Changeset 3155

Timestamp:

03/11/10 14:41:02 (5 months ago)

Author:

martijn

Message:

Biopax conversion added to converter

Location:

trunk

Files:

• build.xml (modified) (1 diff)
• src/core/org/pathvisio/util/Converter.java (modified) (4 diffs)

trunk/build.xml

@@ -266 +266 @@
         <target name="jar" depends="compile-swing" description="Generates pathvisio.jar and pathvisio_core.jar">
                 <manifestclasspath property="manifest.cp" jarfile="pathvisio.jar">
-                        <classpath refid="standalone.libs" />
+                        <classpath>
+                                <path refid="standalone.libs" />
+                        <!--extra transient dependencies for biopax conversion -->
+                                <pathelement location="Biopax3GPML.jar"/>
+                        </classpath>
                 </manifestclasspath>
 

trunk/src/core/org/pathvisio/util/Converter.java

@@ -35 +35 @@
 import org.pathvisio.model.MappFormat;
 import org.pathvisio.model.Pathway;
+import org.pathvisio.model.PathwayExporter;
+import org.pathvisio.model.PathwayImporter;
 import org.pathvisio.model.RasterImageExporter;
 import org.pathvisio.preferences.GlobalPreference;
@@ -71 +73 @@
     public static void main(String[] args)
     {
-                PreferenceManager.init();
+        // Handle command line arguments
+        // Check for custom output path
+        Logger.log.setStream (System.err);
+                                                //debug, trace, info, warn, error, fatal
+        Logger.log.setLogLevel (false, false, true, true, true, true);
+
+        PreferenceManager.init();
         Engine engine = new Engine();
         engine.addPathwayImporter(new GpmlFormat());
@@ -84 +92 @@
                 engine.addPathwayExporter(new DataNodeListExporter());
 
+                // Transient dependency on Biopax converter
+                try
+                {
+                        Class<?> c = Class.forName("org.pathvisio.biopax3.BiopaxFormat");
+                        Object o  = c.newInstance();
+                        engine.addPathwayExporter((PathwayExporter)o);
+                        engine.addPathwayImporter((PathwayImporter)o);
+                }
+                catch (ClassNotFoundException ex)
+                {
+                        Logger.log.warn("BioPAX converter not in classpath, BioPAX conversion not available today.");
+                }
+                catch (InstantiationException e)
+                {
+                        Logger.log.error("BioPAX instantiation error", e);
+                }
+                catch (IllegalAccessException e)
+                {
+                        Logger.log.warn("Access to BioPAX class is Illegal", e);
+                }
+                
                 //Enable MiM support (for export to graphics formats)
                 PreferenceManager.getCurrent().setBoolean(GlobalPreference.MIM_SUPPORT, true);
@@ -90 +119 @@
         File inputFile = null;
         File outputFile = null;
-
-        // Handle command line arguments
-        // Check for custom output path
-        Logger.log.setStream (System.err);
-                                                //debug, trace, info, warn, error, fatal
-        Logger.log.setLogLevel (false, false, true, true, true, true);
 
                 boolean error = false;