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[sbml-svn] SF.net SVN: sbml:[20938] branches/libsbml-experimental
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From: <sar...@us...> - 2014-07-29 07:47:41
|
Revision: 20938
http://sourceforge.net/p/sbml/code/20938
Author: sarahkeating
Date: 2014-07-29 07:47:34 +0000 (Tue, 29 Jul 2014)
Log Message:
-----------
Merged revision(s) 20839-20937 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/CMakeLists.txt
branches/libsbml-experimental/NEWS.txt
branches/libsbml-experimental/docs/src/Makefile.in
branches/libsbml-experimental/docs/src/SBMLDoclet.java
branches/libsbml-experimental/docs/src/common-text/xmlid-syntax.html
branches/libsbml-experimental/docs/src/css/libsbml-base-stylesheet.css
branches/libsbml-experimental/docs/src/css/libsbml-doxygen-stylesheet.css
branches/libsbml-experimental/docs/src/css/libsbml-javadoc-stylesheet.css
branches/libsbml-experimental/docs/src/doxygen-config-common.txt
branches/libsbml-experimental/docs/src/filters/doc-filter-python.py
branches/libsbml-experimental/docs/src/libsbml-accessing.html.in
branches/libsbml-experimental/docs/src/libsbml-java-reading.html
branches/libsbml-experimental/docs/src/libsbml-programming.txt
branches/libsbml-experimental/docs/src/libsbml-python-creating-model.txt
branches/libsbml-experimental/docs/src/python-substitutions/CompPkgNamespaces.py
branches/libsbml-experimental/docs/src/python-substitutions/FbcPkgNamespaces.py
branches/libsbml-experimental/docs/src/python-substitutions/LayoutPkgNamespaces.py
branches/libsbml-experimental/docs/src/python-substitutions/QualPkgNamespaces.py
branches/libsbml-experimental/examples/python/createSimpleModel.py
branches/libsbml-experimental/src/bindings/csharp/Makefile.in
branches/libsbml-experimental/src/bindings/matlab/OutputSBML.c
branches/libsbml-experimental/src/bindings/matlab/TranslateSBML.c
branches/libsbml-experimental/src/bindings/python/local-contrib.i
branches/libsbml-experimental/src/bindings/python/local-doc-extras.i
branches/libsbml-experimental/src/bindings/python/local.i
branches/libsbml-experimental/src/bindings/r/CMakeLists.txt
branches/libsbml-experimental/src/bindings/swig/libsbml.i
branches/libsbml-experimental/src/bindings/swig/swigdoc.py
branches/libsbml-experimental/src/sbml/Rule.h
branches/libsbml-experimental/src/sbml/SBase.cpp
branches/libsbml-experimental/src/sbml/SBase.h
branches/libsbml-experimental/src/sbml/annotation/RDFAnnotationParser.h
branches/libsbml-experimental/src/sbml/conversion/SBMLFunctionDefinitionConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLIdConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLInferUnitsConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLInitialAssignmentConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLLevelVersionConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLLocalParameterConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLReactionConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLRuleConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLStripPackageConverter.h
branches/libsbml-experimental/src/sbml/conversion/SBMLUnitsConverter.h
branches/libsbml-experimental/src/sbml/math/ASTNode.h
branches/libsbml-experimental/src/sbml/math-legacy/ASTNode.cpp
branches/libsbml-experimental/src/sbml/math-legacy/MathML.cpp
branches/libsbml-experimental/src/sbml/packages/comp/extension/CompExtension.h
branches/libsbml-experimental/src/sbml/packages/comp/util/CompFlatteningConverter.h
branches/libsbml-experimental/src/sbml/packages/fbc/util/CobraToFbcConverter.h
branches/libsbml-experimental/src/sbml/packages/fbc/util/FbcToCobraConverter.h
branches/libsbml-experimental/src/sbml/packages/layout/extension/LayoutExtension.h
branches/libsbml-experimental/src/sbml/validator/constraints/ConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/validator/constraints/UnitConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/validator/test/test-data/libsbml-constraints/99508-fail-01-02.xml
branches/libsbml-experimental/src/sbml/xml/XMLNode.h
branches/libsbml-experimental/src/sbml/xml/XMLOutputStream.h
Added Paths:
-----------
branches/libsbml-experimental/src/bindings/r/Makevars.in
branches/libsbml-experimental/src/bindings/r/Makevars.win
branches/libsbml-experimental/src/bindings/r/configure
branches/libsbml-experimental/src/bindings/r/configure.in
branches/libsbml-experimental/src/bindings/r/configure.win
branches/libsbml-experimental/src/bindings/r/create_package.cmake
branches/libsbml-experimental/src/sbml/validator/test/test-data/libsbml-constraints/99508-fail-01-01-20616.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20507-fail-01-11.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20508-fail-01-11.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-unit-constraints/20509-fail-01-13-99508.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-unit-constraints/20608-fail-01-18-99508.xml
Removed Paths:
-------------
branches/libsbml-experimental/src/sbml/validator/test/test-data/libsbml-constraints/99508-fail-01-01.xml
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental 2014-07-29 07:47:34 UTC (rev 20938)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -2,4 +2,4 ##
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
/branches/libsbml-ast-plugin:16251-19654
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-20838
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-20937
\ No newline at end of property
Modified: branches/libsbml-experimental/CMakeLists.txt
===================================================================
--- branches/libsbml-experimental/CMakeLists.txt 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/CMakeLists.txt 2014-07-29 07:47:34 UTC (rev 20938)
@@ -1008,6 +1008,10 @@
message(STATUS " Using Matlab = ${MATLAB_ROOT_PATH}")
endif()
+if(WITH_R)
+ message(STATUS " Using R = ${R_INTERPRETER}")
+endif()
+
if(WITH_CHECK)
message(STATUS " Using libcheck = ${LIBCHECK_LIBRARY}")
Modified: branches/libsbml-experimental/NEWS.txt
===================================================================
--- branches/libsbml-experimental/NEWS.txt 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/NEWS.txt 2014-07-29 07:47:34 UTC (rev 20938)
@@ -16,6 +16,10 @@
* Bug fixes
+ - Code checking the values of units attributes was incorrectly
+ allowing the default Level 2 units, such as substance, to
+ be used in Level 3. This has been corrected.
+
- 'comp' package-specific bug fixes:
- 'fbc' package-specific bug fixes:
- 'layout' package-specific bug fixes:
Modified: branches/libsbml-experimental/docs/src/Makefile.in
===================================================================
--- branches/libsbml-experimental/docs/src/Makefile.in 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/Makefile.in 2014-07-29 07:47:34 UTC (rev 20938)
@@ -123,16 +123,10 @@
doxygen-config-octave.txt \
doxygen-config-perl.txt \
doxygen-config-python.txt \
- libsbml-accessing.html \
- libsbml-converters.txt \
- libsbml-group-comp-intro.html \
- libsbml-group-core-intro.html \
- libsbml-group-fbc-intro.html \
- libsbml-group-layout-intro.html \
- libsbml-group-qual-intro.html \
- libsbml-installation.html \
perlmod \
- xml
+ xml \
+ $(other-generated-files) \
+ $(expanded-html-files)
