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From: <ajo...@us...> - 2008-07-31 22:52:34
|
Revision: 7800
http://sbml.svn.sourceforge.net/sbml/?rev=7800&view=rev
Author: ajouraku
Date: 2008-07-31 22:52:31 +0000 (Thu, 31 Jul 2008)
Log Message:
-----------
Added missing configure's check for file existence for ruby and python.
Modified Paths:
--------------
trunk/libsbml/config/python.m4
trunk/libsbml/config/ruby.m4
trunk/libsbml/configure
Modified: trunk/libsbml/config/python.m4
===================================================================
--- trunk/libsbml/config/python.m4 2008-07-31 12:47:42 UTC (rev 7799)
+++ trunk/libsbml/config/python.m4 2008-07-31 22:52:31 UTC (rev 7800)
@@ -56,6 +56,11 @@
AC_PATH_PROG([PYTHON], [python])
fi
+ if test -z $PYTHON || ! test -f $PYTHON;
+ then
+ AC_MSG_ERROR([*** python missing - please install first or check config.log ***])
+ fi
+
dnl check version if required
m4_ifvaln([$1], [
AC_MSG_CHECKING($PYTHON version >= $1)
@@ -64,6 +69,7 @@
AC_MSG_RESULT(ok)
else
AC_MSG_RESULT(no)
+ AC_MSG_ERROR([*** python version $1 or later is required ***])
fi
])
@@ -77,6 +83,15 @@
PYTHON_NAME="python${PYTHON_VERSION}"
+ PYTHON_H="${PYTHON_PREFIX}/include/${PYTHON_NAME}/Python.h"
+ AC_MSG_CHECKING(for Python.h)
+ if test -z $PYTHON_H || ! test -f $PYTHON_H;
+ then
+ AC_MSG_RESULT(no)
+ AC_MSG_ERROR([*** $PYTHON_H missing - please install first or check config.log ***])
+ fi
+ AC_MSG_RESULT(yes)
+
dnl Figure out the last bits for linking.
dnl This comes in part from SWIG 1.3.31's configure.ac file.
Modified: trunk/libsbml/config/ruby.m4
===================================================================
--- trunk/libsbml/config/ruby.m4 2008-07-31 12:47:42 UTC (rev 7799)
+++ trunk/libsbml/config/ruby.m4 2008-07-31 22:52:31 UTC (rev 7800)
@@ -41,11 +41,11 @@
[with_ruby=$withval],
[with_ruby=no])
- if test $with_ruby != no; then
+ if test "x$with_ruby" != xno; then
dnl Find a ruby executable.
- if test $with_ruby != yes;
+ if test "x$with_ruby" != xyes;
then
dnl Remove needless trailing slashes because it can confuse tests later.
with_ruby=`echo $with_ruby | sed -e 's,\(.*\)/$,\1,g'`
@@ -56,6 +56,11 @@
AC_PATH_PROG([RUBY], [ruby])
fi
+ if test -z $RUBY || ! test -f $RUBY;
+ then
+ AC_MSG_ERROR([*** ruby missing - please install first or check config.log ***])
+ fi
+
dnl check version if required
m4_ifvaln([$1], [
AC_MSG_CHECKING($RUBY version >= $1)
@@ -64,6 +69,7 @@
AC_MSG_RESULT(ok)
else
AC_MSG_RESULT(no)
+ AC_MSG_ERROR([*** ruby version $1 or later is required ***])
fi
])
@@ -77,6 +83,18 @@
else
RUBY_ARCHDIR=`$RUBY -rrbconfig -e ["include Config; puts CONFIG['archdir']"]`
fi
+
+ RUBY_H="${RUBY_ARCHDIR}/ruby.h"
+ AC_MSG_CHECKING(for ruby.h)
+ if test -z $RUBY_H || ! test -f $RUBY_H;
+ then
+ AC_MSG_RESULT(no)
+
+ AC_MSG_ERROR([*** $RUBY_H missing - please install first or check config.log ***])
+ fi
+ AC_MSG_RESULT(yes)
+
+
RUBY_LIBDIR=`$RUBY -rrbconfig -e ["include Config; puts CONFIG['libdir']"]`
RUBY_NAME=`$RUBY -rrbconfig -e ["include Config; puts CONFIG['RUBY_SO_NAME']"]`
Modified: trunk/libsbml/configure
===================================================================
--- trunk/libsbml/configure 2008-07-31 12:47:42 UTC (rev 7799)
+++ trunk/libsbml/configure 2008-07-31 22:52:31 UTC (rev 7800)
@@ -1,5 +1,5 @@
#! /bin/sh
-# From configure.ac Revision: 7725 .
+# From configure.ac Revision: 7762 .
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.60 for libSBML 3.1.1.
#
@@ -4375,8 +4375,15 @@
fi
+ if test -z $PYTHON || ! test -f $PYTHON;
+ then
+ { { echo "$as_me:$LINENO: error: *** python missing - please install first or check config.log ***" >&5
+echo "$as_me: error: *** python missing - please install first or check config.log ***" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+
{ echo "$as_me:$LINENO: checking for Python prefix" >&5
echo $ECHO_N "checking for Python prefix... $ECHO_C" >&6; }
PYTHON_PREFIX=`("$PYTHON" -c "import sys; print sys.prefix") 2>/dev/null`
@@ -4389,7 +4396,21 @@
PYTHON_NAME="python${PYTHON_VERSION}"
+ PYTHON_H="${PYTHON_PREFIX}/include/${PYTHON_NAME}/Python.h"
+ { echo "$as_me:$LINENO: checking for Python.h" >&5
+echo $ECHO_N "checking for Python.h... $ECHO_C" >&6; }
+ if test -z $PYTHON_H || ! test -f $PYTHON_H;
+ then
+ { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+ { { echo "$as_me:$LINENO: error: *** $PYTHON_H missing - please install first or check config.log ***" >&5
+echo "$as_me: error: *** $PYTHON_H missing - please install first or check config.log ***" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ { echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+
case $host in
*darwin*)
@@ -5707,7 +5728,7 @@
else
ac_cv_FUNC_LISPEXIT=no-exit
for ex in "sb-ext:quit :unix-status" "lisp:exit" "excl:exit" "sys:exit" "ext:quit" "unix:unix-exit" "no-exit" ; do
- echo "configure:5710 trying $ex ..." >&5
+ echo "configure:5731 trying $ex ..." >&5
echo "(ignore-errors ($ex 127))"|$LISP 2>&5 1>&5
if test "$?" = "127" ; then
ac_cv_FUNC_LISPEXIT=$ex
@@ -6090,10 +6111,10 @@
fi
- if test $with_ruby != no; then
+ if test "x$with_ruby" != xno; then
- if test $with_ruby != yes;
+ if test "x$with_ruby" != xyes;
then
with_ruby=`echo $with_ruby | sed -e 's,\(.*\)/$,\1,g'`
@@ -6181,8 +6202,15 @@
fi
+ if test -z $RUBY || ! test -f $RUBY;
+ then
+ { { echo "$as_me:$LINENO: error: *** ruby missing - please install first or check config.log ***" >&5
+echo "$as_me: error: *** ruby missing - please install first or check config.log ***" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+
{ echo "$as_me:$LINENO: checking for ruby prefix" >&5
echo $ECHO_N "checking for ruby prefix... $ECHO_C" >&6; }
RUBY_PREFIX=`$RUBY -rrbconfig -e "include Config; puts CONFIG['prefix']"`
@@ -6195,6 +6223,23 @@
else
RUBY_ARCHDIR=`$RUBY -rrbconfig -e "include Config; puts CONFIG['archdir']"`
fi
+
+ RUBY_H="${RUBY_ARCHDIR}/ruby.h"
+ { echo "$as_me:$LINENO: checking for ruby.h" >&5
+echo $ECHO_N "checking for ruby.h... $ECHO_C" >&6; }
+ if test -z $RUBY_H || ! test -f $RUBY_H;
+ then
+ { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+
+ { { echo "$as_me:$LINENO: error: *** $RUBY_H missing - please install first or check config.log ***" >&5
+echo "$as_me: error: *** $RUBY_H missing - please install first or check config.log ***" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ { echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+
+
RUBY_LIBDIR=`$RUBY -rrbconfig -e "include Config; puts CONFIG['libdir']"`
RUBY_NAME=`$RUBY -rrbconfig -e "include Config; puts CONFIG['RUBY_SO_NAME']"`
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-31 12:47:46
|
Revision: 7799
http://sbml.svn.sourceforge.net/sbml/?rev=7799&view=rev
Author: sarahkeating
Date: 2008-07-31 12:47:42 +0000 (Thu, 31 Jul 2008)
Log Message:
-----------
Fixed bug reported by Lukas Endler via sbml-discuss: when determining the units resulting from a division operation if the operation reduced the units to dimensionless the resulting unitDefinition contains no units rather than containing a dimensionless unit.
Modified Paths:
--------------
trunk/libsbml/src/sbml/UnitDefinition.cpp
Modified: trunk/libsbml/src/sbml/UnitDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/UnitDefinition.cpp 2008-07-30 15:24:00 UTC (rev 7798)
+++ trunk/libsbml/src/sbml/UnitDefinition.cpp 2008-07-31 12:47:42 UTC (rev 7799)
@@ -494,6 +494,13 @@
delete units->remove(n-1);
}
}
+
+ /* if all units have been cancelled need to add dimensionless */
+ if (units->size() == 0)
+ {
+ unit = new Unit("dimensionless");
+ ud->addUnit(unit);
+ }
}
/** @cond doxygen-libsbml-internal */
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 15:24:20
|
Revision: 7798
http://sbml.svn.sourceforge.net/sbml/?rev=7798&view=rev
Author: sarahkeating
Date: 2008-07-30 15:24:00 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
initial import
Added Paths:
-----------
trunk/test-suite/cases/syntactic/00001/
trunk/test-suite/cases/syntactic/00001/00001-model.m
trunk/test-suite/cases/syntactic/00001/00001-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00002/
trunk/test-suite/cases/syntactic/00002/00002-model.m
trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00003/
trunk/test-suite/cases/syntactic/00003/00003-model.m
trunk/test-suite/cases/syntactic/00003/00003-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00004/
trunk/test-suite/cases/syntactic/00004/00004-model.m
trunk/test-suite/cases/syntactic/00004/00004-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00005/
trunk/test-suite/cases/syntactic/00005/00005-model.m
trunk/test-suite/cases/syntactic/00005/00005-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00006/
trunk/test-suite/cases/syntactic/00006/00006-model.m
trunk/test-suite/cases/syntactic/00006/00006-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00007/
trunk/test-suite/cases/syntactic/00007/00007-model.m
trunk/test-suite/cases/syntactic/00007/00007-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00008/
trunk/test-suite/cases/syntactic/00008/00008-model.m
trunk/test-suite/cases/syntactic/00008/00008-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00009/
trunk/test-suite/cases/syntactic/00009/00009-model.m
trunk/test-suite/cases/syntactic/00009/00009-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v1.xml
trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v2.xml
trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v3.xml
trunk/test-suite/cases/syntactic/00010/
trunk/test-suite/cases/syntactic/00010/00010-model.m
trunk/test-suite/cases/syntactic/00010/00010-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00011/
trunk/test-suite/cases/syntactic/00011/00011-model.m
trunk/test-suite/cases/syntactic/00011/00011-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00012/
trunk/test-suite/cases/syntactic/00012/00012-model.m
trunk/test-suite/cases/syntactic/00012/00012-sbml-l1v2.xml
trunk/test-suite/cases/syntactic/00013/
trunk/test-suite/cases/syntactic/00013/00013-model.m
trunk/test-suite/cases/syntactic/00013/00013-sbml-l1v2.xml
Added: trunk/test-suite/cases/syntactic/00001/00001-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00001/00001-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00001/00001-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,20 @@
+category: XML
+synopsis: Element tag mismatch or missing tag.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Fail
+
+This model is missing the closing tag '/' of the parameter element on line 12:
+
+{>}%<%parameter id="p" value="1" units="second" constant="false" %>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| XML |
+| *Status:*| Fail |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00001/00001-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00001/00001-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00001/00001-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="minutes">
+ <listOfUnits>
+ <unit kind="second" exponent="1" multiplier="60"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfParameters>
+ <parameter id="p" value="1" units="second" constant="false">
+ <parameter id="p1" value="1" units="minutes" constant="false"/>
+ <parameter id="p2" constant="false"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="minutes">
+ <listOfUnits>
+ <unit kind="second" exponent="1" multiplier="60"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfParameters>
+ <parameter id="p" value="1" units="second" constant="false">
+ <parameter id="p1" value="1" units="minutes" constant="false"/>
+ <parameter id="p2" constant="false"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="minutes">
+ <listOfUnits>
+ <unit kind="second" exponent="1" multiplier="60"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfParameters>
+ <parameter id="p" value="1" units="second" constant="false">
+ <parameter id="p1" value="1" units="minutes" constant="false"/>
+ <parameter id="p2" constant="false"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00001/00001-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="minutes">
+ <listOfUnits>
+ <unit kind="second" exponent="1" multiplier="60"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfParameters>
+ <parameter id="p" value="1" units="second" constant="false">
+ <parameter id="p1" value="1" units="minutes" constant="false"/>
+ <parameter id="p2" constant="false"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00002/00002-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00002/00002-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00002/00002-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,28 @@
+category: SBML_MATHML
+synopsis: Permitted attribute encoding in MathML.
+levels: 2.1, 2.2, 2.3
+status: Fail
+
+This model fails SBML validation rule *10203*:
+
+In the SBML subset of MathML 2.0, the MathML attribute _encoding_ is only
+permitted on *csymbol*, *annotation* and *annotation-xml*. No other MathML
+elements may have an _encoding_ attribute.
+
+References: L2V2 Section 3.5.1; L2V3 Section 3.4.1.
+
+
+The model uses the _encoding_ attribute on the ci element on line 17:
+
+{>}%<%ci encoding="text"%>% p %<%/ci%>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML_MATHML |
+| *Status:*| Fail |
+| *Levels:*| L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfParameters>
+ <parameter id="p" value="1" constant="false"/>
+ <parameter id="p1" units="metre" value="1" constant="false"/>
+ <parameter id="delta_t" units="second" value="1" constant="false"/>
+ </listOfParameters>
+ <listOfRules>
+ <algebraicRule>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci encoding="text"> p </ci>
+ <apply>
+ <csymbol encoding="text"
+ definitionURL="http://www.sbml.org/sbml/symbols/delay">
+ delay
+ </csymbol>
+ <ci> p1 </ci>
+ <ci> delta_t </ci>
+ </apply>
+ </apply>
+ </math>
+ </algebraicRule>
+ </listOfRules>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfParameters>
+ <parameter id="p" value="1" constant="false"/>
+ <parameter id="p1" units="metre" value="1" constant="false"/>
+ <parameter id="delta_t" units="second" value="1" constant="false"/>
+ </listOfParameters>
+ <listOfRules>
+ <algebraicRule>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci encoding="text"> p </ci>
+ <apply>
+ <csymbol encoding="text"
+ definitionURL="http://www.sbml.org/sbml/symbols/delay">
+ delay
+ </csymbol>
+ <ci> p1 </ci>
+ <ci> delta_t </ci>
+ </apply>
+ </apply>
+ </math>
+ </algebraicRule>
+ </listOfRules>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00002/00002-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfParameters>
+ <parameter id="p" value="1" constant="false"/>
+ <parameter id="p1" units="metre" value="1" constant="false"/>
+ <parameter id="delta_t" units="second" value="1" constant="false"/>
+ </listOfParameters>
+ <listOfRules>
+ <algebraicRule>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci encoding="text"> p </ci>
+ <apply>
+ <csymbol encoding="text"
+ definitionURL="http://www.sbml.org/sbml/symbols/delay">
+ delay
+ </csymbol>
+ <ci> p1 </ci>
+ <ci> delta_t </ci>
+ </apply>
+ </apply>
+ </math>
+ </algebraicRule>
+ </listOfRules>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00003/00003-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00003/00003-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00003/00003-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,26 @@
+category: SBML
+synopsis: A species requires a compartment.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Pass
+
+This model passes SBML validation rule *20204*:
+
+If a model defines any *species*, then the model must also define at
+least one *compartment*. This is an implication of the fact that the
+_compartment_ attribute on the *%<%species%>%* element is not optional.
+
+
+References: L2V1 Section 4.5; L2V2 Section 4.8.3; L2V3 Section
+4.8.3.
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Pass |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00003/00003-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00003/00003-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00003/00003-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species name="s" compartment="c" initialAmount="0"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment id="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="s" compartment="c"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment id="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="s" compartment="c"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00003/00003-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+ <listOfCompartments>
+ <compartment id="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="s" compartment="c"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00004/00004-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00004/00004-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00004/00004-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,29 @@
+category: SBML
+synopsis: Missing SBML namespace.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Fail
+
+This model fails SBML validation rule *20101*:
+
+The *%<%sbml%>%* container element must declare the XML Namespace for SBML,
+and this declaration must be consistent with the values of the _level_
+and _version_ attributes on the *%<%sbml%>%* element.
+
+References: L2V2 Section 4.1; L2V3 Section 4.1.
+
+
+The _namespace_ attribute is missing from the sbml element on line 2:
+
+{>}%<%sbml level="2" version="3"%>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Fail |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00004/00004-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00004/00004-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00004/00004-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="1" version="2">
+<model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="2" version="1">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="2" version="2">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00004/00004-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="2" version="3">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00005/00005-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00005/00005-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00005/00005-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,24 @@
+category: SBML
+synopsis: Missing SBML namespace.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Pass
+
+This model passes SBML validation rule *20101*:
+
+The *%<%sbml%>%* container element must declare the XML Namespace for SBML,
+and this declaration must be consistent with the values of the _level_
+and _version_ attributes on the *%<%sbml%>%* element.
+
+References: L2V2 Section 4.1; L2V3 Section 4.1.
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Pass |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00005/00005-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00005/00005-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00005/00005-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00005/00005-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00006/00006-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00006/00006-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00006/00006-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,29 @@
+category: SBML
+synopsis: Inconsistent SBML level.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Fail
+
+This model fails SBML validation rule *20102*:
+
+The *%<%sbml%>%* container element must declare the SBML Level using the
+attribute _level_, and this declaration must be consistent with the XML
+Namespace declared for the *%<%sbml%>%* element.
+
+
+References: L2V2 Section 4.1; L2V3 Section 4.1.
+
+The _level_ attribute is inconsistent with the namespace declared on the sbml element on line 2:
+
+{>}%<%sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="1" version="3"%>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Fail |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00006/00006-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00006/00006-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00006/00006-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="2" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment id="c"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="1" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <specie name="s" compartment="c" initialAmount="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction name="r">
+ <listOfReactants>
+ <specieReference specie="s"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00006/00006-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="1" version="3">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00007/00007-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00007/00007-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00007/00007-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,25 @@
+category: SBML
+synopsis: Inconsistent SBML level.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Pass
+
+This model passes SBML validation rule *20102*:
+
+The *%<%sbml%>%* container element must declare the SBML Level using the
+attribute _level_, and this declaration must be consistent with the XML
+Namespace declared for the *%<%sbml%>%* element.
+
+
+References: L2V2 Section 4.1; L2V3 Section 4.1.
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Pass |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00007/00007-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00007/00007-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00007/00007-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00007/00007-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00008/00008-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00008/00008-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00008/00008-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,29 @@
+category: SBML
+synopsis: Inconsistent SBML version.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Fail
+
+This model fails SBML validation rule *20103*:
+
+The *%<%sbml%>%* container element must declare the SBML Version using the
+attribute _version_, and this declaration must be consistent with the XML
+Namespace declared for the *%<%sbml%>%* element.
+
+
+References: L2V2 Section 4.1; L2V3 Section 4.1.
+
+The _version_ attribute is inconsistent with the namespace declared on the sbml element on line 2:
+
+{>}%<%sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="2"%>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Fail |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00008/00008-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00008/00008-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00008/00008-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="3">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species name="s" compartment="c" initialAmount="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction name="r">
+ <listOfReactants>
+ <speciesReference species="s"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="2">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="1">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00008/00008-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="2">
+ <model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00009/00009-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00009/00009-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00009/00009-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,25 @@
+category: SBML
+synopsis: Inconsistent SBML version.
+levels: 1.2, 2.1, 2.2, 2.3
+status: Pass
+
+This model fails SBML validation rule *20103*:
+
+The *%<%sbml%>%* container element must declare the SBML Version using the
+attribute _version_, and this declaration must be consistent with the XML
+Namespace declared for the *%<%sbml%>%* element.
+
+
+References: L2V2 Section 4.1; L2V3 Section 4.1.
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Pass |
+| *Levels:*| L1V2 |
+| | L2V1 |
+| | L2V2 |
+| | L2V3 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00009/00009-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00009/00009-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00009/00009-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v1.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v1.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v3.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00009/00009-sbml-l2v3.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+<model>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00010/00010-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00010/00010-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00010/00010-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,25 @@
+category: SBML
+synopsis: Annotation/notes not allowed on sbml element.
+levels: 1.2
+status: Fail
+
+This model fails SBML validation rule *20104*:
+
+The *%<%sbml%>%* container element cannot contain *%<%notes%>%* or *%<%annotations%>%* in
+an SBML Level 1 document.
+
+References: L1V2 Appendix B
+
+There is a notes element within the sbml element on line 3:
+
+{>}%<%sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2"%>%\\
+%<%notes/%>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Fail |
+| *Levels:*| L1V2 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00010/00010-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00010/00010-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00010/00010-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <center>
+ <h2>A Simple Mitotic Oscillator</h2>
+ </center>
+ <p>A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase</p>
+ </html>
+ </notes>
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00011/00011-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00011/00011-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00011/00011-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,25 @@
+category: SBML
+synopsis: Annotation/notes not allowed on sbml element.
+levels: 1.2
+status: Fail
+
+This model fails SBML validation rule *20104*:
+
+The *%<%sbml%>%* container element cannot contain *%<%notes%>%* or *%<%annotations%>%* in
+an SBML Level 1 document.
+
+References: L1V2 Appendix B
+
+There is an annotation element within the sbml element on line 3:
+
+{>}%<%sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2"%>%\\
+%<%annotation/%>%
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Fail |
+| *Levels:*| L1V2 |]
\ No newline at end of file
Added: trunk/test-suite/cases/syntactic/00011/00011-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00011/00011-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00011/00011-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <annotation/>
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00012/00012-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00012/00012-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00012/00012-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,20 @@
+category: SBML
+synopsis: Annotation/notes not allowed on sbml element.
+levels: 1.2
+status: Pass
+
+This model passes SBML validation rule *20104*:
+
+The *%<%sbml%>%* container element cannot contain *%<%notes%>%* or *%<%annotations%>%* in
+an SBML Level 1 document.
+
+References: L1V2 Appendix B
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Pass |
+| *Levels:*| L1V2 |]
Added: trunk/test-suite/cases/syntactic/00012/00012-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00012/00012-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00012/00012-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+</model>
+</sbml>
Added: trunk/test-suite/cases/syntactic/00013/00013-model.m
===================================================================
--- trunk/test-suite/cases/syntactic/00013/00013-model.m (rev 0)
+++ trunk/test-suite/cases/syntactic/00013/00013-model.m 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,20 @@
+category: SBML
+synopsis: Annotation/notes not allowed on sbml element.
+levels: 1.2
+status: Pass
+
+This model passes SBML validation rule *20104*:
+
+The *%<%sbml%>%* container element cannot contain *%<%notes%>%* or *%<%annotations%>%* in
+an SBML Level 1 document.
