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Reaction.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Reaction.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -162,32 +162,36 @@
  */
 Reaction& Reaction::operator=(const Reaction& rhs)
 {
-  this->SBase::operator =(rhs);
-  mReversible = rhs.mReversible ;
-  mFast       = rhs.mFast       ;
-  mIsSetFast  = rhs.mIsSetFast  ;
-  mReactants  = rhs.mReactants  ;
-  mProducts   = rhs.mProducts   ;
-  mModifiers  = rhs.mModifiers  ;
-  mId = rhs.mId;
-  mName = rhs.mName;
-  if (rhs.getNumReactants() > 0)
+  if(&rhs!=this)
   {
-    mReactants.setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    mReversible = rhs.mReversible ;
+    mFast       = rhs.mFast       ;
+    mIsSetFast  = rhs.mIsSetFast  ;
+    mReactants  = rhs.mReactants  ;
+    mProducts   = rhs.mProducts   ;
+    mModifiers  = rhs.mModifiers  ;
+    mId = rhs.mId;
+    mName = rhs.mName;
+    if (rhs.getNumReactants() > 0)
+    {
+      mReactants.setParentSBMLObject(this);
+    }
+    if (rhs.getNumProducts() > 0)
+    {
+      mProducts.setParentSBMLObject(this);
+    }
+    if (rhs.getNumModifiers() > 0)
+    {
+      mModifiers.setParentSBMLObject(this);
+    }
+    if (rhs.mKineticLaw)
+    {
+      mKineticLaw = static_cast<KineticLaw*>( rhs.mKineticLaw->clone() );
+      mKineticLaw->setParentSBMLObject(this);
+    }
   }
-  if (rhs.getNumProducts() > 0)
-  {
-    mProducts.setParentSBMLObject(this);
-  }
-  if (rhs.getNumModifiers() > 0)
-  {
-    mModifiers.setParentSBMLObject(this);
-  }
-  if (rhs.mKineticLaw)
-  {
-    mKineticLaw = static_cast<KineticLaw*>( rhs.mKineticLaw->clone() );
-    mKineticLaw->setParentSBMLObject(this);
-  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Rule.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Rule.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Rule.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -121,18 +121,22 @@
  */
 Rule& Rule::operator=(const Rule& rhs)
 {
-  this->SBase::operator =(rhs);
-  mVariable = rhs.mVariable;
-  mFormula = rhs.mFormula ;
-  mUnits   = rhs.mUnits   ;
-  mType    = rhs.mType    ;
-  mL1Type  = rhs.mL1Type  ;
-  mInternalId = rhs.mInternalId;
-  if (rhs.mMath) 
+  if(&rhs!=this)
   {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    mVariable = rhs.mVariable;
+    mFormula = rhs.mFormula ;
+    mUnits   = rhs.mUnits   ;
+    mType    = rhs.mType    ;
+    mL1Type  = rhs.mL1Type  ;
+    mInternalId = rhs.mInternalId;
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/SBase.cpp
===================================================================
--- branches/libsbml-4/src/sbml/SBase.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/SBase.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -253,18 +253,20 @@
  */
 SBase& SBase::operator=(const SBase& orig)
 {
+  if(&orig!=this)
+  {
     this->mMetaId = orig.mMetaId;
 
     if(orig.mNotes) 
       this->mNotes = new XMLNode(*const_cast<SBase&>(orig).getNotes());
     else
       this->mNotes = 0;
-    
+
     if(orig.mAnnotation) 
       this->mAnnotation = new XMLNode(*const_cast<SBase&>(orig).mAnnotation);
     else
       this->mAnnotation = 0;
-    
+
     this->mObjectLevel       = orig.mObjectLevel;
     this->mObjectVersion       = orig.mObjectVersion;
     this->mSBML       = orig.mSBML;
@@ -294,8 +296,9 @@
     }
 
     this->mHasBeenDeleted = orig.mHasBeenDeleted;
-    return *this;
+  }
 
+  return *this;
 }
 
 

Modified: branches/libsbml-4/src/sbml/Species.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Species.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Species.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -116,9 +116,11 @@
  */
 Species& Species::operator=(const Species& orig)
 {
-  this->SBase::operator =(orig);
-  this->mId = orig.mId;
-  this->mName = orig.mName;
+  if(&orig!=this)
+  {
+    this->SBase::operator =(orig);
+    this->mId = orig.mId;
+    this->mName = orig.mName;
     this->mSpeciesType = orig.mSpeciesType;
     this->mCompartment = orig.mCompartment;
 
@@ -136,6 +138,8 @@
     this->mIsSetInitialAmount = orig.mIsSetInitialAmount;
     this->mIsSetInitialConcentration = orig.mIsSetInitialConcentration;
     this->mIsSetCharge = orig.mIsSetCharge;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/SpeciesReference.cpp
===================================================================
--- branches/libsbml-4/src/sbml/SpeciesReference.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/SpeciesReference.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -101,10 +101,14 @@
  */
 SimpleSpeciesReference& SimpleSpeciesReference::operator=(const SimpleSpeciesReference& rhs)
 {
-  this->SBase::operator =(rhs);
-  mId = rhs.mId;
-  mName = rhs.mName;
-  mSpecies = rhs.mSpecies;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mId = rhs.mId;
+    mName = rhs.mName;
+    mSpecies = rhs.mSpecies;
+  }
+
   return *this;
 }
 