# The `make dist' rules for this directory are more complicated than usual.
# There are additional separate rules below.
@@ -677,7 +671,7 @@
# we can't currently do anything about, and that are harmless.
cs-ignorable-warnings = \
- "is not found in the argument list of|explicit link request to 'GO' could not be resolved"
+ "is not found in the argument list of|explicit link request to 'GO' could not be resolved|multiple use of section label"
csharp-manual $(csharp-manual): doxygen-config-csharp.txt $(all-sources) \
$(css-files)
@@ -760,7 +754,7 @@
endef
define adjust_frameset_in_file
- perl -i -pe 's/20%,80%/22%,78%/' $(1)
+ perl -i -pe 's/20%,80%/26%,74%/' $(1)
endef
define fix_broken_highlighting
Modified: branches/libsbml-experimental/docs/src/SBMLDoclet.java
===================================================================
--- branches/libsbml-experimental/docs/src/SBMLDoclet.java 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/SBMLDoclet.java 2014-07-29 07:47:34 UTC (rev 20938)
@@ -388,6 +388,20 @@
return doc.name().startsWith("libsbmlJNI");
}
+ private static boolean isSWIGOwnershipMethod(Doc doc)
+ {
+ if (doc instanceof ProgramElementDoc)
+ {
+ ProgramElementDoc pdoc = (ProgramElementDoc) doc;
+ if (pdoc.qualifiedName().endsWith("swigReleaseOwnership")
+ || pdoc.qualifiedName().endsWith("swigTakeOwnership"))
+ return true;
+ }
+ return (doc.isMethod()
+ && (doc.name().equals("swigReleaseOwnership")
+ || doc.name().equals("swigTakeOwnership")));
+ }
+
private static boolean isDeleteMethod(Doc doc)
{
if (doc instanceof ProgramElementDoc)
@@ -425,7 +439,8 @@
if (markedInternal(item))
continue;
- if (isSWIGWrapper(item) || isJNIclass(item))
+ if (isSWIGWrapper(item) || isJNIclass(item) ||
+ isSWIGOwnershipMethod(item))
{
if (m_list_skipped)
{
Modified: branches/libsbml-experimental/docs/src/common-text/xmlid-syntax.html
===================================================================
--- branches/libsbml-experimental/docs/src/common-text/xmlid-syntax.html 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/common-text/xmlid-syntax.html 2014-07-29 07:47:34 UTC (rev 20938)
@@ -2,8 +2,8 @@
<a target="_blank" href="http://www.w3.org/TR/REC-xml/#id">ID</a>. We
express the syntax using an extended form of BNF notation:
<p>
-<nobr><code style="margin-left: 2em">NCNameChar ::= letter | digit | '.' | '-' | '_' | ':' | CombiningChar | Extender</code><br></nobr>
-<code style="margin-left: 2em">ID ::= ( letter | '_' | ':' ) NCNameChar*</code><br>
+<nobr><code style="margin-left: 2em; letter-spacing: -1px">NCNameChar ::= letter | digit | '.' | '-' | '_' | ':' | CombiningChar | Extender</code><br></nobr>
+<code style="margin-left: 2em; letter-spacing: -1px">ID ::= ( letter | '_' | ':' ) NCNameChar*</code><br>
<p>
The characters <code>(</code> and <code>)</code> are used for grouping, the
character <code>*</code> means "zero or more times", and the character
Modified: branches/libsbml-experimental/docs/src/css/libsbml-base-stylesheet.css
===================================================================
--- branches/libsbml-experimental/docs/src/css/libsbml-base-stylesheet.css 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/css/libsbml-base-stylesheet.css 2014-07-29 07:47:34 UTC (rev 20938)
@@ -66,6 +66,13 @@
padding-bottom: 2px;
}
+h2 code
+{
+ font-size: 18px;
+ padding-left: 3px;
+ padding-right: 3px;
+}
+
/* This is for the words "Detailed Description" in Doxygen class pages. */
h2.groupheader {
font-size: 16pt;
@@ -125,18 +132,30 @@
font-weight: 700;
}
-ul
+ul, ol
{
margin-top: 0.75em;
margin-bottom: 0.75em;
+ padding: 0;
}
-ul li
+ul li,
+ol li
{
margin-top: 0.75em;
margin-bottom: 0.75em;
+ margin-left: 2.5em;
}
+.tabs ul li,
+.tabs2 ul li,
+.tabs3 ul li,
+.tabs4 ul li
+{
+ margin-left: 0;
+}
+
+ul li p,
ul li p
{
margin: 0px;
@@ -162,8 +181,8 @@
font-family: 'Anonymous Pro', 'Courier New', Courier, monospace, fixed;
font-weight: 700;
font-size: 13px;
- padding-left: 2px;
- padding-right: 2px;
+ padding-left: 1px;
+ padding-right: 0px;
color: black;
margin-top: 1em;
margin-bottom: 1em;
Modified: branches/libsbml-experimental/docs/src/css/libsbml-doxygen-stylesheet.css
===================================================================
--- branches/libsbml-experimental/docs/src/css/libsbml-doxygen-stylesheet.css 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/css/libsbml-doxygen-stylesheet.css 2014-07-29 07:47:34 UTC (rev 20938)
@@ -102,6 +102,8 @@
font-family: 'Anonymous Pro', 'Courier New', Courier, monospace, fixed;
font-weight: 700;
font-size: 10pt;
+ padding-left: 1px;
+ padding-right: 0px;
}
a.code, a.code:visited {
@@ -669,8 +671,10 @@
table.directory td.entry {
border-bottom: 1px dotted #ccc;
- min-width: 235px;
- padding-top: 5px;
+ min-width: 240px;
+ padding-top: 3px;
+ padding-bottom: 3px;
+ vertical-align: middle;
}
table.directory td.entry a.el {
@@ -1312,7 +1316,7 @@
pre.signature {
font-size: 13px;
font-weight: 700;
- margin-left: 12px;
+ margin-left: 15px;
white-space: -moz-pre-wrap;
white-space: -o-pre-wrap;
word-wrap: break-word;
@@ -1355,11 +1359,6 @@
padding-right: 1em;
}
-.textblock ul,
-.textblock ol {
- padding-left: 2.5em;
-}
-
.textblock ul li p.startli,
#doc-content ul li p.startli {
padding: 0px;
Modified: branches/libsbml-experimental/docs/src/css/libsbml-javadoc-stylesheet.css
===================================================================
--- branches/libsbml-experimental/docs/src/css/libsbml-javadoc-stylesheet.css 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/css/libsbml-javadoc-stylesheet.css 2014-07-29 07:47:34 UTC (rev 20938)
@@ -196,6 +196,15 @@
font-weight: bold;
}
+/* This next one catches the most common use of li for us inside
+method documentation, namely for return types. Hacky, this is. */
+
+dl dd dl dd ul li
+{
+ margin-top: 0.25em;
+ margin-bottom: 0.25em;
+}
+
td, th
{
padding: 2px;
Modified: branches/libsbml-experimental/docs/src/doxygen-config-common.txt
===================================================================
--- branches/libsbml-experimental/docs/src/doxygen-config-common.txt 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/doxygen-config-common.txt 2014-07-29 07:47:34 UTC (rev 20938)
@@ -196,7 +196,7 @@
ALIASES += sbmlfunction{2}="@if clike SBML_\1()@endif @if csharp SBML_\1()@endif @if python @link libsbml.\1() \1()@endlink@endif@~"
-ALIASES += sbmlconstant{2}="@if clike @link \2#\1 \1@endlink@endif @if csharp @link libsbmlcs#\1 \1@endlink@endif @if python @link libsbml#\1 \1@endlink@endif @if java @link libsbmlConstants#\1 \1@endlink@endif@~"
+ALIASES += sbmlconstant{2}="@if clike @link \2#\1 \1@endlink@endif @if csharp @link libsbml#\1 \1@endlink@endif @if python @link libsbml#\1 \1@endlink@endif @if java @link libsbmlConstants#\1 \1@endlink@endif@~"
# This tag can be used to specify a number of word-keyword mappings (TCL only).
# A mapping has the form "name=value". For example adding "class=itcl::class"
Modified: branches/libsbml-experimental/docs/src/filters/doc-filter-python.py
===================================================================
--- branches/libsbml-experimental/docs/src/filters/doc-filter-python.py 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/filters/doc-filter-python.py 2014-07-29 07:47:34 UTC (rev 20938)
@@ -46,14 +46,14 @@
def reformatDocString (match):
text = match.group(1)
- # First, a regexp we use more than once below.
