[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Sat Jun 16 15:34:36 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv32758/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentGUI.java 
Log Message:
Restored system properties for JAXp and JAXT because default transformer on Windows doesn't work properly
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentGUI.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java	2007/06/09 22:16:54	1.11
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java	2007/06/16 19:34:36	1.12
@@ -747,7 +747,12 @@
 		logger.warn("Cannot process close tab event: tab " + activeTabIndex +" no longer exists");
 		return;
 	    }
-	    tabbedPane.remove(activeTabIndex);
+	    if(tabbedPane.getComponentAt(activeTabIndex) instanceof MobyContentClipboard){
+		// Don't close clipboard, if somehow we were asked...
+	    }
+	    else{
+		tabbedPane.remove(activeTabIndex);
+	    }
 	}
 	else if(MobyContentClipboard.CLEAR_CLIPBOARD_OPTION.equals(cmd)){
 	    clipboard.clearData();
@@ -908,26 +913,31 @@
 	java.util.Locale.setDefault(java.util.Locale.ENGLISH);
 
 	// Unless overridden on the command line, use xerces
-	//if(System.getProperty("javax.xml.parsers.DocumentBuilderFactory") == null){
-	//    System.setProperty("javax.xml.parsers.DocumentBuilderFactory",
-	//		       "org.apache.xerces.jaxp.DocumentBuilderFactoryImpl");
-	//}
+	if(System.getProperty("javax.xml.parsers.DocumentBuilderFactory") == null){
+	    System.setProperty("javax.xml.parsers.DocumentBuilderFactory",
+			       "org.apache.xerces.jaxp.DocumentBuilderFactoryImpl");
+	}
 
 	// Unless overridden on the command line, use xalan
-	//if(System.getProperty("javax.xml.transform.TransformerFactory") == null){
-	//    System.setProperty("javax.xml.transform.TransformerFactory",
-	//		       "org.apache.xalan.processor.TransformerFactoryImpl");
-	//}
+	if(System.getProperty("javax.xml.transform.TransformerFactory") == null){
+	    System.setProperty("javax.xml.transform.TransformerFactory",
+			       "org.apache.xalan.processor.TransformerFactoryImpl");
+	}
 
 	// Setting this explicitly prevents repeated calls to the META-INF file encoding the same 
-	//if(System.getProperty("org.apache.xerces.xni.parser.XMLParserConfiguration") == null){
-	//   System.setProperty("org.apache.xerces.xni.parser.XMLParserConfiguration",
-	//		       "org.apache.xerces.parsers.StandardParserConfiguration");
-	//}
+	if(System.getProperty("org.apache.xerces.xni.parser.XMLParserConfiguration") == null){
+	   System.setProperty("org.apache.xerces.xni.parser.XMLParserConfiguration",
+			       "org.apache.xerces.parsers.StandardParserConfiguration");
+	}
 
 	// First, restore any user preferences (uses default settings file location)
-	SeahawkOptions.restoreSettings();
-
+	try{
+	    SeahawkOptions.restoreSettings();
+	} catch(Exception e){
+	    e.printStackTrace();
+	    System.err.println("Using default settings, could not restore Seahawk settings from file " +
+			       SeahawkOptions.getDefaultsFile()+": "+ e);
+	}
 	// Asynchronously load up ontology data so it's ready when the user needs it.
 	cacheOntologies();