@@ -512,15 +516,19 @@
  */
 SpeciesReference& SpeciesReference::operator=(const SpeciesReference& rhs)
 {
-  this->SBase::operator =(rhs);
-  this->SimpleSpeciesReference::operator = ( rhs );
-  mStoichiometry = rhs.mStoichiometry ;
-  mDenominator = rhs.mDenominator   ;
-  if (rhs.mStoichiometryMath)
+  if(&rhs!=this)
   {
-    mStoichiometryMath = new StoichiometryMath(*rhs.getStoichiometryMath());
-    mStoichiometryMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    this->SimpleSpeciesReference::operator = ( rhs );
+    mStoichiometry = rhs.mStoichiometry ;
+    mDenominator = rhs.mDenominator   ;
+    if (rhs.mStoichiometryMath)
+    {
+      mStoichiometryMath = new StoichiometryMath(*rhs.getStoichiometryMath());
+      mStoichiometryMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/SpeciesType.cpp
===================================================================
--- branches/libsbml-4/src/sbml/SpeciesType.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/SpeciesType.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -89,9 +89,13 @@
  */
 SpeciesType& SpeciesType::operator=(const SpeciesType& rhs)
 {
-  this->SBase::operator =(rhs);
-  mId = rhs.mId;
-  mName = rhs.mName;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mId = rhs.mId;
+    mName = rhs.mName;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/StoichiometryMath.cpp
===================================================================
--- branches/libsbml-4/src/sbml/StoichiometryMath.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/StoichiometryMath.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -101,13 +101,17 @@
  */
 StoichiometryMath& StoichiometryMath::operator=(const StoichiometryMath& rhs)
 {
-  this->SBase::operator =(rhs);
-  this->mInternalId = rhs.mInternalId;
-  if (rhs.mMath) 
+  if(&rhs!=this)
   {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    this->mInternalId = rhs.mInternalId;
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Trigger.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Trigger.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Trigger.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -99,12 +99,16 @@
  */
 Trigger& Trigger::operator=(const Trigger& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) 
+  if(&rhs!=this)
   {
-    mMath = rhs.mMath->deepCopy();
-    mMath->setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) 
+    {
+      mMath = rhs.mMath->deepCopy();
+      mMath->setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/Unit.cpp
===================================================================
--- branches/libsbml-4/src/sbml/Unit.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/Unit.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -95,12 +95,16 @@
  */
 Unit& Unit::operator=(const Unit& rhs)
 {
-  this->SBase::operator =(rhs);
-  mKind       = rhs.mKind       ;
-  mExponent   = rhs.mExponent   ;
-  mScale      = rhs.mScale      ;
-  mMultiplier = rhs.mMultiplier ;
-  mOffset     = rhs.mOffset     ;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mKind       = rhs.mKind       ;
+    mExponent   = rhs.mExponent   ;
+    mScale      = rhs.mScale      ;
+    mMultiplier = rhs.mMultiplier ;
+    mOffset     = rhs.mOffset     ;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/UnitDefinition.cpp
===================================================================
--- branches/libsbml-4/src/sbml/UnitDefinition.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/UnitDefinition.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -100,14 +100,18 @@
  */
 UnitDefinition& UnitDefinition::operator=(const UnitDefinition& rhs)
 {
-  this->SBase::operator =(rhs);
-  mId = rhs.mId;
-  mName = rhs.mName;
-  mUnits = rhs.mUnits;
-  if (rhs.getNumUnits() > 0)
+  if(&rhs!=this)
   {
-    mUnits.setParentSBMLObject(this);
+    this->SBase::operator =(rhs);
+    mId = rhs.mId;
+    mName = rhs.mName;
+    mUnits = rhs.mUnits;
+    if (rhs.getNumUnits() > 0)
+    {
+      mUnits.setParentSBMLObject(this);
+    }
   }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/sbml/layout/BoundingBox.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/BoundingBox.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/BoundingBox.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -80,12 +80,16 @@
  */
 BoundingBox& BoundingBox::operator=(const BoundingBox& orig)
 {
+  if(&orig!=this)
+  {
     this->SBase::operator=(orig);
   
     this->mId = orig.mId;
     this->mPosition=orig.mPosition;
     this->mDimensions=orig.mDimensions;
-    return *this;
+  }
+  
+  return *this;
 }
 
 

Modified: branches/libsbml-4/src/sbml/layout/CompartmentGlyph.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/CompartmentGlyph.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/CompartmentGlyph.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -127,9 +127,13 @@
  */
 CompartmentGlyph& CompartmentGlyph::operator=(const CompartmentGlyph& source)
 {
+  if(&source!=this)
+  {
     GraphicalObject::operator=(source);
     this->mCompartment=source.getCompartmentId();    
-    return *this;
+  }
+  
+  return *this;
 }
 
 /**

Modified: branches/libsbml-4/src/sbml/layout/CubicBezier.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/CubicBezier.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/CubicBezier.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -130,14 +130,12 @@
  */
 CubicBezier& CubicBezier::operator=(const CubicBezier& orig)
 {
-//    this->mId=orig.mId;
+  if(&orig!=this)
+  {
     this->mStartPoint=orig.mStartPoint;
     this->mEndPoint=orig.mEndPoint;
     this->mBasePoint1=orig.mBasePoint1;
     this->mBasePoint2=orig.mBasePoint2;
-    // attributes of SBase
-//    this->mId=orig.mId;
-//    this->mName=orig.mName;
     this->mMetaId=orig.mMetaId;
     delete this->mNotes;
     this->mNotes=NULL;
@@ -160,7 +158,9 @@
         this->mCVTerms->add(static_cast<CVTerm*>(orig.mCVTerms->get(i))->clone());
       }
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 

Modified: branches/libsbml-4/src/sbml/layout/Curve.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/Curve.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/Curve.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -285,11 +285,15 @@
  */
 Curve& Curve::operator=(const Curve& source)
 {
+  if(&source!=this)
+  {
     this->SBase::operator=(source);
     // copy the line segments
     this->mCurveSegments=*source.getListOfCurveSegments();
     
-    return *this;
+  }
+  
+  return *this;
 }
 
 
@@ -392,6 +396,8 @@
 
 ListOfLineSegments& ListOfLineSegments::operator=(const ListOfLineSegments& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -419,7 +425,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfLineSegments::ListOfLineSegments(const ListOfLineSegments& source)

Modified: branches/libsbml-4/src/sbml/layout/Dimensions.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/Dimensions.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/Dimensions.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -103,12 +103,11 @@
 
 Dimensions& Dimensions::operator=(const Dimensions& orig)
 {
+  if(&orig!=this)
+  {
     this->mH=orig.mH;
     this->mW=orig.mW;
     this->mD=orig.mD;
-    // attributes of SBase
-//    this->mId=orig.mId;
-//   this->mName=orig.mName;
     this->mMetaId=orig.mMetaId;
     delete this->mNotes;
     this->mNotes=NULL;
@@ -131,7 +130,9 @@
         this->mCVTerms->add(static_cast<CVTerm*>(orig.mCVTerms->get(i))->clone());
       }
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 /**

Modified: branches/libsbml-4/src/sbml/layout/GraphicalObject.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/GraphicalObject.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/GraphicalObject.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -174,11 +174,14 @@
  */
 GraphicalObject& GraphicalObject::operator=(const GraphicalObject& source)
 {
+  if(&source!=this)
+  {
     this->SBase::operator=(source);
     this->mId = source.mId;
     this->mBoundingBox=*source.getBoundingBox();
-        
-    return *this;
+  }
+
+  return *this;
 }
 
 /**

Modified: branches/libsbml-4/src/sbml/layout/Layout.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/Layout.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/Layout.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -274,6 +274,8 @@
  */
 Layout& Layout::operator=(const Layout& source)
 {
+  if(&source!=this)
+  {
     this->SBase::operator=(source);
     this->mId = source.mId;
     this->mDimensions=*source.getDimensions();
@@ -282,8 +284,9 @@
     this->mReactionGlyphs=*source.getListOfReactionGlyphs();
     this->mTextGlyphs=*source.getListOfTextGlyphs();
     this->mAdditionalGraphicalObjects=*source.getListOfAdditionalGraphicalObjects();
-       
-    return *this;
+  }
+  
+  return *this;
 }
 