- # This regexp matches signatures of the following form:
+ # First, define some regexps we use more than once below.
+ # The regexp matches signatures of the following form:
# foo()
# foo() -> result(arg, arg, ...)
# foo(arg, arg, ...) -> result(arg, arg, ...)
- sigLHS = '\w+\([\w()=*:"<>?,.\n ]*\)'
- sigRHS = '( -> [\w()=*:"<>?|, \t]+)?'
+ sigLHS = '\w+\([-\w()=&*:"<>?,.\n ]*\)'
+ sigRHS = '( -> [-\w()=&*:"<>?|, \t]+)?'
sigLine = sigLHS + sigRHS
# We start by fixing some wonkiness with the output from SWIG: it sometimes
@@ -105,13 +105,23 @@
p = re.compile(' -> ')
text = p.sub(r' ' + newArrow + ' ', text)
- # Now we do a final transformation: bring up the brief description, if there
- # is one, to make it the first line of the doc string.
+ # Now we do some final transformations.
- start = '<pre class="signature">'
+ start = '<pre class=["\']signature["\']>'
+ middle = '.*?'
+ end = '</pre>'
+
+ # First, clean up whitespace in the method signature strings (and not the
+ # rest of the doc body, because that will mess up code example blocks).
+
+ p = re.compile(start + '(' + middle + ')' + end, re.DOTALL)
+ text = p.sub(clean_up_spaces, text)
+
+ # Next, bring up the brief description, if there is one, to make it the
+ # first line of the doc string.
+
brief = '\w[^.]+\.'
-
- p = re.compile('(' + start + r'.*?)<p>\s*(' + brief + ')\s(.*)', re.DOTALL)
+ p = re.compile('(' + start + middle + end + '\s*?)<p>\s*(' + brief + ')\s(.*)', re.DOTALL)
text = p.sub(r'\2\n\n' + r'\1' + r'\3', text)
# Crucial detail: need a '!' character after the opening triple quotes or
@@ -120,6 +130,15 @@
return "\"\"\"!" + text + "\"\"\""
+def clean_up_spaces(match):
+ normalized = re.sub(' +', ' ', match.group(0)) # Multiple spaces.
+ normalized = re.sub('^ +', '', normalized, flags=re.MULTILINE) # Leading spaces.
+ normalized = normalized.replace(' , ', ', ') # Space before comma.
+ normalized = normalized.replace('( ', '(') # Space after paren.
+ normalized = normalized.replace(' )', ')') # Space before paren.
+ return normalized
+
+
def filterDocStrings (contents):
# Make the docstrings more readable.
p = re.compile('\"\"\"(.+?)\"\"\"', re.DOTALL | re.MULTILINE)
@@ -171,6 +190,9 @@
# Other simple type replacements.
contents = contents.replace('an unsigned int', 'a long integer')
contents = contents.replace('unsigned int', 'long')
+ contents = contents.replace('const int&', 'int')
+ contents = contents.replace('const long&', 'long')
+ contents = contents.replace('const bool&', 'bool')
contents = contents.replace('const std.string&', 'string')
contents = contents.replace('const std.string', 'string')
contents = contents.replace('SBMLConstructorException', 'ValueError')
@@ -179,6 +201,14 @@
contents = contents.replace('const ', '')
contents = contents.replace('char *', 'string')
contents = contents.replace('string *', 'string')
+ contents = contents.replace('string &', 'string')
+ contents = contents.replace('double *', 'float')
+ contents = contents.replace('double &', 'float')
+ contents = contents.replace('float &', 'float')
+ contents = contents.replace('float&', 'float')
+ contents = contents.replace('bool &', 'bool')
+ contents = contents.replace('long &', 'long')
+ contents = contents.replace('int &', 'int')
return contents
@@ -266,9 +296,3 @@
if __name__ == '__main__':
main(sys.argv)
-
-
-# Misc. code from previous iterations that I don't want to throw
-# away just yet:
-#
-# text = p.sub(r'\1<table class="signatureTable"><tr><td class="signatureIntro"><b>Python method signature(s)</b>:</td><td class="signatureBlock">\2</td></tr></table>\1<p>', text)
Modified: branches/libsbml-experimental/docs/src/libsbml-accessing.html.in
===================================================================
--- branches/libsbml-experimental/docs/src/libsbml-accessing.html.in 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/libsbml-accessing.html.in 2014-07-29 07:47:34 UTC (rev 20938)
@@ -206,41 +206,72 @@
to use the Java-libSBML interface in an application.
-<h4>Step 1: set LD_LIBRARY_PATH (Linux), DYLD_LIBRARY_PATH
-(Mac OS X), or PATH (Windows)</h4>
+<h4>Step 1: set the run-time library search path</h4>
-First, please follow the instructions for configuring the
-<code>LD_LIBRARY_PATH</code> (under Linux, Unix, Cygwin),
-<code>DYLD_LIBRARY_PATH</code> (under Mac OS X) or <code>PATH</code> (under
-Windows) variables described in the beginning of this section. This is
-necessary so that, before the operating system starts a Java application,
-the system loaders can find libSBML's native library components.
+<p> This is necessary so that, before the operating system starts a Java
+application, the system loaders can find libSBML's native library components.