+
+References: L1V2 Appendix B
+\\
+\\
+----
+
+[{width:10em}| | |
+|2> *TEST SUMMARY* |
+| *Category:*| SBML |
+| *Status:*| Pass |
+| *Levels:*| L1V2 |]
Added: trunk/test-suite/cases/syntactic/00013/00013-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/syntactic/00013/00013-sbml-l1v2.xml (rev 0)
+++ trunk/test-suite/cases/syntactic/00013/00013-sbml-l1v2.xml 2008-07-30 15:24:00 UTC (rev 7798)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+</model>
+</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 10:03:15
|
Revision: 7797
http://sbml.svn.sourceforge.net/sbml/?rev=7797&view=rev
Author: sarahkeating
Date: 2008-07-30 10:03:11 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
changed model so that compartment value actually varied and updated results to be correct data
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00106/00106-model.m
trunk/test-suite/cases/semantic/00106/00106-results.csv
trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml
trunk/test-suite/cases/semantic/00106/00106-settings.txt
Added Paths:
-----------
trunk/test-suite/cases/semantic/00106/00106-plot.jpg
Modified: trunk/test-suite/cases/semantic/00106/00106-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-model.m 2008-07-30 09:56:40 UTC (rev 7796)
+++ trunk/test-suite/cases/semantic/00106/00106-model.m 2008-07-30 10:03:11 UTC (rev 7797)
@@ -58,7 +58,7 @@
addSpecies[ S4, initialAmount -> 1.5 10^-15];
addParameter[ k1, value -> 0.75 10^15 ];
addParameter[ k2, value -> 0.25 10^15 ];
-addParameter[ p1, value -> 0.1 10^-15];
+addParameter[ p1, value -> 0.001];
addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 + S2 -> S3 + S4, reversible -> False,
kineticLaw -> multiply[k1,multiply[S1,S2]] * C ];
Property changes on: trunk/test-suite/cases/semantic/00106/00106-plot.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/test-suite/cases/semantic/00106/00106-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-results.csv 2008-07-30 09:56:40 UTC (rev 7796)
+++ trunk/test-suite/cases/semantic/00106/00106-results.csv 2008-07-30 10:03:11 UTC (rev 7797)
@@ -1,52 +1,52 @@
-time,case00106`S1,case00106`S2,case00106`S3,case00106`S4
-0,5.e-16,1.e-15,2.e-15,1.5e-15
-0.04,5.183932008295898e-16,1.01839320082959e-15,1.989606799170409e-15,1.48960679917041e-15
-0.08,5.356245724165928e-16,1.035624572416593e-15,1.980375427583407e-15,1.480375427583407e-15
-0.12,5.517693633244673e-16,1.051769363324467e-15,1.972230636675532e-15,1.472230636675532e-15
-0.16,5.66899508626493e-16,1.066899508626493e-15,1.965100491373506e-15,1.465100491373506e-15
-0.2,5.810835403665686e-16,1.081083540366569e-15,1.95891645963343e-15,1.458916459633431e-15
-0.24,5.943865476476662e-16,1.094386547647666e-15,1.953613452352332e-15,1.453613452352333e-15
-0.28,6.068701736249535e-16,1.106870173624954e-15,1.949129826375045e-15,1.449129826375046e-15
-0.32,6.185926473913734e-16,1.118592647391374e-15,1.945407352608625e-15,1.445407352608626e-15
-0.36,6.296088456534946e-16,1.129608845653495e-15,1.942391154346504e-15,1.442391154346505e-15
-0.4,6.399703652087813e-16,1.139970365208781e-15,1.940029634791218e-15,1.440029634791218e-15
-0.44,6.497256373607358e-16,1.149725637360736e-15,1.938274362639263e-15,1.438274362639263e-15
-0.48,6.589200211919006e-16,1.1589200211919e-15,1.937079978808098e-15,1.437079978808099e-15
-0.52,6.675959407850369e-16,1.167595940785037e-15,1.936404059214962e-15,1.436404059214962e-15
-0.56,6.757930125313641e-16,1.175793012531364e-15,1.936206987468635e-15,1.436206987468635e-15
-0.6,6.835481436858873e-16,1.183548143685887e-15,1.936451856314111e-15,1.436451856314112e-15
-0.64,6.90895727546337e-16,1.190895727546337e-15,1.937104272453662e-15,1.437104272453662e-15
-0.68,6.978677376624494e-16,1.197867737662449e-15,1.938132262337549e-15,1.43813226233755e-15
-0.72,7.044938717271642e-16,1.204493871727164e-15,1.939506128272834e-15,1.439506128272835e-15
-0.76,7.108016829169708e-16,1.21080168291697e-15,1.941198317083028e-15,1.441198317083029e-15
-0.8,7.168167066400683e-16,1.216816706640068e-15,1.943183293359931e-15,1.443183293359931e-15
-0.84,7.225625874499309e-16,1.222562587449931e-15,1.945437412550068e-15,1.445437412550068e-15
-0.88,7.280612002448261e-16,1.228061200244826e-15,1.947938799755173e-15,1.447938799755173e-15
-0.92,7.33332765521555e-16,1.233332765521555e-15,1.950667234478444e-15,1.450667234478444e-15
-0.96,7.383959595141569e-16,1.238395959514156e-15,1.953604040485842e-15,1.453604040485842e-15
-1.,7.432680187196353e-16,1.243268018719635e-15,1.956731981280364e-15,1.456731981280364e-15
-1.04,7.479648415985539e-16,1.247964841598554e-15,1.960035158401445e-15,1.460035158401445e-15
-1.08,7.525010776181062e-16,1.252501077618106e-15,1.963498922381893e-15,1.463498922381892e-15
-1.12,7.568902205993101e-16,1.25689022059931e-15,1.967109779400689e-15,1.467109779400688e-15
-1.16,7.611446912479119e-16,1.261144691247912e-15,1.970855308752087e-15,1.470855308752087e-15
-1.2,7.652759157668415e-16,1.265275915766841e-15,1.974724084233158e-15,1.474724084233157e-15
-1.24,7.692943994604221e-16,1.269294399460422e-15,1.978705600539577e-15,1.478705600539577e-15
-1.28,7.732097959136278e-16,1.273209795913628e-15,1.982790204086371e-15,1.482790204086371e-15
-1.32,7.770309715215534e-16,1.277030971521553e-15,1.986969028478446e-15,1.486969028478445e-15
-1.36,7.807660656257176e-16,1.280766065625718e-15,1.991233934374281e-15,1.491233934374281e-15
-1.4,7.844225465423753e-16,1.284422546542375e-15,1.995577453457623e-15,1.495577453457623e-15
-1.44,7.880072636978634e-16,1.288007263697863e-15,1.999992736302135e-15,1.499992736302135e-15
-1.48,7.915264960848098e-16,1.29152649608481e-15,2.004473503915189e-15,1.504473503915189e-15
-1.52,7.949859972501382e-16,1.294985997250138e-15,2.009014002749861e-15,1.509014002749861e-15
-1.56,7.983910374559504e-16,1.29839103745595e-15,2.013608962544049e-15,1.513608962544049e-15
-1.6,8.017464398914329e-16,1.301746439891433e-15,2.018253560108567e-15,1.518253560108566e-15
-1.64,8.0505662161216e-16,1.30505662161216e-15,2.022943378387839e-15,1.522943378387839e-15
-1.68,8.083256225412779e-16,1.308325622541277e-15,2.027674377458722e-15,1.527674377458721e-15
-1.72,8.115571357664221e-16,1.311557135766422e-15,2.032442864233577e-15,1.532442864233577e-15
-1.76,8.147545371569455e-16,1.314754537156945e-15,2.037245462843054e-15,1.537245462843053e-15
-1.8,8.179209119227102e-16,1.31792091192271e-15,2.042079088077289e-15,1.542079088077289e-15
-1.84,8.210590784960751e-16,1.321059078496074e-15,2.046940921503924e-15,1.546940921503924e-15
-1.88,8.241716105763129e-16,1.324171610576312e-15,2.051828389423687e-15,1.551828389423686e-15
-1.92,8.272608574424397e-16,1.327260857442439e-15,2.05673914255756e-15,1.55673914255756e-15
-1.96,8.303289617015514e-16,1.33032896170155e-15,2.061671038298448e-15,1.561671038298448e-15
-2.,8.333778783067955e-16,1.333377878306795e-15,2.066622121693204e-15,1.566622121693204e-15
\ No newline at end of file
+time,S1,S2,S3,S4,C
+0,5e-016,1e-015,2e-015,1.5e-015,1
+0.04,5.146228769548965e-016,1.014822916960231e-015,1.986377323071773e-015,1.486177283066439e-015,0.9996000799893344
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+0.16,5.521946297198331e-016,1.052995270061303e-015,1.951808571987517e-015,1.451007931646047e-015,0.9984012793176064
+0.2,5.628631873922665e-016,1.063864188059267e-015,1.942141815942734e-015,1.441140815275734e-015,0.9980019986673332
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+0.28,5.818109409945442e-016,1.083212902825159e-015,1.925198868158529e-015,1.423796906327914e-015,0.9972039163438931
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+0.36,5.979565101643971e-016,1.099759754055899e-015,1.911059709293112e-015,1.40925646540161e-015,0.9964064722309934
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+0.44,6.117082606038317e-016,1.113913107710314e-015,1.899315974928579e-015,1.397111127822097e-015,0.9956096658182702
+0.48,6.177990472942015e-016,1.120204816521271e-015,1.894229798841148e-015,1.391824029614078e-015,0.9952115015900974
+0.52,6.234202004340541e-016,1.126026972166636e-015,1.889613658228855e-015,1.387006886496273e-015,0.9948134965957669
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+1.16,6.725376433081983e-016,1.178371413760959e-015,1.856631208955602e-015,1.350797438502842e-015,0.988467020603353
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+1.76,6.875432910015664e-016,1.196421187322275e-015,1.856846190601975e-015,1.347968294281267e-015,0.9825539753546042
+1.8,6.881553829820655e-016,1.197236871176963e-015,1.857252057992419e-015,1.348170569797522e-015,0.9821610323583009
+1.84,6.887393863227572e-016,1.198024547844882e-015,1.857686421287866e-015,1.348401259765741e-015,0.9817682465077648
+1.88,6.892976595309174e-016,1.198786575865897e-015,1.858146922143979e-015,1.348658005809e-015,0.9813756177401503
+1.92,6.898323614582323e-016,1.199525114124295e-015,1.858631401872076e-015,1.348938649206015e-015,0.9809831459926367
+1.96,6.903454770062062e-016,1.200242147554192e-015,1.859137875733722e-015,1.349241205185736e-015,0.9805908312024285
+2,6.908388218050461e-016,1.200939491818425e-015,1.859664528261843e-015,1.349563858248465e-015,0.9801986733067555
Modified: trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml 2008-07-30 09:56:40 UTC (rev 7796)
+++ trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml 2008-07-30 10:03:11 UTC (rev 7797)
@@ -32,7 +32,7 @@
<listOfParameters>
<parameter id="k1" name="k1" value="750000000000000"/>
<parameter id="k2" name="k2" value="250000000000000"/>
- <parameter id="p1" name="p1" value="1e-016"/>
+ <parameter id="p1" name="p1" value="0.001"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="rule1" variable="C">
Modified: trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml 2008-07-30 09:56:40 UTC (rev 7796)
+++ trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml 2008-07-30 10:03:11 UTC (rev 7797)
@@ -32,7 +32,7 @@
<listOfParameters>
<parameter id="k1" name="k1" value="750000000000000"/>
<parameter id="k2" name="k2" value="250000000000000"/>
- <parameter id="p1" name="p1" value="1e-016"/>
+ <parameter id="p1" name="p1" value="0.001"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="rule1" variable="C">
Modified: trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml 2008-07-30 09:56:40 UTC (rev 7796)
+++ trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml 2008-07-30 10:03:11 UTC (rev 7797)
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 30-July-2008 10:32:56.7968750 -->
+<!-- Generated 30-July-2008 10:57:32.8125000 -->
<!-- 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"
@@ -82,7 +82,7 @@
value="2.5e14"/>
<parameter id="p1"
name="p1"
- value="1.0000000000000001e-16"/>
+ value="0.001"/>
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
Modified: trunk/test-suite/cases/semantic/00106/00106-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-settings.txt 2008-07-30 09:56:40 UTC (rev 7796)
+++ trunk/test-suite/cases/semantic/00106/00106-settings.txt 2008-07-30 10:03:11 UTC (rev 7797)
@@ -1,6 +1,6 @@
start: 0
duration: 2
steps: 50
-variables: S1, S2, S3, S4
+variables: S1, S2, S3, S4, C
absolute: 1.000000e-018
relative: 0.0001
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 09:56:42
|
Revision: 7796
http://sbml.svn.sourceforge.net/sbml/?rev=7796&view=rev
Author: sarahkeating
Date: 2008-07-30 09:56:40 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
fixed typo in description
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00104/00104-model.m
Modified: trunk/test-suite/cases/semantic/00104/00104-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00104/00104-model.m 2008-07-30 09:56:00 UTC (rev 7795)
+++ trunk/test-suite/cases/semantic/00104/00104-model.m 2008-07-30 09:56:40 UTC (rev 7796)
@@ -34,7 +34,7 @@
|Initial amount of S1 |$1.5 \x 10^-15$ |mole |
|Initial amount of S2 |$1.5 \x 10^-15$ |mole |
|Value of parameter k1 |$ 1$ |second^-1^ |
-|Value of parameter p1 |$0.1 \x 10^-12$ |second^-1^ |
+|Value of parameter p1 |$0.01$ |second^-1^ |
|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 09:56:05
|
Revision: 7795
http://sbml.svn.sourceforge.net/sbml/?rev=7795&view=rev
Author: sarahkeating
Date: 2008-07-30 09:56:00 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
changed model so that compartment value actually varied and updated results to be correct data
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00105/00105-model.m
trunk/test-suite/cases/semantic/00105/00105-results.csv
trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml
trunk/test-suite/cases/semantic/00105/00105-settings.txt
Added Paths:
-----------
trunk/test-suite/cases/semantic/00105/00105-plot.jpg
Modified: trunk/test-suite/cases/semantic/00105/00105-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-model.m 2008-07-30 09:34:29 UTC (rev 7794)
+++ trunk/test-suite/cases/semantic/00105/00105-model.m 2008-07-30 09:56:00 UTC (rev 7795)
@@ -37,7 +37,7 @@
|Initial amount of S3 |$1.0 \x 10^-15$ |mole |
|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |
|Value of parameter k2 |$ 0.25$ |second^-1^ |
-|Value of parameter p1 |$0.1 \x 10^-15$ |second^-1^ |
+|Value of parameter p1 |$0.01$ |second^-1^ |
|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
@@ -56,7 +56,7 @@
addSpecies[ S3, initialAmount -> 1.0 10^-15];
addParameter[ k1, value -> 0.75 ];
addParameter[ k2, value -> 0.25 ];
-addParameter[ p1, value -> 0.1 10^-15];
+addParameter[ p1, value -> 0.01];
addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 + S2 -> S3, reversible -> False,
kineticLaw -> multiply[k1, S1, S2] * C ];
Property changes on: trunk/test-suite/cases/semantic/00105/00105-plot.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/test-suite/cases/semantic/00105/00105-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-results.csv 2008-07-30 09:34:29 UTC (rev 7794)
+++ trunk/test-suite/cases/semantic/00105/00105-results.csv 2008-07-30 09:56:00 UTC (rev 7795)
@@ -1,52 +1,52 @@
-time,case00105`S1,case00105`S2,case00105`S3
-0,1.e-15,2.e-15,1.e-15
-0.2,1.069262345304718e-15,2.069262345304721e-15,9.707376546952808e-16
-0.4,1.137097549188241e-15,2.137097549188243e-15,9.429024508117581e-16
-0.6,1.203575214416944e-15,2.203575214416946e-15,9.164247855830553e-16
-0.8,1.268761548189663e-15,2.268761548189665e-15,8.912384518103355e-16
-1.,1.332719530243869e-15,2.332719530243871e-15,8.672804697561302e-16
-1.2,1.395509068025646e-15,2.395509068025649e-15,8.444909319743527e-16
-1.4,1.45718714718702e-15,2.457187147187022e-15,8.228128528129792e-16
-1.6,1.517807974064076e-15,2.517807974064078e-15,8.02192025935923e-16
-1.8,1.577423109036011e-15,2.577423109036013e-15,7.825768909639874e-16
-2.,1.63608160555532e-15,2.636081605555321e-15,7.639183944446793e-16
-2.2,1.693830114809568e-15,2.69383011480957e-15,7.461698851904312e-16
-2.4,1.750713025285632e-15,2.750713025285634e-15,7.292869747143667e-16
-2.6,1.806772542700282e-15,2.806772542700283e-15,7.132274572997172e-16
-2.8,1.862048825883399e-15,2.862048825883401e-15,6.979511741165994e-16
-3.,1.916580073927837e-15,2.916580073927838e-15,6.83419926072162e-16
-3.2,1.97040262379434e-15,2.970402623794341e-15,6.69597376205659e-16
-3.4,2.023551040932291e-15,3.023551040932293e-15,6.564489590677078e-16
-3.6,2.076058205098659e-15,3.076058205098661e-15,6.439417949013397e-16
-3.8,2.127955389376565e-15,3.127955389376566e-15,6.320446106234343e-16
-4.,2.179272340777585e-15,3.179272340777587e-15,6.207276592224137e-16
-4.2,2.230037356555639e-15,3.23003735655564e-15,6.099626434443602e-16
-4.4,2.280277372693742e-15,3.280277372693743e-15,5.997226273062575e-16
-4.6,2.330017972022762e-15,3.330017972022764e-15,5.899820279772365e-16
-4.8,2.379283484763584e-15,3.379283484763586e-15,5.807165152364151e-16
-5.,2.428097125161876e-15,3.428097125161878e-15,5.719028748381229e-16
-5.2,2.476480942254798e-15,3.4764809422548e-15,5.635190577452004e-16
-5.4,2.524455846733046e-15,3.524455846733048e-15,5.555441532669522e-16
-5.6,2.572041831354125e-15,3.572041831354126e-15,5.479581686458743e-16
-5.8,2.619257840298244e-15,3.619257840298245e-15,5.407421597017553e-16
-6.,2.666121903991882e-15,3.666121903991883e-15,5.338780960081175e-16
-6.2,2.712651228741169e-15,3.712651228741171e-15,5.273487712588301e-16
-6.4,2.758862095412414e-15,3.758862095412415e-15,5.21137904587585e-16
-6.6,2.804770058595554e-15,3.804770058595555e-15,5.152299414044451e-16
-6.8,2.850389897491634e-15,3.850389897491636e-15,5.096101025083651e-16
-7.,2.89573563487505e-15,3.895735634875052e-15,5.042643651249492e-16
-7.2,2.940820674951731e-15,3.940820674951733e-15,4.991793250482678e-16
-7.4,2.985657707961185e-15,3.985657707961188e-15,4.943422920388134e-16
-7.6,3.030258829030322e-15,4.030258829030325e-15,4.897411709696765e-16
-7.8,3.074635566274989e-15,4.074635566274992e-15,4.853644337250094e-16
-8.,3.118798833021574e-15,4.118798833021577e-15,4.812011669784244e-16
-8.2,3.162759061525616e-15,4.162759061525619e-15,4.772409384743826e-16
-8.4,3.206526150666501e-15,4.206526150666504e-15,4.734738493334972e-16
-8.6,3.250109505470003e-15,4.250109505470005e-15,4.698904945299957e-16
-8.8,3.293518111059588e-15,4.293518111059591e-15,4.664818889404106e-16
-9.,3.336760472398896e-15,4.336760472398899e-15,4.632395276011024e-16
-9.2,3.379844702260638e-15,4.379844702260641e-15,4.601552977393611e-16
-9.4,3.422778508295157e-15,4.422778508295161e-15,4.572214917048415e-16
-9.6,3.465569230102062e-15,4.465569230102065e-15,4.544307698979366e-16
-9.8,3.508223855587295e-15,4.508223855587298e-15,4.517761444127034e-16
-10.,3.550749000825274e-15,4.550749000825277e-15,4.492509991747247e-16
\ No newline at end of file
+time,S1,S2,S3,C
+0,1e-015,2e-015,1e-015,1
+0.3,1.075478115418725e-015,2.078482619922103e-015,9.305308935880295e-016,0.9970044955033727
+0.6,1.146148325655529e-015,2.152166361709594e-015,8.65887746452601e-016,0.9940179640539351
+0.9,1.21234594226877e-015,2.221386564042638e-015,8.057353012789661e-016,0.9910403787728835
+1.2,1.274382985243909e-015,2.286455274109987e-015,7.497615924882467e-016,0.9880717128619306
+1.5,1.3325498032583e-015,2.347662867874019e-015,6.976763259731387e-016,0.9851119396030627
+1.8,1.387116577140175e-015,2.405279553529968e-015,6.492093756394136e-016,0.9821610323583006
+2.1,1.438334722109561e-015,2.45955677374709e-015,6.041093811654972e-016,0.9792189645694592
+2.4,1.486438191711842e-015,2.510728509602464e-015,5.621424440694019e-016,0.9762857097579091
+2.7,1.531644692100289e-015,2.559012494863778e-015,5.230909134266899e-016,0.9733612415243368
+3,1.574156811783858e-015,2.604611345737375e-015,4.867522561231761e-016,0.9704455335485082
+3.3,1.614163066797061e-015,2.647713606038367e-015,4.529380116855506e-016,0.9675385595890317
+3.6,1.651838879586936e-015,2.688494726077859e-015,4.214728133949132e-016,0.9646402934831225
+3.9,1.687347491233406e-015,2.727117974883563e-015,3.921934760669104e-016,0.9617507091463666
+4.2,1.720840810705144e-015,2.763735289455906e-015,3.649481467963832e-016,0.9588697805724845
+4.5,1.752460195281393e-015,2.79848805519011e-015,3.395955245360422e-016,0.9559974818330994
+4.8,1.782337182909763e-015,2.831507838234234e-015,3.160041277391792e-016,0.9531337870775043
+5.1,1.81059418084573e-015,2.862917074128934e-015,2.940516057206777e-016,0.950278670532427
+5.4,1.837345101351014e-015,2.892829703506094e-015,2.736241029591472e-016,0.947432106501798
+5.7,1.862695939994574e-015,2.921351750390075e-015,2.546156807964283e-016,0.9445940693665226
+6,1.886745333752821e-015,2.948581880298181e-015,2.369277593378983e-016,0.9417645335842487
+6.3,1.909585079087177e-015,2.974611918318483e-015,2.204685993754349e-016,0.9389434736891329
+6.6,1.931300592095259e-015,2.999527309261253e-015,2.051528422367303e-016,0.936130864291618
+6.9,1.951971358332338e-015,3.023407567480684e-015,1.909010599643545e-016,0.933326680078202
+7.2,1.971671354930351e-015,3.046326698994165e-015,1.776393331972781e-016,0.9305308958112052
+7.5,1.990469414419558e-015,3.06835356530419e-015,1.652988873497079e-016,0.9277434863285519
+7.8,2.008429593935375e-015,3.089552252605458e-015,1.538157234047918e-016,0.9249644265435393
+8.1,2.02561151203288e-015,3.109982408599641e-015,1.43130281100644e-016,0.9221936914446069
+8.4,2.042070637859193e-015,3.129699531668019e-015,1.331871497584613e-016,0.9194312560951242
+8.7,2.057858601694804e-015,3.148755281413082e-015,1.239347577417534e-016,0.9166770956331518
+9,2.073023447325491e-015,3.167197731030704e-015,1.153251200849337e-016,0.9139311852712267
+9.3,2.087609881439749e-015,3.185071616707831e-015,1.07313589096416e-016,0.9111935002961407
+9.6,2.101659519695532e-015,3.202418583689513e-015,9.985860829243103e-017,0.9084640160687044
+9.9,2.115211077129172e-015,3.219277376688054e-015,9.292152198859275e-017,0.9057427080235484
+10.2,2.128300597662924e-015,3.23568406939086e-015,8.64663457929466e-017,0.9030295516688753
+10.5,2.140961613892602e-015,3.251672224248309e-015,8.045960681881162e-017,0.9003245225862647
+10.8,2.153225340863251e-015,3.26727308624972e-015,7.487014990968713e-017,0.8976275964304339
+11.1,2.165120826468799e-015,3.28251573332326e-015,6.966898724012286e-017,0.8949387489290293
+11.4,2.176675103882204e-015,3.297427228766357e-015,6.482914588610525e-017,0.8922579558824078
+11.7,2.187913337236116e-015,3.312032766926656e-015,6.032552214496531e-017,0.8895851931634088
+12,2.198858939769316e-015,3.326355791348693e-015,5.613476338943771e-017,0.886920436717157
+12.3,2.209533711557877e-015,3.340418132505371e-015,5.223513033711035e-017,0.8842636625608178
+12.6,2.219957932584744e-015,3.354240100867771e-015,4.860640398130801e-017,0.8816148467834155
+12.9,2.230150489028761e-015,3.367840613194497e-015,4.522975930271261e-017,0.8789739655455797
+13.2,2.240128948861136e-015,3.381237268128373e-015,4.208768967333753e-017,0.8763409950793725
+13.5,2.249909674060567e-015,3.394446458411886e-015,3.916389464207192e-017,0.8737159116880311
+13.8,2.259507885725152e-015,3.407483435999333e-015,3.644321482320883e-017,0.8710986917457972
+14.1,2.268937759184223e-015,3.420362407168972e-015,3.391153678527395e-017,0.8684893116976649
+14.4,2.278212483840428e-015,3.433096592365344e-015,3.155573320940396e-017,0.8658877480592035
+14.7,2.287344340978643e-015,3.4456983040085e-015,2.936358508107005e-017,0.8632939774163188
+15,2.296344762086996e-015,3.458179004815279e-015,2.732372336957123e-017,0.8607079764250579
Modified: trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml 2008-07-30 09:34:29 UTC (rev 7794)
+++ trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml 2008-07-30 09:56:00 UTC (rev 7795)
@@ -35,7 +35,7 @@
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
<parameter id="k2" name="k2" value="0.25"/>
- <parameter id="p1" name="p1" value="1e-016"/>
+ <parameter id="p1" name="p1" value="0.01"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="rule1" variable="C">
Modified: trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml 2008-07-30 09:34:29 UTC (rev 7794)
+++ trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml 2008-07-30 09:56:00 UTC (rev 7795)
@@ -35,7 +35,7 @@
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
<parameter id="k2" name="k2" value="0.25"/>
- <parameter id="p1" name="p1" value="1e-016"/>
+ <parameter id="p1" name="p1" value="0.01"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="rule1" variable="C">
Modified: trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml 2008-07-30 09:34:29 UTC (rev 7794)
+++ trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml 2008-07-30 09:56:00 UTC (rev 7795)
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 30-July-2008 10:24:00.1406250 -->
+<!-- Generated 30-July-2008 10:42:45.4218750 -->
<!-- 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"
@@ -78,7 +78,7 @@
value="0.25"/>
<parameter id="p1"
name="p1"
- value="1.0000000000000001e-16"/>
+ value="0.01"/>
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
Modified: trunk/test-suite/cases/semantic/00105/00105-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-settings.txt 2008-07-30 09:34:29 UTC (rev 7794)
+++ trunk/test-suite/cases/semantic/00105/00105-settings.txt 2008-07-30 09:56:00 UTC (rev 7795)
@@ -1,6 +1,6 @@
start: 0
-duration: 10.0
+duration: 15.0
steps: 50
-variables: S1, S2, S3
+variables: S1, S2, S3, C
absolute: 1.000000e-018
relative: 0.0001
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 09:34:35
|
Revision: 7794
http://sbml.svn.sourceforge.net/sbml/?rev=7794&view=rev
Author: sarahkeating
Date: 2008-07-30 09:34:29 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
changed compartment id to C
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00105/00105-model.m
trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml
trunk/test-suite/cases/semantic/00106/00106-model.m
trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml
Modified: trunk/test-suite/cases/semantic/00105/00105-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-model.m 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00105/00105-model.m 2008-07-30 09:34:29 UTC (rev 7794)
@@ -9,18 +9,18 @@
levels: 2.1, 2.2, 2.3
generatedBy: Numeric
-The model contains one varying compartment called "compartment". There are three
+The model contains one varying compartment called C. There are three
species called S1, S2 and S3 and three parameters called k1, k2 and p1. The
model contains two reactions defined as:
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
-| S1 + S2 -> S3 | $multiply(k1, S1, S2) * compartment$ |
-| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]
+| S1 + S2 -> S3 | $multiply(k1, S1, S2) * C$ |
+| S3 -> S1 + S2 | $k2 * S3 * C$ |]
The model contains one rule:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Rate | compartment | $-p1 * compartment$ |]
+ | Rate | C | $-p1 * C$ |]
The model contains one functionDefinition defined as:
@@ -38,7 +38,7 @@
|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |
|Value of parameter k2 |$ 0.25$ |second^-1^ |
|Value of parameter p1 |$0.1 \x 10^-15$ |second^-1^ |
-|Volume of compartment "compartment" |$ 1$ |litre |]
+|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
use the model in a discrete stochastic simulator, but (as per usual SBML
@@ -50,17 +50,17 @@
newcase[ "00105" ];
addFunction[ multiply, arguments -> {x, y, z}, math -> x * y * z];
-addCompartment[ compartment, constant -> False, size -> 1 ];
+addCompartment[ C, constant -> False, size -> 1 ];
addSpecies[ S1, initialAmount -> 1.0 10^-15];
addSpecies[ S2, initialAmount -> 2.0 10^-15];
addSpecies[ S3, initialAmount -> 1.0 10^-15];
addParameter[ k1, value -> 0.75 ];
addParameter[ k2, value -> 0.25 ];
addParameter[ p1, value -> 0.1 10^-15];
-addRule[ type->RateRule, variable -> compartment, math -> -p1 * compartment];
+addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 + S2 -> S3, reversible -> False,
- kineticLaw -> multiply[k1, S1, S2] * compartment ];
+ kineticLaw -> multiply[k1, S1, S2] * C ];
addReaction[ S3 -> S1 + S2, reversible -> False,
- kineticLaw -> k2 * S3 * compartment ];
+ kineticLaw -> k2 * S3 * C ];
makemodel[]
Modified: trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00105/00105-sbml-l2v1.xml 2008-07-30 09:34:29 UTC (rev 7794)
@@ -25,12 +25,12 @@
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1e-015" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="2e-015" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="1e-015" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1e-015" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="2e-015" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="1e-015" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
@@ -38,12 +38,12 @@
<parameter id="p1" name="p1" value="1e-016"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -62,7 +62,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
@@ -85,7 +85,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00105/00105-sbml-l2v2.xml 2008-07-30 09:34:29 UTC (rev 7794)
@@ -25,12 +25,12 @@
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1e-015" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="2e-015" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="1e-015" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1e-015" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="2e-015" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="1e-015" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
@@ -38,12 +38,12 @@
<parameter id="p1" name="p1" value="1e-016"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -62,7 +62,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
@@ -85,7 +85,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00105/00105-sbml-l2v3.xml 2008-07-30 09:34:29 UTC (rev 7794)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 12-February-2008 12:55:20.9687500 -->
-<!-- Generated by MathSBML 2.7.2b -->
+<!-- Generated 30-July-2008 10:24:00.1406250 -->
+<!-- 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"
level="2"
@@ -36,17 +36,17 @@
<!-- <listOfCompartmentTypes/> -->
<!-- <listOfSpeciesTypes/> -->
<listOfCompartments>
- <compartment id="compartment"
- name="compartment"
+ <compartment id="C"
+ name="C"
spatialDimensions="3"
units="volume"
- size="1"
+ size="1."
constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1"
name="S1"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.e-15"
@@ -54,7 +54,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S2"
name="S2"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="2.e-15"
@@ -62,7 +62,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S3"
name="S3"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.e-15"
@@ -82,7 +82,7 @@
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
- <rateRule variable="compartment"
+ <rateRule variable="C"
metaid="rule1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -90,7 +90,7 @@
<apply>
<times/>
<cn type="integer">-1</cn>
- <ci>compartment</ci>
+ <ci>C</ci>
</apply>
<ci>p1</ci>
</apply>
@@ -115,7 +115,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<apply>
<ci>multiply</ci>
<ci>k1</ci>
@@ -143,7 +143,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k2</ci>
<ci>S3</ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00106/00106-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-model.m 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00106/00106-model.m 2008-07-30 09:34:29 UTC (rev 7794)
@@ -9,18 +9,18 @@
levels: 2.1, 2.2, 2.3
generatedBy: Numeric
-The model contains one varying compartment called "compartment". There are four
+The model contains one varying compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.
The model contains two reactions defined as:
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
-| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * compartment$ |
-| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]
+| S1 + S2 -> S3 + S4 | $multiply(k1,multiply(S1,S2)) * C$ |
+| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]
The model contains one rule:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Rate | compartment | $-p1 * compartment$ |]
+ | Rate | C | $-p1 * C$ |]
The model contains one functionDefinition defined as:
@@ -39,7 +39,7 @@
|Value of parameter k1 |$0.75 \x 10^15$ |litre mole^-1^ second^-1^ |
|Value of parameter k2 |$0.25 \x 10^15$ |litre mole^-1^ second^-1^ |
|Value of parameter p1 |$0.1 \x 10^-15$ |second^-1^ |
-|Volume of compartment "compartment" |$ 1$ |litre |]
+|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
use the model in a discrete stochastic simulator, but (as per usual SBML
@@ -51,7 +51,7 @@
newcase[ "00106" ];
addFunction[ multiply, arguments -> {x, y}, math -> x * y];
-addCompartment[ compartment, constant -> False, size -> 1 ];
+addCompartment[ C, constant -> False, size -> 1 ];
addSpecies[ S1, initialAmount -> 0.5 10^-15];
addSpecies[ S2, initialAmount -> 1.0 10^-15];
addSpecies[ S3, initialAmount -> 2.0 10^-15];
@@ -59,10 +59,10 @@
addParameter[ k1, value -> 0.75 10^15 ];
addParameter[ k2, value -> 0.25 10^15 ];
addParameter[ p1, value -> 0.1 10^-15];
-addRule[ type->RateRule, variable -> compartment, math -> -p1 * compartment];
+addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 + S2 -> S3 + S4, reversible -> False,
- kineticLaw -> multiply[k1,multiply[S1,S2]] * compartment ];
+ kineticLaw -> multiply[k1,multiply[S1,S2]] * C ];
addReaction[ S3 + S4 -> S1 + S2, reversible -> False,
- kineticLaw -> k2 * S3 * S4 * compartment ];
+ kineticLaw -> k2 * S3 * S4 * C ];
makemodel[]
Modified: trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00106/00106-sbml-l2v1.xml 2008-07-30 09:34:29 UTC (rev 7794)
@@ -21,13 +21,13 @@
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="5e-016" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="1e-015" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="2e-015" substanceUnits="substance"/>
- <species id="S4" name="S4" compartment="compartment" initialAmount="1.5e-015" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="5e-016" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="1e-015" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="2e-015" substanceUnits="substance"/>
+ <species id="S4" name="S4" compartment="C" initialAmount="1.5e-015" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="750000000000000"/>
@@ -35,12 +35,12 @@
<parameter id="p1" name="p1" value="1e-016"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -60,7 +60,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
@@ -87,7 +87,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
<ci> S4 </ci>
Modified: trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00106/00106-sbml-l2v2.xml 2008-07-30 09:34:29 UTC (rev 7794)
@@ -21,13 +21,13 @@
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="5e-016" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="1e-015" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="2e-015" substanceUnits="substance"/>
- <species id="S4" name="S4" compartment="compartment" initialAmount="1.5e-015" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="5e-016" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="1e-015" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="2e-015" substanceUnits="substance"/>
+ <species id="S4" name="S4" compartment="C" initialAmount="1.5e-015" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="750000000000000"/>
@@ -35,12 +35,12 @@
<parameter id="p1" name="p1" value="1e-016"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -60,7 +60,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
@@ -87,7 +87,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
<ci> S4 </ci>
Modified: trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml 2008-07-30 09:16:38 UTC (rev 7793)
+++ trunk/test-suite/cases/semantic/00106/00106-sbml-l2v3.xml 2008-07-30 09:34:29 UTC (rev 7794)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 12-February-2008 13:06:11.8750000 -->
-<!-- Generated by MathSBML 2.7.2b -->
+<!-- Generated 30-July-2008 10:32:56.7968750 -->
+<!-- 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"
level="2"
@@ -32,17 +32,17 @@
<!-- <listOfCompartmentTypes/> -->
<!-- <listOfSpeciesTypes/> -->
<listOfCompartments>
- <compartment id="compartment"
- name="compartment"
+ <compartment id="C"
+ name="C"
spatialDimensions="3"
units="volume"
- size="1"
+ size="1."
constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1"
name="S1"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="5.e-16"
@@ -50,7 +50,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S2"
name="S2"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.e-15"
@@ -58,7 +58,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S3"
name="S3"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="2.e-15"
@@ -66,7 +66,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S4"
name="S4"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.5000000000000001e-15"
@@ -86,7 +86,7 @@
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
- <rateRule variable="compartment"
+ <rateRule variable="C"
metaid="rule1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -94,7 +94,7 @@
<apply>
<times/>
<cn type="integer">-1</cn>
- <ci>compartment</ci>
+ <ci>C</ci>
</apply>
<ci>p1</ci>
</apply>
@@ -120,7 +120,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<apply>
<ci>multiply</ci>
<ci>k1</ci>
@@ -152,7 +152,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k2</ci>
<ci>S3</ci>
<ci>S4</ci>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 09:16:42
|
Revision: 7793
http://sbml.svn.sourceforge.net/sbml/?rev=7793&view=rev
Author: sarahkeating
Date: 2008-07-30 09:16:38 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
added appropriate plot
Added Paths:
-----------
trunk/test-suite/cases/semantic/00104/00104-plot.jpg
Property changes on: trunk/test-suite/cases/semantic/00104/00104-plot.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 09:01:04
|
Revision: 7792
http://sbml.svn.sourceforge.net/sbml/?rev=7792&view=rev
Author: sarahkeating
Date: 2008-07-30 09:01:00 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
updated results to be correct data
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00053/00053-results.csv
trunk/test-suite/cases/semantic/00053/00053-settings.txt
Added Paths:
-----------
trunk/test-suite/cases/semantic/00053/00053-plot.jpg
Property changes on: trunk/test-suite/cases/semantic/00053/00053-plot.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/test-suite/cases/semantic/00053/00053-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-results.csv 2008-07-30 08:59:20 UTC (rev 7791)
+++ trunk/test-suite/cases/semantic/00053/00053-results.csv 2008-07-30 09:01:00 UTC (rev 7792)
@@ -1,52 +1,52 @@
-time,case00053`S1,case00053`S2,case00053`S3,case00053`S4
-0,1.,1.5,2.,1.
-0.1,0.9547401205663916,1.45474012056639,2.065259879433609,1.065259879433608
-0.2,0.9215220752496508,1.421522075249649,2.11847792475035,1.118477924750349
-0.3,0.8974386177956833,1.397438617795681,2.162561382204317,1.162561382204316
-0.4,0.8803399133661962,1.380339913366194,2.199660086633804,1.199660086633803
-0.5,0.86861590976735,1.368615909767348,2.231384090232651,1.23138409023265
-0.6,0.8610485489050505,1.361048548905049,2.25895145109495,1.258951451094949
-0.7,0.8567088660340734,1.356708866034072,2.283291133965928,1.283291133965926
-0.8,0.8548837884382997,1.354883788438298,2.305116211561701,1.3051162115617
-0.9,0.8550230956387744,1.355023095638773,2.324976904361227,1.324976904361225
-1.,0.8567004347889322,1.356700434788931,2.34329956521107,1.343299565211068
-1.1,0.8595843087788959,1.359584308778895,2.360415691221106,1.360415691221104
-1.2,0.8634162161943472,1.363416216194346,2.376583783805655,1.376583783805652
-1.3,0.8679941307430115,1.36799413074301,2.392005869256991,1.392005869256988
-1.4,0.8731598252902629,1.373159825290261,2.40684017470974,1.406840174709737
-1.5,0.8787891787150732,1.378789178715072,2.421210821284929,1.421210821284927
-1.6,0.8847846678000366,1.384784667800035,2.435215332199966,1.435215332199963
-1.7,0.8910695815289824,1.391069581528981,2.44893041847102,1.448930418471018
-1.8,0.8975834974139653,1.397583497413964,2.462416502586037,1.462416502586035
-1.9,0.9042787753619724,1.404278775361971,2.47572122463803,1.475721224638027
-2.,0.911117820026747,1.411117820026746,2.488882179973256,1.488882179973253
-2.1,0.9180709313761873,1.418070931376186,2.501929068623816,1.501929068623812
-2.2,0.9251146264535078,1.425114626453507,2.514885373546495,1.514885373546492
-2.3,0.9322303248308527,1.432230324830852,2.527769675169151,1.527769675169147
-2.4,0.9394033111673288,1.439403311167328,2.540596688832674,1.540596688832671
-2.5,0.9466219228003856,1.446621922800385,2.553378077199617,1.553378077199614
-2.6,0.9538769093414765,1.453876909341475,2.566123090658526,1.566123090658523
-2.7,0.9611609283280944,1.461160928328093,2.578839071671908,1.578839071671906
-2.8,0.9684681471690065,1.468468147169006,2.591531852830996,1.591531852830993
-2.9,0.9757939297378457,1.475793929737845,2.604206070262157,1.604206070262154
-3.,0.9831345886246126,1.483134588624611,2.61686541137539,1.616865411375387
-3.1,0.9904871877311115,1.49048718773111,2.629512812268891,1.629512812268888
-3.2,0.9978493891348748,1.497849389134873,2.642150610865127,1.642150610865125
-3.3,1.005219329594069,1.505219329594068,2.654780670405932,1.65478067040593
-3.4,1.012595522581616,1.512595522581615,2.667404477418386,1.667404477418383
-3.5,1.019976782476649,1.519976782476648,2.680023217523352,1.68002321752335
-3.6,1.027362162564536,1.527362162564535,2.692637837435466,1.692637837435464
-3.7,1.034750906666504,1.534750906666503,2.705249093333497,1.705249093333496
-3.8,1.042142410827598,1.542142410827597,2.717857589172403,1.717857589172401
-3.9,1.049536192086436,1.549536192086435,2.730463807913566,1.730463807913564
-4.,1.056931864738437,1.556931864738436,2.743068135261565,1.743068135261563
-4.1,1.064329120189219,1.564329120189218,2.755670879810783,1.755670879810781
-4.2,1.071727712071447,1.571727712071445,2.768272287928556,1.768272287928553
-4.3,1.079127443457697,1.579127443457696,2.780872556542305,1.780872556542302
-4.4,1.086528157206943,1.586528157206942,2.793471842793059,1.793471842793056
-4.5,1.093929728063429,1.593929728063428,2.806070271936573,1.80607027193657
-4.6,1.101332056258547,1.601332056258546,2.818667943741456,1.818667943741453
-4.7,1.108735062626829,1.608735062626828,2.831264937373173,1.831264937373171
-4.8,1.116138684446917,1.616138684446916,2.843861315553085,1.843861315553082
-4.9,1.123542872253727,1.623542872253726,2.856457127746276,1.856457127746273
-5.,1.13094758727918,1.630947587279179,2.869052412720823,1.869052412720819
\ No newline at end of file
+time,S1,S2,S3,S4,C
+0,1,1.5,2,1,1
+0.1,0.954232701,1.459257785,2.0759178,1.065867633,0.990049834
+0.2,0.919902473,1.430003143,2.140701547,1.120500207,0.980198673
+0.3,0.894525137,1.409752404,2.196838465,1.166383931,0.970445534
+0.4,0.876197558,1.396602946,2.246234764,1.20542399,0.960789439
+0.5,0.863445577,1.389081125,2.290367712,1.239096616,0.951229425
+0.6,0.855117765,1.386036038,2.330391875,1.268555328,0.941764534
+0.7,0.850309052,1.386563142,2.367215492,1.294707311,0.93239382
+0.8,0.848304531,1.389948065,2.401556672,1.318269604,0.923116346
+0.9,0.848537834,1.395624976,2.433985017,1.339810733,0.913931185
+1,0.850560094,1.403145553,2.46495266,1.359781742,0.904837418
+1.1,0.854014514,1.412153549,2.494819698,1.378541627,0.895834135
+1.2,0.858617262,1.422365688,2.523873293,1.396376441,0.886920437
+1.3,0.864143939,1.43355813,2.552341211,1.413512828,0.878095431
+1.4,0.870415797,1.445552696,2.5804056,1.430131801,0.869358235
+1.5,0.877291732,1.458208853,2.608210996,1.446376754,0.860707976
+1.6,0.884660376,1.471415811,2.635872237,1.462361366,0.852143789
+1.7,0.892433468,1.485085894,2.663481086,1.478176234,0.843664817
+1.8,0.900542383,1.499151064,2.691109707,1.493892343,0.835270211
+1.9,0.908932533,1.513557332,2.71881626,1.509566662,0.826959134
+2,0.917562098,1.528263477,2.746646176,1.525243418,0.818730753
+2.1,0.926397954,1.543236984,2.774636226,1.540958166,0.810584246
+2.2,0.935414764,1.558453129,2.802815428,1.556738698,0.802518798
+2.3,0.944593185,1.57389319,2.831206844,1.572606834,0.794533603
+2.4,0.95391776,1.589542336,2.859829691,1.58858054,0.786627861
+2.5,0.963377774,1.605390482,2.888698476,1.604673059,0.778800783
+2.6,0.972964222,1.621429265,2.917826038,1.620895951,0.771051586
+2.7,0.982670863,1.637653089,2.947222489,1.637258038,0.763379494
+2.8,0.992493437,1.654058343,2.976896,1.653766188,0.755783741
+2.9,1.002428167,1.670641911,3.006854297,1.670426809,0.748263568
+3,1.012472964,1.687402367,3.037103459,1.687244652,0.740818221
+3.1,1.022626651,1.704339208,3.067648691,1.704223577,0.733446956
+3.2,1.032888048,1.72145193,3.098495245,1.721367481,0.726149037
+3.3,1.043256672,1.738740736,3.129647714,1.738679585,0.718923733
+3.4,1.053732841,1.756206637,3.16110993,1.75616234,0.711770323
+3.5,1.064316787,1.773850561,3.192885859,1.773818311,0.70468809
+3.6,1.075008664,1.791673372,3.224979579,1.791650165,0.697676326
+3.7,1.085809177,1.809676484,3.257394667,1.809660053,0.690734331
+3.8,1.096719291,1.827861586,3.290134478,1.827849888,0.683861409
+3.9,1.107739859,1.846230256,3.323202523,1.846221729,0.677056874
+4,1.118871622,1.864783971,3.356602471,1.864777773,0.670320046
+4.1,1.130115483,1.883524375,3.390337873,1.883520088,0.66365025
+4.2,1.141472625,1.902453403,3.424412042,1.902450486,0.65704682
+4.3,1.152944172,1.921572933,3.4588284,1.921570876,0.650509095
+4.4,1.164531195,1.940884804,3.493590461,1.940883242,0.644036421
+4.5,1.176234723,1.960390815,3.528701834,1.960389648,0.637628152
+4.6,1.188055881,1.980092873,3.564166075,1.98009209,0.631283645
+4.7,1.199995901,1.999992998,3.59998668,1.999992486,0.625002268
+4.8,1.212055978,2.020093179,3.636167229,2.020092827,0.618783392
+4.9,1.224237303,2.040395413,3.672711357,2.040395137,0.612626394
+5,1.236541061,2.060901696,3.709622751,2.060901481,0.60653066
Modified: trunk/test-suite/cases/semantic/00053/00053-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-settings.txt 2008-07-30 08:59:20 UTC (rev 7791)
+++ trunk/test-suite/cases/semantic/00053/00053-settings.txt 2008-07-30 09:01:00 UTC (rev 7792)
@@ -1,6 +1,6 @@
start: 0
duration: 5.0
steps: 50
-variables: S1, S2, S3, S4
+variables: S1, S2, S3, S4, C
absolute: 1.000000e-003
relative: 0.0001
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 08:59:24
|
Revision: 7791
http://sbml.svn.sourceforge.net/sbml/?rev=7791&view=rev
Author: sarahkeating
Date: 2008-07-30 08:59:20 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
changed compartment id to C
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00053/00053-model.m
trunk/test-suite/cases/semantic/00053/00053-sbml-l1v2.xml
trunk/test-suite/cases/semantic/00053/00053-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00053/00053-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00053/00053-sbml-l2v3.xml
Modified: trunk/test-suite/cases/semantic/00053/00053-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-model.m 2008-07-30 08:23:24 UTC (rev 7790)
+++ trunk/test-suite/cases/semantic/00053/00053-model.m 2008-07-30 08:59:20 UTC (rev 7791)
@@ -9,19 +9,19 @@
levels: 1.2, 2.1, 2.2, 2.3
generatedBy: Numeric
-The model contains one varying compartment called "compartment". There are four
+The model contains one varying compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.
The model contains two reactions defined as:
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
-| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * compartment$ |
-| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * compartment$ |]
+| S1 + S2 -> S3 + S4 | $k1 * S1 * S2 * C$ |
+| S3 + S4 -> S1 + S2 | $k2 * S3 * S4 * C$ |]
The model contains one rule which defines the rate at which the volume of
the compartment is changing:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Rate | compartment | $-p1 * compartment$ |]
+ | Rate | C | $-p1 * C$ |]
The initial conditions are as follows:
@@ -33,7 +33,7 @@
|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |
|Value of parameter k2 |$ 0.25$ |litre mole^-1^ second^-1^ |
|Value of parameter p1 |$ 0.1$ |second^-1^ |
-|Volume of compartment "compartment" |$ 1$ |litre |]
+|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
use the model in a discrete stochastic simulator, but (as per usual SBML
@@ -44,7 +44,7 @@
newcase[ "00053" ];
-addCompartment[ compartment, constant->False, size -> 1 ];
+addCompartment[ C, constant->False, size -> 1 ];
addSpecies[ S1, initialAmount -> 1.0];
addSpecies[ S2, initialAmount -> 1.5];
addSpecies[ S3, initialAmount -> 2.0];
@@ -52,10 +52,10 @@
addParameter[ k1, value -> 0.75 ];
addParameter[ k2, value -> 0.25 ];
addParameter[ p1, value -> 0.1 ];
-addRule[ type->RateRule, variable -> compartment, math -> -p1 * compartment];
+addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 + S2 -> S3 + S4, reversible -> False,
- kineticLaw -> k1 * S1 * S2 * compartment ];
+ kineticLaw -> k1 * S1 * S2 * C ];
addReaction[ S3 + S4 -> S1 + S2, reversible -> False,
- kineticLaw -> k2 * S3 * S4 * compartment ];
+ kineticLaw -> k2 * S3 * S4 * C ];
makemodel[]
Modified: trunk/test-suite/cases/semantic/00053/00053-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-sbml-l1v2.xml 2008-07-30 08:23:24 UTC (rev 7790)
+++ trunk/test-suite/cases/semantic/00053/00053-sbml-l1v2.xml 2008-07-30 08:59:20 UTC (rev 7791)
@@ -2,13 +2,13 @@
<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
<model name="case00053">
<listOfCompartments>
- <compartment name="compartment" volume="1" units="volume"/>
+ <compartment name="C" volume="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
- <species name="S1" compartment="compartment" initialAmount="1" units="substance"/>
- <species name="S2" compartment="compartment" initialAmount="1.5" units="substance"/>
- <species name="S3" compartment="compartment" initialAmount="2" units="substance"/>
- <species name="S4" compartment="compartment" initialAmount="1" units="substance"/>
+ <species name="S1" compartment="C" initialAmount="1" units="substance"/>
+ <species name="S2" compartment="C" initialAmount="1.5" units="substance"/>
+ <species name="S3" compartment="C" initialAmount="2" units="substance"/>
+ <species name="S4" compartment="C" initialAmount="1" units="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter name="k1" value="0.75"/>
@@ -16,7 +16,7 @@
<parameter name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <compartmentVolumeRule formula="-1 * compartment * p1" type="rate" compartment="compartment"/>
+ <compartmentVolumeRule formula="-1 * C * p1" type="rate" compartment="C"/>
</listOfRules>
<listOfReactions>
<reaction name="reaction1" reversible="false">
@@ -28,7 +28,7 @@
<speciesReference species="S3"/>
<speciesReference species="S4"/>
</listOfProducts>
- <kineticLaw formula="compartment * k1 * S1 * S2"/>
+ <kineticLaw formula="C * k1 * S1 * S2"/>
</reaction>
<reaction name="reaction2" reversible="false">
<listOfReactants>
@@ -39,7 +39,7 @@
<speciesReference species="S1"/>
<speciesReference species="S2"/>
</listOfProducts>
- <kineticLaw formula="compartment * k2 * S3 * S4"/>
+ <kineticLaw formula="C * k2 * S3 * S4"/>
</reaction>
</listOfReactions>
</model>
Modified: trunk/test-suite/cases/semantic/00053/00053-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-sbml-l2v1.xml 2008-07-30 08:23:24 UTC (rev 7790)
+++ trunk/test-suite/cases/semantic/00053/00053-sbml-l2v1.xml 2008-07-30 08:59:20 UTC (rev 7791)
@@ -2,13 +2,13 @@
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model metaid="_case00053" id="case00053" name="case00053">
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="1.5" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="2" substanceUnits="substance"/>
- <species id="S4" name="S4" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="1.5" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="2" substanceUnits="substance"/>
+ <species id="S4" name="S4" compartment="C" initialAmount="1" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
@@ -16,12 +16,12 @@
<parameter id="p1" name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -41,7 +41,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k1 </ci>
<ci> S1 </ci>
<ci> S2 </ci>
@@ -62,7 +62,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
<ci> S4 </ci>
Modified: trunk/test-suite/cases/semantic/00053/00053-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-sbml-l2v2.xml 2008-07-30 08:23:24 UTC (rev 7790)
+++ trunk/test-suite/cases/semantic/00053/00053-sbml-l2v2.xml 2008-07-30 08:59:20 UTC (rev 7791)
@@ -2,13 +2,13 @@
<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
<model metaid="_case00053" id="case00053" name="case00053">
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="1.5" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="2" substanceUnits="substance"/>
- <species id="S4" name="S4" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="1.5" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="2" substanceUnits="substance"/>
+ <species id="S4" name="S4" compartment="C" initialAmount="1" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
@@ -16,12 +16,12 @@
<parameter id="p1" name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -41,7 +41,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k1 </ci>
<ci> S1 </ci>
<ci> S2 </ci>
@@ -62,7 +62,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
<ci> S4 </ci>
Modified: trunk/test-suite/cases/semantic/00053/00053-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-sbml-l2v3.xml 2008-07-30 08:23:24 UTC (rev 7790)
+++ trunk/test-suite/cases/semantic/00053/00053-sbml-l2v3.xml 2008-07-30 08:59:20 UTC (rev 7791)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 7-February-2008 14:54:06.6250000 -->
-<!-- Generated by MathSBML 2.7.1 (7 December 2007) -->
+<!-- Generated 30-July-2008 09:39:08.4218750 -->
+<!-- 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"
level="2"
@@ -13,17 +13,17 @@
<!-- <listOfCompartmentTypes/> -->
<!-- <listOfSpeciesTypes/> -->
<listOfCompartments>
- <compartment id="compartment"
- name="compartment"
+ <compartment id="C"
+ name="C"
spatialDimensions="3"
units="volume"
- size="1"
+ size="1."
constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1"
name="S1"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1."
