[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui/menus AnalysisMenu.java, 1.9, 1.10 AnnotationMenu.java, 1.156, 1.157

[elee <gk...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/gui/menus
In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv22005/gui/menus

Modified Files:
	AnalysisMenu.java AnnotationMenu.java 
Log Message:
+ Added support for remote analysis: BLAST and Primer BLAST
+ Added new glyph for displaying primers



Index: AnalysisMenu.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/menus/AnalysisMenu.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** AnalysisMenu.java	9 Aug 2004 15:31:15 -0000	1.9
--- AnalysisMenu.java	24 Feb 2009 17:27:39 -0000	1.10
***************
*** 2,5 ****
--- 2,7 ----
  
  import apollo.config.Config;
+ import apollo.config.PropertyScheme;
+ import apollo.config.TierProperty;
  import apollo.gui.*;
  import apollo.gui.drawable.DrawableAnnotationConstants;
***************
*** 10,13 ****
--- 12,18 ----
  import apollo.gui.tweeker.Tweeker;
  import apollo.analysis.AnalysisDataAdapterI;
+ import apollo.analysis.AnalysisGUI;
+ import apollo.analysis.BlastXMLParser;
+ import apollo.analysis.RemoteBlastNCBI;
  import apollo.analysis.SeqAnalysisI;
  
***************
*** 52,57 ****
      add(gcplot);
      add(restriction);
!     //    addSeparator();
!     //    add(analyze);  // Not working yet--don't add
  
      analyze.addActionListener(this);
--- 57,62 ----
      add(gcplot);
      add(restriction);
!     addSeparator();
!     add(analyze);  // Not working yet--don't add
  
      analyze.addActionListener(this);
***************
*** 84,90 ****
        gcplot.setEnabled(haveSequence());
        restriction.setEnabled(haveSequence());
!       //      analyze.setEnabled(frame.haveSequence());
        // analyze is not working yet
!       analyze.setEnabled(false);
      } 
      public void menuDeselected(MenuEvent e) {}
--- 89,95 ----
        gcplot.setEnabled(haveSequence());
        restriction.setEnabled(haveSequence());
!       analyze.setEnabled(haveSequence());
        // analyze is not working yet
!       //analyze.setEnabled(false);
      } 
      public void menuDeselected(MenuEvent e) {}
***************
*** 103,106 ****
--- 108,112 ----
      if (e.getSource() == analyze) {
        //      SequenceI seq = frame.getSeqFromClipboard();
+       /*
        DataAdapterChooser chooser 
  	= new DataAdapterChooser(Config.getAdapterRegistry(),
***************
*** 110,113 ****
--- 116,121 ----
  				 false);
        chooser.show();
+       */
+       new AnalysisGUI();
      }
    }

Index: AnnotationMenu.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/menus/AnnotationMenu.java,v
retrieving revision 1.156
retrieving revision 1.157
diff -C2 -d -r1.156 -r1.157
*** AnnotationMenu.java	10 Jun 2008 23:11:39 -0000	1.156
--- AnnotationMenu.java	24 Feb 2009 17:27:39 -0000	1.157
***************
*** 3,6 ****
--- 3,7 ----
  import apollo.editor.AnnotationEditor;
  import apollo.editor.UserName;
+ import apollo.analysis.AnalysisGUI;
  import apollo.config.Config;
  import apollo.gui.*;
***************
*** 80,83 ****
--- 81,86 ----
    
    JMenuItem preferences;
+   
+   JMenuItem analysis;
  
    AnnotationView  annotView;
***************
*** 186,189 ****
--- 189,194 ----
      preferences = new JMenuItem("Preferences");
      
+     analysis = new JMenuItem("Analyze region");
+     
      add(sequence);
      haveResidues = false;
***************
*** 324,327 ****
--- 329,336 ----
  
      preferences.setEnabled(haveAnnots());
+     analysis.setEnabled(haveAnnots());
+     
+     addSeparator();
+     add(analysis);
      
      addSeparator();
***************
*** 384,387 ****
--- 393,397 ----
      //    hideTier    .setMnemonic('H');
      // Shortcuts don't work for popup menus, as far as Steve and Nomi know.
+     analysis.addActionListener(this);
    }
  
***************
*** 525,528 ****
--- 535,542 ----
        PreferenceWindow.getInstance(selection).setVisible(true);
      }
+     else if (e.getSource() == analysis) {
+       FeatureList fl = selection.getSelectedData();
+       new AnalysisGUI(selection.getSelectedData(0).getLow(), fl.getFeature(fl.size() - 1).getHigh(), fl);
+     }