+For Java, there are two ways of doing this:
+<ol>
+
+<li style="margin-bottom: 1em"><em>Approach 1</em>: follow the instructions
+for configuring the <code>LD_LIBRARY_PATH</code> (under Linux, Unix, Cygwin),
+<code>DYLD_LIBRARY_PATH</code> (under Mac OS X) or
+<code>PATH</code> (under Windows) variables described in the <a
+href="#common">beginning of this section</a>.</li>
-<h4>Step 2: adjust the application's class search path</h4>
+<li><em>Approach 2</em>: start your Java interpreter with a value for the
+flag <code>-Djava.library.path</code> equal to the directory containing the
+libSBML library files (i.e., the <code>.jnilib</code>, <code>.dylib</code>
+and/or <code>.dll</code> files for libSBML, depending on the operating
+system—<em>not</em> the JAR file). For example, suppose that you
+configured libSBML to be installed into <code>/usr/local</code> on a Linux
+system. Then, you could start your application using a command that begins
+as follows:
-Java applications separately need to have their class search paths include
-the libSBML <code>.jar</code> and binary object files. This is often most
-easily done by setting the <code>CLASSPATH</code> environment variable, but
-other methods are possible. The exact recipe also depends on the operating
-system in use, as follows:
+<pre class="fragment">
+java -Djava.library.path=/usr/local/lib -cp .:/usr/local/share/java/libsbmlj.jar <span class="placeholder">APPLICATION</span>
+</pre></li>
+</ol>
+
+<p> If the library search path is <em>not</em> set, your application will
+encounter a <code>java.lang.UnsatisfiedLinkError</code> at run time when it
+attempts to call <code>System.loadLibrary("sbmlj")</code> (discussed in
+Step 3 below). Here is an example of such an error message printed by
+the Java interpreter:
+
+<pre class="fragment">
+Exception in thread "main" java.lang.UnsatisfiedLinkError: no libsbmlj in java.library.path
+ at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1764)
+ at java.lang.Runtime.loadLibrary0(Runtime.java:823)
+ at java.lang.System.loadLibrary(System.java:1044)
+ at test.<clinit>(test.java:31)
+</pre>
+
+
+<h4>Step 2: set the application's Java class search path</h4>
+
+Java applications separately <strong>also</strong> need to have their class
+search paths set up such that they include the libSBML <code>.jar</code>
+file. This is often most easily done by setting the <code>CLASSPATH</code>
+environment variable, but other methods are possible. The exact recipe also
+depends on the operating system in use, as follows:
+
<ul>
<li><em>Java on Linux, Mac OS X and similar Unix-like systems:</em>
-<p style="margin-top: 0.5em;"> You must either (1) set
-your <code>CLASSPATH</code> environment variable to include
-the <code>.jar</code> file, or (2) the <code>.jar</code> file must be listed
-in the <nobr><code>-classpath</code></nobr> option passed to the Java
-interpreter when it is started. As an example of the former approach,
-if you had configured libSBML to install itself into
-<code>/usr/local</code> (e.g., by using
-<nobr><code>--prefix=/usr/local</code></nobr> when configuring libSBML
-using the <code>configure</code> system),
-the <code>libsbmlj.jar</code> file will end up as
-<code>/usr/local/share/java/libsbmlj.jar</code> and your environment
-variable would at minimum need to be set as follows:
+<p style="margin-top: 0.5em;"> You must either (1) set your
+<code>CLASSPATH</code> environment variable to include the <code>.jar</code>
+file, or (2) the libSBML <code>.jar</code> file must be listed in the
+<nobr><code>-classpath</code></nobr> option passed to the Java interpreter
+when it is started. As an example of the former approach, if you had
+configured libSBML to be installed into <code>/usr/local</code>, the
+<code>libsbmlj.jar</code> file will end up as
+<code>/usr/local/share/java/libsbmlj.jar</code> on Linux and
+Mac OS X and your environment variable would at minimum need to be
+set as follows:
<pre class="fragment">
CLASSPATH=.:/usr/local/share/java/libsbmlj.jar
@@ -265,15 +296,33 @@
</li>
</ul>
+<p> If the Java class search path is <em>not</em> set, then your application
+will encounter a <code>java.lang.ClassNotFoundException</code> error at run
+time when it first attempts to access a libSBML class. Here is an example
+of such an error message:
+<pre class="fragment">
+Exception in thread "main" java.lang.NoClassDefFoundError: org/sbml/libsbml/XMLOutputStream
+ at test.main(test.java:15)
+Caused by: java.lang.ClassNotFoundException: org.sbml.libsbml.XMLOutputStream
+ at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
+ at java.security.AccessController.doPrivileged(Native Method)
+ at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
+ at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
+ at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
+ at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
+ ... 1 more
+</pre>
+
+
<h4>Step 3: load the libSBML JNI library in the application</h4>
-Finally, because of how JNI works in Java, an explicit call to
+<p> Finally, because of how JNI works in Java, an explicit call to
<code>System.loadLibrary</code> is needed in an application to load the
native language library portion of libSBML. This involves putting a Java
<code>static</code> block of code somewhere in your application, usually in
-the application's main class. The following example illustrates one way of
-doing this.
+the application's main class. The following is an example of the minimum
+code for doing this:
<pre class="fragment"><span style="color: #777">import org.sbml.libsbml.*;
@@ -290,6 +339,32 @@
*/
static
{
+ System.loadLibrary("sbmlj");
+ }
+}
+</pre>
+
+<p> For real applications, it is often useful to catch run-time exceptions
+and try to interpret the causes on users' behalf. The following is a more
+elaborate example of code to load libSBML that tries to catch exceptions at
+run-time, interpret their meaning, and provide informative error messages
+about their causes. (Note that the following is an entirely optional
+replacement for the simpler version above.)
+
+<pre class="fragment"><span style="color: #777">import org.sbml.libsbml.*;
+public class YourMainApplicationClass
+{
+ public static void main (String[] args)
+ {
+ /* Whatever your application does here ... */
+ }
+</span>
+ /**
+ * The following static block is needed in order to load the
+ * libSBML Java interface library when the application starts.
+ */
+ static
+ {
String varname;
String shlibname;
@@ -298,9 +373,14 @@
varname = "DYLD_LIBRARY_PATH"; // We're on a Mac.
shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
}
+ else if (System.getProperty("os.name").startsWith("Windows"))
+ {
+ varname = "PATH"; // We're on Windows.
+ shlibname = "sbmlj.dll and/or libsbml.dll";
+ }
else
{
- varname = "LD_LIBRARY_PATH"; // We're not on a Mac.
+ varname = "LD_LIBRARY_PATH"; // Linux or possibly some other Unix.
shlibname = "libsbmlj.so and/or libsbml.so";
}
Modified: branches/libsbml-experimental/docs/src/libsbml-java-reading.html
===================================================================
--- branches/libsbml-experimental/docs/src/libsbml-java-reading.html 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/libsbml-java-reading.html 2014-07-29 07:47:34 UTC (rev 20938)
@@ -58,17 +58,7 @@
static
{
- try
- {
- System.loadLibrary("sbmlj");
- /* Extra check to be sure we have access to libSBML: */
- Class.forName("org.sbml.libsbml.libsbml");
- }
- catch (Exception e)
- {
- System.err.println("Error: could not load the libSBML library");
- System.exit(1);
- }
+ System.loadLibrary("sbmlj");
}
}
</pre>
Modified: branches/libsbml-experimental/docs/src/libsbml-programming.txt
===================================================================
--- branches/libsbml-experimental/docs/src/libsbml-programming.txt 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/libsbml-programming.txt 2014-07-29 07:47:34 UTC (rev 20938)
@@ -14,8 +14,8 @@
@endif
@if python
- @subpage libsbml-python-reading-files
+- @subpage libsbml-python-creating-model
- @subpage libsbml-math
-- @subpage libsbml-python-creating-model
- @subpage libsbml-python-example-files
@endif
@if conly
Modified: branches/libsbml-experimental/docs/src/libsbml-python-creating-model.txt
===================================================================
--- branches/libsbml-experimental/docs/src/libsbml-python-creating-model.txt 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/libsbml-python-creating-model.txt 2014-07-29 07:47:34 UTC (rev 20938)
@@ -19,16 +19,21 @@
@endcode
Next, we define a simple function to check the return values of libSBML calls
-and report any errors encountered. This function is designed to work with
-null values and error code values.
+and report any errors encountered. This function uses a generic parameter
+for the value (the first argument), and tests the value against nulls as well
+as integer codes. This makes it suitable for testing the return values from
+any libSBML function, whether the function returns an object or an integer
+status codes. The benefit of this will become clear in the code further
+below.
@code{.py}
def check(value, message):
- """If the value is None, prints the message and exit with status code 1.