 
@@ -1328,6 +1331,8 @@
 
 ListOfLayouts& ListOfLayouts::operator=(const ListOfLayouts& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -1355,7 +1360,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfLayouts::ListOfLayouts(const ListOfLayouts& source)
@@ -1454,6 +1461,8 @@
 
 ListOfCompartmentGlyphs& ListOfCompartmentGlyphs::operator=(const ListOfCompartmentGlyphs& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     // clear the old list
     this->mLine=source.getLine();
@@ -1481,7 +1490,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfCompartmentGlyphs::ListOfCompartmentGlyphs(const ListOfCompartmentGlyphs& source)
@@ -1584,6 +1595,8 @@
 
 ListOfSpeciesGlyphs& ListOfSpeciesGlyphs::operator=(const ListOfSpeciesGlyphs& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -1611,7 +1624,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 
@@ -1713,6 +1728,8 @@
 
 ListOfReactionGlyphs& ListOfReactionGlyphs::operator=(const ListOfReactionGlyphs& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -1740,7 +1757,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfReactionGlyphs::ListOfReactionGlyphs(const ListOfReactionGlyphs& source)
@@ -1842,6 +1861,8 @@
 
 ListOfTextGlyphs& ListOfTextGlyphs::operator=(const ListOfTextGlyphs& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -1868,7 +1889,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfTextGlyphs::ListOfTextGlyphs(const ListOfTextGlyphs& source)
@@ -1969,6 +1992,8 @@
 
 ListOfGraphicalObjects& ListOfGraphicalObjects::operator=(const ListOfGraphicalObjects& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -1996,7 +2021,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfGraphicalObjects::ListOfGraphicalObjects(const ListOfGraphicalObjects& source)

Modified: branches/libsbml-4/src/sbml/layout/LineSegment.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/LineSegment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/LineSegment.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -110,11 +110,15 @@
  */
 LineSegment& LineSegment::operator=(const LineSegment& orig)
 {
+  if(&orig!=this)
+  {
     this->SBase::operator=(orig);
     this->mId = orig.mId;
     this->mStartPoint=orig.mStartPoint;
     this->mEndPoint=orig.mEndPoint;
-    return *this;
+  }
+  
+  return *this;
 }
 
 

Modified: branches/libsbml-4/src/sbml/layout/Point.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/Point.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/Point.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -97,14 +97,13 @@
 
 Point& Point::operator=(const Point& orig)
 {
+  if(&orig!=this)
+  {
     this->mXOffset=orig.mXOffset;
     this->mYOffset=orig.mYOffset;
     this->mZOffset=orig.mZOffset;
     this->mElementName=orig.mElementName;
 
-    // attributes of SBase
-    //this->mId=orig.mId;
-    //this->mName=orig.mName;
     this->mMetaId=orig.mMetaId;
     delete this->mNotes;
     this->mNotes=NULL;
@@ -133,7 +132,9 @@
         this->mCVTerms->add(static_cast<CVTerm*>(orig.mCVTerms->get(i))->clone());
       }
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 

Modified: branches/libsbml-4/src/sbml/layout/ReactionGlyph.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/ReactionGlyph.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/ReactionGlyph.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -187,11 +187,15 @@
  */
 ReactionGlyph& ReactionGlyph::operator=(const ReactionGlyph& source)
 {
+  if(&source!=this)
+  {
     GraphicalObject::operator=(source);
     this->mReaction=source.getReactionId();
     this->mCurve=*source.getCurve();
     this->mSpeciesReferenceGlyphs=*source.getListOfSpeciesReferenceGlyphs();
-    return *this;
+  }
+  
+  return *this;
 }
 
 
@@ -603,6 +607,8 @@
 
 ListOfSpeciesReferenceGlyphs& ListOfSpeciesReferenceGlyphs::operator=(const ListOfSpeciesReferenceGlyphs& source)
 {
+  if(&source!=this)
+  {
     copySBaseAttributes(source,*this);
     this->mLine=source.getLine();
     this->mColumn=source.getColumn();
@@ -630,7 +636,9 @@
       this->append(source.get(i));
       ++i;
     }
-    return *this;
+  }
+  
+  return *this;
 }
 
 ListOfSpeciesReferenceGlyphs::ListOfSpeciesReferenceGlyphs(const ListOfSpeciesReferenceGlyphs& source)

Modified: branches/libsbml-4/src/sbml/layout/SpeciesGlyph.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/SpeciesGlyph.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/SpeciesGlyph.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -128,9 +128,13 @@
  */
 SpeciesGlyph& SpeciesGlyph::operator=(const SpeciesGlyph& source)
 {
+  if(&source!=this)
+  {
     GraphicalObject::operator=(source);
     this->mSpecies=source.getSpeciesId();    
-    return *this;
+  }
+  
+  return *this;
 }
 
 

Modified: branches/libsbml-4/src/sbml/layout/SpeciesReferenceGlyph.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/SpeciesReferenceGlyph.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/SpeciesReferenceGlyph.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -174,12 +174,16 @@
  */
 SpeciesReferenceGlyph& SpeciesReferenceGlyph::operator=(const SpeciesReferenceGlyph& source)
 {
+  if(&source!=this)
+  {
     GraphicalObject::operator=(source);
     this->mSpeciesReference=source.getSpeciesReferenceId();
     this->mSpeciesGlyph=source.getSpeciesGlyphId();
     this->mRole=source.getRole();
     this->mCurve=*source.getCurve();
-    return *this;
+  }
+  
+  return *this;
 }
 
 /**

Modified: branches/libsbml-4/src/sbml/layout/TextGlyph.cpp
===================================================================
--- branches/libsbml-4/src/sbml/layout/TextGlyph.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/sbml/layout/TextGlyph.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -130,11 +130,15 @@
  */
 TextGlyph& TextGlyph::operator=(const TextGlyph& source)
 {
+  if(&source!=this)
+  {
     GraphicalObject::operator=(source);
     this->mText=source.getText();
     this->mOriginOfText=source.getOriginOfTextId();
     this->mGraphicalObject=source.getGraphicalObjectId();    
-    return *this;
+  }
+  
+  return *this;
 }
 
 /**

Modified: branches/libsbml-4/src/xml/XMLAttributes.cpp
===================================================================
--- branches/libsbml-4/src/xml/XMLAttributes.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/xml/XMLAttributes.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -89,10 +89,14 @@
 XMLAttributes& 
 XMLAttributes::operator=(const XMLAttributes& orig)
 {
-  this->mNames.assign( orig.mNames.begin(), orig.mNames.end() ); 
-  this->mValues.assign( orig.mValues.begin(), orig.mValues.end() ); 
-  this->mElementName = orig.mElementName;
-  this->mLog = orig.mLog;
+  if(&orig!=this)
+  {
+    this->mNames.assign( orig.mNames.begin(), orig.mNames.end() ); 
+    this->mValues.assign( orig.mValues.begin(), orig.mValues.end() ); 
+    this->mElementName = orig.mElementName;
+    this->mLog = orig.mLog;
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/xml/XMLNamespaces.cpp
===================================================================
--- branches/libsbml-4/src/xml/XMLNamespaces.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/xml/XMLNamespaces.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -68,7 +68,11 @@
 XMLNamespaces& 
 XMLNamespaces::operator=(const XMLNamespaces& orig)
 {
-  this->mNamespaces.assign( orig.mNamespaces.begin(), orig.mNamespaces.end() ); 
+  if(&orig!=this)
+  {
+    this->mNamespaces.assign( orig.mNamespaces.begin(), orig.mNamespaces.end() ); 
+  }
+  
   return *this;
 }
 