@@ -31,7 +31,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S2"
name="S2"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.5"
@@ -39,7 +39,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S3"
name="S3"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="2."
@@ -47,7 +47,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S4"
name="S4"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1."
@@ -67,7 +67,7 @@
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
- <rateRule variable="compartment"
+ <rateRule variable="C"
metaid="rule1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -75,7 +75,7 @@
<apply>
<times/>
<cn type="integer">-1</cn>
- <ci>compartment</ci>
+ <ci>C</ci>
</apply>
<ci>p1</ci>
</apply>
@@ -101,7 +101,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k1</ci>
<ci>S1</ci>
<ci>S2</ci>
@@ -127,7 +127,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k2</ci>
<ci>S3</ci>
<ci>S4</ci>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-30 08:23:28
|
Revision: 7790
http://sbml.svn.sourceforge.net/sbml/?rev=7790&view=rev
Author: sarahkeating
Date: 2008-07-30 08:23:24 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
removed incorrect plots
Removed Paths:
-------------
trunk/test-suite/cases/semantic/00104/00104-plot.eps
trunk/test-suite/cases/semantic/00104/00104-plot.jpg
trunk/test-suite/cases/semantic/00105/00105-plot.eps
trunk/test-suite/cases/semantic/00105/00105-plot.jpg
trunk/test-suite/cases/semantic/00106/00106-plot.eps
trunk/test-suite/cases/semantic/00106/00106-plot.jpg
Deleted: trunk/test-suite/cases/semantic/00104/00104-plot.eps
===================================================================
--- trunk/test-suite/cases/semantic/00104/00104-plot.eps 2008-07-30 08:20:03 UTC (rev 7789)
+++ trunk/test-suite/cases/semantic/00104/00104-plot.eps 2008-07-30 08:23:24 UTC (rev 7790)
@@ -1,1949 +0,0 @@
-%!PS-Adobe-2.0 EPSF-1.2
-%%BoundingBox: 88 4 376 144
-%%HiResBoundingBox: 88 4 376 143.563
-%%Creator: (Mathematica 5.2 for Microsoft Windows)
-%%CreationDate: (Tuesday, February 12, 2008) (12:48:13)
-%%Title: Clipboard
-%%DocumentNeededResources: font Math1Mono
-%%+ font Courier
-%%DocumentSuppliedResources:
-%%DocumentNeededFonts: Math1Mono
-%%+ Courier
-%%DocumentSuppliedFonts:
-%%DocumentFonts: Math1Mono
-%%+ Courier
-%%EndComments
-0 147.563 translate 1 -1 scale
-150 dict begin
-/Mfixwid true def
-/Mrot 0 def
-/Mpstart {
- MathPictureStart
-} bind def
-/Mpend {
- MathPictureEnd
-} bind def
-/Mscale {
- 0 1 0 1
- 5 -1 roll
- MathScale
-} bind def
-/Plain /Courier findfont def
-/Bold /Courier-Bold findfont def
-/Italic /Courier-Oblique findfont def
-/MathPictureStart {
- /Mimatrix
- matrix currentmatrix
- def
- gsave
- newpath
- Mleft
- Mbottom
- translate
- /Mtmatrix
- matrix currentmatrix
- def
- Plain
- Mfontsize scalefont
- setfont
- 0 setgray
- 0 setlinewidth
-} bind def
-/MathPictureEnd {
- grestore
-} bind def
-/MathSubStart {
- Momatrix
- Mgmatrix Mtmatrix
- Mleft Mbottom
- Mwidth Mheight
- 9 -2 roll
- moveto
- Mtmatrix setmatrix
- currentpoint
- Mgmatrix setmatrix
- 11 -2 roll
- moveto
- Mtmatrix setmatrix
- currentpoint
- 2 copy translate
- /Mtmatrix matrix currentmatrix def
- /Mleft 0 def
- /Mbottom 0 def
- 3 -1 roll
- exch sub
- /Mheight exch def
- sub
- /Mwidth exch def
-} bind def
-/MathSubEnd {
- /Mheight exch def
- /Mwidth exch def
- /Mbottom exch def
- /Mleft exch def
- /Mtmatrix exch def
- dup setmatrix
- /Mgmatrix exch def
- /Momatrix exch def
-} bind def
-/Mdot {
- moveto
- 0 0 rlineto
- stroke
-} bind def
-/Mtetra {
- moveto
- lineto
- lineto
- lineto
- fill
-} bind def
-/Metetra {
- moveto
- lineto
- lineto
- lineto
- closepath
- gsave
- fill
- grestore
- 0 setgray
- stroke
-} bind def
-/Mistroke {
- flattenpath
- 0 0 0
- {
- 4 2 roll
- pop pop
- }
- {
- 4 -1 roll
- 2 index
- sub dup mul
- 4 -1 roll
- 2 index
- sub dup mul
- add sqrt
- 4 -1 roll
- add
- 3 1 roll
- }
- {
- stop
- }
- {
- stop
- }
- pathforall
- pop pop
- currentpoint
- stroke
- moveto
- currentdash
- 3 -1 roll
- add
- setdash
-} bind def
-/Mfstroke {
- stroke
- currentdash
- pop 0
- setdash
-} bind def
-/Mrotsboxa {
- gsave
- dup
- /Mrot
- exch def
- Mrotcheck
- Mtmatrix
- dup
- setmatrix
- 7 1 roll
- 4 index
- 4 index
- translate
- rotate
- 3 index
- -1 mul
- 3 index
- -1 mul
- translate
- /Mtmatrix
- matrix
- currentmatrix
- def
- grestore
- Msboxa
- 3 -1 roll
- /Mtmatrix
- exch def
- /Mrot
- 0 def
-} bind def
-/Msboxa {
- newpath
- 5 -1 roll
- Mvboxa
- pop
- Mboxout
- 6 -1 roll
- 5 -1 roll
- 4 -1 roll
- Msboxa1
- 5 -3 roll
- Msboxa1
- Mboxrot
- [
- 7 -2 roll
- 2 copy
- [
- 3 1 roll
- 10 -1 roll
- 9 -1 roll
- ]
- 6 1 roll
- 5 -2 roll
- ]
-} bind def
-/Msboxa1 {
- sub
- 2 div
- dup
- 2 index
- 1 add
- mul
- 3 -1 roll
- -1 add
- 3 -1 roll
- mul
-} bind def
-/Mvboxa {
- Mfixwid
- {
- Mvboxa1
- }
- {
- dup
- Mwidthcal
- 0 exch
- {
- add
- }
- forall
- exch
- Mvboxa1
- 4 index
- 7 -1 roll
- add
- 4 -1 roll
- pop
- 3 1 roll
- }
- ifelse
-} bind def
-/Mvboxa1 {
- gsave
- newpath
- [ true
- 3 -1 roll
- {
- Mbbox
- 5 -1 roll
- {
- 0
- 5 1 roll
- }
- {
- 7 -1 roll
- exch sub
- (m) stringwidth pop
- .3 mul
- sub
- 7 1 roll
- 6 -1 roll
- 4 -1 roll
- Mmin
- 3 -1 roll
- 5 index
- add
- 5 -1 roll
- 4 -1 roll
- Mmax
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From: <sar...@us...> - 2008-07-30 08:20:07
|
Revision: 7789
http://sbml.svn.sourceforge.net/sbml/?rev=7789&view=rev
Author: sarahkeating
Date: 2008-07-30 08:20:03 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
removed incorrect plots
Removed Paths:
-------------
trunk/test-suite/cases/semantic/00053/00053-plot.eps
trunk/test-suite/cases/semantic/00053/00053-plot.jpg
Deleted: trunk/test-suite/cases/semantic/00053/00053-plot.eps
===================================================================
--- trunk/test-suite/cases/semantic/00053/00053-plot.eps 2008-07-30 08:19:22 UTC (rev 7788)
+++ trunk/test-suite/cases/semantic/00053/00053-plot.eps 2008-07-30 08:20:03 UTC (rev 7789)
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From: <sar...@us...> - 2008-07-30 08:19:26
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Revision: 7788
http://sbml.svn.sourceforge.net/sbml/?rev=7788&view=rev
Author: sarahkeating
Date: 2008-07-30 08:19:22 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
removed incorrect plots
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-------------
trunk/test-suite/cases/semantic/00052/00052-plot.eps
trunk/test-suite/cases/semantic/00052/00052-plot.jpg
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From: <sar...@us...> - 2008-07-30 08:18:09
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Revision: 7787
http://sbml.svn.sourceforge.net/sbml/?rev=7787&view=rev
Author: sarahkeating
Date: 2008-07-30 08:18:05 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
removed incorrect plots
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trunk/test-suite/cases/semantic/00051/00051-plot.eps
trunk/test-suite/cases/semantic/00051/00051-plot.jpg
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-30 05:03:51
|
Revision: 7786
http://sbml.svn.sourceforge.net/sbml/?rev=7786&view=rev
Author: kbegley
Date: 2008-07-30 05:03:48 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
updated root level jar file
Modified Paths:
--------------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestCaseUpdater.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$1.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$aboutActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$checkUpdatesActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$helpActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$newActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$quitActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/dist/SBMLTestSuite.jar
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite.jar
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-30 04:59:47
|
Revision: 7785
http://sbml.svn.sourceforge.net/sbml/?rev=7785&view=rev
Author: kbegley
Date: 2008-07-30 04:59:43 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
updated javadoc comments
Modified Paths:
--------------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseUpdater.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestRunnerView.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestTabPane.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/UpdateDownloader.java
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseUpdater.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseUpdater.java 2008-07-30 04:40:24 UTC (rev 7784)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseUpdater.java 2008-07-30 04:59:43 UTC (rev 7785)
@@ -1,35 +1,66 @@
-/*
- * TestCaseUpdater.java
- *
- * Created on July 11, 2008, 5:59 PM
- */
+// @file TestCaseUpdater.java
+// @brief TestCaseUpdater class for SBML Standalone application
+// @author Kimberly Begley
+//
+//
+//<!---------------------------------------------------------------------------
+// This file is part of the SBML Test Suite. Please visit http://sbml.org for
+// more information about SBML, and the latest version of the SBML Test Suite.
+//
+// Copyright 2008 California Institute of Technology.
+// Copyright 2004-2007 California Institute of Technology (USA) and
+// University of Hertfordshire (UK).
+//
+// The SBML Test Suite 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. A copy of the license
+// agreement is provided in the file named "LICENSE.txt" included with
+// this software distribution and also available at
+// http://sbml.org/Software/SBML_Test_Suite/license.html
+//------------------------------------------------------------------------- -->
+// Class for updating the test cases via the internet.
+//
+
package sbml.test;
/**
- *
+ * TestCaseUpdater class creates the dialog window for the test case downloads and has many methods used in the process.
* @author Kimberly Begley
* @version 2.0
*/
public class TestCaseUpdater extends javax.swing.JDialog {
- /** Creates new form TestCaseUpdater */
+
+ /**
+ * Creates new form TestCaseUpdater
+ * @param parent is the parent frame
+ * @param modal boolean value for indicating if the dialog is modal or not
+ */
public TestCaseUpdater(java.awt.Frame parent, boolean modal) {
super(parent, modal);
initComponents();
this.setVisible(true);
}
-
+ /**
+ * checkForUpdates creates a new UpdateDownloader and checks for updates
+ */
public void checkForUpdates() {
UpdateDownloader ud = new UpdateDownloader(this);
ud.start();
}
-
+ /**
+ * appendToLog appends a string to the log
+ * @param string
+ */
void appendToLog(String string) {
jTextArea1.append(string);
}
-
+ /**
+ * setFinished sets the progress bar details to finished with the message parameter given
+ * @param message the message to set the string in the progress bar to
+ */
void setFinished(String message) {
jProgressBar1.setIndeterminate(false);
jProgressBar1.setMaximum(100);
@@ -37,26 +68,41 @@
jProgressBar1.setString(message);
jProgressBar1.setStringPainted(true);
}
-
+ /**
+ * setLocalTimestamp sets the local timestamp
+ * @param ts the value to set the timestamp to
+ */
void setLocalTimestamp(String ts) {
currentVersionLabel.setText(ts);
}
-
+ /**
+ * setNewTimestamp sets the new timestamp value
+ * @param logLine the value to set the timestamp to
+ */
void setNewTimestamp(String logLine) {
latestVersionLabel.setText(logLine);
}
-
+ /**
+ * setProgressBarIndeterminant - sets the progress bar to an interterminant type if indicated by ind
+ * @param ind the boolean value indicating whether to set the progress bar to indeterminant or not
+ */
void setProgressBarIndeterminate(boolean ind) {
jProgressBar1.setStringPainted(!ind);
jProgressBar1.setIndeterminate(ind);
}
-
+ /**
+ * setProgressBarMax - sets the max value for the progress bar
+ * @param i the value to set as max for the progress bar
+ */
void setProgressBarMax(int i) {
jProgressBar1.setMaximum(i);
jProgressBar1.setString("0 MB of "+i/(1024*1024)+" MB");
jProgressBar1.setStringPainted(true);
}
-
+ /**
+ * setProgressBarProgress - updates the progress of the progress bar
+ * @param i the value to set the progress to
+ */
void setProgressBarProgress(int i) {
jProgressBar1.setValue(i);
jProgressBar1.setString(i/(1024*1024)+" MB of "+jProgressBar1.getMaximum()/(1024*1024)+" MB");
@@ -125,7 +171,10 @@
pack();
}// </editor-fold>//GEN-END:initComponents
-
+ /**
+ * jButtonActionPerformed is the listener event that occurs when the cancel button is clicked on
+ * @param evt it sets the window to invisible
+ */
private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton1ActionPerformed
// Cancel button selected
this.setVisible(false);
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestRunnerView.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestRunnerView.java 2008-07-30 04:40:24 UTC (rev 7784)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestRunnerView.java 2008-07-30 04:59:43 UTC (rev 7785)
@@ -47,11 +47,12 @@
import javax.swing.ImageIcon;
import java.net.URL;
import java.util.HashMap;
-//import javax.help.HelpBroker;
-//import javax.help.HelpSet;
+
public class TestRunnerView extends JFrame implements WindowListener {
- /** Creates new form TestRunnerView */
+ /**
+ * Creates new form for TestRunnerView
+ */
public TestRunnerView() {
super("SBML TestRunner");
initComponents();
@@ -68,7 +69,9 @@
public static HashMap<String, Object> currentvalues;
// public static HelpDialog helpdialog;
TestRunnerWorker worker;
-
+ /**
+ * initComponents - initializes the components for the TestRunnerView
+ */
private void initComponents() {
testCaseListModel = new TestCaseListModel();
failedTestCaseListModel = new FailedTestCaseListModel();
@@ -198,7 +201,10 @@
}
});
}
-
+ /**
+ * quit - closes the application
+ * @return returns a boolean value if user wants to quit
+ */
public boolean quit() {
int option = JOptionPane.showConfirmDialog(this, "Are you sure you want to quit?", "Quit?", JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION) {
@@ -207,92 +213,137 @@
return (option == JOptionPane.YES_OPTION);
}
-
+ /**
+ * about - sets the about box contents
+ */
public void about() {
// aboutBox.setLocation((int)this.getLocation().getX() + 22, (int)this.getLocation().getY() + 22);
// aboutBox.setVisible(true);
// Display the about box here
ImageIcon icon = new ImageIcon(getClass().getResource("resources/SBML.png"));
- JOptionPane.showMessageDialog(this, "<html><p>SBML Test Suite V1.0 2008</p></html>", "About SBML Test Suite", JOptionPane.PLAIN_MESSAGE, icon);
+ JOptionPane.showMessageDialog(this, "<html><p>SBML Test Suite V2.0 2008</p></html>", "About SBML Test Suite", JOptionPane.PLAIN_MESSAGE, icon);
}
-
+ /**
+ * openHelp opens the help dialog
+ */
public void openHelp() {
HelpDialog displayHelp = new HelpDialog(this);
}
- // General preferences dialog; fed to the OSXAdapter as the method to call when
- // "Preferences..." is selected from the application menu
+
+ /**
+ * General preferences dialog; fed to the OSXAdapter as the method to call when
+ * "Preferences..." is selected from the application menu
+ */
public void preferences() {
currentvalues = PreferencesDialog.getValue(this, currentvalues);
}
-
+ /**
+ * getLoggingInfo - gets the hashmap containing the logging info from the dialog
+ * @return
+ */
public HashMap<String, Object> getLoggingInfo() {
return currentvalues;
}
-
+ /**
+ * performUpdate - is run when the user selects to "check for new test cases" from the menu
+ */
public void performUpdate() {
// connect to server and get latest copy of zip file if newer than packaged copy
TestCaseUpdater testCaseUpdater = new TestCaseUpdater(this, false);
testCaseUpdater.checkForUpdates();
testCaseUpdater.setModal(true);
}
-
+ /**
+ * windowOpened - can uncomment the performUpdate line to have it automatically check for updates as soon as the app is started
+ * @param e
+ */
public void windowOpened(WindowEvent e) {
// performUpdate();
// throw new UnsupportedOperationException("Not supported yet.");
}
-
+ /**
+ * windowClosing - exits the program
+ * @param e
+ */
public void windowClosing(WindowEvent e) {
if (quit()) {
System.exit(0);
}
//throw new UnsupportedOperationException("Not supported yet.");
}
-
+ /**
+ * updateProgress updates the progess bar information
+ * @param progress total number of tests taken so far
+ * @param failed number of failed tests so far
+ * @param skipped number of skipped tests so far
+ * @param passed number of passed tests so far
+ * @param finish indicates whether at the end of test set or not
+ */
public void updateProgress(int progress, int failed, int skipped, int passed, int finish) {
testTabPane.updateProgress(progress, failed, skipped, passed, finish);
}
-
+ /**
+ * sets the selections hashmap
+ * @param tconfiguration hashmap to set
+ */
public void setSelections(HashMap<String, Object> tconfiguration) {
testTabPane.setConfigurations(tconfiguration);
}
-
+ /**
+ * setStartButton - enables the start button
+ */
public void setStartButton() {
testTabPane.enableStart();
}
-
+ /**
+ * disableStartButton - disables the start button
+ */
public void disableStartButton() {
testTabPane.disableStart();
}
-
+ /**
+ * setStopButton - sets the stop button
+ */
public void setStopButton() {
testTabPane.enableStop();
}
-
+ /**
+ * disableStopButton - disables the stop button
+ */
public void disableStopButton() {
testTabPane.disableStop();
}
-
+ /**
+ * setResetButton - sets the reset button
+ */
public void setResetButton() {
testTabPane.enableReset();
}
-
+ /**
+ * disableResetButton - disables the reset button
+ */
public void disableResetButton() {
testTabPane.disableReset();
}
-
+ /**
+ * displayWrapperError - displays the wrapper error diaglog
+ */
public void displayWrapperError() {
testTabPane.wrapperError();
}
-
+ /**
+ * windowClosed event - nothing happens yet
+ * @param e
+ */
public void windowClosed(WindowEvent e) {
// throw new UnsupportedOperationException("Not supported yet.");
}
-
+
public void windowIconified(WindowEvent e) {
// throw new UnsupportedOperationException("Not supported yet.");
}
@@ -313,6 +364,9 @@
// public static TestRunnerView getApplication() {
// return Application.getInstance(TestRunnerView.class);
// }
+ /**
+ * registerForMacOSXEvents - sets the mac os look and feel for the quit, about and preferences menu items
+ */
public void registerForMacOSXEvents() {
if (MAC_OS_X) {
try {
@@ -328,7 +382,10 @@
}
}
}
-
+ /**
+ * startTest - starts a test
+ * @param testConfiguration test parameters for the test
+ */
public void startTest(TestConfiguration testConfiguration) {
// final TestConfiguration finalTestConfig = testConfiguration;
@@ -347,11 +404,15 @@
worker = new TestRunnerWorker(this, testConfiguration);
worker.start();
}
-
+ /**
+ * stopTest sends an interrupt to the worker thread
+ */
public void stopTest() {
worker.interrupt();
}
-
+ /**
+ * newActionClass is called when a new test is selected from the menu
+ */
public class newActionClass extends AbstractAction {
TestRunnerView parent;
@@ -368,7 +429,9 @@
wizard.runWizard();
}
}
-
+ /**
+ * checkUpdatesActionClass is called when the menu is selected to check for new test cases
+ */
public class checkUpdatesActionClass extends AbstractAction {
public checkUpdatesActionClass(String text) {
@@ -384,7 +447,9 @@
performUpdate();
}
}
-
+ /**
+ * quitActionClass is called when the quit menu is selected
+ */
public class quitActionClass extends AbstractAction {
public quitActionClass(String text) {
@@ -396,7 +461,9 @@
quit();
}
}
-
+ /**
+ * aboutActionClass is called when about is selected from the menu
+ */
public class aboutActionClass extends AbstractAction {
public aboutActionClass(String text) {
@@ -408,7 +475,9 @@
about();
}
}
-
+ /**
+ * helpActionClass is called when help is selected from the menu
+ */
public class helpActionClass extends AbstractAction {
public helpActionClass(String text) {
@@ -420,7 +489,9 @@
openHelp();
}
}
-
+ /**
+ * preferencesActionClass is called when the preferences are selected from the menu
+ */
public class preferencesActionClass extends AbstractAction {
public preferencesActionClass(String text) {
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestTabPane.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestTabPane.java 2008-07-30 04:40:24 UTC (rev 7784)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestTabPane.java 2008-07-30 04:59:43 UTC (rev 7785)
@@ -92,7 +92,7 @@
ButtonGroup controlButtons = new ButtonGroup();
- JButton configureButton = new JButton(new ImageIcon(getClass().getResource("resources/config.png")));
+ JButton configureButton = new JButton(new ImageIcon(getClass().getResource("resources/configure3.png")));
if (MAC_OS_X) {
configureButton.putClientProperty("JButton.buttonType", "segmentedCapsule");
@@ -101,7 +101,7 @@
}
configureButton.setToolTipText("Configure");
- configureButton.setAction(new settingsActionClass("", new ImageIcon(getClass().getResource("resources/config.png"))));
+ configureButton.setAction(new settingsActionClass("", new ImageIcon(getClass().getResource("resources/configure3.png"))));
startButton = new JButton(new ImageIcon(getClass().getResource("resources/start.png")));
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/UpdateDownloader.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/UpdateDownloader.java 2008-07-30 04:40:24 UTC (rev 7784)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/UpdateDownloader.java 2008-07-30 04:59:43 UTC (rev 7785)
@@ -1,7 +1,26 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
+// @file UpdateDownloader.java
+// @brief UpdateDownloader class for SBML Standalone application
+// @author Kimberly Begley
+//
+
+//
+//<!---------------------------------------------------------------------------
+// This file is part of the SBML Test Suite. Please visit http://sbml.org for
+// more information about SBML, and the latest version of the SBML Test Suite.
+//
+// Copyright 2008 California Institute of Technology.
+// Copyright 2004-2007 California Institute of Technology (USA) and
+// University of Hertfordshire (UK).