- If the value is an integer, checks if it's equal to LIBSBML_OPERATION_SUCCESS.
- If if is, returns without further action; if it's a different integer, prints
- the message along with text from libSBML explaining the meaning of the code,
- and exits with status code 1.
+ """If 'value' is None, prints an error message constructed using
+ 'message' and then exits with status code 1. If 'value' is an integer,
+ it assumes it is a libSBML return status code. If the code value is
+ LIBSBML_OPERATION_SUCCESS, returns without further action; if it is not,
+ prints an error message constructed using 'message' along with text from
+ libSBML explaining the meaning of the code, and exits with status code 1.
"""
if value == None:
print('LibSBML returned a null value trying to ' + message + '.')
@@ -47,18 +52,22 @@
return
@endcode
-Now we get to the real business of building the model. Here we encapsulated
-the entire model in one function to make the example simpler, but in a real
-application, it would likely be more effective to decompose the function
-further. For example, an improvement would be to abstract away the
-construction of major pieces such as SBML species into functions that
-encapsulate repeated code for setting the component's attributes.
+Now we get to the real business of building the model. Here we
+encapsulated the entire model in one function to make the example
+simpler, but in a real application, it would likely be more effective to
+decompose the function further. For example, an improvement would be to
+abstract away the construction of major pieces such as SBML species into
+functions that encapsulate repeated code for setting the component's
+attributes.
@code{.py}
def create_model():
"""Returns a simple but complete SBML Level 3 model for illustration."""
- # Create an empty SBMLDocument object:
+ # Create an empty SBMLDocument object. It's a good idea to check for
+ # possible errors. Even when the parameter values are hardwired like
+ # this, it is still possible for a failure to occur (e.g., if the
+ # operating system runs out of memory).
try:
document = SBMLDocument(3, 1)
@@ -66,7 +75,12 @@
print('Could not create SBMLDocumention object')
sys.exit(1)
- # Create the basic Model object inside the SBMLDocument object:
+ # Create the basic Model object inside the SBMLDocument object. To
+ # produce a model with complete units for the reaction rates, we need
+ # to set the 'timeUnits' and 'extentUnits' attributes on Model. We
+ # set 'substanceUnits' too, for good measure, though it's not strictly
+ # necessary here because we also set the units for invididual species
+ # in their definitions.
model = document.createModel()
check(model, 'create model')
@@ -74,7 +88,9 @@
check(model.setExtentUnits("mole"), 'set model units of extent')
check(model.setSubstanceUnits('mole'), 'set model substance units')
- # Create a unit definition we will need later:
+ # Create a unit definition we will need later. Note that SBML Unit
+ # objects must have all four attributes 'kind', 'exponent', 'scale'
+ # and 'multiplier' defined.
per_second = model.createUnitDefinition()
check(per_second, 'create unit definition')
@@ -86,7 +102,8 @@
check(unit.setScale(0), 'set unit scale')
check(unit.setMultiplier(1), 'set unit multiplier')
- # Create components inside the model:
+ # Create a compartment inside this model, and set the required
+ # attributes for an SBML compartment in SBML Level 3.
c1 = model.createCompartment()
check(c1, 'create compartment')
@@ -96,6 +113,12 @@
check(c1.setSpatialDimensions(3), 'set compartment dimensions')
check(c1.setUnits('litre'), 'set compartment size units')
+ # Create two species inside this model, set the required attributes
+ # for each species in SBML Level 3 (which are the 'id', 'compartment',
+ # 'constant', 'hasOnlySubstanceUnits', and 'boundaryCondition'
+ # attributes), and initialize the amount of the species along with the
+ # units of the amount.
+
s1 = model.createSpecies()
check(s1, 'create species s1')
check(s1.setId('s1'), 'set species s1 id')
@@ -116,13 +139,23 @@
check(s2.setBoundaryCondition(False), 'set "boundaryCondition" on s2')
check(s2.setHasOnlySubstanceUnits(False), 'set "hasOnlySubstanceUnits" on s2')
+ # Create a parameter object inside this model, set the required
+ # attributes 'id' and 'constant' for a parameter in SBML Level 3, and
+ # initialize the parameter with a value along with its units.
+
k = model.createParameter()
check(k, 'create parameter k')
check(k.setId('k'), 'set parameter k id')
+ check(k.setConstant(True), 'set parameter k "constant"')
check(k.setValue(1), 'set parameter k value')
check(k.setUnits('per_second'), 'set parameter k units')
- check(k.setConstant(True), 'set parameter k "constant"')
+ # Create a reaction inside this model, set the reactants and products,
+ # and set the reaction rate expression (the SBML "kinetic law"). We
+ # set the minimum required attributes for all of these objects. The
+ # units of the reaction rate are determined from the 'timeUnits' and
+ # 'extentUnits' attributes on the Model object.
+
r1 = model.createReaction()
check(r1, 'create reaction')
check(r1.setId('r1'), 'set reaction id')
@@ -146,7 +179,8 @@
check(kinetic_law, 'create kinetic law')
check(kinetic_law.setMath(math_ast), 'set math on kinetic law')
- # Done. Return a text string containing the model.
+ # And we're done creating the basic model.
+ # Now return a text string containing the model in XML format.
return writeSBMLToString(document)
@endcode
Modified: branches/libsbml-experimental/docs/src/python-substitutions/CompPkgNamespaces.py
===================================================================
--- branches/libsbml-experimental/docs/src/python-substitutions/CompPkgNamespaces.py 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/python-substitutions/CompPkgNamespaces.py 2014-07-29 07:47:34 UTC (rev 20938)
@@ -2,9 +2,7 @@
"""
@sbmlpackage{comp}
- @htmlinclude pkg-marker-comp.html Class to store SBML Level, Version, and XML
- namespace for the SBML Hierarchical Model Composition (“comp”)
- package.
+ @htmlinclude pkg-marker-comp.html SBMLNamespaces extension for the package.
@htmlinclude not-sbml-warning.html
Modified: branches/libsbml-experimental/docs/src/python-substitutions/FbcPkgNamespaces.py
===================================================================
--- branches/libsbml-experimental/docs/src/python-substitutions/FbcPkgNamespaces.py 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/python-substitutions/FbcPkgNamespaces.py 2014-07-29 07:47:34 UTC (rev 20938)
@@ -2,9 +2,7 @@
"""
@sbmlpackage{fbc}
- @htmlinclude pkg-marker-fbc.html Class to store SBML Level, Version, and XML
- namespace for the SBML Flux Balance Constraints (“fbc”)
- package.
+ @htmlinclude pkg-marker-fbc.html SBMLNamespaces extension for the package.
@htmlinclude not-sbml-warning.html
Modified: branches/libsbml-experimental/docs/src/python-substitutions/LayoutPkgNamespaces.py
===================================================================
--- branches/libsbml-experimental/docs/src/python-substitutions/LayoutPkgNamespaces.py 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/python-substitutions/LayoutPkgNamespaces.py 2014-07-29 07:47:34 UTC (rev 20938)
@@ -2,8 +2,7 @@
"""
@sbmlpackage{layout}
- @htmlinclude pkg-marker-layout.html Class to store SBML Level, Version, and XML
- namespace for the SBML Layout (“layout”) package.
+ @htmlinclude pkg-marker-layout.html SBMLNamespaces extension for the package.