Modified: branches/libsbml-4/src/xml/XMLNode.cpp
===================================================================
--- branches/libsbml-4/src/xml/XMLNode.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/xml/XMLNode.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -182,8 +182,12 @@
 XMLNode& 
 XMLNode::operator=(const XMLNode& orig)
 {
-  this->XMLToken::operator=(orig);
-  this->mChildren.assign( orig.mChildren.begin(), orig.mChildren.end() ); 
+  if(&orig!=this)
+  {
+    this->XMLToken::operator=(orig);
+    this->mChildren.assign( orig.mChildren.begin(), orig.mChildren.end() ); 
+  }
+
   return *this;
 }
 

Modified: branches/libsbml-4/src/xml/XMLToken.cpp
===================================================================
--- branches/libsbml-4/src/xml/XMLToken.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/xml/XMLToken.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -166,29 +166,32 @@
 XMLToken& 
 XMLToken::operator=(const XMLToken& orig)
 {
-  if (orig.mTriple.isEmpty())
-    mTriple = XMLTriple();
-  else
-    mTriple = XMLTriple(orig.getName(), orig.getURI(), orig.getPrefix());
-  
-  if (orig.mAttributes.isEmpty())
-    mAttributes = XMLAttributes();
-  else
-    mAttributes = XMLAttributes(orig.getAttributes());
-  
-  if (orig.mNamespaces.isEmpty())
-    mNamespaces = XMLNamespaces();
-  else
-    mNamespaces = XMLNamespaces(orig.getNamespaces());
+  if(&orig!=this)
+  {
+    if (orig.mTriple.isEmpty())
+      mTriple = XMLTriple();
+    else
+      mTriple = XMLTriple(orig.getName(), orig.getURI(), orig.getPrefix());
+    
+    if (orig.mAttributes.isEmpty())
+      mAttributes = XMLAttributes();
+    else
+      mAttributes = XMLAttributes(orig.getAttributes());
+    
+    if (orig.mNamespaces.isEmpty())
+      mNamespaces = XMLNamespaces();
+    else
+      mNamespaces = XMLNamespaces(orig.getNamespaces());
 
-  mChars = orig.mChars;
+    mChars = orig.mChars;
 
-  mIsStart = orig.mIsStart;
-  mIsEnd = orig.mIsEnd;
-  mIsText = orig.mIsText;
+    mIsStart = orig.mIsStart;
+    mIsEnd = orig.mIsEnd;
+    mIsText = orig.mIsText;
 
-  mLine = orig.mLine;
-  mColumn = orig.mColumn;
+    mLine = orig.mLine;
+    mColumn = orig.mColumn;
+  }
 
   return *this;
 }

Modified: branches/libsbml-4/src/xml/XMLTriple.cpp
===================================================================
--- branches/libsbml-4/src/xml/XMLTriple.cpp	2009-04-16 15:53:39 UTC (rev 9441)
+++ branches/libsbml-4/src/xml/XMLTriple.cpp	2009-04-16 16:48:09 UTC (rev 9442)
@@ -107,9 +107,12 @@
 XMLTriple& 
 XMLTriple::operator=(const XMLTriple& orig)
 {
-  mName   = orig.mName;
-  mURI    = orig.mURI;
-  mPrefix = orig.mPrefix;
+  if(&orig!=this)
+  {
+    mName   = orig.mName;
+    mURI    = orig.mURI;
+    mPrefix = orig.mPrefix;
+  }
 
   return *this;
 }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9441
          http://sbml.svn.sourceforge.net/sbml/?rev=9441&view=rev
Author:   sarahkeating
Date:     2009-04-16 15:53:39 +0000 (Thu, 16 Apr 2009)

Log Message:
-----------
assignment operator should check for self-assignment

Modified Paths:
--------------
    trunk/libsbml/src/annotation/CVTerm.cpp
    trunk/libsbml/src/annotation/ModelHistory.cpp
    trunk/libsbml/src/sbml/Compartment.cpp
    trunk/libsbml/src/sbml/CompartmentType.cpp
    trunk/libsbml/src/sbml/Constraint.cpp
    trunk/libsbml/src/sbml/Delay.cpp
    trunk/libsbml/src/sbml/Event.cpp
    trunk/libsbml/src/sbml/EventAssignment.cpp
    trunk/libsbml/src/sbml/FunctionDefinition.cpp
    trunk/libsbml/src/sbml/InitialAssignment.cpp
    trunk/libsbml/src/sbml/KineticLaw.cpp
    trunk/libsbml/src/sbml/ListOf.cpp
    trunk/libsbml/src/sbml/Model.cpp
    trunk/libsbml/src/sbml/Parameter.cpp
    trunk/libsbml/src/sbml/Reaction.cpp
    trunk/libsbml/src/sbml/Rule.cpp
    trunk/libsbml/src/sbml/SBase.cpp
    trunk/libsbml/src/sbml/Species.cpp
    trunk/libsbml/src/sbml/SpeciesReference.cpp
    trunk/libsbml/src/sbml/SpeciesType.cpp
    trunk/libsbml/src/sbml/StoichiometryMath.cpp
    trunk/libsbml/src/sbml/Trigger.cpp
    trunk/libsbml/src/sbml/Unit.cpp
    trunk/libsbml/src/sbml/UnitDefinition.cpp
    trunk/libsbml/src/xml/XMLAttributes.cpp
    trunk/libsbml/src/xml/XMLNamespaces.cpp
    trunk/libsbml/src/xml/XMLNode.cpp
    trunk/libsbml/src/xml/XMLToken.cpp
    trunk/libsbml/src/xml/XMLTriple.cpp

Modified: trunk/libsbml/src/annotation/CVTerm.cpp
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/annotation/CVTerm.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -157,11 +157,15 @@
 CVTerm& 
 CVTerm::operator=(const CVTerm& rhs)
 {
-  mQualifier       = rhs.mQualifier;
-  mModelQualifier  = rhs.mModelQualifier;
-  mBiolQualifier   = rhs.mBiolQualifier;
+  if(&rhs!=this)
+  {
+    mQualifier       = rhs.mQualifier;
+    mModelQualifier  = rhs.mModelQualifier;
+    mBiolQualifier   = rhs.mBiolQualifier;
 
