Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826)

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 067b3d2..4f60de3 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -113,6 +113,13 @@ public class GAlignFrame extends JInternalFrame
 
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+  // protected JRadioButtonMenuItem covariationColour = new
+  // JRadioButtonMenuItem();
+
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -121,7 +128,7 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 
   JMenuItem htmlMenuItem = new JMenuItem();
 
@@ -149,8 +156,6 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 
-  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
   JMenuItem deleteGroups = new JMenuItem();
 
   JMenuItem delete = new JMenuItem();
@@ -217,10 +222,16 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem annotationColour = new JMenuItem();
 
+  JMenuItem rnahelicesColour = new JMenuItem();
+
   JMenuItem associatedData = new JMenuItem();
 
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
+  protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
   JMenu addSequenceMenu = new JMenu();
 
   JMenuItem addFromFile = new JMenuItem();
@@ -363,8 +374,7 @@ public class GAlignFrame extends JInternalFrame
             if (evt.isControlDown()
                     || SwingUtilities.isRightMouseButton(evt))
             {
-              radioItem
-                      .removeActionListener(radioItem.getActionListeners()[0]);
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
@@ -414,6 +424,8 @@ public class GAlignFrame extends JInternalFrame
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
+    colours.add(purinePyrimidineColour);
+    // colours.add(covariationColour);
 
     setColourSelected(jalview.bin.Cache
             .getDefault("DEFAULT_COLOUR", "None"));
@@ -430,9 +442,6 @@ public class GAlignFrame extends JInternalFrame
 
       switch (index)
       {
-      case ColourSchemeProperty.NONE:
-        noColourmenuItem.setSelected(true);
-        break;
       case ColourSchemeProperty.CLUSTAL:
         clustalColour.setSelected(true);
 
@@ -487,10 +496,25 @@ public class GAlignFrame extends JInternalFrame
 
         break;
 
+      case ColourSchemeProperty.PURINEPYRIMIDINE:
+        purinePyrimidineColour.setSelected(true);
+
+        break;
+      /*
+       * case ColourSchemeProperty.COVARIATION:
+       * covariationColour.setSelected(true);
+       * 
+       * break;
+       */
       case ColourSchemeProperty.USER_DEFINED:
         userDefinedColour.setSelected(true);
 
         break;
+      case ColourSchemeProperty.NONE:
+      default:
+        noColourmenuItem.setSelected(true);
+        break;
+
       }
     }
 
@@ -656,9 +680,9 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    showUnconservedMenuItem.setText("Show Unconserved");
-    showUnconservedMenuItem.setState(false);
-    showUnconservedMenuItem
+    showNonconservedMenuItem.setText("Show nonconserved");
+    showNonconservedMenuItem.setState(false);
+    showNonconservedMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
               public void actionPerformed(ActionEvent e)
@@ -845,6 +869,31 @@ public class GAlignFrame extends JInternalFrame
         BLOSUM62Colour_actionPerformed(e);
       }
     });
+    nucleotideColour.setText("Nucleotide");
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideColour_actionPerformed(e);
+      }
+    });
+
+    purinePyrimidineColour.setText("Purine/Pyrimidine");
+    purinePyrimidineColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                purinePyrimidineColour_actionPerformed(e);
+              }
+            });
+    /*
+     * covariationColour.setText("Covariation");
+     * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+     * public void actionPerformed(ActionEvent e) {
+     * covariationColour_actionPerformed(e); } });
+     */
+
     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
     avDistanceTreeBlosumMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -1384,6 +1433,16 @@ public class GAlignFrame extends JInternalFrame
         annotationColour_actionPerformed(e);
       }
     });
+
+    rnahelicesColour.setText("By RNA helices");
+    rnahelicesColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        rnahelicesColour_actionPerformed(e);
+      }
+    });
+
     associatedData.setText("Load Features / Annotations");
     associatedData.addActionListener(new ActionListener()
     {
@@ -1402,6 +1461,29 @@ public class GAlignFrame extends JInternalFrame
         autoCalculate_actionPerformed(e);
       }
     });
+    sortByTree.setText("Sort Alignment With New Tree");
+    sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
+    sortByTree.setState(jalview.bin.Cache.getDefault(
+            "SORT_BY_TREE", false));
+    sortByTree.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortByTreeOption_actionPerformed(e);
+      }
+    });
+
+    listenToViewSelections.setText("Listen for selections");
+    listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
+    listenToViewSelections.setState(false); 
+    listenToViewSelections.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        listenToViewSelections_actionPerformed(e);
+      }
+    });
+
     addSequenceMenu.setText("Add Sequences");
     addFromFile.setText("From File");
     addFromFile.addActionListener(new ActionListener()
@@ -1732,6 +1814,8 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
+    colourMenu.add(purinePyrimidineColour);
+    // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -1739,6 +1823,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
+    colourMenu.add(rnahelicesColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
@@ -1748,6 +1833,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(showTranslation);
     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
+    calculateMenu.add(sortByTree);
     calculateMenu.addSeparator();
     calculateMenu.add(extractScores);
     webServiceNoServices = new JMenuItem("<No Services>");
@@ -1794,7 +1880,7 @@ public class GAlignFrame extends JInternalFrame
     formatMenu.add(colourTextMenuItem);
     formatMenu.add(renderGapsMenuItem);
     formatMenu.add(centreColumnLabelsMenuItem);
-    formatMenu.add(showUnconservedMenuItem);
+    formatMenu.add(showNonconservedMenuItem);
     selectMenu.add(findMenuItem);
     selectMenu.addSeparator();
     selectMenu.add(selectAllSequenceMenuItem);
@@ -1803,6 +1889,15 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(invertColSel);
     selectMenu.add(deleteGroups);
     selectMenu.add(grpsFromSelection);
+    // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
+    //selectMenu.addSeparator();
+    //selectMenu.add(listenToViewSelections);
+  }
+
+  protected void listenToViewSelections_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
   }
 
   protected void showAllhidden_actionPerformed(ActionEvent e)
@@ -2103,6 +2198,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /*
+   * protected void covariationColour_actionPerformed(ActionEvent e) { }
+   */
+
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -2255,6 +2358,11 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  public void rnahelicesColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   public void associatedData_actionPerformed(ActionEvent e)
   {
 
@@ -2265,6 +2373,11 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  public void sortByTreeOption_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   public void showAllSeqs_actionPerformed(ActionEvent e)
   {