@htmlinclude not-sbml-warning.html
Modified: branches/libsbml-experimental/docs/src/python-substitutions/QualPkgNamespaces.py
===================================================================
--- branches/libsbml-experimental/docs/src/python-substitutions/QualPkgNamespaces.py 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/docs/src/python-substitutions/QualPkgNamespaces.py 2014-07-29 07:47:34 UTC (rev 20938)
@@ -2,8 +2,7 @@
"""
@sbmlpackage{qual}
- @htmlinclude pkg-marker-qual.html Class to store SBML Level, Version, and XML
- namespace for the SBML Qualitative Models (“qual”) package.
+ @htmlinclude pkg-marker-qual.html SBMLNamespaces extension for the package.
@htmlinclude not-sbml-warning.html
Modified: branches/libsbml-experimental/examples/python/createSimpleModel.py
===================================================================
--- branches/libsbml-experimental/examples/python/createSimpleModel.py 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/examples/python/createSimpleModel.py 2014-07-29 07:47:34 UTC (rev 20938)
@@ -44,11 +44,12 @@
def check(value, message):
- """If the value is None, prints the message and exit with status code 1.
- If the value is an integer, checks if it's equal to LIBSBML_OPERATION_SUCCESS.
- If it is, returns without further action; if it's a different integer, prints
- the message along with text from libSBML explaining the meaning of the code,
- and exits with status code 1.
+ """If 'value' is None, prints an error message constructed using
+ 'message' and then exits with status code 1. If 'value' is an integer,
+ it assumes it is a libSBML return status code. If the code value is
+ LIBSBML_OPERATION_SUCCESS, returns without further action; if it is not,
+ prints an error message constructed using 'message' along with text from
+ libSBML explaining the meaning of the code, and exits with status code 1.
"""
if value == None:
print('LibSBML returned a null value trying to ' + message + '.')
@@ -70,15 +71,23 @@
def create_model():
"""Returns a simple but complete SBML Level 3 model for illustration."""
- # Create an empty SBMLDocument object:
+ # Create an empty SBMLDocument object. It's a good idea to check for
+ # possible errors. Even when the parameter values are hardwired like
+ # this, it is still possible for a failure to occur (e.g., if the
+ # operating system runs out of memory).
try:
document = SBMLDocument(3, 1)
except ValueError:
- print('Could not create SBMLDocument object')
+ print('Could not create SBMLDocumention object')
sys.exit(1)
- # Create the basic Model object inside the SBMLDocument object:
+ # Create the basic Model object inside the SBMLDocument object. To
+ # produce a model with complete units for the reaction rates, we need
+ # to set the 'timeUnits' and 'extentUnits' attributes on Model. We
+ # set 'substanceUnits' too, for good measure, though it's not strictly
+ # necessary here because we also set the units for invididual species
+ # in their definitions.
model = document.createModel()
check(model, 'create model')
@@ -86,7 +95,9 @@
check(model.setExtentUnits("mole"), 'set model units of extent')
check(model.setSubstanceUnits('mole'), 'set model substance units')
- # Create a unit definition we will need later:
+ # Create a unit definition we will need later. Note that SBML Unit
+ # objects must have all four attributes 'kind', 'exponent', 'scale'
+ # and 'multiplier' defined.
per_second = model.createUnitDefinition()
check(per_second, 'create unit definition')
@@ -98,7 +109,8 @@
check(unit.setScale(0), 'set unit scale')
check(unit.setMultiplier(1), 'set unit multiplier')
- # Create components inside the model:
+ # Create a compartment inside this model, and set the required
+ # attributes for an SBML compartment in SBML Level 3.
c1 = model.createCompartment()
check(c1, 'create compartment')
@@ -108,6 +120,12 @@
check(c1.setSpatialDimensions(3), 'set compartment dimensions')
check(c1.setUnits('litre'), 'set compartment size units')
+ # Create two species inside this model, set the required attributes
+ # for each species in SBML Level 3 (which are the 'id', 'compartment',
+ # 'constant', 'hasOnlySubstanceUnits', and 'boundaryCondition'
+ # attributes), and initialize the amount of the species along with the
+ # units of the amount.
+
s1 = model.createSpecies()
check(s1, 'create species s1')
check(s1.setId('s1'), 'set species s1 id')
@@ -128,13 +146,23 @@
check(s2.setBoundaryCondition(False), 'set "boundaryCondition" on s2')
check(s2.setHasOnlySubstanceUnits(False), 'set "hasOnlySubstanceUnits" on s2')
+ # Create a parameter object inside this model, set the required
+ # attributes 'id' and 'constant' for a parameter in SBML Level 3, and
+ # initialize the parameter with a value along with its units.
+
k = model.createParameter()
check(k, 'create parameter k')
check(k.setId('k'), 'set parameter k id')
+ check(k.setConstant(True), 'set parameter k "constant"')
check(k.setValue(1), 'set parameter k value')
check(k.setUnits('per_second'), 'set parameter k units')
- check(k.setConstant(True), 'set parameter k "constant"')
+ # Create a reaction inside this model, set the reactants and products,
+ # and set the reaction rate expression (the SBML "kinetic law"). We
+ # set the minimum required attributes for all of these objects. The
+ # units of the reaction rate are determined from the 'timeUnits' and
+ # 'extentUnits' attributes on the Model object.
+
r1 = model.createReaction()
check(r1, 'create reaction')
check(r1.setId('r1'), 'set reaction id')
@@ -158,7 +186,8 @@
check(kinetic_law, 'create kinetic law')
check(kinetic_law.setMath(math_ast), 'set math on kinetic law')
- # Done. Return a text string containing the model.
+ # And we're done creating the basic model.
+ # Now return a text string containing the model in XML format.
return writeSBMLToString(document)
Modified: branches/libsbml-experimental/src/bindings/csharp/Makefile.in
===================================================================
--- branches/libsbml-experimental/src/bindings/csharp/Makefile.in 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/src/bindings/csharp/Makefile.in 2014-07-29 07:47:34 UTC (rev 20938)
@@ -360,7 +360,7 @@
all:
@echo
@echo "Reconfigure libSBML using --with-csharp to enable CSharp support.";
- @echo "(--with-cli-interpreter=path" and/or --with-csharp-compiler=path may be required.)";
+ @echo "(--with-cli-interpreter=path and/or --with-csharp-compiler=path may be required.)";
@echo
@exit 1
endif
@@ -368,8 +368,25 @@
# Until we improve swigdoc.py, the following warnings are spurious and annoying
# and we don't need to see them.
-CSC_NOWARN = -nowarn:108,109,219
+# the compile run disables the following warnings
+# - 105: duplicated using statement, due to the patch above
+# - 108: 'method name' hides inherited member 'base member name'. Use the
+# new keyword if hiding was intended.
+# - 114: 'method name' hides inherited member 'base member name'. To make
+# the current member override that implementation, add the override
+# keyword. Otherwise add the new keyword.
+# - 1570: XML comment on 'class name' has badly formed XML.
+# - 1572: XML comment on 'method name' has a param tag for 'parameter name'
+# but there is no parameter by that name.
+# - 1573: Parameter 'parameter name' has no matching param tag in the XML
+# comment for 'method name' (but other parameters do).
+# - 1574: XML comment on 'method name' has cref attribute 'method name'
+# that could not be resolved.