-  mResources=new XMLAttributes(*rhs.mResources);
+    mResources=new XMLAttributes(*rhs.mResources);
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/annotation/ModelHistory.cpp
===================================================================
--- trunk/libsbml/src/annotation/ModelHistory.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/annotation/ModelHistory.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -90,18 +90,22 @@
   */
 Date& Date::operator=(const Date& orig)
 {
-  mYear   = orig.mYear;
-  mMonth  = orig.mMonth;
-  mDay    = orig.mDay;
-  mHour   = orig.mHour;  
-  mMinute = orig.mMinute;
-  mSecond = orig.mSecond;
-  
-  mSignOffset     = orig.mSignOffset;
-  mHoursOffset    = orig.mHoursOffset;
-  mMinutesOffset  = orig.mMinutesOffset;;
+  if(&orig!=this)
+  {
+    mYear   = orig.mYear;
+    mMonth  = orig.mMonth;
+    mDay    = orig.mDay;
+    mHour   = orig.mHour;  
+    mMinute = orig.mMinute;
+    mSecond = orig.mSecond;
+    
+    mSignOffset     = orig.mSignOffset;
+    mHoursOffset    = orig.mHoursOffset;
+    mMinutesOffset  = orig.mMinutesOffset;;
 
-  mDate = orig.mDate;
+    mDate = orig.mDate;
+  }
+
   return *this;
 }
 
@@ -566,10 +570,14 @@
   */
 ModelCreator& ModelCreator::operator=(const ModelCreator& orig)
 {
-  mFamilyName   = orig.mFamilyName;
-  mGivenName    = orig.mGivenName;
-  mEmail        = orig.mEmail;
-  mOrganization = orig.mOrganization;
+  if(&orig!=this)
+  {
+    mFamilyName   = orig.mFamilyName;
+    mGivenName    = orig.mGivenName;
+    mEmail        = orig.mEmail;
+    mOrganization = orig.mOrganization;
+  }
+
   return *this;
 }
 
@@ -778,18 +786,21 @@
 ModelHistory& 
 ModelHistory::operator=(const ModelHistory& orig)
 {
-  unsigned int i;
-  for (i = 0; i < orig.mCreators->getSize(); i++)
+  if(&orig!=this)
   {
-    addCreator(static_cast<ModelCreator*>(orig.mCreators->get(i)));
+    unsigned int i;
+    for (i = 0; i < orig.mCreators->getSize(); i++)
+    {
+      addCreator(static_cast<ModelCreator*>(orig.mCreators->get(i)));
+    }
+
+    for (i = 0; i < orig.mModifiedDates->getSize(); i++)
+    {
+      addModifiedDate(static_cast<Date*>(orig.mModifiedDates->get(i)));
+    }
+    if (orig.mCreatedDate) setCreatedDate(orig.mCreatedDate);
   }
 
-  for (i = 0; i < orig.mModifiedDates->getSize(); i++)
-  {
-    addModifiedDate(static_cast<Date*>(orig.mModifiedDates->get(i)));
-  }
-  if (orig.mCreatedDate) setCreatedDate(orig.mCreatedDate);
-//  if (orig.mModifiedDate)setModifiedDate(orig.mModifiedDate);
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Compartment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -99,14 +99,18 @@
  */
 Compartment& Compartment::operator=(const Compartment& rhs)
 {
-  this->SBase::operator =(rhs);
-  mSpatialDimensions= rhs.mSpatialDimensions  ;
-  mSize             = rhs.mSize      ;
-  mConstant         = rhs.mConstant     ;
-  mIsSetSize        = rhs.mIsSetSize    ;
-  mCompartmentType  = rhs.mCompartmentType;
-  mUnits            = rhs.mUnits ;
-  mOutside          = rhs.mOutside ;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mSpatialDimensions= rhs.mSpatialDimensions  ;
+    mSize             = rhs.mSize      ;
+    mConstant         = rhs.mConstant     ;
+    mIsSetSize        = rhs.mIsSetSize    ;
+    mCompartmentType  = rhs.mCompartmentType;
+    mUnits            = rhs.mUnits ;
+    mOutside          = rhs.mOutside ;
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/CompartmentType.cpp
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/CompartmentType.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -85,7 +85,11 @@
  */
 CompartmentType& CompartmentType::operator=(const CompartmentType& rhs)
 {
-  this->SBase::operator =(rhs);
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Constraint.cpp
===================================================================
--- trunk/libsbml/src/sbml/Constraint.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Constraint.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -101,10 +101,13 @@
  */
 Constraint& Constraint::operator=(const Constraint& rhs)
 {
-  this->SBase::operator =(rhs);
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
 
-  if (rhs.mMath)    mMath    = rhs.mMath->deepCopy();
-  if (rhs.mMessage) mMessage = new XMLNode(*rhs.mMessage);
+    if (rhs.mMath)    mMath    = rhs.mMath->deepCopy();
+    if (rhs.mMessage) mMessage = new XMLNode(*rhs.mMessage);
+  }
 
   return *this;
 }

Modified: trunk/libsbml/src/sbml/Delay.cpp
===================================================================
--- trunk/libsbml/src/sbml/Delay.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Delay.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -96,8 +96,12 @@
  */
 Delay& Delay::operator=(const Delay& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Event.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -106,15 +106,18 @@
  */
 Event& Event::operator=(const Event& rhs)
 {
-  this->SBase::operator =(rhs);
- 
-  mTimeUnits        = rhs.mTimeUnits        ;
-  mUseValuesFromTriggerTime = rhs.mUseValuesFromTriggerTime;
-  mInternalIdOnly   = rhs.mInternalIdOnly   ;
-  mEventAssignments = rhs.mEventAssignments ;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+   
+    mTimeUnits        = rhs.mTimeUnits        ;
+    mUseValuesFromTriggerTime = rhs.mUseValuesFromTriggerTime;
+    mInternalIdOnly   = rhs.mInternalIdOnly   ;
+    mEventAssignments = rhs.mEventAssignments ;
 
