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Created release 1.1.
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draeger committed Apr 25, 2013
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4 changes: 2 additions & 2 deletions build.xml
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<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib}/jsbml-1.0-a1-with-dependencies.jar"/>
<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib}/SimulationCoreLibrary_v1.3_slim.jar"/>
<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib}/sysbio.jar"/>
<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib-garuda}/garuda-csr.jar"/>
<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib-garuda}/jsonic-1.2.10.jar"/>
<!--<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib-garuda}/garuda-csr.jar"/>
<zipfileset excludes="META-INF/**, COPYING.txt, licenses/COPYING.txt, overview.html, AUTHORS.txt" src="${lib-garuda}/jsonic-1.2.10.jar"/>-->
</jar>

</target>
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250 changes: 250 additions & 0 deletions dist/SBMLsimulator-1.1/releaseNotes1.1.html
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<h1>Release notes of SBMLsimulator version 1.1</h1>
<h2>New features</h2>
<ul>
<li>Includes version 1.3 of the <a href="http://simulation-core.sourceforge.net/">Systems Biology Simulation Core Library</a></li>
</ul>

<h2>Bugs that were fixed</h2>
<ul>
<li>All issues related to the simulation of SBML files that were fixed in the <a href="http://simulation-core.sourceforge.net/">Systems Biology Simulation Core Library</a></li>
</ul>

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Last changes: 24.04.2013, 17:32 CEST &nbsp;&#124;&nbsp;&copy; 2001-2011&nbsp;&#124;&nbsp;University of T&uuml;bingen&nbsp;&#124;&nbsp;<a href="/impressum.html">Impressum</a>
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2 changes: 1 addition & 1 deletion dist/SBMLsimulator-latest.jnlp
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
<resources>
<!-- Application Resources -->
<j2se version="1.6+" initial-heap-size="64m" max-heap-size="256m" java-vm-args="-splash:org/sbml/simulator/gui/img/Splash.gif" href="http://java.sun.com/products/autodl/j2se"/>
<jar href="SBMLsimulator-1.1.jar" main="true"/>
<jar href="SBMLsimulator-latest.jar" main="true"/>
</resources>
<application-desc name="SBMLsimulator" main-class="org.sbml.simulator.SBMLsimulator" width="640" height="480"/>
<update check="background"/>
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13 changes: 10 additions & 3 deletions src/org/sbml/simulator/SBMLsimulator.java
Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,11 @@ public class SBMLsimulator extends Launcher {
* The package where all ODE solvers are assumed to be located.
*/
public static final String SOLVER_PACKAGE = "org.simulator.math.odes";

/**
*
*/
public static final boolean garuda = true;

/**
* An array of all available implementations of distance functions to judge
Expand Down Expand Up @@ -290,7 +295,9 @@ public List<Class<? extends KeyProvider>> getCmdLineOptions() {
defAndKeys.add(GUIOptions.class);
defAndKeys.add(PlotOptions.class);
defAndKeys.add(CSVOptions.class);
defAndKeys.add(GarudaOptions.class);
if (garuda) {
defAndKeys.add(GarudaOptions.class);
}
return defAndKeys;
}

Expand Down Expand Up @@ -365,9 +372,9 @@ public short getYearWhenProjectWasStarted() {
*/
public BaseFrame initGUI(AppConf appConf) {
final BaseFrame gui = new SimulatorUI(appConf);
if (getCmdLineOptions().contains(GarudaOptions.class)
if (garuda && (getCmdLineOptions().contains(GarudaOptions.class)
&& (!appConf.getCmdArgs().containsKey(GarudaOptions.CONNECT_TO_GARUDA) ||
appConf.getCmdArgs().getBoolean(GarudaOptions.CONNECT_TO_GARUDA))) {
appConf.getCmdArgs().getBoolean(GarudaOptions.CONNECT_TO_GARUDA)))) {
new Thread(new Runnable() {
/* (non-Javadoc)
* @see java.lang.Runnable#run()
Expand Down
4 changes: 2 additions & 2 deletions src/org/sbml/simulator/gui/SimulatorUI.java
Original file line number Diff line number Diff line change
Expand Up @@ -327,8 +327,8 @@ protected JMenuItem[] additionalEditMenuItems() {
optimization.setEnabled(false);
items.add(optimization);

if (!appConf.getCmdArgs().containsKey(GarudaOptions.CONNECT_TO_GARUDA)
|| appConf.getCmdArgs().getBoolean(GarudaOptions.CONNECT_TO_GARUDA)) {
if (SBMLsimulator.garuda && (!appConf.getCmdArgs().containsKey(GarudaOptions.CONNECT_TO_GARUDA)
|| appConf.getCmdArgs().getBoolean(GarudaOptions.CONNECT_TO_GARUDA))) {
items.add(GarudaGUIfactory.createGarudaMenu(EventHandler.create(ActionListener.class, this, "sendToGaruda")));
}

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