+# - 1591: Missing XML comment for publicly visible type or member 'method
+# name'
+CSC_NOWARN = -nowarn:105,108,109,114,1570,1572,1573,1574,1591
+
$(csproxy_lib): $(outpath)/libsbml.cs $(dllimport_lib)
-"$(SN)" -k $(sn_keyfile)
"$(CSHARP_COMPILER)" $(CSC_OPT_SHARED) $(CSC_NOWARN) \
@@ -464,6 +481,13 @@
# stand-in for the .cs files. Their creation results in the creation of the .cs
# files too -- both are made by running swig.
+patch-swig-output:
+ @list='$(wildcard $(outpath)/*.cs)'; for file in $$list; do \
+ echo 'using System;\nusing System.Runtime.InteropServices;\n\n' > $(outpath)/.tmpfile; \
+ cat $$file >> $(outpath)/.tmpfile; \
+ mv -f $(outpath)/.tmpfile $$file; \
+ done
+
# for non-Windows
libsbml_wrap.cpp $(outpath) : $(swig_sources) $(main_sources) csdoc.i \
$(shell $(call check_comp)) $(shell $(call check_fbc)) \
@@ -473,6 +497,7 @@
"$(SWIG)" $(SWIGFLAGS) $(sort $(default_includes) $(INCLUDES)) \
-c++ -csharp -namespace libsbmlcs -dllimport $(dllimport_name) \
-outdir $(outpath) -o libsbml_wrap.cpp libsbml.i
+ make patch-swig-output
# for Windows
libsbml_wrap-win.cpp $(outpath_win) : $(swig_sources) $(main_sources) csdoc.i \
Modified: branches/libsbml-experimental/src/bindings/matlab/OutputSBML.c
===================================================================
--- branches/libsbml-experimental/src/bindings/matlab/OutputSBML.c 2014-07-29 07:22:58 UTC (rev 20937)
+++ branches/libsbml-experimental/src/bindings/matlab/OutputSBML.c 2014-07-29 07:47:34 UTC (rev 20938)
@@ -55,6 +55,108 @@
#endif
+
+#if defined(WIN32) && !defined(CYGWIN) && !defined(USE_OCTAVE)
+#define FILE_CHAR wchar_t*
+#define FILE_FOPEN(file) _wfopen(file, L"r")
+#define USE_FILE_WCHAR 1
+#else
+#define FILE_CHAR char*
+#define FILE_FOPEN(file) fopen(file, "r")
+#endif
+
+#ifndef uint16_t
+#define uint16_t unsigned short
+#endif
+
+FILE_CHAR readUnicodeString(const mxArray *prhs, mwSize length)
+{
+#ifdef USE_OCTAVE
+ char* ansii = (char *) mxCalloc(length, sizeof(char));
+ mxGetString(prhs, ansii, length);
+ return ansii;
+#else
+ wchar_t* utf16 = (wchar_t *) mxCalloc(length, sizeof(wchar_t));
+ char* utf8 = NULL;
+ uint16_T *ch = (uint16_T *) mxGetData(prhs);
+ wchar_t* p = utf16;
+ mwSize i;
+ for ( i = 0; i < length-1; ++i)
+ *p++ = *ch++;
+ *p = 0;
+
+#if USE_FILE_WCHAR
+ return utf16;
+#else
+
+ utf8 = (char*)mxCalloc(length*2, sizeof(char));
+
+ wcstombs(utf8, utf16, length*2);
+
+ /*mxFree(utf16);*/
+
+ if (utf8 != NULL && strlen(utf8) == 0 && length > 0)
+ {
+ mexErrMsgTxt("This string uses characters that cannot be expressed in UTF8, please rename the file.");
+ }
+
+ return utf8;
+#endif /* USE_FILE_WCHAR */
+
+#endif /* USE_OCTAVE*/
+
+}
+
+
+FILE_CHAR readUnicodeStringFromArrays(mxArray *mxFilename[2])
+
+{
+ mwSize nBuflen = (mxGetM(mxFilename[0])*mxGetN(mxFilename[0])+1);
+ FILE_CHAR pacTempString1 = readUnicodeString(mxFilename[0],nBuflen);
+
+ mwSize nBufferLen = (mxGetM(mxFilename[1])*mxGetN(mxFilename[1])+1);
+ FILE_CHAR pacTempString2 = readUnicodeString(mxFilename[1],nBufferLen);
+
+#if USE_FILE_WCHAR
+ FILE_CHAR pacFilename = (wchar_t *) mxCalloc(nBufferLen+nBuflen, sizeof(wchar_t));
+ wcscpy(pacFilename, pacTempString2);
+ wcscpy(pacFilename, pacTempString1);
+#else
+ FILE_CHAR pacFilename = (char *) mxCalloc(nBufferLen+nBuflen, sizeof(char));
+ strcpy(pacFilename, pacTempString2);
+ strcat(pacFilename, pacTempString1);
+#endif
+
+ /*mxFree(pacTempString1);*/
+ /*mxFree(pacTempString2);*/
+ return pacFilename;
+}
+
+#if USE_FILE_WCHAR
+
+int endsWith(const wchar_t* fileName, const char* ext)
+{
+ size_t len = wcslen(fileName), i;
+ size_t targetLen = strlen(ext);
+ wchar_t* temp1 = (wchar_t*)mxCalloc(targetLen, sizeof(wchar_t));
+ char* temp2 = (char*)mxCalloc(targetLen, sizeof(char));
+ int result = 0;
+
+ for (i = 0; i < targetLen; ++i)
+ {
+ temp1[i] = fileName[len - targetLen + i];
+ }
+
+ wcstombs(temp2,temp1, targetLen);
+ result = strcmp_insensitive(temp2, ext);
+
+ /*mxFree(temp1);*/
+ /*mxFree(temp2);*/
+ return result;
+}
+
+#endif
+
static char * timeSymbol = NULL;
static char * delaySymbol = NULL;
static char * avoSymbol = NULL;
@@ -136,36 +238,37 @@
mexFunction (int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
- mxArray * mxCheckStructure[2];
- mxArray * mxFilename[2], * mxExt[1];
- int nStatus;
- char *pacFilename = NULL, *pacTempString1 = NULL, *pacTempString2 = NULL;
+ mxArray * mxCheckStructure[2];
+ mxArray * mxFilename[2], * mxExt[1];
+ int nStatus;
+ FILE_CHAR pacFilename = NULL;
+ char *pacTempString1 = NULL, *pacTempString2 = NULL;
size_t nBuflen, nBufferLen;
-
- SBMLDocument_t *sbmlDocument;
+
+ SBMLDocument_t *sbmlDocument;
SBMLNamespaces_t *ns;
XMLNamespaces_t *xmlns;
- Model_t *sbmlModel;
+ Model_t *sbmlModel;
- mxArray * mxLevel, * mxVersion, * mxNotes, * mxAnnotations, * mxFBCVersion;
+ mxArray * mxLevel, * mxVersion, * mxNotes, * mxAnnotations, * mxFBCVersion;
mxArray * mxName, * mxId, *mxNamespaces, *mxMetaid, *mxTimeSymbol;
mxArray * mxSubstanceUnits, * mxTimeUnits, *mxLengthUnits, *mxAreaUnits;
mxArray * mxVolumeUnits, * mxExtentUnits, *mxConversionFactor;
mxArray * mxDelaySymbol, *mxAvoSymbol, *mxActiveObjective;
- unsigned int nLevel, nVersion, nFBCVersion;
- char * pacNotes, * pacAnnotations;
+ unsigned int nLevel, nVersion, nFBCVersion;
+ char * pacNotes, * pacAnnotations;
char * pacName, * pacId, *pacMetaid;
char * pacSubstanceUnits, * pacTimeUnits, *pacLengthUnits, *pacAreaUnits;
char * pacVolumeUnits, * pacExtentUnits, *pacConversionFactor, *pacActiveObjective;
int nSBOTerm;
-
+
SBasePlugin_t * plugin;
- mxArray * mxParameters, * mxCompartments, * mxFunctionDefinitions;