-  if (rhs.mTrigger) mTrigger = new Trigger(*rhs.getTrigger());
-  if (rhs.mDelay) mDelay = new Delay(*rhs.getDelay());
+    if (rhs.mTrigger) mTrigger = new Trigger(*rhs.getTrigger());
+    if (rhs.mDelay) mDelay = new Delay(*rhs.getDelay());
+  }
 
   return *this;
 }

Modified: trunk/libsbml/src/sbml/EventAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/EventAssignment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -96,8 +96,12 @@
  */
 EventAssignment& EventAssignment::operator=(const EventAssignment& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/FunctionDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/FunctionDefinition.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/FunctionDefinition.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -109,8 +109,12 @@
  */
 FunctionDefinition& FunctionDefinition::operator=(const FunctionDefinition& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/InitialAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/InitialAssignment.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -92,8 +92,12 @@
  */
 InitialAssignment& InitialAssignment::operator=(const InitialAssignment& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/KineticLaw.cpp
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/KineticLaw.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -122,12 +122,16 @@
  */
 KineticLaw& KineticLaw::operator=(const KineticLaw& rhs)
 {
-  this->SBase::operator =(rhs);
-  mFormula        = rhs.mFormula        ;
-  mTimeUnits      = rhs.mTimeUnits      ;
-  mSubstanceUnits = rhs.mSubstanceUnits ;
-  mParameters     = rhs.mParameters     ;
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mFormula        = rhs.mFormula        ;
+    mTimeUnits      = rhs.mTimeUnits      ;
+    mSubstanceUnits = rhs.mSubstanceUnits ;
+    mParameters     = rhs.mParameters     ;
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/ListOf.cpp
===================================================================
--- trunk/libsbml/src/sbml/ListOf.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/ListOf.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -85,11 +85,15 @@
  */
 ListOf& ListOf::operator=(const ListOf& rhs)
 {
-  this->SBase::operator =(rhs);
-  // Deletes existing items
-  for_each( mItems.begin(), mItems.end(), Delete() );
-  mItems.resize( rhs.size() );
-  transform( rhs.mItems.begin(), rhs.mItems.end(), mItems.begin(), Clone() );
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    // Deletes existing items
+    for_each( mItems.begin(), mItems.end(), Delete() );
+    mItems.resize( rhs.size() );
+    transform( rhs.mItems.begin(), rhs.mItems.end(), mItems.begin(), Clone() );
+  }
+  
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Model.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -141,45 +141,48 @@
  */
 Model& Model::operator=(const Model& rhs)
 {
-  this->SBase::operator = (rhs);
-  mFunctionDefinitions  = rhs.mFunctionDefinitions;
-  mUnitDefinitions      = rhs.mUnitDefinitions;
-  mCompartmentTypes     = rhs.mCompartmentTypes;
-  mSpeciesTypes         = rhs.mSpeciesTypes;
-  mCompartments         = rhs.mCompartments;
-  mSpecies              = rhs.mSpecies;
-  mParameters           = rhs.mParameters;
-  mInitialAssignments   = rhs.mInitialAssignments;
-  mRules                = rhs.mRules;
-  mConstraints          = rhs.mConstraints;
-  mReactions            = rhs.mReactions;
-  mEvents               = rhs.mEvents;
-#ifdef USE_LAYOUT
-  mLayouts              = rhs.mLayouts;
-#endif
-  if (rhs.mHistory)
+  if(&rhs!=this)
   {
-    this->mHistory = rhs.mHistory->clone();
-  }
-  else
-  {
-    this->mHistory = 0;
-  }
-  if(rhs.mFormulaUnitsData)
-  {
-    this->mFormulaUnitsData  = new List();
-    unsigned int i,iMax = rhs.mFormulaUnitsData->getSize();
-    for(i = 0; i < iMax; ++i)
+    this->SBase::operator = (rhs);
+    mFunctionDefinitions  = rhs.mFunctionDefinitions;
+    mUnitDefinitions      = rhs.mUnitDefinitions;
+    mCompartmentTypes     = rhs.mCompartmentTypes;
+    mSpeciesTypes         = rhs.mSpeciesTypes;
+    mCompartments         = rhs.mCompartments;
+    mSpecies              = rhs.mSpecies;
+    mParameters           = rhs.mParameters;
+    mInitialAssignments   = rhs.mInitialAssignments;
+    mRules                = rhs.mRules;
+    mConstraints          = rhs.mConstraints;
+    mReactions            = rhs.mReactions;
+    mEvents               = rhs.mEvents;
+  #ifdef USE_LAYOUT
+    mLayouts              = rhs.mLayouts;
+  #endif
+    if (rhs.mHistory)
     {
-      this->mFormulaUnitsData
-        ->add(static_cast<FormulaUnitsData*>
-                                 (rhs.mFormulaUnitsData->get(i))->clone());
+      this->mHistory = rhs.mHistory->clone();
     }
+    else
+    {
+      this->mHistory = 0;
+    }
+    if(rhs.mFormulaUnitsData)
+    {
+      this->mFormulaUnitsData  = new List();
+      unsigned int i,iMax = rhs.mFormulaUnitsData->getSize();
+      for(i = 0; i < iMax; ++i)
+      {
+        this->mFormulaUnitsData
+          ->add(static_cast<FormulaUnitsData*>
+                                   (rhs.mFormulaUnitsData->get(i))->clone());
+      }
+    }
+    else
+    {
+      this->mFormulaUnitsData = 0;
+    }
   }
-  else
-  {
-    this->mFormulaUnitsData = 0;
-  }
 
   return *this;
 }

Modified: trunk/libsbml/src/sbml/Parameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/Parameter.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Parameter.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -116,11 +116,15 @@
  */
 Parameter& Parameter::operator=(const Parameter& rhs)
 {
-  this->SBase::operator =(rhs);
-     mValue      = rhs.mValue    ;
-     mUnits      = rhs.mUnits    ;
-     mConstant   = rhs.mConstant ;
-     mIsSetValue = rhs.mIsSetValue;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mValue      = rhs.mValue    ;
+    mUnits      = rhs.mUnits    ;
+    mConstant   = rhs.mConstant ;
+    mIsSetValue = rhs.mIsSetValue;
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Reaction.cpp
===================================================================
--- trunk/libsbml/src/sbml/Reaction.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Reaction.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -149,17 +149,21 @@
  */
 Reaction& Reaction::operator=(const Reaction& rhs)
 {
-  this->SBase::operator =(rhs);
- mReversible = rhs.mReversible ;
- mFast       = rhs.mFast       ;
- mIsSetFast  = rhs.mIsSetFast  ;
- mReactants  = rhs.mReactants  ;
- mProducts   = rhs.mProducts   ;
- mModifiers  = rhs.mModifiers  ;
-  if (rhs.mKineticLaw)
+  if(&rhs!=this)
   {
-    mKineticLaw = static_cast<KineticLaw*>( rhs.mKineticLaw->clone() );
+    this->SBase::operator =(rhs);
+    mReversible = rhs.mReversible ;
+    mFast       = rhs.mFast       ;
+    mIsSetFast  = rhs.mIsSetFast  ;
+    mReactants  = rhs.mReactants  ;
+    mProducts   = rhs.mProducts   ;
+    mModifiers  = rhs.mModifiers  ;
+    if (rhs.mKineticLaw)
+    {
+      mKineticLaw = static_cast<KineticLaw*>( rhs.mKineticLaw->clone() );
+    }
   }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Rule.cpp
===================================================================
--- trunk/libsbml/src/sbml/Rule.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Rule.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -109,12 +109,16 @@
  */
 Rule& Rule::operator=(const Rule& rhs)
 {
-  this->SBase::operator =(rhs);
-  mFormula = rhs.mFormula ;
-  mUnits   = rhs.mUnits   ;
-  mType    = rhs.mType    ;
-  mL1Type  = rhs.mL1Type  ;
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mFormula = rhs.mFormula ;
+    mUnits   = rhs.mUnits   ;
+    mType    = rhs.mType    ;
+    mL1Type  = rhs.mL1Type  ;
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/SBase.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -246,6 +246,8 @@
  */
 SBase& SBase::operator=(const SBase& orig)
 {
+  if(&orig!=this)
+  {
     this->mId     = orig.mId;
     this->mName   = orig.mName;
     this->mMetaId = orig.mMetaId;
@@ -254,12 +256,12 @@
       this->mNotes = new XMLNode(*const_cast<SBase&>(orig).getNotes());
     else
       this->mNotes = 0;
-    
+
     if(orig.mAnnotation) 
       this->mAnnotation = new XMLNode(*const_cast<SBase&>(orig).mAnnotation);
     else
       this->mAnnotation = 0;
-    
+
     this->mObjectLevel       = orig.mObjectLevel;
     this->mObjectVersion       = orig.mObjectVersion;
     this->mSBML       = orig.mSBML;
@@ -289,8 +291,9 @@
     }
 