+//
+// The SBML Test Suite 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. A copy of the license
+// agreement is provided in the file named "LICENSE.txt" included with
+// this software distribution and also available at
+// http://sbml.org/Software/SBML_Test_Suite/license.html
+//------------------------------------------------------------------------- -->
+// UpdateDownloader will download new SBML test case files from SourceForge.net
+//
package sbml.test;
import java.io.BufferedInputStream;
@@ -28,7 +47,7 @@
import javax.swing.SwingUtilities;
/**
- * UpdateDownloader will download new TestCase files from SourceForge.net
+ * UpdateDownloader will download new SBML test case files from SourceForge.net
*
*
* @author Kimberly Begley
@@ -41,7 +60,10 @@
private DataInputStream in;
private static String timestampURL = "http://sbml.svn.sf.net/viewvc/*checkout*/sbml/trunk/test-suite/.cases-archive-date";
private TestCaseUpdater tcu;
-
+ /**
+ * UpdateDownloader has one constructor
+ * @param tcu takes a TestCaseUpdater as input
+ */
public UpdateDownloader(TestCaseUpdater tcu) {
super();
this.tcu = tcu;
@@ -59,6 +81,7 @@
});
try {
+ // Looks for the timestamp file in the .sbmltestrunner directory - this should have the timestamp for the latest installed version of cases
File localtimestampfile = new File(((String) System.getProperty("user.home")) + File.separator + ".sbmltestrunner" + File.separator + "sbml-test-suite" + File.separator + "timestamp");
BufferedReader br = new BufferedReader(new FileReader(localtimestampfile));
localtimestamp = br.readLine();
@@ -188,7 +211,7 @@
try {
- // unzip the file
+ // unzip the files
FileInputStream newcasesfile = new FileInputStream(((String) System.getProperty("java.io.tmpdir")) + File.separator + "testoutputfile.zip");
ZipInputStream zipFile = new ZipInputStream(new BufferedInputStream(newcasesfile));
ZipEntry entry;
@@ -271,7 +294,10 @@
return true;
}
-
+ /**
+ * reportToDialog - appends the string to the dialog
+ * @param message the string to append
+ */
private void reportToDialog(String message) {
final String m = message;
SwingUtilities.invokeLater(new Runnable() {
@@ -280,7 +306,13 @@
}
});
}
-
+ /**
+ * checkIfUpdateNecessary
+ * @param servertimestamp
+ * @param localtimestamp
+ * @return
+ * @throws java.lang.NumberFormatException
+ */
private boolean checkIfUpdateNecessary(String servertimestamp, String localtimestamp) throws NumberFormatException {
Calendar localdate = new GregorianCalendar();
@@ -290,7 +322,12 @@
return serverdate.after(localdate);
}
-
+ /**
+ * getReaderOnURL
+ * @param inputurl
+ * @return
+ * @throws java.io.IOException
+ */
private BufferedReader getReaderOnURL(URL inputurl) throws IOException {
HttpURLConnection urlConn = null;
InputStreamReader inStream = null;
@@ -308,7 +345,12 @@
return buff;
}
-
+ /**
+ * getHttpURLConnectionFromURL
+ * @param inputurl
+ * @return
+ * @throws java.io.IOException
+ */
private HttpURLConnection getHttpURLConnectionFromURL(URL inputurl) throws IOException {
HttpURLConnection urlConn = null;
URL url = inputurl;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-30 04:40:26
|
Revision: 7784
http://sbml.svn.sourceforge.net/sbml/?rev=7784&view=rev
Author: kbegley
Date: 2008-07-30 04:40:24 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
added new config icon
Added Paths:
-----------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/resources/configure3.png
Property changes on: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/resources/configure3.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-30 04:37:16
|
Revision: 7783
http://sbml.svn.sourceforge.net/sbml/?rev=7783&view=rev
Author: kbegley
Date: 2008-07-30 04:37:12 +0000 (Wed, 30 Jul 2008)
Log Message:
-----------
updated javadocs
Modified Paths:
--------------
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/overview-tree.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/package-list
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/FailedTestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/HelpDialog.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/ListViewPane.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/MapViewPane.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/PassedTestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/PreferencesDialog.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SBMLTestCase.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SBMLTestRunnerApp.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SBMLTestSelection.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SkippedTestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SwingWorker.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestCaseUpdater.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestConfiguration.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestResultDetails.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestResultMap.FieldListener.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestResultMap.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.aboutActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.checkUpdatesActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.helpActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.newActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.preferencesActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.quitActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerWorker.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.openBrowserActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.resetActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.settingsActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.startActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.stopActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/package-frame.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/package-summary.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/package-tree.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/serialized-form.html
Modified: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html 2008-07-29 14:15:10 UTC (rev 7782)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html 2008-07-30 04:37:12 UTC (rev 7783)
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<!-- Generated by javadoc (build 1.5.0_13) on Wed Jul 30 14:32:24 EST 2008 -->
<TITLE>
All Classes
</TITLE>
@@ -20,22 +20,46 @@
<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
<TR>
-<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard" target="classFrame">ComponentTagsSelectorPanel</A>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="sbml/test/FailedTestCaseListModel.html" title="class in sbml.test" target="classFrame">FailedTestCaseListModel</A>
<BR>
-<A HREF="sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard" target="classFrame">CreateTestWizard</A>
+<A HREF="sbml/test/HelpDialog.html" title="class in sbml.test" target="classFrame">HelpDialog</A>
<BR>
-<A HREF="sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard" target="classFrame">LevelSelectorPanel</A>
+<A HREF="sbml/test/ListViewPane.html" title="class in sbml.test" target="classFrame">ListViewPane</A>
<BR>
-<A HREF="sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard" target="classFrame">TestTagSelectionPanel</A>
+<A HREF="sbml/test/MapViewPane.html" title="class in sbml.test" target="classFrame">MapViewPane</A>
<BR>
-<A HREF="sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard" target="classFrame">TestTypeSelectorPanel</A>
+<A HREF="sbml/test/PassedTestCaseListModel.html" title="class in sbml.test" target="classFrame">PassedTestCaseListModel</A>
<BR>
-<A HREF="sbml/test/Wizard/WizardPanel.html" title="class in sbml.test.Wizard" target="classFrame">WizardPanel</A>
+<A HREF="sbml/test/PreferencesDialog.html" title="class in sbml.test" target="classFrame">PreferencesDialog</A>
<BR>
-<A HREF="sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard" target="classFrame"><I>WizardPanelInterface</I></A>
+<A HREF="sbml/test/SBMLTestCase.html" title="class in sbml.test" target="classFrame">SBMLTestCase</A>
<BR>
-<A HREF="sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard" target="classFrame">WrapperConfigurationPanel</A>
+<A HREF="sbml/test/SBMLTestRunnerApp.html" title="class in sbml.test" target="classFrame">SBMLTestRunnerApp</A>
<BR>
+<A HREF="sbml/test/SBMLTestSelection.html" title="class in sbml.test" target="classFrame">SBMLTestSelection</A>
+<BR>
+<A HREF="sbml/test/SkippedTestCaseListModel.html" title="class in sbml.test" target="classFrame">SkippedTestCaseListModel</A>
+<BR>
+<A HREF="sbml/test/SwingWorker.html" title="class in sbml.test" target="classFrame">SwingWorker</A>
+<BR>
+<A HREF="sbml/test/TestCaseListModel.html" title="class in sbml.test" target="classFrame">TestCaseListModel</A>
+<BR>
+<A HREF="sbml/test/TestCaseUpdater.html" title="class in sbml.test" target="classFrame">TestCaseUpdater</A>
+<BR>
+<A HREF="sbml/test/TestConfiguration.html" title="class in sbml.test" target="classFrame">TestConfiguration</A>
+<BR>
+<A HREF="sbml/test/TestResultDetails.html" title="class in sbml.test" target="classFrame">TestResultDetails</A>
+<BR>
+<A HREF="sbml/test/TestResultMap.html" title="class in sbml.test" target="classFrame">TestResultMap</A>
+<BR>
+<A HREF="sbml/test/TestRunnerView.html" title="class in sbml.test" target="classFrame">TestRunnerView</A>
+<BR>
+<A HREF="sbml/test/TestRunnerWorker.html" title="class in sbml.test" target="classFrame">TestRunnerWorker</A>
+<BR>
+<A HREF="sbml/test/TestTabPane.html" title="class in sbml.test" target="classFrame">TestTabPane</A>
+<BR>
+<A HREF="sbml/test/UpdateDownloader.html" title="class in sbml.test" target="classFrame">UpdateDownloader</A>
+<BR>
</FONT></TD>
</TR>
</TABLE>
Modified: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html 2008-07-29 14:15:10 UTC (rev 7782)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html 2008-07-30 04:37:12 UTC (rev 7783)
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<!-- Generated by javadoc (build 1.5.0_13) on Wed Jul 30 14:32:24 EST 2008 -->
<TITLE>
All Classes
</TITLE>
@@ -20,22 +20,46 @@
<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
<TR>
-<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="sbml/test/FailedTestCaseListModel.html" title="class in sbml.test">FailedTestCaseListModel</A>
<BR>
-<A HREF="sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<A HREF="sbml/test/HelpDialog.html" title="class in sbml.test">HelpDialog</A>
<BR>
-<A HREF="sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<A HREF="sbml/test/ListViewPane.html" title="class in sbml.test">ListViewPane</A>
<BR>
-<A HREF="sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<A HREF="sbml/test/MapViewPane.html" title="class in sbml.test">MapViewPane</A>
<BR>
-<A HREF="sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<A HREF="sbml/test/PassedTestCaseListModel.html" title="class in sbml.test">PassedTestCaseListModel</A>
<BR>
-<A HREF="sbml/test/Wizard/WizardPanel.html" title="class in sbml.test.Wizard">WizardPanel</A>
+<A HREF="sbml/test/PreferencesDialog.html" title="class in sbml.test">PreferencesDialog</A>
<BR>
-<A HREF="sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard"><I>WizardPanelInterface</I></A>
+<A HREF="sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
<BR>
-<A HREF="sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<A HREF="sbml/test/SBMLTestRunnerApp.html" title="class in sbml.test">SBMLTestRunnerApp</A>
<BR>
+<A HREF="sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<BR>
+<A HREF="sbml/test/SkippedTestCaseListModel.html" title="class in sbml.test">SkippedTestCaseListModel</A>
+<BR>
+<A HREF="sbml/test/SwingWorker.html" title="class in sbml.test">SwingWorker</A>
+<BR>
+<A HREF="sbml/test/TestCaseListModel.html" title="class in sbml.test">TestCaseListModel</A>
+<BR>
+<A HREF="sbml/test/TestCaseUpdater.html" title="class in sbml.test">TestCaseUpdater</A>
+<BR>
+<A HREF="sbml/test/TestConfiguration.html" title="class in sbml.test">TestConfiguration</A>
+<BR>
+<A HREF="sbml/test/TestResultDetails.html" title="class in sbml.test">TestResultDetails</A>
+<BR>
+<A HREF="sbml/test/TestResultMap.html" title="class in sbml.test">TestResultMap</A>
+<BR>
+<A HREF="sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<BR>
+<A HREF="sbml/test/TestRunnerWorker.html" title="class in sbml.test">TestRunnerWorker</A>
+<BR>
+<A HREF="sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<BR>
+<A HREF="sbml/test/UpdateDownloader.html" title="class in sbml.test">UpdateDownloader</A>
+<BR>
</FONT></TD>
</TR>
</TABLE>
Modified: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html 2008-07-29 14:15:10 UTC (rev 7782)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html 2008-07-30 04:37:12 UTC (rev 7783)
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<!-- Generated by javadoc (build 1.5.0_13) on Wed Jul 30 14:32:24 EST 2008 -->
<TITLE>
Constant Field Values
</TITLE>
@@ -33,9 +33,9 @@
<A NAME="navbar_top_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
@@ -93,9 +93,9 @@
<A NAME="navbar_bottom_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
Modified: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html 2008-07-29 14:15:10 UTC (rev 7782)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html 2008-07-30 04:37:12 UTC (rev 7783)
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<!-- Generated by javadoc (build 1.5.0_13) on Wed Jul 30 14:32:24 EST 2008 -->
<TITLE>
Deprecated List
</TITLE>
@@ -33,9 +33,9 @@
<A NAME="navbar_top_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
@@ -93,9 +93,9 @@
<A NAME="navbar_bottom_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
Modified: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html 2008-07-29 14:15:10 UTC (rev 7782)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html 2008-07-30 04:37:12 UTC (rev 7783)
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<!-- Generated by javadoc (build 1.5.0_13) on Wed Jul 30 14:32:24 EST 2008 -->
<TITLE>
API Help
</TITLE>
@@ -33,9 +33,9 @@
<A NAME="navbar_top_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
@@ -160,9 +160,9 @@
<A NAME="navbar_bottom_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
<TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
Modified: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html 2008-07-29 14:15:10 UTC (rev 7782)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html 2008-07-30 04:37:12 UTC (rev 7783)
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<!-- Generated by javadoc (build 1.5.0_13) on Wed Jul 30 14:32:24 EST 2008 -->
<TITLE>
Index
</TITLE>
@@ -33,9 +33,9 @@
<A NAME="navbar_top_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
<TR ALIGN="center" VALIGN="top">
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./sbml/test/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./sbml/test/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
<TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
<TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
@@ -72,331 +72,772 @@
<A NAME="skip-navbar_top"></A>
<!-- ========= END OF TOP NAVBAR ========= -->
-<A HREF="#_A_">A</A> <A HREF="#_C_">C</A> <A HREF="#_G_">G</A> <A HREF="#_I_">I</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <HR>
+<A HREF="#_A_">A</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_Q_">Q</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <HR>
<A NAME="_A_"><!-- --></A><H2>
<B>A</B></H2>
<DL>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.cancelActionClass</A>
+<DT><A HREF="./sbml/test/TestRunnerView.html#about()"><B>about()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<DD>about - sets the about box contents
+<DT><A HREF="./sbml/test/SBMLTestCase.html#abs"><B>abs</B></A> -
+Variable in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.finishActionClass</A>
+<DT><A HREF="./sbml/test/HelpDialog.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/HelpDialog.html" title="class in sbml.test">HelpDialog</A>
+<DD>actionPerformed Listener that listens for the close action of the help dialog
+<DT><A HREF="./sbml/test/TestRunnerView.aboutActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.aboutActionClass.html" title="class in sbml.test">TestRunnerView.aboutActionClass</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.nextActionClass</A>
+<DT><A HREF="./sbml/test/TestRunnerView.checkUpdatesActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.checkUpdatesActionClass.html" title="class in sbml.test">TestRunnerView.checkUpdatesActionClass</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.previousActionClass</A>
+<DT><A HREF="./sbml/test/TestRunnerView.helpActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.helpActionClass.html" title="class in sbml.test">TestRunnerView.helpActionClass</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#addPropertyChangeListener(java.beans.PropertyChangeListener)"><B>addPropertyChangeListener(PropertyChangeListener)</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
-<DD>addPropertyChangeListener - adds a new propertychangelistener
-</DL>
-<HR>
-<A NAME="_C_"><!-- --></A><H2>
-<B>C</B></H2>
-<DL>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#changeCard(java.lang.String)"><B>changeCard(String)</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
-<DD>changeCard changes the viewable pages on the wizard
-<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard"><B>ComponentTagsSelectorPanel</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>ComponentTagsSelectorPanel is the class responsible for the component tag selection for the test wizard.<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#ComponentTagsSelectorPanel(sbml.test.Wizard.CreateTestWizard)"><B>ComponentTagsSelectorPanel(CreateTestWizard)</B></A> -
-Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
-<DD>ComponentTagSelectorPanel has one constructor that initializes the components for the wizard interface
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard"><B>CreateTestWizard</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>CreateTestWizard is the main class for creating a new test wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#CreateTestWizard(sbml.test.TestRunnerView)"><B>CreateTestWizard(TestRunnerView)</B></A> -
-Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
-<DD>CreateTestWizard constructor initializes componenet for the wizard and adds a listener for the selections
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.cancelActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>cancelActionClass - closes the wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html#CreateTestWizard.cancelActionClass(java.lang.String)"><B>CreateTestWizard.cancelActionClass(String)</B></A> -
-Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.cancelActionClass</A>
+<DT><A HREF="./sbml/test/TestRunnerView.newActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.newActionClass.html" title="class in sbml.test">TestRunnerView.newActionClass</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.finishActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>finishActionClass completes the wizard and closes it and passes variables onto the test.<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html#CreateTestWizard.finishActionClass(java.lang.String)"><B>CreateTestWizard.finishActionClass(String)</B></A> -
-Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.finishActionClass</A>
+<DT><A HREF="./sbml/test/TestRunnerView.preferencesActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.preferencesActionClass.html" title="class in sbml.test">TestRunnerView.preferencesActionClass</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.nextActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>nextActionClass sets the next page on the wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html#CreateTestWizard.nextActionClass(java.lang.String)"><B>CreateTestWizard.nextActionClass(String)</B></A> -
-Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.nextActionClass</A>
+<DT><A HREF="./sbml/test/TestRunnerView.quitActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.quitActionClass.html" title="class in sbml.test">TestRunnerView.quitActionClass</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.previousActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>previousActionClass sets the previous page on the wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html#CreateTestWizard.previousActionClass(java.lang.String)"><B>CreateTestWizard.previousActionClass(String)</B></A> -
-Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.previousActionClass</A>
+<DT><A HREF="./sbml/test/TestTabPane.openBrowserActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.openBrowserActionClass.html" title="class in sbml.test">TestTabPane.openBrowserActionClass</A>
<DD>
+<DT><A HREF="./sbml/test/TestTabPane.resetActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.resetActionClass.html" title="class in sbml.test">TestTabPane.resetActionClass</A>
+<DD>actionPerformed for the reset button - it stops the current thread and enables the start button
+<DT><A HREF="./sbml/test/TestTabPane.settingsActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.settingsActionClass.html" title="class in sbml.test">TestTabPane.settingsActionClass</A>
+<DD>actionPerformed - action performed when the configuration button is pushed - it launches a new test wizard
+<DT><A HREF="./sbml/test/TestTabPane.startActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.startActionClass.html" title="class in sbml.test">TestTabPane.startActionClass</A>
+<DD>actionPerformed - sets the action for the start button - it starts a new test with the same configurations as indicated in the wizard
+<DT><A HREF="./sbml/test/TestTabPane.stopActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.stopActionClass.html" title="class in sbml.test">TestTabPane.stopActionClass</A>
+<DD>actionPerformed - sets the action for the stop button - by calling the stopTest method.
+<DT><A HREF="./sbml/test/FailedTestCaseListModel.html#addElement(sbml.test.TestResultDetails)"><B>addElement(TestResultDetails)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/FailedTestCaseListModel.html" title="class in sbml.test">FailedTestCaseListModel</A>
+<DD>Adds a new data structure of result details to the failed list.
+<DT><A HREF="./sbml/test/PassedTestCaseListModel.html#addElement(sbml.test.TestResultDetails)"><B>addElement(TestResultDetails)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/PassedTestCaseListModel.html" title="class in sbml.test">PassedTestCaseListModel</A>
+<DD>addElement adds a TestResultDetails object to the list anf fires an event to record this.
+<DT><A HREF="./sbml/test/SkippedTestCaseListModel.html#addElement(sbml.test.TestResultDetails)"><B>addElement(TestResultDetails)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SkippedTestCaseListModel.html" title="class in sbml.test">SkippedTestCaseListModel</A>
+<DD>addElement - adds an element to the skipped list and fires an interval change.
+<DT><A HREF="./sbml/test/TestCaseListModel.html#addElement(sbml.test.TestResultDetails)"><B>addElement(TestResultDetails)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestCaseListModel.html" title="class in sbml.test">TestCaseListModel</A>
+<DD>addElement - adds a case ojbect to the list
+<DT><A HREF="./sbml/test/TestResultMap.html#addItemListener(java.awt.event.ItemListener)"><B>addItemListener(ItemListener)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultMap.html" title="class in sbml.test">TestResultMap</A>
+<DD>addItemListener - adds an item listener to the list
+<DT><A HREF="./sbml/test/SBMLTestCase.html#analyzeResults(java.math.BigDecimal[][], java.math.BigDecimal[][], int, java.math.BigDecimal, java.math.BigDecimal)"><B>analyzeResults(BigDecimal[][], BigDecimal[][], int, BigDecimal, BigDecimal)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Looks at the allowable difference and how it compares to the differences of the user and control files
</DL>
<HR>
-<A NAME="_G_"><!-- --></A><H2>
-<B>G</B></H2>
+<A NAME="_C_"><!-- --></A><H2>
+<B>C</B></H2>
<DL>
-<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
-<DD>getIdentifier
-<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#category"><B>category</B></A> -
+Variable in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DT><A HREF="./sbml/test/TestTabPane.html#changedUpdate(javax.swing.event.DocumentEvent)"><B>changedUpdate(DocumentEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>changedUpdate - not in use
+<DT><A HREF="./sbml/test/TestCaseUpdater.html#checkForUpdates()"><B>checkForUpdates()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestCaseUpdater.html" title="class in sbml.test">TestCaseUpdater</A>
+<DD>checkForUpdates creates a new UpdateDownloader and checks for updates
+<DT><A HREF="./sbml/test/SBMLTestCase.html#compareResults(java.math.BigDecimal[][], java.math.BigDecimal[][], int, int)"><B>compareResults(BigDecimal[][], BigDecimal[][], int, int)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Subtracts the corresponding fields to give the difference between the values in the user and control result files
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#componenttags"><B>componenttags</B></A> -
+Variable in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DT><A HREF="./sbml/test/SwingWorker.html#construct()"><B>construct()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SwingWorker.html" title="class in sbml.test">SwingWorker</A>
+<DD>Compute the value to be returned by the <code>get</code> method.
+<DT><A HREF="./sbml/test/TestRunnerWorker.html#construct()"><B>construct()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerWorker.html" title="class in sbml.test">TestRunnerWorker</A>
+<DD>construct method basically does all the testing of the selected tests.
+<DT><A HREF="./sbml/test/UpdateDownloader.html#construct()"><B>construct()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/UpdateDownloader.html" title="class in sbml.test">UpdateDownloader</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getIdentifier()"><B>getIdentifier()</B></A> -
-Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#containsComponent(java.lang.String)"><B>containsComponent(String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Returns a boolean value as to whether a test case contains a specified component
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#containsLevel(java.lang.String)"><B>containsLevel(String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Returns a boolean value as to whether a test case contains a specified level
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#containsTag(java.lang.String)"><B>containsTag(String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Returns a boolean value as to whether a test case contains a specified tag
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#containsTesttype(java.lang.String)"><B>containsTesttype(String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Returns a boolean value as to whether a test case contains the specified test type
+<DT><A HREF="./sbml/test/FailedTestCaseListModel.html#contentsChanged(javax.swing.event.ListDataEvent)"><B>contentsChanged(ListDataEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/FailedTestCaseListModel.html" title="class in sbml.test">FailedTestCaseListModel</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DT><A HREF="./sbml/test/PassedTestCaseListModel.html#contentsChanged(javax.swing.event.ListDataEvent)"><B>contentsChanged(ListDataEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/PassedTestCaseListModel.html" title="class in sbml.test">PassedTestCaseListModel</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getInputPath()"><B>getInputPath()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DT><A HREF="./sbml/test/SkippedTestCaseListModel.html#contentsChanged(javax.swing.event.ListDataEvent)"><B>contentsChanged(ListDataEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SkippedTestCaseListModel.html" title="class in sbml.test">SkippedTestCaseListModel</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getNext()"><B>getNext()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
-<DD>getNext
-<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getNext()"><B>getNext()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DT><A HREF="./sbml/test/TestCaseListModel.html#contentsChanged(javax.swing.event.ListDataEvent)"><B>contentsChanged(ListDataEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestCaseListModel.html" title="class in sbml.test">TestCaseListModel</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getNext()"><B>getNext()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DT><A HREF="./sbml/test/TestResultMap.html#contentsChanged(javax.swing.event.ListDataEvent)"><B>contentsChanged(ListDataEvent)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultMap.html" title="class in sbml.test">TestResultMap</A>
+<DD>contentsChanged - currently has no function
+<DT><A HREF="./sbml/test/TestRunnerView.html#currentvalues"><B>currentvalues</B></A> -
+Static variable in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getNext()"><B>getNext()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+</DL>
+<HR>
+<A NAME="_D_"><!-- --></A><H2>
+<B>D</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/SBMLTestCase.html#deleteDirectory(java.io.File)"><B>deleteDirectory(File)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Deletes a directory containing uploaded test cases.
+<DT><A HREF="./sbml/test/TestTabPane.html#disableReset()"><B>disableReset()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>disableReset disables the reset button
+<DT><A HREF="./sbml/test/TestRunnerView.html#disableResetButton()"><B>disableResetButton()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<DD>disableResetButton - disables the reset button
+<DT><A HREF="./sbml/test/TestTabPane.html#disableStart()"><B>disableStart()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>disableStart disables the start button
+<DT><A HREF="./sbml/test/TestRunnerView.html#disableStartButton()"><B>disableStartButton()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<DD>disableStartButton - disables the start button
+<DT><A HREF="./sbml/test/TestTabPane.html#disableStop()"><B>disableStop()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>disableStop disables the stop button
+<DT><A HREF="./sbml/test/TestRunnerView.html#disableStopButton()"><B>disableStopButton()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<DD>disableStopButton - disables the stop button
+<DT><A HREF="./sbml/test/TestRunnerView.html#displayWrapperError()"><B>displayWrapperError()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<DD>displayWrapperError - displays the wrapper error diaglog
+<DT><A HREF="./sbml/test/SBMLTestCase.html#duration"><B>duration</B></A> -
+Variable in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getNext()"><B>getNext()</B></A> -
-Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+</DL>
+<HR>
+<A NAME="_E_"><!-- --></A><H2>
+<B>E</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/TestTabPane.html#enableReset()"><B>enableReset()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>enableReset enables the reset button
+<DT><A HREF="./sbml/test/TestTabPane.html#enableStart()"><B>enableStart()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>enableStart enables the start button
+<DT><A HREF="./sbml/test/TestTabPane.html#enableStop()"><B>enableStop()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestTabPane.html" title="class in sbml.test">TestTabPane</A>
+<DD>enableStop enables the stop button
+</DL>
+<HR>
+<A NAME="_F_"><!-- --></A><H2>
+<B>F</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/FailedTestCaseListModel.html" title="class in sbml.test"><B>FailedTestCaseListModel</B></A> - Class in <A HREF="./sbml/test/package-summary.html">sbml.test</A><DD>This class provides a list model for the list of failed test cases.<DT><A HREF="./sbml/test/TestRunnerView.html#failedTestCaseListModel"><B>failedTestCaseListModel</B></A> -
+Static variable in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getNext()"><B>getNext()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DT><A HREF="./sbml/test/SwingWorker.html#finished()"><B>finished()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SwingWorker.html" title="class in sbml.test">SwingWorker</A>
+<DD>Called on the event dispatching thread (not on the worker thread)
+ after the <code>construct</code> method has returned.