+ mxArray * mxParameters, * mxCompartments, * mxFunctionDefinitions;
mxArray * mxUnitDefinitions, *mxSBOTerm;
- mxArray * mxSpecies, * mxRules, * mxReactions, * mxEvents, * mxConstraints;
- mxArray * mxSpeciesTypes, * mxCompartmentTypes, * mxInitialAssignments;
+ mxArray * mxSpecies, * mxRules, * mxReactions, * mxEvents, * mxConstraints;
+ mxArray * mxSpeciesTypes, * mxCompartmentTypes, * mxInitialAssignments;
mxArray * mxFluxBounds, *mxObjectives, *mxFluxObjectives;
unsigned int usingOctave = 0;
mxArray * mxOctave[1];
@@ -176,136 +279,130 @@
/* determine whether we are in octave or matlab */
mexCallMATLAB(1, mxOctave, 0, NULL, "isoctave");
-
+
nBuflen = (mxGetM(mxOctave[0])*mxGetN(mxOctave[0])+1);
pacTempString1 = (char *) mxCalloc(nBuflen, sizeof(char));
nStatus = mxGetString(mxOctave[0], pacTempString1, (mwSize)(nBuflen));
if (nStatus != 0)
{
- mexErrMsgTxt("Could not determine platform");
+ mexErrMsgTxt("Could not determine platform");
}
if (!(strcmp_insensitive(pacTempString1, "0") == 0))
usingOctave = 1;
-/*************************************************************************************
- * validate inputs and outputs
- **********************************************************************************/
+ /*************************************************************************************
+ * validate inputs and outputs
+ **********************************************************************************/
if (nrhs < 1)
{
- mexErrMsgTxt("Must supply at least the model as an output argument\n"
- "USAGE: OutputSBML(SBMLModel, (filename))");
+ mexErrMsgTxt("Must supply at least the model as an output argument\n"
+ "USAGE: OutputSBML(SBMLModel, (filename))");
}
if (usingOctave == 1 && nrhs < 2)
{
- mexErrMsgTxt("Octave requires the filename to be specified\n"
- "USAGE: OutputSBML(SBMLModel, filename)");
+ mexErrMsgTxt("Octave requires the filename to be specified\n"
+ "USAGE: OutputSBML(SBMLModel, filename)");
}
if (nrhs > 3)
{
inInstaller = 1;
}
-/**
- * create a copy of the input
- */
- mxModel[0] = mxDuplicateArray(prhs[0]);
- mexMakeArrayPersistent(mxModel[0]);
- mexAtExit(FreeMem);
+ /**
+ * create a copy of the input
+ */
+ mxModel[0] = mxDuplicateArray(prhs[0]);
+ mexMakeArrayPersistent(mxModel[0]);
+ mexAtExit(FreeMem);
-/**
- * we know have the option of a third argument that indicates that we
- * want the structure to ONLY contain expected fields or not
- */
-if (nrhs > 2)
-{
- mxModel[1] = (mxArray *)prhs[2];
-}
-else
-{
- mxModel[1] = mxCreateDoubleScalar(1);
-}
-
-/**
- * check number and type of output arguments
- * SHOULDNT BE ANY
- */
- if (nlhs > 0)
- {
- mexErrMsgTxt("Too many output arguments\n"
- "USAGE: OutputSBML(SBMLModel, (filename))");
- }
+ /**
+ * we know have the option of a third argument that indicates that we
+ * want the structure to ONLY contain expected fields or not
+ */
+ if (nrhs > 2)
+ {
+ mxModel[1] = (mxArray *)prhs[2];
+ }
+ else
+ {
+ mxModel[1] = mxCreateDoubleScalar(1);
+ }
-/**
- * check number and type of input arguments
- * must be a valid MATLAB_SBML structure
- * and optionally the filename
- */
-
- if (nrhs > 4)
- {
- mexErrMsgTxt("Too many input arguments\n"
- "USAGE: OutputSBML(SBMLModel, (filename), (exclusive))");
- }
-
- nStatus = mexCallMATLAB(2, mxCheckStructure, 2, mxModel, "isSBML_Model");
-
- if ((nStatus != 0) || (mxIsLogicalScalarTrue(mxCheckStructure[0]) != 1))
- {
- /* there are errors - use the pacFilename char * to list these to the user */
+ /**
+ * check number and type of output arguments
+ * SHOULDNT BE ANY
+ */
+ if (nlhs > 0)
+ {
+ mexErrMsgTxt("Too many output arguments\n"
+ "USAGE: OutputSBML(SBMLModel, (filename))");
+ }
+
+ /**
+ * check number and type of input arguments
+ * must be a valid MATLAB_SBML structure
+ * and optionally the filename
+ */
+
+ if (nrhs > 4)
+ {
+ mexErrMsgTxt("Too many input arguments\n"
+ "USAGE: OutputSBML(SBMLModel, (filename), (exclusive))");
+ }
+
+ nStatus = mexCallMATLAB(2, mxCheckStructure, 2, mxModel, "isSBML_Model");
+
+ if ((nStatus != 0) || (mxIsLogicalScalarTrue(mxCheckStructure[0]) != 1))
+ {
+ /* there are errors - use the pacTempString1 char * to list these to the user */
nBuflen = (mxGetM(mxCheckStructure[1])*mxGetN(mxCheckStructure[1])+1);
- pacFilename = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxCheckStructure[1], pacFilename, (mwSize)(nBuflen));
+ pacTempString1 = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxCheckStructure[1], pacTempString1, (mwSize)(nBuflen));
if (nStatus == 0)
{
msgTxt = (char *) mxCalloc(200+nBuflen, sizeof(char));
sprintf(msgTxt, "\n%s\n\nErrors reported: %s%s\n", "First input must be a valid MATLAB_SBML Structure",
- pacFilename, "USAGE: OutputSBML(SBMLModel, (filename))");
+ pacTempString1, "USAGE: OutputSBML(SBMLModel, (filename))");
mexErrMsgTxt(msgTxt);
}
else
{
msgTxt = (char *) mxCalloc(200, sizeof(char));
sprintf(msgTxt, "%s\n%s", "First input must be a valid MATLAB_SBML Structure",
- "USAGE: OutputSBML(SBMLModel, (filename))");
+ "USAGE: OutputSBML(SBMLModel, (filename))");
mexErrMsgTxt(msgTxt);
}
- }
+ }
if (nrhs >= 2)
{
-
- if (mxIsChar(prhs[1]) != 1)
- {
- mexErrMsgTxt("Second input must be a filename\n"
- "USAGE: OutputSBML(SBMLModel, (filename))");
- }
- nBuflen = (mxGetM(prhs[1])*mxGetN(prhs[1])+1);
- pacFilename = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(prhs[1], pacFilename, (mwSize)(nBuflen));
-
- if (nStatus != 0)
+ if (mxIsChar(prhs[1]) != 1)
{
- mexErrMsgTxt("Cannot copy filename");
+ mexErrMsgTxt("Second input must be a filename\n"
+ "USAGE: OutputSBML(SBMLMod...
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