     this->mHasBeenDeleted = orig.mHasBeenDeleted;
-    return *this;
-
+  }
+  
+  return *this;
 }
 
 

Modified: trunk/libsbml/src/sbml/Species.cpp
===================================================================
--- trunk/libsbml/src/sbml/Species.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Species.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -120,7 +120,9 @@
  */
 Species& Species::operator=(const Species& orig)
 {
-  this->SBase::operator =(orig);
+  if(&orig!=this)
+  {
+    this->SBase::operator =(orig);
     this->mSpeciesType = orig.mSpeciesType;
     this->mCompartment = orig.mCompartment;
 
@@ -138,6 +140,8 @@
     this->mIsSetInitialAmount = orig.mIsSetInitialAmount;
     this->mIsSetInitialConcentration = orig.mIsSetInitialConcentration;
     this->mIsSetCharge = orig.mIsSetCharge;
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/SpeciesReference.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesReference.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/SpeciesReference.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -98,8 +98,12 @@
  */
 SimpleSpeciesReference& SimpleSpeciesReference::operator=(const SimpleSpeciesReference& rhs)
 {
-  this->SBase::operator =(rhs);
-  mSpecies = rhs.mSpecies;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mSpecies = rhs.mSpecies;
+  }
+
   return *this;
 }
 
@@ -349,14 +353,18 @@
  */
 SpeciesReference& SpeciesReference::operator=(const SpeciesReference& rhs)
 {
-  this->SBase::operator =(rhs);
-  this->SimpleSpeciesReference::operator = ( rhs );
-  mStoichiometry = rhs.mStoichiometry ;
-  mDenominator = rhs.mDenominator   ;
-  if (rhs.mStoichiometryMath)
+  if(&rhs!=this)
   {
-    mStoichiometryMath = new StoichiometryMath(*rhs.getStoichiometryMath());
+    this->SBase::operator =(rhs);
+    this->SimpleSpeciesReference::operator = ( rhs );
+    mStoichiometry = rhs.mStoichiometry ;
+    mDenominator = rhs.mDenominator   ;
+    if (rhs.mStoichiometryMath)
+    {
+      mStoichiometryMath = new StoichiometryMath(*rhs.getStoichiometryMath());
+    }
   }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/SpeciesType.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesType.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/SpeciesType.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -85,7 +85,11 @@
  */
 SpeciesType& SpeciesType::operator=(const SpeciesType& rhs)
 {
-  this->SBase::operator =(rhs);
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/StoichiometryMath.cpp
===================================================================
--- trunk/libsbml/src/sbml/StoichiometryMath.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/StoichiometryMath.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -96,8 +96,12 @@
  */
 StoichiometryMath& StoichiometryMath::operator=(const StoichiometryMath& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Trigger.cpp
===================================================================
--- trunk/libsbml/src/sbml/Trigger.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Trigger.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -96,8 +96,12 @@
  */
 Trigger& Trigger::operator=(const Trigger& rhs)
 {
-  this->SBase::operator =(rhs);
-  if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    if (rhs.mMath) mMath = rhs.mMath->deepCopy();
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/Unit.cpp
===================================================================
--- trunk/libsbml/src/sbml/Unit.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/Unit.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -121,12 +121,16 @@
  */
 Unit& Unit::operator=(const Unit& rhs)
 {
-  this->SBase::operator =(rhs);
-  mKind       = rhs.mKind       ;
-  mExponent   = rhs.mExponent   ;
-  mScale      = rhs.mScale      ;
-  mMultiplier = rhs.mMultiplier ;
-  mOffset     = rhs.mOffset     ;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mKind       = rhs.mKind       ;
+    mExponent   = rhs.mExponent   ;
+    mScale      = rhs.mScale      ;
+    mMultiplier = rhs.mMultiplier ;
+    mOffset     = rhs.mOffset     ;
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/sbml/UnitDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/UnitDefinition.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/sbml/UnitDefinition.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -89,8 +89,12 @@
  */
 UnitDefinition& UnitDefinition::operator=(const UnitDefinition& rhs)
 {
-  this->SBase::operator =(rhs);
-  mUnits = rhs.mUnits;
+  if(&rhs!=this)
+  {
+    this->SBase::operator =(rhs);
+    mUnits = rhs.mUnits;
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/xml/XMLAttributes.cpp
===================================================================
--- trunk/libsbml/src/xml/XMLAttributes.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/xml/XMLAttributes.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -89,10 +89,14 @@
 XMLAttributes& 
 XMLAttributes::operator=(const XMLAttributes& orig)
 {
-  this->mNames.assign( orig.mNames.begin(), orig.mNames.end() ); 
-  this->mValues.assign( orig.mValues.begin(), orig.mValues.end() ); 
-  this->mElementName = orig.mElementName;
-  this->mLog = orig.mLog;
+  if(&orig!=this)
+  {
+    this->mNames.assign( orig.mNames.begin(), orig.mNames.end() ); 
+    this->mValues.assign( orig.mValues.begin(), orig.mValues.end() ); 
+    this->mElementName = orig.mElementName;
+    this->mLog = orig.mLog;
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/xml/XMLNamespaces.cpp
===================================================================
--- trunk/libsbml/src/xml/XMLNamespaces.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/xml/XMLNamespaces.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -68,7 +68,11 @@
 XMLNamespaces& 
 XMLNamespaces::operator=(const XMLNamespaces& orig)
 {
-  this->mNamespaces.assign( orig.mNamespaces.begin(), orig.mNamespaces.end() ); 
+  if(&orig!=this)
+  {
+    this->mNamespaces.assign( orig.mNamespaces.begin(), orig.mNamespaces.end() ); 
+  }
+  
   return *this;
 }
 

