Author: rodche
Date: 2011-08-16 12:29:37 -0700 (Tue, 16 Aug 2011)
New Revision: 26572
Modified:
core3/gui-distribution/trunk/distribution/src/main/bin/cytoscape.sh
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchBoxPanel.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/cPathSearchPanel.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProperties.java
Log:
Added debug opts (commented out) to the sh script. Fixed "organisms" list in
the combo box in the Pathway Commons plugin UI.
Modified: core3/gui-distribution/trunk/distribution/src/main/bin/cytoscape.sh
===================================================================
--- core3/gui-distribution/trunk/distribution/src/main/bin/cytoscape.sh
2011-08-16 18:00:21 UTC (rev 26571)
+++ core3/gui-distribution/trunk/distribution/src/main/bin/cytoscape.sh
2011-08-16 19:29:37 UTC (rev 26572)
@@ -1,3 +1,8 @@
#!/bin/bash
-java -jar -Xss10M -Xmx1550M -Dawt.useSystemAAFontSettings=lcd
-Dapple.laf.useScreenMenuBar=true -Dapple.awt.rendering=speed
-Dapple.awt.fileDialogForDirectories=true
-Dcom.apple.mrj.application.apple.menu.about.name="Cytoscape 3"
-Dorg.ops4j.pax.logging.DefaultServiceLog.level=NONE
-Dbundles.configuration.location=bundles/configurations
-Dfelix.fileinstall.dir=bundles/plugins cytoscape-launcher.jar
+CY3_OPTIONS="-Xss10M -Xmx1550M -Dawt.useSystemAAFontSettings=lcd
-Dapple.laf.useScreenMenuBar=true -Dapple.awt.rendering=speed
-Dapple.awt.fileDialogForDirectories=true
-Dcom.apple.mrj.application.apple.menu.about.name="Cytoscape 3"
-Dorg.ops4j.pax.logging.DefaultServiceLog.level=NONE
-Dbundles.configuration.location=bundles/configurations
-Dfelix.fileinstall.dir=bundles/plugins"
+
+java $CY3_OPTIONS -jar cytoscape-launcher.jar
+
+# use this instead with a java debugger
+#java $CY3_OPTIONS -Xdebug
-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=12345 -jar
cytoscape-launcher.jar
\ No newline at end of file
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchBoxPanel.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchBoxPanel.java
2011-08-16 18:00:21 UTC (rev 26571)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchBoxPanel.java
2011-08-16 19:29:37 UTC (rev 26572)
@@ -120,10 +120,9 @@
*/
private JComboBox createOrganismComboBox() {
// Organism List is currently hard-coded.
- Vector organismList = new Vector();
+ Vector<Organism> organismList = new Vector<Organism>();
organismList.add(new Organism("All Organisms", -1));
- CPathProperties props = CPathProperties.getInstance();
- organismList.addAll(props.getOrganismList());
+ organismList.addAll(CPathProperties.getInstance().getOrganismList());
DefaultComboBoxModel organismComboBoxModel = new
DefaultComboBoxModel(organismList);
JComboBox organismComboBox = new JComboBox(organismComboBoxModel);
organismComboBox.setToolTipText("Select Organism");
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/cPathSearchPanel.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/cPathSearchPanel.java
2011-08-16 18:00:21 UTC (rev 26571)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/cPathSearchPanel.java
2011-08-16 19:29:37 UTC (rev 26572)
@@ -73,7 +73,6 @@
JPanel aboutPanel = new JPanel();
aboutPanel.setLayout(new BorderLayout());
GradientHeader header = new GradientHeader("About");
-
aboutPanel.add(header, BorderLayout.NORTH);
JTextPane textPane =
PhysicalEntityDetailsPanel.createHtmlTextPane(factory.getOpenBrowser());
textPane.setText(CPathProperties.getInstance().getCPathBlurb());
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProperties.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProperties.java
2011-08-16 18:00:21 UTC (rev 26571)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProperties.java
2011-08-16 19:29:37 UTC (rev 26572)
@@ -37,11 +37,6 @@
public static final String ICON_FILE_NAME = new String
("cpath2.icon_file_name");
/**
- * Property: Organism.
- */
- public static final String ORGANISM_PREFIX = new String
("cpath2.organism");
-
- /**
* Download Networks in Full BioPAX Mode.
*/
public final static int DOWNLOAD_FULL_BIOPAX = 1;
@@ -109,23 +104,12 @@
"involving proteins, DNA, RNA, small molecules and complexes.";
}
- int index = 0;
- String orgField = pluginProperties.getProperty(ORGANISM_PREFIX +
index);
- while (orgField != null) {
- String parts[] = orgField.split(":");
- Organism organism = new Organism();
- if (parts != null && parts.length == 2) {
- organism.setSpeciesName(parts[0]);
- try {
- organism.setNcbiTaxonomyId(Integer.parseInt(parts[1]));
- organismList.add(organism);
- } catch(NumberFormatException e) {
- }
- }
- index++;
- orgField = pluginProperties.getProperty(ORGANISM_PREFIX + index);
- }
-
+ organismList.add(new Organism("Human", 9606));
+ organismList.add(new Organism("Fruit Fly", 7227));
+ organismList.add(new Organism("Mouse", 10090));
+ organismList.add(new Organism("Rat", 10116));
+ organismList.add(new Organism("C. elegans", 6239));
+ organismList.add(new Organism("S. cerevisiae", 4932));
}
/**
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