+<DT><A HREF="./sbml/test/TestRunnerWorker.html#finished()"><B>finished()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerWorker.html" title="class in sbml.test">TestRunnerWorker</A>
<DD>
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getOutputPath()"><B>getOutputPath()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getPrevious()"><B>getPrevious()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
-<DD>getPrevious
-<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getPrevious()"><B>getPrevious()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getPrevious()"><B>getPrevious()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getPrevious()"><B>getPrevious()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getPrevious()"><B>getPrevious()</B></A> -
-Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getPrevious()"><B>getPrevious()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
-<DD>getQualifiedName
-<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
-Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
-<DD>
-<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#getSelections()"><B>getSelections()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
-<DD>getSelections gets the selection hashmap
-<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getWrapperPath()"><B>getWrapperPath()</B></A> -
-Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
-<DD>
</DL>
<HR>
+<A NAME="_G_"><!-- --></A><H2>
+<B>G</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/SwingWorker.html#get()"><B>get()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SwingWorker.html" title="class in sbml.test">SwingWorker</A>
+<DD>Return the value created by the <code>construct</code> method.
+<DT><A HREF="./sbml/test/TestConfiguration.html#get(java.lang.String)"><B>get(String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestConfiguration.html" title="class in sbml.test">TestConfiguration</A>
+<DD>get - gets a value from the selections hashmap
+<DT><A HREF="./sbml/test/SBMLTestCase.html#getAbs()"><B>getAbs()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Gets the Absolute allowable difference
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#getComponenttags()"><B>getComponenttags()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Gets the component tags of a test case
+<DT><A HREF="./sbml/test/SBMLTestCase.html#getControlResults(java.lang.String, java.lang.String)"><B>getControlResults(String, String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Gets the control results for a given test case.
+<DT><A HREF="./sbml/test/TestResultDetails.html#getCtags()"><B>getCtags()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultDetails.html" title="class in sbml.test">TestResultDetails</A>
+<DD>getCtags gets the component tags associated with the TestResultDetails oject
+<DT><A HREF="./sbml/test/TestResultDetails.html#getCtagsString()"><B>getCtagsString()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultDetails.html" title="class in sbml.test">TestResultDetails</A>
+<DD>getCtagsString gets the component tags in a string as opposed to a vector
+<DT><A HREF="./sbml/test/TestResultDetails.html#getDescription()"><B>getDescription()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultDetails.html" title="class in sbml.test">TestResultDetails</A>
+<DD>getDescription gets the description line of the TestResultDetails object
+<DT><A HREF="./sbml/test/SBMLTestCase.html#getDuration()"><B>getDuration()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Gets the duration of the test
+<DT><A HREF="./sbml/test/FailedTestCaseListModel.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/FailedTestCaseListModel.html" title="class in sbml.test">FailedTestCaseListModel</A>
+<DD>getElementAt - Returns the element at specified index.
+<DT><A HREF="./sbml/test/PassedTestCaseListModel.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/PassedTestCaseListModel.html" title="class in sbml.test">PassedTestCaseListModel</A>
+<DD>getElementAt returns the string value of the testname of the object at the specified index.
+<DT><A HREF="./sbml/test/SkippedTestCaseListModel.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SkippedTestCaseListModel.html" title="class in sbml.test">SkippedTestCaseListModel</A>
+<DD>getElementAt gets the test name of the test case in the list a the specified index
+<DT><A HREF="./sbml/test/TestCaseListModel.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestCaseListModel.html" title="class in sbml.test">TestCaseListModel</A>
+<DD>getElementAt - gets the testname of the case at the specified index
+<DT><A HREF="./sbml/test/TestResultDetails.html#getHtml()"><B>getHtml()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultDetails.html" title="class in sbml.test">TestResultDetails</A>
+<DD>getHtml gets the html file path of the TestResultDetails object
+<DT><A HREF="./sbml/test/SBMLTestCase.html#getHtmlFile(java.lang.String, java.lang.String)"><B>getHtmlFile(String, String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTestCase</A>
+<DD>Gets the html file path for a given test case
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#getLevels()"><B>getLevels()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Gets the SBML levels of a test case
+<DT><A HREF="./sbml/test/TestRunnerView.html#getLoggingInfo()"><B>getLoggingInfo()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestRunnerView.html" title="class in sbml.test">TestRunnerView</A>
+<DD>getLoggingInfo - gets the hashmap containing the logging info from the dialog
+<DT><A HREF="./sbml/test/SBMLTestSelection.html#getModelFile(java.lang.String, java.lang.String)"><B>getModelFile(String, String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestSelection.html" title="class in sbml.test">SBMLTestSelection</A>
+<DD>Gets the model file for a particular test case
+<DT><A HREF="./sbml/test/TestResultDetails.html#getPlot()"><B>getPlot()</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/TestResultDetails.html" title="class in sbml.test">TestResultDetails</A>
+<DD>getPlot gets the plot path of the TestResultDetails ojbect
+<DT><A HREF="./sbml/test/SBMLTestCase.html#getPlotFile(java.lang.String, java.lang.String)"><B>getPlotFile(String, String)</B></A> -
+Method in class sbml.test.<A HREF="./sbml/test/SBMLTestCase.html" title="class in sbml.test">SBMLTes...
[truncated message content] |
|
From: <sar...@us...> - 2008-07-29 14:15:13
|
Revision: 7782
http://sbml.svn.sourceforge.net/sbml/?rev=7782&view=rev
Author: sarahkeating
Date: 2008-07-29 14:15:10 +0000 (Tue, 29 Jul 2008)
Log Message:
-----------
added new validation rule 10219- additional file FunctionNoArgsMathCheck
Modified Paths:
--------------
trunk/libsbml/win32/MSVC7/libsbml.vcproj
trunk/libsbml/win32/MSVC7/libsbml_expat.vcproj
trunk/libsbml/win32/MSVC7/libsbml_xml.vcproj
trunk/libsbml/win32/MSVC8/libsbml.vcproj
trunk/libsbml/win32/MSVC8/libsbml_expat.vcproj
trunk/libsbml/win32/MSVC8/libsbml_xml.vcproj
Modified: trunk/libsbml/win32/MSVC7/libsbml.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC7/libsbml.vcproj 2008-07-29 14:14:05 UTC (rev 7781)
+++ trunk/libsbml/win32/MSVC7/libsbml.vcproj 2008-07-29 14:15:10 UTC (rev 7782)
@@ -249,6 +249,9 @@
RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.cpp">
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp">
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp">
</File>
<File
@@ -721,6 +724,9 @@
RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.h">
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h">
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h">
</File>
<File
Modified: trunk/libsbml/win32/MSVC7/libsbml_expat.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC7/libsbml_expat.vcproj 2008-07-29 14:14:05 UTC (rev 7781)
+++ trunk/libsbml/win32/MSVC7/libsbml_expat.vcproj 2008-07-29 14:15:10 UTC (rev 7782)
@@ -258,6 +258,9 @@
RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.cpp">
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp">
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp">
</File>
<File
@@ -727,6 +730,9 @@
RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.h">
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h">
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h">
</File>
<File
Modified: trunk/libsbml/win32/MSVC7/libsbml_xml.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC7/libsbml_xml.vcproj 2008-07-29 14:14:05 UTC (rev 7781)
+++ trunk/libsbml/win32/MSVC7/libsbml_xml.vcproj 2008-07-29 14:15:10 UTC (rev 7782)
@@ -249,6 +249,9 @@
RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.cpp">
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp">
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp">
</File>
<File
@@ -721,6 +724,9 @@
RelativePath="..\..\src\validator\constraints\FunctionDefinitionVars.h">
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h">
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h">
</File>
<File
Modified: trunk/libsbml/win32/MSVC8/libsbml.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC8/libsbml.vcproj 2008-07-29 14:14:05 UTC (rev 7781)
+++ trunk/libsbml/win32/MSVC8/libsbml.vcproj 2008-07-29 14:15:10 UTC (rev 7782)
@@ -371,6 +371,10 @@
>
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp">
+ >
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp"
>
</File>
@@ -967,6 +971,10 @@
>
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h">
+ >
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h"
>
</File>
Modified: trunk/libsbml/win32/MSVC8/libsbml_expat.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC8/libsbml_expat.vcproj 2008-07-29 14:14:05 UTC (rev 7781)
+++ trunk/libsbml/win32/MSVC8/libsbml_expat.vcproj 2008-07-29 14:15:10 UTC (rev 7782)
@@ -380,6 +380,10 @@
>
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp">
+ >
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp"
>
</File>
@@ -964,6 +968,10 @@
>
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h">
+ >
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h"
>
</File>
Modified: trunk/libsbml/win32/MSVC8/libsbml_xml.vcproj
===================================================================
--- trunk/libsbml/win32/MSVC8/libsbml_xml.vcproj 2008-07-29 14:14:05 UTC (rev 7781)
+++ trunk/libsbml/win32/MSVC8/libsbml_xml.vcproj 2008-07-29 14:15:10 UTC (rev 7782)
@@ -368,6 +368,10 @@
>
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.cpp">
+ >
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.cpp"
>
</File>
@@ -956,6 +960,10 @@
>
</File>
<File
+ RelativePath="..\..\src\validator\constraints\FunctionNoArgsMathCheck.h">
+ >
+ </File>
+ <File
RelativePath="..\..\src\validator\constraints\FunctionReferredToExists.h"
>
</File>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-29 14:14:11
|
Revision: 7781
http://sbml.svn.sourceforge.net/sbml/?rev=7781&view=rev
Author: sarahkeating
Date: 2008-07-29 14:14:05 +0000 (Tue, 29 Jul 2008)
Log Message:
-----------
added new validation rule 10219
Modified Paths:
--------------
trunk/libsbml/src/validator/constraints/Makefile.in
trunk/libsbml/src/validator/constraints/MathMLConsistencyConstraints.cpp
trunk/libsbml/src/validator/constraints/NumberArgsMathCheck.cpp
Added Paths:
-----------
trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.cpp
trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.h
Added: trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.cpp
===================================================================
--- trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.cpp (rev 0)
+++ trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.cpp 2008-07-29 14:14:05 UTC (rev 7781)
@@ -0,0 +1,163 @@
+/**
+ * @file FunctionNoArgsMathCheck.cpp
+ * @brief Ensures correct number of arguments to a function definition.
+ * @author Sarah Keating
+ *
+ * $Id: FunctionNoArgsMathCheck.cpp 7249 2008-06-26 22:48:40Z mhucka $
+ * $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.cpp $
+ */
+/* Copyright 2005 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. A copy of the license agreement is
+ * provided in the file named "LICENSE.txt" included with this software
+ * distribution. It is also available online at
+ * http://sbml.org/software/libsbml/license.html
+ *
+ * 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.
+ */
+
+#include <sbml/Model.h>
+#include <sbml/Compartment.h>
+#include <sbml/Species.h>
+#include <sbml/Parameter.h>
+#include <sbml/UnitDefinition.h>
+#include <sbml/Event.h>
+#include <sbml/Reaction.h>
+#include <sbml/EventAssignment.h>
+#include <sbml/SpeciesReference.h>
+#include <sbml/Rule.h>
+#include <sbml/math/FormulaFormatter.h>
+
+#include <sbml/units/UnitFormulaFormatter.h>
+
+#include "FunctionNoArgsMathCheck.h"
+
+static const char* PREAMBLE =
+ "The number of arguments used in a call to a function defined by a "
+ "<functionDefinition> must equal the number of arguments accepted by "
+ "that function, or in other words, the number of <bvar> elements "
+ "inside the <lambda> element of the function definition. "
+ "(References: L2V4 Section 4.3.4.)";
+
+/** @cond doxygen-ignored */
+
+using namespace std;
+
+/** @endcond doxygen-ignored */
+
+
+/**
+ * Creates a new Constraint with the given id.
+ */
+FunctionNoArgsMathCheck::FunctionNoArgsMathCheck (unsigned int id, Validator& v) : MathMLBase(id, v)
+{
+}
+
+
+/**
+ * Destroys this Constraint.
+ */
+FunctionNoArgsMathCheck::~FunctionNoArgsMathCheck ()
+{
+}
+
+
+/**
+ * @return the preamble to use when logging constraint violations.
+ */
+const char*
+FunctionNoArgsMathCheck::getPreamble ()
+{
+ return PREAMBLE;
+}
+
+
+/**
+ * Checks the MathML of the ASTnode
+ * is appropriate for the function being performed
+ *
+ * If an inconsistency is found, an error message is logged.
+ */
+void
+FunctionNoArgsMathCheck::checkMath (const Model& m, const ASTNode& node, const SBase & sb)
+{
+ ASTNodeType_t type = node.getType();
+
+ switch (type)
+ {
+ case AST_FUNCTION:
+
+ checkNumArgs(m, node, sb);
+ break;
+
+ default:
+
+ checkChildren(m, node, sb);
+ break;
+
+ }
+}
+
+
+/**
+ * Checks that the functionDefinition referred to by a <ci> element
+ * has the appropriate number of arguments.
+ *
+ * If not, an error message is logged.
+ */
+void
+FunctionNoArgsMathCheck::checkNumArgs (const Model& m, const ASTNode& node,
+ const SBase & sb)
+{
+ /* this rule was only introduced level 2 version 4 */
+ if (m.getLevel() == 2 && m.getVersion() == 4)
+ {
+ if (m.getFunctionDefinition(node.getName()))
+ {
+ /* functiondefinition math */
+ const ASTNode * fdMath = m.getFunctionDefinition(node.getName())->getMath();
+ if (fdMath != NULL)
+ {
+ /* We have a definition for this function. Does the defined number
+ of arguments equal the number used here? */
+
+ if (node.getNumChildren() + 1 != fdMath->getNumChildren())
+ {
+ logMathConflict(node, sb);
+ }
+ }
+
+ }
+ }
+}
+
+
+/**
+ * @return the error message to use when logging constraint violations.
+ * This method is called by logFailure.
+ *
+ * Returns a message that the given id and its corresponding object are
+ * in conflict with an object previously defined.
+ */
+const string
+FunctionNoArgsMathCheck::getMessage (const ASTNode& node, const SBase& object)
+{
+
+ ostringstream msg;
+
+ //msg << getPreamble();
+ char * formula = SBML_formulaToString(&node);
+ msg << "\nThe formula '" << formula;
+ msg << "' in the " << getFieldname() << " element of the ";
+ msg << getTypename(object);
+ msg << " uses the function '" << node.getName() << "' which requires ";
+ msg << "a different number of arguments than the number supplied.";
+ safe_free(formula);
+
+ return msg.str();
+}
Added: trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.h
===================================================================
--- trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.h (rev 0)
+++ trunk/libsbml/src/validator/constraints/FunctionNoArgsMathCheck.h 2008-07-29 14:14:05 UTC (rev 7781)
@@ -0,0 +1,99 @@
+/**
+ * @file FunctionNoArgsMathCheck.h
+ * @brief Ensures correct number of arguments to a function definition.
+ * @author Sarah Keating
+ *
+ * $Id: $
+ * $HeadURL: $
+ */
+/* Copyright 2005 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. A copy of the license agreement is
+ * provided in the file named "LICENSE.txt" included with this software
+ * distribution. It is also available online at
+ * http://sbml.org/software/libsbml/license.html
+ *
+ * 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.
+ */
+
+
+#ifndef FunctionNoArgsMathCheck_h
+#define FunctionNoArgsMathCheck_h
+
+
+#ifdef __cplusplus
+
+
+#include <string>
+#include <sstream>
+#include <math.h>
+
+#include <sbml/validator/VConstraint.h>
+
+#include "MathMLBase.h"
+
+
+class ASTNode;
+
+
+class FunctionNoArgsMathCheck: public MathMLBase
+{
+public:
+
+ /**
+ * Creates a new Constraint with the given id.
+ */
+ FunctionNoArgsMathCheck (unsigned int id, Validator& v);
+
+ /**
+ * Destroys this Constraint.
+ */
+ virtual ~FunctionNoArgsMathCheck ();
+
+
+protected:
+
+ /**
+ * Checks the MathML of the ASTnode
+ * is appropriate for the function being performed
+ *
+ * If an inconsistency is found, an error message is logged.
+ */
+ virtual void checkMath (const Model& m, const ASTNode& node, const SBase & sb);
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+ * preamble will be prepended to each log message. If not overriden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+
+ /**
+ * Checks that the functionDefinition referred to by a <ci> element
+ * has the appropriate number of arguments.
+ *
+ * If not, an error message is logged.
+ */
+ void checkNumArgs (const Model& m, const ASTNode& node, const SBase & sb);
+
+ /**
+ * @return the error message to use when logging constraint violations.
+ * This method is called by logFailure.
+ *
+ * If at all possible please use getPreamble() and getFieldname() when
+ * constructing error messages. This will help to make your constraint
+ * easily customizable.
+ */
+ virtual const std::string
+ getMessage (const ASTNode& node, const SBase& object);
+
+};
+
+
+#endif /* __cplusplus */
+#endif /* FunctionNoArgsMathCheck_h */
Modified: trunk/libsbml/src/validator/constraints/Makefile.in
===================================================================
--- trunk/libsbml/src/validator/constraints/Makefile.in 2008-07-29 14:12:56 UTC (rev 7780)
+++ trunk/libsbml/src/validator/constraints/Makefile.in 2008-07-29 14:14:05 UTC (rev 7781)
@@ -80,9 +80,10 @@
CompartmentOutsideCycles.cpp \
ConsistencyConstraints.cpp \
EqualityArgsMathCheck.cpp \
- ExponentUnitsCheck.cpp \
+ ExponentUnitsCheck.cpp \
FunctionApplyMathCheck.cpp \
FunctionDefinitionVars.cpp \
+ FunctionNoArgsMathCheck.cpp \
FunctionReferredToExists.cpp \
IdBase.cpp \
IdentifierConsistencyConstraints.cpp \
@@ -145,6 +146,7 @@
ExponentUnitsCheck.h \
FunctionApplyMathCheck.h \
FunctionDefinitionVars.h \
+ FunctionNoArgsMathCheck.h \
FunctionReferredToExists.h \
KineticLawVars.h \
LambdaMathCheck.h \
Modified: trunk/libsbml/src/validator/constraints/MathMLConsistencyConstraints.cpp
===================================================================
--- trunk/libsbml/src/validator/constraints/MathMLConsistencyConstraints.cpp 2008-07-29 14:12:56 UTC (rev 7780)
+++ trunk/libsbml/src/validator/constraints/MathMLConsistencyConstraints.cpp 2008-07-29 14:14:05 UTC (rev 7781)
@@ -38,6 +38,7 @@
#include "NumericReturnMathCheck.h"
#include "LocalParameterMathCheck.h"
#include "NumberArgsMathCheck.h"
+#include "FunctionNoArgsMathCheck.h"
#endif
@@ -79,5 +80,6 @@
EXTERN_CONSTRAINT( 10216, LocalParameterMathCheck)
EXTERN_CONSTRAINT( 10217, NumericReturnMathCheck )
EXTERN_CONSTRAINT( 10218, NumberArgsMathCheck )
+EXTERN_CONSTRAINT( 10219, FunctionNoArgsMathCheck )
Modified: trunk/libsbml/src/validator/constraints/NumberArgsMathCheck.cpp
===================================================================
--- trunk/libsbml/src/validator/constraints/NumberArgsMathCheck.cpp 2008-07-29 14:12:56 UTC (rev 7780)
+++ trunk/libsbml/src/validator/constraints/NumberArgsMathCheck.cpp 2008-07-29 14:14:05 UTC (rev 7781)
@@ -154,23 +154,29 @@
checkSpecialCases(m, node, sb);
break;
+
case AST_FUNCTION:
+ /* the case for a functionDefinition has its own rule
+ from l2v4*/
- if (m.getFunctionDefinition(node.getName()))
+ if (!(m.getLevel() == 2 && m.getVersion() == 4))
{
- /* functiondefinition math */
- const ASTNode * fdMath = m.getFunctionDefinition(node.getName())->getMath();
- if (fdMath != NULL)
+ if (m.getFunctionDefinition(node.getName()))
{
- /* We have a definition for this function. Does the defined number
- of arguments equal the number used here? */
+ /* functiondefinition math */
+ const ASTNode * fdMath = m.getFunctionDefinition(node.getName())->getMath();
+ if (fdMath != NULL)
+ {
+ /* We have a definition for this function. Does the defined number
+ of arguments equal the number used here? */
- if (node.getNumChildren() + 1 != fdMath->getNumChildren())
- {
- logMathConflict(node, sb);
- }
+ if (node.getNumChildren() + 1 != fdMath->getNumChildren())
+ {
+ logMathConflict(node, sb);
+ }
+ }
+
}
-
}
break;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-29 14:13:03
|
Revision: 7780
http://sbml.svn.sourceforge.net/sbml/?rev=7780&view=rev
Author: sarahkeating
Date: 2008-07-29 14:12:56 +0000 (Tue, 29 Jul 2008)
Log Message:
-----------
added new validation rule 10219
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBMLError.h
trunk/libsbml/src/sbml/SBMLErrorTable.h
Modified: trunk/libsbml/src/sbml/SBMLError.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLError.h 2008-07-29 05:38:58 UTC (rev 7779)
+++ trunk/libsbml/src/sbml/SBMLError.h 2008-07-29 14:12:56 UTC (rev 7780)
@@ -115,6 +115,7 @@
* <tr><td><em>KineticLawParametersAreLocalOnly</em></td><td>SBML L2v3 validation rule #10216</td>
* <tr><td><em>MathResultMustBeNumeric</em></td><td>SBML L2v3 validation rule #10217</td>
* <tr><td><em>OpsNeedCorrectNumberOfArgs</em></td><td>SBML L2v3 validation rule #10218</td>
+ * <tr><td><em>InvalidNoArgsPassedToFunctionDef</em></td><td>SBML L2v4 validation rule #10219</td>
* <tr><td><em>DuplicateComponentId</em></td><td>SBML L2v3 validation rule #10301</td>
* <tr><td><em>DuplicateUnitDefinitionId</em></td><td>SBML L2v3 validation rule #10302</td>
* <tr><td><em>DuplicateLocalParameterId</em></td><td>SBML L2v3 validation rule #10303</td>
@@ -454,6 +455,7 @@
, KineticLawParametersAreLocalOnly = 10216 /*!< SBML L2v3 validation rule #10216 */
, MathResultMustBeNumeric = 10217 /*!< SBML L2v3 validation rule #10217 */
, OpsNeedCorrectNumberOfArgs = 10218 /*!< SBML L2v3 validation rule #10218 */
+ , InvalidNoArgsPassedToFunctionDef = 10219 /*!< SBML L2v4 validation rule #10219 */
, DuplicateComponentId = 10301 /*!< SBML L2v3 validation rule #10301 */
, DuplicateUnitDefinitionId = 10302 /*!< SBML L2v3 validation rule #10302 */
, DuplicateLocalParameterId = 10303 /*!< SBML L2v3 validation rule #10303 */
Modified: trunk/libsbml/src/sbml/SBMLErrorTable.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorTable.h 2008-07-29 05:38:58 UTC (rev 7779)
+++ trunk/libsbml/src/sbml/SBMLErrorTable.h 2008-07-29 14:12:56 UTC (rev 7780)
@@ -419,6 +419,23 @@
"SBML 3.5.1; L2V3 Section 3.4.1.)"
},
+ //10219
+ {
+ InvalidNoArgsPassedToFunctionDef,
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_NOT_APPLICABLE,
+ LIBSBML_SEV_NOT_APPLICABLE,
+ LIBSBML_SEV_NOT_APPLICABLE,
+ LIBSBML_SEV_NOT_APPLICABLE,
+ LIBSBML_SEV_NOT_APPLICABLE,
+ LIBSBML_SEV_ERROR,
+ "The number of arguments used in a call to a function defined by a "
+ "<functionDefinition> must equal the number of arguments accepted by "
+ "that function, or in other words, the number of <bvar> elements "
+ "inside the <lambda> element of the function definition. "
+ "(References: L2V4 Section 4.3.4.)"
+ },
+
//10301
{
DuplicateComponentId,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-29 05:39:02
|
Revision: 7779
http://sbml.svn.sourceforge.net/sbml/?rev=7779&view=rev
Author: kbegley
Date: 2008-07-29 05:38:58 +0000 (Tue, 29 Jul 2008)
Log Message:
-----------
updated stand alone jar file
Modified Paths:
--------------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/ListViewPane.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/MapViewPane.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/PassedTestCaseListModel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/SBMLTestCase.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/SBMLTestRunnerApp.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/SBMLTestSelection.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/SkippedTestCaseListModel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestCaseListModel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestCaseUpdater.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestConfiguration.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestResultDetails.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestResultMap$FieldListener.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestResultMap.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$1.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$aboutActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$checkUpdatesActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$helpActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$newActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView$quitActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerView.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerWorker$1.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestRunnerWorker.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane$openBrowserActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane$resetActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane$settingsActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane$startActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane$stopActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/TestTabPane.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/ComponentTagsSelectorPanel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/CreateTestWizard$1.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/CreateTestWizard$cancelActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/CreateTestWizard$finishActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/CreateTestWizard$nextActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/CreateTestWizard$previousActionClass.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/CreateTestWizard.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/LevelSelectorPanel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/TestTagSelectionPanel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/TestTypeSelectorPanel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/WizardPanel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/build/classes/sbml/test/Wizard/WrapperConfigurationPanel.class
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/dist/SBMLTestSuite.jar
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite.jar
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-29 05:34:30
|
Revision: 7778
http://sbml.svn.sourceforge.net/sbml/?rev=7778&view=rev
Author: kbegley
Date: 2008-07-29 05:34:26 +0000 (Tue, 29 Jul 2008)
Log Message:
-----------
updated stand alone app
Modified Paths:
--------------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/FailedTestCaseListModel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/HelpDialog.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/ListViewPane.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/MapViewPane.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PassedTestCaseListModel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PreferencesDialog.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestCase.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestRunnerApp.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestSelection.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SkippedTestCaseListModel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseListModel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseUpdater.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestConfiguration.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestResultDetails.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestResultMap.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestRunnerView.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestRunnerWorker.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestTabPane.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/ComponentTagsSelectorPanel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/CreateTestWizard.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/LevelSelectorPanel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/TestTagSelectionPanel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/TestTypeSelectorPanel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/WizardPanel.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/WizardPanelInterface.java
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/Wizard/WrapperConfigurationPanel.java
Added Paths:
-----------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/TestCaseUpdater.form
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/UpdateDownloader.java
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/FailedTestCaseListModel.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/FailedTestCaseListModel.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/FailedTestCaseListModel.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -36,7 +36,7 @@
* list view of the SBML Test Suite.