Modified: trunk/libsbml/src/xml/XMLNode.cpp
===================================================================
--- trunk/libsbml/src/xml/XMLNode.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/xml/XMLNode.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -182,8 +182,12 @@
 XMLNode& 
 XMLNode::operator=(const XMLNode& orig)
 {
-  this->XMLToken::operator=(orig);
-  this->mChildren.assign( orig.mChildren.begin(), orig.mChildren.end() ); 
+  if(&orig!=this)
+  {
+    this->XMLToken::operator=(orig);
+    this->mChildren.assign( orig.mChildren.begin(), orig.mChildren.end() ); 
+  }
+
   return *this;
 }
 

Modified: trunk/libsbml/src/xml/XMLToken.cpp
===================================================================
--- trunk/libsbml/src/xml/XMLToken.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/xml/XMLToken.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -166,29 +166,32 @@
 XMLToken& 
 XMLToken::operator=(const XMLToken& orig)
 {
-  if (orig.mTriple.isEmpty())
-    mTriple = XMLTriple();
-  else
-    mTriple = XMLTriple(orig.getName(), orig.getURI(), orig.getPrefix());
-  
-  if (orig.mAttributes.isEmpty())
-    mAttributes = XMLAttributes();
-  else
-    mAttributes = XMLAttributes(orig.getAttributes());
-  
-  if (orig.mNamespaces.isEmpty())
-    mNamespaces = XMLNamespaces();
-  else
-    mNamespaces = XMLNamespaces(orig.getNamespaces());
+  if(&orig!=this)
+  {
+    if (orig.mTriple.isEmpty())
+      mTriple = XMLTriple();
+    else
+      mTriple = XMLTriple(orig.getName(), orig.getURI(), orig.getPrefix());
+    
+    if (orig.mAttributes.isEmpty())
+      mAttributes = XMLAttributes();
+    else
+      mAttributes = XMLAttributes(orig.getAttributes());
+    
+    if (orig.mNamespaces.isEmpty())
+      mNamespaces = XMLNamespaces();
+    else
+      mNamespaces = XMLNamespaces(orig.getNamespaces());
 
-  mChars = orig.mChars;
+    mChars = orig.mChars;
 
-  mIsStart = orig.mIsStart;
-  mIsEnd = orig.mIsEnd;
-  mIsText = orig.mIsText;
+    mIsStart = orig.mIsStart;
+    mIsEnd = orig.mIsEnd;
+    mIsText = orig.mIsText;
 
-  mLine = orig.mLine;
-  mColumn = orig.mColumn;
+    mLine = orig.mLine;
+    mColumn = orig.mColumn;
+  }
 
   return *this;
 }

Modified: trunk/libsbml/src/xml/XMLTriple.cpp
===================================================================
--- trunk/libsbml/src/xml/XMLTriple.cpp	2009-04-15 20:55:35 UTC (rev 9440)
+++ trunk/libsbml/src/xml/XMLTriple.cpp	2009-04-16 15:53:39 UTC (rev 9441)
@@ -107,9 +107,12 @@
 XMLTriple& 
 XMLTriple::operator=(const XMLTriple& orig)
 {
-  mName   = orig.mName;
-  mURI    = orig.mURI;
-  mPrefix = orig.mPrefix;
+  if(&orig!=this)
+  {
+    mName   = orig.mName;
+    mURI    = orig.mURI;
+    mPrefix = orig.mPrefix;
+  }
 
   return *this;
 }


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Revision: 9440
          http://sbml.svn.sourceforge.net/sbml/?rev=9440&view=rev
Author:   sarahkeating
Date:     2009-04-15 20:55:35 +0000 (Wed, 15 Apr 2009)

Log Message:
-----------
Tracker issue #2748785
Fixed memory leak. Thanks to Lucian Smith for reporting these.

Modified Paths:
--------------
    branches/libsbml-4/src/validator/constraints/AssignmentCycles.cpp

Modified: branches/libsbml-4/src/validator/constraints/AssignmentCycles.cpp
===================================================================
--- branches/libsbml-4/src/validator/constraints/AssignmentCycles.cpp	2009-04-15 20:54:00 UTC (rev 9439)
+++ branches/libsbml-4/src/validator/constraints/AssignmentCycles.cpp	2009-04-15 20:55:35 UTC (rev 9440)
@@ -594,6 +594,8 @@
     if (!(strcmp(variable.c_str(), name)))
       logMathRefersToSelf(*(object.getMath()), object);
   }
+
+  delete variables;
 }
 
 void 
@@ -617,6 +619,8 @@
       if (!(strcmp(variable.c_str(), name)))
         logMathRefersToSelf(*(object.getKineticLaw()->getMath()), object);
     }
+    
+    delete variables;
   }
 }
 
@@ -636,6 +640,8 @@
     if (!(strcmp(variable.c_str(), name)))
       logMathRefersToSelf(*(object.getMath()), object);
   }
+  
+  delete variables;
 }
 
   
@@ -668,6 +674,8 @@
       logImplicitReference(object, *(s));
     }
   }
+  
+  delete variables;
 }
  
 
@@ -700,6 +708,8 @@
       logImplicitReference(object, *(s));
     }
   }
+  
+  delete variables;
 }
 
 /**


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 9439
          http://sbml.svn.sourceforge.net/sbml/?rev=9439&view=rev
Author:   sarahkeating
Date:     2009-04-15 20:54:00 +0000 (Wed, 15 Apr 2009)

Log Message:
-----------
Tracker issue #2748785
Fixed memory leak. Thanks to Lucian Smith for reporting these.

Modified Paths:
--------------
    trunk/libsbml/src/validator/constraints/AssignmentCycles.cpp

Modified: trunk/libsbml/src/validator/constraints/AssignmentCycles.cpp
===================================================================
--- trunk/libsbml/src/validator/constraints/AssignmentCycles.cpp	2009-04-15 20:14:33 UTC (rev 9438)
+++ trunk/libsbml/src/validator/constraints/AssignmentCycles.cpp	2009-04-15 20:54:00 UTC (rev 9439)
@@ -594,6 +594,8 @@
     if (!(strcmp(variable.c_str(), name)))
       logMathRefersToSelf(*(object.getMath()), object);
   }
+
+  delete variables;
 }
 
 void 
@@ -617,6 +619,8 @@
       if (!(strcmp(variable.c_str(), name)))
         logMathRefersToSelf(*(object.getKineticLaw()->getMath()), object);
     }
+    
+    delete variables;
   }
 }
 
@@ -636,6 +640,8 @@
     if (!(strcmp(variable.c_str(), name)))
       logMathRefersToSelf(*(object.getMath()), object);
   }
+  
+  delete variables;
 }
 
   
@@ -668,6 +674,8 @@
       logImplicitReference(object, *(s));
     }
   }
+  
+  delete variables;
 }
  
 
@@ -700,6 +708,8 @@
       logImplicitReference(object, *(s));
     }
   }
+  
+  delete variables;
 }
 
 /**


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