*
* @author Kimberly Begley
- * @version 1.0
+ * @version 2.0
*/
public class FailedTestCaseListModel extends AbstractListModel implements ListDataListener{
@@ -69,9 +69,9 @@
}
/**
- *
- * @param index
- * @return
+ * remove - Function to remove a list item.
+ * @param index Index of list item to be removed
+ * @return nothing
*/
public TestResultDetails remove(int index) {
TestResultDetails o = failedData.remove(index);
@@ -80,7 +80,7 @@
}
/**
- *
+ * removeAllElements - Function to remove all items in a list.
*/
public void removeAllElements() {
if (getSize() > 0 ) {
@@ -90,24 +90,24 @@
}
}
/**
- *
- * @return
+ * getSize - Get the size of the list.
+ * @return - Returns an integer value of the size of the list.
*/
public int getSize() {
return failedData.size();
}
/**
- *
- * @param index
- * @return
+ * getElementAt - Returns the element at specified index.
+ * @param index Index of element to return
+ * @return returns the String representation of the test name of the elemnent requested
*/
public Object getElementAt(int index) {
return (failedData.get(index)).getTestname();
}
/**
- *
- * @param index
- * @return
+ * getRawElementAt - Gets the TestResultDetails object at the specified index.
+ * @param index Index of the element to return.
+ * @return returns a TestResultDetails object.
*/
public TestResultDetails getRawElementAt(int index) {
return failedData.get(index);
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/HelpDialog.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/HelpDialog.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/HelpDialog.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -41,7 +41,18 @@
public class HelpDialog extends JDialog implements ActionListener{
+
+/**
+ * This class provides help dialog for the Standalone SBML Test Suite.
+ *
+ * @author Kimberly Begley
+ * @version 2.0
+ */
+ /**
+ * HelpDialog has one constructor to create and fill the content of the frame that contains the help dialog.
+ * @param parent the parent JFrame of the calling class.
+ */
public HelpDialog(JFrame parent) {
super(parent, "Help", false);
setVisible(true);
@@ -107,8 +118,11 @@
setLocationRelativeTo(getParent());
backButton.addActionListener(this);
- }
-*/
+ } */
+/**
+ * actionPerformed Listener that listens for the close action of the help dialog
+ * @param e the actionEvent called when the close button is selected.
+ */
public void actionPerformed (ActionEvent e) {
// this.hide();
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/ListViewPane.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/ListViewPane.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/ListViewPane.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -1,4 +1,3 @@
-
package sbml.test;
// @file ListViewPane.java
@@ -24,7 +23,6 @@
//------------------------------------------------------------------------- -->
// Creates the list view pane for the main Stand alone application view.
//
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
@@ -35,68 +33,79 @@
import java.io.FileNotFoundException;
import java.io.IOException;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
-import javax.swing.ImageIcon;
+import javax.swing.JEditorPane;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
-import javax.swing.JTextPane;
import javax.swing.ListSelectionModel;
import javax.swing.border.Border;
import javax.swing.border.LineBorder;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
-
+/**
+ * This class provides the list view pane of the stand alone SBML Test Suite. It is the default view of the application and contains
+ * a selectable listing of passed, failed and skipped tests with case lists on the left hand side of the pane and a details panel to
+ * be filled in when a user selects a particular case from the displayed list.
+ * @author Kimberly Begley
+ * @version 2.0
+ */
public class ListViewPane extends JPanel implements ListSelectionListener, ItemListener {
- private JPanel bottomLeftPanel, selectPanel, detailPane, findPanel, detailContainer;
+ /**
+ *
+ */
+ private JPanel bottomLeftPanel, selectPanel, detailPane, findPanel, detailContainer;
private String[] panelTitles = {"Listing selection", "Details", "Jump to test case result"};
-
PassedTestCaseListModel passedList;
FailedTestCaseListModel failedList;
SkippedTestCaseListModel skippedList;
-
JScrollPane scrollList, scrollPane;
- JTextPane summaryLabel;
-
+ // JTextPane summaryEditorPane;
+ JEditorPane summaryEditorPane;
JTextField searchField;
JList testList, passList, failList, skipList;
JLabel shortDetailLabel, plotLabel, synopsisLabel;
JRadioButton passedRadioButton, failedRadioButton, skippedRadioButton;
+ /**
+ * ListViewPane has one constructor that initializes the components of the panel.
+ */
public ListViewPane() {
super();
initComponents();
}
+ /**
+ * initComponents initializes the viewable panel for the list view tab.
+ */
private void initComponents() {
setOpaque(false);
selectPanel = new JPanel();
- selectPanel.setLayout(new FlowLayout(FlowLayout.CENTER,20,0));
+ selectPanel.setLayout(new FlowLayout(FlowLayout.CENTER, 20, 0));
bottomLeftPanel = new JPanel();
findPanel = new JPanel();
-
-
+
+
+ // detailPane = new JPanel(new BorderLayout(10, 10));
detailPane = new JPanel();
+ detailPane.setLayout(new BoxLayout(detailPane, BoxLayout.PAGE_AXIS));
detailContainer = new JPanel(new BorderLayout());
-
- scrollPane = new JScrollPane(detailPane);
- scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
- scrollPane.getViewport().setViewPosition(new java.awt.Point(0,0));
+
+
this.setLayout(new BorderLayout(7, 7));
-
- detailContainer.add(scrollPane, BorderLayout.CENTER);
+
bottomLeftPanel.setLayout(new BorderLayout(7, 7));
this.add(bottomLeftPanel, BorderLayout.CENTER);
bottomLeftPanel.add(selectPanel, BorderLayout.PAGE_START);
- // bottomLeftPanel.add(scrollPane, BorderLayout.CENTER);
+ // bottomLeftPanel.add(scrollPane, BorderLayout.CENTER);
bottomLeftPanel.add(detailContainer, BorderLayout.CENTER);
this.add(findPanel, BorderLayout.LINE_START);
@@ -104,13 +113,13 @@
this.setOpaque(false);
findPanel.setLayout(new BorderLayout(5, 10));
-
+
passedList = TestRunnerView.passedTestCaseListModel;
failedList = TestRunnerView.failedTestCaseListModel;
skippedList = TestRunnerView.skippedTestCaseListModel;
-
-
-
+
+
+
passList = new JList(passedList);
passList.addListSelectionListener(this);
passList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
@@ -121,26 +130,39 @@
scrollList.setPreferredSize(new Dimension(150, 80));
findPanel.add(scrollList, BorderLayout.CENTER);
- // findPanel.add(new JLabel("<html>Jump to test case result</html>"), BorderLayout.PAGE_START);
+ // findPanel.add(new JLabel("<html>Jump to test case result</html>"), BorderLayout.PAGE_START);
shortDetailLabel = new JLabel("No dataset selected");
-
-
+
+
detailPane.setLayout(new BorderLayout(10, 10));
plotLabel = new JLabel("");
synopsisLabel = new JLabel("");
-
- summaryLabel = new JTextPane();
- summaryLabel.setPreferredSize(new Dimension(525,600));
-
+
+ summaryEditorPane = new JEditorPane();
+ summaryEditorPane.setEditable(false);
+ // summaryEditorPane.setPreferredSize(new Dimension(525,600));
+
//detailPane.add(sdlPanel,BorderLayout.PAGE_START);
detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
//detailPane.add(synopsisLabel, BorderLayout.PAGE_END);
detailPane.add(plotLabel, BorderLayout.WEST);
- detailPane.add(summaryLabel, BorderLayout.PAGE_END);
+ // detailPane.add(summaryEditorPane, BorderLayout.PAGE_END);
detailPane.setBackground(Color.white);
-
+ summaryEditorPane.setContentType("text/html");
+ summaryEditorPane.setText("<html>No dataset selected</html>");
+
+
+ scrollPane = new JScrollPane(summaryEditorPane);
+ scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+ scrollPane.getViewport().setViewPosition(new java.awt.Point(0, 0));
+ detailContainer.add(scrollPane, BorderLayout.CENTER);
+
+
+ // summaryEditorPane.setLineWrap(true);
+
JPanel[] namedPanel = new JPanel[3];
namedPanel[0] = selectPanel;
namedPanel[1] = detailContainer;
@@ -163,12 +185,12 @@
passedRadioButton.setOpaque(false);
failedRadioButton.setOpaque(false);
skippedRadioButton.setOpaque(false);
-
- // RadioListener radioListener = new RadioListener();
+
+ // RadioListener radioListener = new RadioListener();
failedRadioButton.addItemListener(this);
passedRadioButton.addItemListener(this);
skippedRadioButton.addItemListener(this);
-
+
listingButtonGroup.add(passedRadioButton);
listingButtonGroup.add(failedRadioButton);
listingButtonGroup.add(skippedRadioButton);
@@ -176,142 +198,167 @@
selectPanel.add(passedRadioButton);
selectPanel.add(failedRadioButton);
selectPanel.add(skippedRadioButton);
-
+
}
+ /**
+ * valueChanged records the ListSelectionEvent that occurs when the user selects a test case from selection list.
+ * @param e
+ */
public void valueChanged(ListSelectionEvent e) {
- if(e.getValueIsAdjusting() == false) {
+ if (e.getValueIsAdjusting() == false) {
JList list = (JList) e.getSource();
int index = list.getSelectedIndex();
updateDetails(index, list);
}
}
- public void updateDetails(int index, JList list){
- detailPane.remove(shortDetailLabel);
- detailPane.remove(plotLabel);
- detailPane.remove(summaryLabel);
- //detailPane.remove(synopsisLabel);
- String html_content = "";
- String plotpath = "";
- String description_path = "";
-
-
- if(list == passList){
- shortDetailLabel = new JLabel("<html><p>Test Case " + passedList.getElementAt(index) + "</p><p>Passed!</p></html>");
- detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
- String synopsis = passedList.getRawElementAt(index).getDescription();
- synopsisLabel = new JLabel(synopsis);
+
+ /**
+ * updateDetails updates the list in the selection panel to reflect the list selected in the list, called by valueChanged.
+ * @param index The index of the list of the selected item.
+ * @param list The name of the list in the list selections - ie passed, failed or skipped.
+ */
+ public void updateDetails(int index, JList list) {
+
+ String html_content = "";
+ String plotpath = "";
+ String description_path = "";
+
+ StringBuffer buffer = new StringBuffer();
+
+ if (list == passList) {
+ // shortDetailLabel.setText("<html><p>Test Case " + passedList.getElementAt(index) + "</p><p>Passed!</p></html>");
+ buffer.append("<p><b>Test Case</b> " + passedList.getElementAt(index) + "</p><p>Passed!</p>");
+ // detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
+ String synopsis = passedList.getRawElementAt(index).getDescription();
+ synopsisLabel.setText(synopsis);
plotpath = passedList.getRawElementAt(index).getPlot();
description_path = passedList.getRawElementAt(index).getHtml();
-
- }
- else if(list == failList){
- shortDetailLabel = new JLabel("<html><p>Test Case " + failedList.getElementAt(index) + "</p><p>Failed at " + failedList.getRawElementAt(index).getResult() + " points</p></html>");
- detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
- String synopsis = failedList.getRawElementAt(index).getDescription();
- synopsisLabel = new JLabel(synopsis);
+
+ } else if (list == failList) {
+ // shortDetailLabel.setText("<html><p>Test Case " + failedList.getElementAt(index) + "</p><p>Failed at " + failedList.getRawElementAt(index).getResult() + " points</p></html>");
+ buffer.append("<p>Test Case " + failedList.getElementAt(index) + "</p><p>Failed at " + failedList.getRawElementAt(index).getResult() + " points</p>");
+ // detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
+ String synopsis = failedList.getRawElementAt(index).getDescription();
+ synopsisLabel.setText(synopsis);
plotpath = failedList.getRawElementAt(index).getPlot();
description_path = failedList.getRawElementAt(index).getHtml();
-
- }
- else if(list == skipList){
- shortDetailLabel = new JLabel("<html><p>Test Case " + skippedList.getRawElementAt(index).getTestname() + " </p><p>Skipped: " + skippedList.getRawElementAt(index).getWarnings() + "</p></html>");
- detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
- String synopsis = skippedList.getRawElementAt(index).getDescription();
- synopsisLabel = new JLabel(synopsis);
+
+ } else if (list == skipList) {
+ // shortDetailLabel.setText("<html><p>Test Case " + skippedList.getRawElementAt(index).getTestname() + " </p><p>Skipped: " + skippedList.getRawElementAt(index).getWarnings() + "</p></html>");
+ buffer.append("<p>Test Case " + skippedList.getRawElementAt(index).getTestname() + " </p><p>Skipped: " + skippedList.getRawElementAt(index).getWarnings() + "</p>");
+
+ // detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
+ String synopsis = skippedList.getRawElementAt(index).getDescription();
+ synopsisLabel.setText(synopsis);
plotpath = skippedList.getRawElementAt(index).getPlot();
description_path = skippedList.getRawElementAt(index).getHtml();
-
- }
-
+
+ }
+
try {
FileInputStream fis = new FileInputStream(description_path);
int x = fis.available();
byte b[] = new byte[x];
fis.read(b);
html_content = new String(b);
-
+
} catch (FileNotFoundException e) {
System.out.println("didn't find the html file");
} catch (IOException e) {
System.out.println("caught an io exception opening html file");
}
- summaryLabel.setContentType("text/html");
- summaryLabel.setText("<html>" + html_content + "</html>");
-
- plotLabel = new JLabel(new ImageIcon(plotpath));
- detailPane.add(summaryLabel, BorderLayout.PAGE_END);
- // detailPane.add(synopsisLabel, BorderLayout.PAGE_END);
- detailPane.add(plotLabel, BorderLayout.WEST);
- scrollPane.getViewport().setViewPosition(new java.awt.Point(0,0));
-
- }
- public void itemStateChanged(ItemEvent e) {
- //throw new UnsupportedOperationException("Not supported yet.");
- int state = e.getStateChange();
- if(state == ItemEvent.DESELECTED){
- if(e.getSource() == passedRadioButton){
- passList.removeListSelectionListener(this);
- }
- if(e.getSource() == failedRadioButton){
- failList.removeListSelectionListener(this);
- }
- if(e.getSource() == skippedRadioButton){
- skipList.removeListSelectionListener(this);
- }
- }
-
- if(state == ItemEvent.SELECTED) {
- if(e.getSource() == failedRadioButton) {
-
- findPanel.remove(scrollList);
- failList = new JList(failedList);
- failList.addListSelectionListener(this);
- failList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- failList.setLayoutOrientation(JList.VERTICAL);
+ buffer.append("<br><p><img src=\"file://" + convertPathToHTML(plotpath) + "\"></img></p><br>");
+ buffer.append(html_content);
+ summaryEditorPane.setText("<html>" + buffer.toString() + "</html>");
- scrollList = new JScrollPane(failList, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollList.setPreferredSize(new Dimension(150, 80));
- findPanel.add(scrollList, BorderLayout.CENTER);
-
- }
- if(e.getSource() == passedRadioButton){
-
- findPanel.remove(scrollList);
- passList = new JList(passedList);
- passList.addListSelectionListener(this);
- passList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- passList.setLayoutOrientation(JList.VERTICAL);
+ summaryEditorPane.setCaretPosition(0);
+ }
- scrollList = new JScrollPane(passList, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollList.setPreferredSize(new Dimension(150, 80));
+ /**
+ * itemStateChanged records the ItemEvent triggered by a change in the radio button selection list.
+ * @param e The event object containing details of the change.
+ */
+ private String convertPathToHTML(String path) {
+ if ((System.getProperty("os.name").toLowerCase().startsWith("windows"))) {
+ StringBuffer newpath = new StringBuffer("/");
+ newpath.append(path.replaceAll("\\\\", "/").replaceAll(" ", "%20"));
- findPanel.add(scrollList, BorderLayout.CENTER);
-
+ return newpath.toString();
+ } else {
+ return path.replaceAll(" ", "%20");
}
- if(e.getSource() == skippedRadioButton){
-
- findPanel.remove(scrollList);
- skipList = new JList(skippedList);
- skipList.addListSelectionListener(this);
- skipList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- skipList.setLayoutOrientation(JList.VERTICAL);
+ }
+ public void itemStateChanged(ItemEvent e) {
- scrollList = new JScrollPane(skipList, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollList.setPreferredSize(new Dimension(150, 80));
+ int state = e.getStateChange();
+ if (state == ItemEvent.DESELECTED) {
+ if (e.getSource() == passedRadioButton) {
+ passList.removeListSelectionListener(this);
+ }
+ if (e.getSource() == failedRadioButton) {
+ failList.removeListSelectionListener(this);
+ }
+ if (e.getSource() == skippedRadioButton) {
+ skipList.removeListSelectionListener(this);
+ }
+ }
- findPanel.add(scrollList, BorderLayout.CENTER);
-
-
+ if (state == ItemEvent.SELECTED) {
+ if (e.getSource() == failedRadioButton) {
+
+ findPanel.remove(scrollList);
+ failList = new JList(failedList);
+ failList.addListSelectionListener(this);
+ failList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ failList.setLayoutOrientation(JList.VERTICAL);
+
+ scrollList = new JScrollPane(failList, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollList.setPreferredSize(new Dimension(150, 80));
+
+ findPanel.add(scrollList, BorderLayout.CENTER);
+
+ }
+ if (e.getSource() == passedRadioButton) {
+
+ findPanel.remove(scrollList);
+ passList = new JList(passedList);
+ passList.addListSelectionListener(this);
+ passList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ passList.setLayoutOrientation(JList.VERTICAL);
+
+
+ scrollList = new JScrollPane(passList, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollList.setPreferredSize(new Dimension(150, 80));
+
+ findPanel.add(scrollList, BorderLayout.CENTER);
+
+ }
+ if (e.getSource() == skippedRadioButton) {
+
+ findPanel.remove(scrollList);
+ skipList = new JList(skippedList);
+ skipList.addListSelectionListener(this);
+ skipList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ skipList.setLayoutOrientation(JList.VERTICAL);
+
+
+ scrollList = new JScrollPane(skipList, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollList.setPreferredSize(new Dimension(150, 80));
+
+ findPanel.add(scrollList, BorderLayout.CENTER);
+
+
+ }
+
+
}
-
-
}
-}}
+}
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/MapViewPane.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/MapViewPane.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/MapViewPane.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -1,4 +1,3 @@
-
package sbml.test;
// @file MapViewPane.java
@@ -24,71 +23,73 @@
//------------------------------------------------------------------------- -->
// Creates the map view for the main page of the SBML stand alone application.
//
-
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Dimension;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import javax.swing.BorderFactory;
-import javax.swing.ImageIcon;
+import javax.swing.JEditorPane;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
-import javax.swing.JTextPane;
import javax.swing.border.Border;
import javax.swing.border.LineBorder;
-
+/**
+ * This class provides the map view pane of the stand alone SBML Test Suite. It is selected via tab in the default view of the application and contains
+ * a colour coded map of passed failed and skipped test cases whose details can be viewed by mouse clicking on the icons.
+ *
+ * @author Kimberly Begley
+ * @version 2.0
+ */
public class MapViewPane extends JPanel implements ItemListener {
- private JPanel mainPanel, bottomLeftPanel, testResultMapPanel, detailPane, upperFindPanel, detailContainer;
+ private JPanel mainPanel, bottomLeftPanel, testResultMapPanel, detailPane, upperFindPanel, detailContainer;
private String[] panelTitles = {"Test result map", "Details", "Find test case result"};
TestCaseListModel testCaseListModel;
-
JTextField searchField;
JList testList;
JLabel shortDetailLabel, plotLabel, synopsisLabel;
-
- JTextPane summaryLabel;
+ JEditorPane summaryEditorPane;
TestResultMap resultMap;
-
JScrollPane scrollPane;
+ /**
+ * MapViewPane contains one constructor that calls the initComponents method.
+ */
public MapViewPane() {
initComponents();
}
+ /**
+ * initComponents initializes components for the map view.
+ */
private void initComponents() {
mainPanel = this;
testResultMapPanel = new JPanel();
bottomLeftPanel = new JPanel();
detailPane = new JPanel();
detailContainer = new JPanel(new BorderLayout());
-
- scrollPane = new JScrollPane(detailPane);
- scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
- scrollPane.getViewport().setViewPosition(new java.awt.Point(0,0));
+
+
//this.setLayout(new BorderLayout(7, 7));
-
+
//detailPane.setPreferredSize(new Dimension(150,800));
//add(scrollPane, BorderLayout.CENTER);
//detailContainer.setLayout(new BorderLayout(10,10));
- detailContainer.add(scrollPane, BorderLayout.CENTER);
- // detailContainer.setOpaque(false);
-
+ // detailContainer.setOpaque(false);
+
mainPanel.setLayout(new BorderLayout(7, 7));
mainPanel.add(bottomLeftPanel, BorderLayout.CENTER);
-
+
bottomLeftPanel.setLayout(new BorderLayout(7, 7));
bottomLeftPanel.add(testResultMapPanel, BorderLayout.PAGE_START);
- // bottomLeftPanel.add(scrollPane, BorderLayout.CENTER);
+ // bottomLeftPanel.add(scrollPane, BorderLayout.CENTER);
bottomLeftPanel.add(detailContainer, BorderLayout.CENTER);
bottomLeftPanel.setOpaque(false);
@@ -98,121 +99,149 @@
resultMap = new TestResultMap();
testResultMapPanel.add(resultMap);
-
-
+
+
testCaseListModel = TestRunnerView.testCaseListModel;
- // sortedModel = new SortedTestCaseListModel(testCaseListModel);
+ // sortedModel = new SortedTestCaseListModel(testCaseListModel);
resultMap.addItemListener(this);
-
+
shortDetailLabel = new JLabel("No dataset selected");
plotLabel = new JLabel("");
detailPane.setLayout(new BorderLayout(1, 1));
- // detailContainer.setLayout(new BorderLayout(10,10));
-
- summaryLabel = new JTextPane();
- summaryLabel.setPreferredSize(new Dimension(725,600));
+ // detailContainer.setLayout(new BorderLayout(10,10));
+
+ summaryEditorPane = new JEditorPane();
+ summaryEditorPane.setEditable(false);
+
+ // summaryEditorPane.setPreferredSize(new Dimension(725,600));
detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
- detailPane.add(plotLabel,BorderLayout.WEST);
- detailPane.add(summaryLabel,BorderLayout.PAGE_END);
+ detailPane.add(plotLabel, BorderLayout.WEST);
+ detailPane.add(summaryEditorPane, BorderLayout.PAGE_END);
detailPane.setBackground(Color.white);
+
+
+ scrollPane = new JScrollPane(summaryEditorPane);
+ scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+ scrollPane.getViewport().setViewPosition(new java.awt.Point(0, 0));
+ detailContainer.add(scrollPane, BorderLayout.CENTER);
+ summaryEditorPane.setContentType("text/html");
+ summaryEditorPane.setText("<html>No dataset selected</html>");
+
// add the plot when the user clicks on a square
//detailPane.add(new JLabel(new ImageIcon(getClass().getResource("resources/testgraph.jpg"))), BorderLayout.PAGE_END);
-
- // JScrollPane scrollPane = new JScrollPane(detailPane);
- // add(scrollPane, BorderLayout.CENTER);
+ // JScrollPane scrollPane = new JScrollPane(detailPane);
+ // add(scrollPane, BorderLayout.CENTER);
+
JPanel[] namedPanel = new JPanel[3];
namedPanel[0] = testResultMapPanel;
namedPanel[1] = detailContainer;
- // namedPanel[1] = detailPane;
- // namedPanel[2] = findPanel;
+ // namedPanel[1] = detailPane;
+ // namedPanel[2] = findPanel;
//namedPanel[1] = scrollPane;
Border lineborder = new LineBorder(Color.gray, 1, true);
testResultMapPanel.setBorder(
- BorderFactory.createCompoundBorder(
- BorderFactory.createTitledBorder(lineborder, "Test Result Map"),
- BorderFactory.createEmptyBorder(10, 10, 10, 10)));
- testResultMapPanel.setOpaque(false);
-
+ BorderFactory.createCompoundBorder(
+ BorderFactory.createTitledBorder(lineborder, "Test Result Map"),
+ BorderFactory.createEmptyBorder(10, 10, 10, 10)));
+ testResultMapPanel.setOpaque(false);
+
detailContainer.setBorder(
- BorderFactory.createCompoundBorder(
- BorderFactory.createTitledBorder(lineborder, "Details"),
- BorderFactory.createEmptyBorder(10, 10, 10, 10)));
- detailContainer.setOpaque(false);
+ BorderFactory.createCompoundBorder(
+ BorderFactory.createTitledBorder(lineborder, "Details"),
+ BorderFactory.createEmptyBorder(10, 10, 10, 10)));
+ detailContainer.setOpaque(false);
-/* for (int i = 0; i < 2; i++) {
- Border lineborder = new LineBorder(Color.gray, 1, true);
- namedPanel[i].setBorder(
- BorderFactory.createCompoundBorder(
- BorderFactory.createTitledBorder(lineborder, panelTitles[i]),
- BorderFactory.createEmptyBorder(10, 10, 10, 10)));
- namedPanel[i].setOpaque(false);
- }
-*/
-
+ /* for (int i = 0; i < 2; i++) {
+ Border lineborder = new LineBorder(Color.gray, 1, true);
+ namedPanel[i].setBorder(
+ BorderFactory.createCompoundBorder(
+ BorderFactory.createTitledBorder(lineborder, panelTitles[i]),
+ BorderFactory.createEmptyBorder(10, 10, 10, 10)));
+ namedPanel[i].setOpaque(false);
}
+ */
- public void updateMap() {
- resultMap.resetDisplay();
- }
+ }
- public void itemStateChanged(ItemEvent evt) {
- int index = (Integer)evt.getItem();
+ /**
+ * updateMap resets the map display.
+ */
+ public void updateMap() {
+ resultMap.resetDisplay();
+ }
+
+ /**
+ * itemStateChanged records the ItemEvent that occurs when an icon has been selected.
+ * @param evt
+ */
+ public void itemStateChanged(ItemEvent evt) {
+ int index = (Integer) evt.getItem();
updateDetails(index);
}
- public void updateDetails(int index) {
- detailPane.remove(shortDetailLabel);
- detailPane.remove(plotLabel);
- detailPane.remove(summaryLabel);
- String html_content = "";
-
- int result = testCaseListModel.getRawElementAt(index).getResult();
- if(result == 0) {
- shortDetailLabel = new JLabel("<html><p>Test Case " + testCaseListModel.getRawElementAt(index).getTestname() + " </p><p>Passed!</p></html>");
- }
- if(result > 0) {
- shortDetailLabel = new JLabel("<html><p>Test Case " + testCaseListModel.getRawElementAt(index).getTestname() + " </p><p>Failed at " + result +" points</p></html>");
- }
- if(result == -1) {
- shortDetailLabel = new JLabel("<html><p>Test Case " + testCaseListModel.getRawElementAt(index).getTestname() + " </p><p>Skipped: " + testCaseListModel.getRawElementAt(index).getWarnings() + "</p></html>");
- }
-
+ /**
+ * updateDetails is called when an icon has been selected, it updates the details pane of the view to show the details of the selected icon.
+ * @param index
+ */
+ public void updateDetails(int index) {
+
+ String html_content = "";
+
+ StringBuffer buffer = new StringBuffer("");
+
+
+ int result = testCaseListModel.getRawElementAt(index).getResult();
+ if (result == 0) {
+ buffer.append("<p>Test Case " + testCaseListModel.getRawElementAt(index).getTestname() + " </p><p>Passed!</p>");
+ }
+ if (result > 0) {
+ buffer.append("<p>Test Case " + testCaseListModel.getRawElementAt(index).getTestname() + " </p><p>Failed at " + result + " points</p>");
+ }
+ if (result == -1) {
+ buffer.append("<p>Test Case " + testCaseListModel.getRawElementAt(index).getTestname() + " </p><p>Skipped: " + testCaseListModel.getRawElementAt(index).getWarnings() + "</p>");
+ }
+
//detailPane.setLayout(new BorderLayout(10, 10));
- detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
- String description_path = testCaseListModel.getRawElementAt(index).getHtml();
- try {
- FileInputStream fis = new FileInputStream(description_path);
- int x = fis.available();
- byte b[] = new byte[x];
- fis.read(b);
- html_content = new String(b);
-
- }
- catch(FileNotFoundException e){
- System.out.println("didn't find the html file");
- }
- catch(IOException e) {
- System.out.println("caught an io exception opening html file");
- }
-
- //summaryLabel = new JLabel("<html>" + html_content + "</html>");
- String plotpath = testCaseListModel.getRawElementAt(index).getPlot();
- summaryLabel.setContentType("text/html");
- summaryLabel.setText("<html>" + html_content + "</html>");
-
- detailPane.add(summaryLabel, BorderLayout.PAGE_END);
-
- plotLabel = new JLabel(new ImageIcon(plotpath));
- detailPane.add(plotLabel, BorderLayout.WEST);
- scrollPane.getViewport().setViewPosition(new java.awt.Point(0,0));
-
- }
-
+ // detailPane.add(shortDetailLabel, BorderLayout.PAGE_START);
+ String description_path = testCaseListModel.getRawElementAt(index).getHtml();
+ try {
+ FileInputStream fis = new FileInputStream(description_path);
+ int x = fis.available();
+ byte b[] = new byte[x];
+ fis.read(b);
+ html_content = new String(b);
+ } catch (FileNotFoundException e) {
+ System.out.println("didn't find the html file");
+ } catch (IOException e) {
+ System.out.println("caught an io exception opening html file");
+ }
-
+ //summaryEditorPane = new JLabel("<html>" + html_content + "</html>");
+ String plotpath = testCaseListModel.getRawElementAt(index).getPlot();
+ buffer.append("<br><p><img src=\"file://" + convertPathToHTML(plotpath) + "\"></img></p><br>");
+ buffer.append(html_content);
+
+ summaryEditorPane.setText("<html>" + buffer.toString() + "</html>");
+
+ summaryEditorPane.setCaretPosition(0);
+
+
+ }
+
+ private String convertPathToHTML(String path) {
+ if ((System.getProperty("os.name").toLowerCase().startsWith("windows"))) {
+ StringBuffer newpath = new StringBuffer("/");
+ newpath.append(path.replaceAll("\\\\", "/").replaceAll(" ", "%20"));
+
+ return newpath.toString();
+ } else {
+ return path.replaceAll(" ", "%20");
+ }
+ }
}
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PassedTestCaseListModel.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PassedTestCaseListModel.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PassedTestCaseListModel.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -31,28 +31,45 @@
import javax.swing.event.ListDataEvent;
import javax.swing.event.ListDataListener;
+/**
+ * PassedTestCaseListModel is a class that creates a list model of the passed test cases.
+ * @author Kimberly Begley
+ * @version 2.0
+ */
public class PassedTestCaseListModel extends AbstractListModel implements ListDataListener {
Vector<TestResultDetails> passedData;
-
+/**
+ * PassedTestCaseListModel has one constructor that creates a new vector of TestResultDetails for the test case that have passed.
+ */
PassedTestCaseListModel() {
passedData = new Vector<TestResultDetails>();
}
-
+/**
+ * addElement adds a TestResultDetails object to the list anf fires an event to record this.
+ * @param o the TestResultDetails object to add to the list.
+ */
public void addElement(TestResultDetails o) {
passedData.add(o);
fireIntervalAdded(this, getSize() - 1, getSize() - 1);
}
+ /**
+ * remove removes a TestResultObject from the passed test case list model at the specified index.
+ * @param index Index of the item to remove
+ * @return returns the TestResultDetails object that was removed.
+ */
public TestResultDetails remove(int index) {
TestResultDetails o = passedData.remove(index);
fireContentsChanged(this, getSize() - 1, getSize() - 1);
return o;
}
-
+ /**
+ * removeAllElements removes all elements from the PassedTestCaseListModel list.
+ */
public void removeAllElements() {
if (getSize() > 0 ) {
this.fireIntervalRemoved(this, 0, getSize() - 1);
@@ -60,26 +77,47 @@
}
}
+ /**
+ * getSize returns the size of the passed result list.
+ * @return returns an integer value of the size of the PassedTestCaseListModel.
+ */
public int getSize() {
return passedData.size();
}
-
+ /**
+ * getElementAt returns the string value of the testname of the object at the specified index.
+ * @param index the index of the list
+ * @return returns a string value of the test name.
+ */
public Object getElementAt(int index) {
return (passedData.get(index)).getTestname();
}
-
+ /**
+ * getRawElementAt returns the TestResultDetails object at the selected index.
+ * @param index the index for the item in the list.
+ * @return returns a TestResultDetails object of the specified index value.
+ */
public TestResultDetails getRawElementAt(int index) {
return passedData.get(index);
}
-
+ /**
+ *
+ * @param e
+ */
public void intervalAdded(ListDataEvent e) {
throw new UnsupportedOperationException("Not supported yet.");
}
-
+ /**
+ *
+ * @param e
+ */
public void intervalRemoved(ListDataEvent e) {
throw new UnsupportedOperationException("Not supported yet.");
}
-
+ /**
+ *
+ * @param e
+ */
public void contentsChanged(ListDataEvent e) {
throw new UnsupportedOperationException("Not supported yet.");
}
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PreferencesDialog.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PreferencesDialog.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/PreferencesDialog.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -6,10 +6,20 @@
import java.util.HashMap;
import javax.swing.JDialog;
+/**
+ * This class creates the diaglog for the preferences menu item.
+ * @author Kimberly Begley
+ * @version 2.0
+ */
public class PreferencesDialog extends JDialog {
HashMap<String, Object> settings;
/** Creates new form PreferencesDialog */
+ /**
+ * PreferencesDialog creates a new form for Preferences menu item. It has one constructor.
+ * @param parent The parent frame
+ * @param currentsettings A hashmap of the current preferences settings.
+ */
public PreferencesDialog(Frame parent, HashMap<String, Object> currentsettings) {
super(parent, "Preferences",true);
initComponents();
@@ -23,7 +33,9 @@
this.setLocationRelativeTo(parent);
}
-
+/**
+ * initComponents Initializes the components for the preferences dialog.
+ */
@SuppressWarnings("unchecked")
private void initComponents() {
@@ -117,24 +129,38 @@
pack();
}// </editor-fold>//GEN-END:initComponents
-
+/**
+ * applyButtonActionPerformed - gets the values of the varibles set in the dialog and closes the diaglog.
+ * @param evt ActionEvent indicating the Apply button has been selected.
+ */
private void applyButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_applyButtonActionPerformed
settings.put("logging", loggingCheckBox.isSelected());
settings.put("configpath", pathTextField.getText());
this.setVisible(false);// TODO add your handling code here:
}//GEN-LAST:event_applyButtonActionPerformed
-
+/**
+ * cancelButtonActionEvent - closes the dialog
+ * @param evt ActionEvent indicating the Cancel button has been selected.
+ */
private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
this.setVisible(false);// TODO add your handling code here:
}//GEN-LAST:event_cancelButtonActionPerformed
-
+/**
+ * getValue returns the preferences dialog variable settings. It is a static method.
+ * @param parent Frame from which the request is coming
+ * @param currentsettings hashmap of the current variable settings
+ * @return returns the current variable settings
+ */
public static HashMap<String,Object> getValue(Frame parent, HashMap<String, Object> currentsettings) {
PreferencesDialog dlg = new PreferencesDialog(parent, currentsettings);
dlg.setVisible(true);
return dlg.getReturnValue();
}
-
+/**
+ * getReturnValue is the private function to get the settings hashmap
+ * @return returns the settings in a hashmap
+ */
private HashMap<String,Object> getReturnValue() {
return settings;
}
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestCase.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestCase.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestCase.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -35,8 +35,9 @@
import java.applet.*;
/**
- *
- * @author kimberlybegley
+ *This class contains most of the logic for the testing included in the SBML Test Suite.
+ * @author Kimberly Begley
+ * @version 2.0
*/
public class SBMLTestCase {
@@ -48,29 +49,61 @@
public BigDecimal abs;
public BigDecimal rel;
-
+ /**
+ * Gets the start time interval
+ * @return The start time interval
+ */
public int getStart() {
return start;
}
+ /**
+ * Gets the test name
+ * @return The test name
+ */
public String getTestname() {
return testname;
}
+ /**
+ * Gets the duration of the test
+ * @return The duration of the test
+ */
public double getDuration() {
return duration;
}
+ /**
+ * Gets the number of steps
+ * @return The number of steps
+ */
public int getSteps() {
return steps;
}
+ /**
+ * Gets the number of variables
+ * @return The number of varaibles in the test
+ */
public int getVariables_count() {
return variables_count;
}
+ /**
+ * Gets the Absolute allowable difference
+ * @return the absolute allowable difference
+ */
public BigDecimal getAbs() {
return abs;
}
+ /**
+ * Gets the relative allowable difference
+ * @return the relative allowable difference
+ */
public BigDecimal getRel() {
return rel;
}
-
+ /**
+ * Gets the test case directory
+ * @return A string containing the path to the test case directory - Used in web application only
+ * @throws java.io.IOException if the config file cannot be opened
+ * @throws java.io.FileNotFoundException if the config file cannot be found
+ */
public String getSbmlTestdir() throws IOException, FileNotFoundException {
String sbmltestdir = new String();
File sbmlconfigfile = new File("/usr/share/apache-tomcat-5.5.26/webapps/test_suite/WEB-INF/sbml_config_file.txt");
@@ -91,28 +124,48 @@
return sbmltestdir;
}
-
+ /**
+ * Gets the appropriate settings file for a given test case.
+ * @param value the test case name
+ * @param testdir the test case directory
+ * @return returns a path to the settings file
+ */
public String getSettingsFile(String value, String testdir) {
String settingsfile = new String();
settingsfile = testdir + File.separator + value + File.separator + value + "-settings.txt";
return settingsfile;
}
-
+ /**
+ * Gets the control results for a given test case.
+ * @param value the test case name
+ * @param testdir the test case directory
+ * @return returns a path to the test case control results file
+ */
public String getControlResults(String value, String testdir) {
String resultfile = new String();
resultfile = testdir + File.separator + value + File.separator + value + "-results.csv";
return resultfile;
}
-
+ /**
+ * Gets the plot file path for a given test case
+ * @param value the test case name
+ * @param testdir the test case directory
+ * @return returns a path to the test case plot file
+ */
public String getPlotFile(String value, String testdir) {
String plotfile = new String();
plotfile = testdir + File.separator + value + File.separator + value + "-plot.jpg";
return plotfile;
}
-
+ /**
+ * Gets the html file path for a given test case
+ * @param value the test case name
+ * @param testdir the test case directory
+ * @return returns a path to the html file of test case details
+ */
public String getHtmlFile(String value, String testdir) {
String htmlfile = new String();
htmlfile = testdir + File.separator + value + File.separator + value + "-model.html";
@@ -120,7 +173,18 @@
return htmlfile;
}
-
+ /**
+ * Reads the results of a test case result file into a two dimensional bigdecimal array
+ * @param filename filename to read
+ * @param header 1 or 0 indicates the presence of a header - at this time it is always set to 1 expecting all files to have a header
+ * @param steps the number of steps as given in the settings file
+ * @param variables_count the number of variables as giving in the settings file
+ * @return a 2D BigDecimal array of results.
+ * @throws java.io.IOException
+ * @throws java.io.FileNotFoundException
+ * @throws java.lang.NumberFormatException
+ * @throws java.lang.Exception returns an exception if the file does not have the indicated number of variables as read from the settings fiel
+ */
public BigDecimal[][] readResults(String filename, int header, int steps, int variables_count) throws IOException, FileNotFoundException, NumberFormatException, Exception {
/* readResults - returns a csv file as a multidimensional array
Input:a cvs file (filename) along with whether it has a header (header=1/0), step count (steps), number of variables
@@ -164,7 +228,12 @@
return value;
}
-
+ /**
+ * Makes sure the user result file has the same number of timesteps etc as defined in the settings file
+ * @param resultdata control result multidimensional array
+ * @param userresultdata user result multidimensional array
+ * @throws java.lang.Exception throws an exception if there are an inconsistant number of rows between the two input files and if the time step values do not match up
+ */
public void validateResults(BigDecimal [][] resultdata, BigDecimal [][] userresultdata) throws Exception {
/* validateResults - makes sure that the users result file has the same timesteps etc as defined in the settings file
Input: user result mulitidimensional array
@@ -182,7 +251,15 @@
}
}
}
-
+ /**
+ * Subtracts the corresponding fields to give the difference between the values in the user and control result files
+ * @param resultdata control result data multidimensional array
+ * @param inputdata user result data multidimensional array
+ * @param steps the number of steps in the test
+ * @param variables_count the number of variables in the test
+ * @return returns a multidimensional array containing the differences of the compared files.
+ * @throws java.lang.Exception if the files are of different lengths it returns an exception
+ */
public BigDecimal[][] compareResults(BigDecimal [][] resultdata, BigDecimal [][] inputdata, int steps, int variables_count) throws Exception{
/* compareResults - subtracts each corresponding field to give the differences
Input: the multidimensional array from the control result data file and a multidimensional
@@ -214,6 +291,15 @@
}
return result;
}
+ /**
+ * Looks at the allowable difference and how it compares to the differences of the user and control files
+ * @param control control file results multidimensional array
+ * @param differences differences mulitdimensional array (from the compareResults function)
+ * @param variables number of variables
+ * @param absolute the absolute allowable difference from the settings file
+ * @param relative the relative allowable difference from the settings file
+ * @return and integer - the number of failed comparisons in the file - if equal to zero then the test passed.
+ */
public int analyzeResults(BigDecimal [][] control, BigDecimal [][] differences, int variables, BigDecimal absolute, BigDecimal relative) {
/* anaylzeResults - looks at the allowable difference and how it compares to the differences of the user and control files
Input: differences array (from compareResults function), absolute difference, relative difference
@@ -258,7 +344,12 @@
}
return pass_fail;
}
-
+ /**
+ * Reads the values in the settings file
+ * @param filename path to the settings file
+ * @throws java.io.IOException thrown if the settings file cannot be opened.
+ * @throws java.io.FileNotFoundException thrown if the settings file cannot be found.
+ */
public void readSettingsFile(String filename) throws IOException, FileNotFoundException {
/* Read settings file for test into a hash table rea
Input: is settings file name
@@ -337,6 +428,12 @@
}
}
+ /**
+ * Gets the user test file directory and checks the format of the files in the directory - only used in web version of test suite.
+ * @param dirname path to the test case directory
+ * @return a hashmap of the testname and user result file name
+ * @throws java.lang.Exception thrown if the user test file has an incorrect name format.
+ */
public Map getUsertestlist(String dirname) throws Exception{
/* Gets the user file directory and checks the format of the files in the directory
Input: is the directory path
@@ -373,7 +470,11 @@
}
return m;
}
-
+/**
+ * Deletes a directory containing uploaded test cases.
+ * @param path path to test case files
+ * @return boolean value indicating success of deletion.
+ */
public boolean deleteDirectory(File path) {
if( path.exists() ) {
File[] files = path.listFiles();
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestRunnerApp.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestRunnerApp.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestRunnerApp.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -26,7 +26,11 @@
import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;
-
+/**
+ * The class containing the main method for the stand alone application
+ * @author Kimberly Begley
+ * @version 2.0
+ */
public class SBMLTestRunnerApp {
static {
@@ -64,7 +68,10 @@
}
-
+/**
+ * Starts the gui
+ * @param args
+ */
@SuppressWarnings("static-access")
private void startGui(String[] args) {
try {
@@ -84,12 +91,17 @@
TestRunnerView testRunnerView = new TestRunnerView();
testRunnerView.showGui(args);
}
-
+/**
+ * Shows the usage for calling the test suite jar file
+ */
private static void showUsage() {
System.out.println("Usage: java -jar SBMLTestRunner.jar [OPTIONS]");
System.out.println("-nogui Start without GUI (javavm needs to be in headless mode");
}
-
+/**
+ * Starts the command line version
+ * @param args
+ */
private static void startCLI(String[] args) {
System.out.println("Starting without Gui...");
}
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestSelection.java
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestSelection.java 2008-07-28 22:28:53 UTC (rev 7777)
+++ trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite/src/sbml/test/SBMLTestSelection.java 2008-07-29 05:34:26 UTC (rev 7778)
@@ -35,8 +35,9 @@
import java.applet.*;
/**
- *
- * @author kimberlybegley
+ * This class gets various test case elements from test case model files.
+ * @author Kimberly Begley
+ * @version 2.0
*/
public class SBMLTestSelection {
@@ -49,25 +50,53 @@
public Vector<String> levels;
-
+ /**
+ * Gets the test name of a test case
+ * @return a string representation of a test case.
+ */
public String getTestname() {
return testname;
}
+ /**
+ * Gets the synopsis line of a test case
+ * @return a string representation of the synopsis line of a test case.
+ */
public String getSynopsis() {
return synopsis;
}
+ /**
+ * Gets the component tags of a test case
+ * @return a vector containing the component tags of a test case
+ */
public Vector<String> getComponenttags() {
return componenttags;
}
+ /**
+ * Gets the test tags of a test case
+ * @return a vector containing the test tags of a test case
+ */
public Vector<String> getTesttags() {
return testtags;
}
+ /**
+ * Gets the test type of a test case
+ * @return the test type of a test case
+ */
public String getTesttype() {
return testtype;
}
+ /**
+ * Gets the SBML levels of a test case
+ * @return a vector of the levels a test case applies to
+ */
public Vector<String> getLevels() {
return levels;
}
+ /**
+ * Returns a boolean value as to whether a test case contains a specified component
+ * @param component the component to be tested for
+ * @return a boolean value indicating the presence of the component tag in the test case
+ */
public Boolean containsComponent(String component) {
@@ -76,6 +105,11 @@
}
else return false;
}
+ /**
+ * Returns a boolean value as to whether a test case contains a specified tag
+ * @param tag the tag to be tested for
+ * @return a boolean value indicating the presence of the test tag in the test case
+ */
public Boolean containsTag(String tag) {
if(testtags.contains(tag)) {
@@ -83,6 +117,11 @@
}
else return false;
}
+ /**
+ * Returns a boolean value as to whether a test ...
[truncated message content] |
|
From: <mh...@us...> - 2008-07-28 22:28:56
|
Revision: 7777
http://sbml.svn.sourceforge.net/sbml/?rev=7777&view=rev
Author: mhucka
Date: 2008-07-28 22:28:53 +0000 (Mon, 28 Jul 2008)
Log Message:
-----------
[Fix for issue #1830712.] Added new bqbiol MIRIAM qualifiers.
Modified Paths:
--------------
trunk/specifications/sbml-level-2/version-4/spec/annotations.tex
Modified: trunk/specifications/sbml-level-2/version-4/spec/annotations.tex
===================================================================
--- trunk/specifications/sbml-level-2/version-4/spec/annotations.tex 2008-07-28 22:24:14 UTC (rev 7776)
+++ trunk/specifications/sbml-level-2/version-4/spec/annotations.tex 2008-07-28 22:28:53 UTC (rev 7777)
@@ -375,6 +375,18 @@
species or a parameter to the literature that describes the
quantity of the species or the value of the parameter.
+\begin{blockChanged}
+
+\item \token{bqbiol:isEncodedBy} The biological entity represented
+ by the model component is encoded, either directly or by virtue
+ of transitivity, by the subject of the referenced resource.
+
+\item \token{bqbiol:encodes} The biological entity represented by
+ the model component encodes, either directly or by virtue of
+ transitivity, the subject of the referenced resource.
+
+\end{blockChanged}
+
\end{itemize}
%In all cases using the biology qualifiers, the `object' of the
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|
|
From: <mh...@us...> - 2008-07-28 22:24:16
|
Revision: 7776
http://sbml.svn.sourceforge.net/sbml/?rev=7776&view=rev
Author: mhucka
Date: 2008-07-28 22:24:14 +0000 (Mon, 28 Jul 2008)
Log Message:
-----------
[Fix for issue #1811168.] Added text clarifying that compartment inside/outside doesn't affect size, and also that the outside attribute doesn't express containment, only 'surrounding'.
Modified Paths:
--------------
trunk/specifications/sbml-level-2/version-4/spec/components.tex
Modified: trunk/specifications/sbml-level-2/version-4/spec/components.tex
===================================================================
--- trunk/specifications/sbml-level-2/version-4/spec/components.tex 2008-07-28 22:20:17 UTC (rev 7775)
+++ trunk/specifications/sbml-level-2/version-4/spec/components.tex 2008-07-28 22:24:14 UTC (rev 7776)
@@ -1550,7 +1550,22 @@
given in terms of concentrations or densities, the compartment
sizes become factors in the reaction rate expressions.
+\begin{blockChanged}
+A final question to address is, what are the relationships between
+compartment sizes when compartment positioning is expressed using
+the \token{outside} attribute
+(Section~\ref{sec:compartment-outside})? The answer is: none.
+The size of a given compartment does not in any sense include the
+sizes of other compartments having it as the value of their
+\token{outside} attributes. In other words, if a compartment
+\emph{B} has the identifier of compartment \emph{A} as its
+\token{outside} attribute value, the size of \emph{A} does not
+include the size of \emph{B}. The compartment sizes are separate.
+
+\end{blockChanged}
+
+
\subsubsection{The \token{units} attribute}
\label{sec:compartment-units}
@@ -1669,28 +1684,28 @@
\label{sec:compartment-outside}
The optional attribute \token{outside} of type \primtype{SId} can be
-used to express containment relationships between compartments. If
+used to express \changed{one type of positioning} relationship between compartments. If
present, the value of \token{outside} for a given compartment must
be the \token{id} attribute value of another \changed{compartment
defined in the model}. Doing so means that the other compartment
-contains it or is ``outside'' of it. This enables the
+\changed{surrounds} it or is ``outside'' of it. This enables the
representation of simple topological relationships between
compartments, for those simulation systems that can make use of
the information (e.g., for drawing simple diagrams of
compartments).
-There are two restrictions on the containment relationships in SBML.
+There are two restrictions on the \changed{inside/outside} relationships in SBML.
First, because a compartment with
\token{spatialDimensions} of \val{0} has no size, such a
-compartment cannot act as the container of any other compartment
+compartment cannot act as the \changed{``outside''} of any other compartment
\emph{except} compartments that \emph{also} have
\token{spatialDimensions} values of \val{0}. Second, the directed
graph formed by representing \Compartment objects as vertexes
and the \token{outside} attribute values as edges must be acyclic.
The latter condition is imposed to prevent a compartment from
-being contained inside itself.
+being \changed{located} inside itself.
-Although containment relationships are partly taken into account
+Although \changed{inside/outside} relationships are partly taken into account
by the compartmental localization of reactants and products, it is
not always possible to determine purely from the reaction
equations whether \textcolor{black}{one} compartment is meant to be located within
@@ -1703,7 +1718,20 @@
Section~\ref{sec:level-3}, SBML Level~3 is expected introduce the
ability to define geometries and spatial qualities.)
+\begin{blockChanged}
+Finally, as mentioned in Section~\ref{sec:size} above, the
+presence of \token{outside} attributes in compartment definitions
+has no implications whatsoever about the sizes (or any other
+attributes) of the compartments involved. The size of a
+compartment does not include the sizes of any other compartments
+having it as the value of their \token{outside} attributes. The
+\token{outside} attribute only provides semantic information and
+has no impact on mathematical analysis and simulation.
+
+\end{blockChanged}
+
+
\subsubsection{The \token{sboTerm} attribute}
\label{sec:compartment-sboterm}
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|