X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9ed81abb1cb5984c3603944798777a07342f4f66;hb=3e6b14950a06bb87c147493e4dfff0c4491ea25b;hp=5213bad73baeddff6f51b729053c4eeb8caf7155;hpb=eb77addf49f8957e88b61f07ce36414c6619a221;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 5213bad..9ed81ab 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -81,6 +81,8 @@ public class PopupMenu extends JPopupMenu
   JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
   JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
 
   /**
      * Creates a new PopupMenu object.
@@ -178,7 +180,7 @@ public class PopupMenu extends JPopupMenu
           add(menuItem);
 
           if(ap.av.getSelectionGroup() !=null
-             && ap.av.getSelectionGroup().getSize(false)>1)
+             && ap.av.getSelectionGroup().getSize()>1)
           {
             menuItem = new JMenuItem("Represent Group with " + seq.getName());
             menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -510,23 +512,25 @@ public class PopupMenu extends JPopupMenu
         sequenceFeature_actionPerformed(e);
       }
     });
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed(e);
+      }
+    });
+    jMenu1.setText("Group");
     add(groupMenu);
 
     add(sequenceMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
-    groupMenu.addSeparator();
     groupMenu.add(sequenceFeature);
-    groupMenu.addSeparator();
-    groupMenu.add(groupName);
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
-    groupMenu.add(outline);
+    groupMenu.add(jMenu1);
     sequenceMenu.add(sequenceName);
     sequenceMenu.add(pdbMenu);
+    colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
@@ -573,6 +577,13 @@ public class PopupMenu extends JPopupMenu
     pdbMenu.add(pdbFromFile);
     pdbMenu.add(enterPDB);
     pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
     noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
@@ -707,7 +718,7 @@ public class PopupMenu extends JPopupMenu
     protected void clustalColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
-        sg.cs = new ClustalxColourScheme(sg.getSequences(true),
+        sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
                 ap.av.alignment.getWidth());
         refresh();
     }
@@ -814,7 +825,7 @@ public class PopupMenu extends JPopupMenu
         if (abovePIDColour.isSelected())
         {
           sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(true), sg.getStartRes(),
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
               sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
@@ -861,7 +872,7 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
                                                  sg.getStartRes(),
                                                  sg.getEndRes() + 1));
         refresh();
@@ -878,7 +889,7 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
                                                  sg.getStartRes(),
                                                  sg.getEndRes() + 1));
 
@@ -911,7 +922,7 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true),
+                    sg.getSequences(ap.av.hiddenRepSequences),
                     sg.getStartRes(),
                     sg.getEndRes() + 1);
 
@@ -952,31 +963,6 @@ public class PopupMenu extends JPopupMenu
         groupName.setText(reply);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void analyze_actionPerformed(ActionEvent e)
-    {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(cap);
-        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
-
-        SequenceGroup sg = getGroup();
-        StringBuffer sb = new StringBuffer();
-
-        for (int i = 0; i < sg.getSize(false); i++)
-        {
-            Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
-            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-            sb.append("\n");
-        }
-
-        sb.append("Something amazing will happen soon");
-        cap.setText(sb.toString());
-    }
 
     /**
      * DOCUMENT ME!
@@ -1040,13 +1026,15 @@ public class PopupMenu extends JPopupMenu
             }
 
             s = s.replace(' ', '_');
-            sequence.getDatasetSequence().setName(s);
             sequence.setName(s);
             ap.repaint();
         }
 
-        sequence.getDatasetSequence().setDescription(description.getText());
         sequence.setDescription(description.getText());
+
+        ap.av.firePropertyChange("alignment", null,
+                                  ap.av.getAlignment().getSequences());
+
     }
 
     /**
@@ -1136,34 +1124,33 @@ public class PopupMenu extends JPopupMenu
     void hideSequences(boolean representGroup)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
-      if(sg==null || sg.getSize(false)<1)
+      if(sg==null || sg.getSize()<1)
       {
         ap.av.hideSequence(new SequenceI[]{sequence});
         return;
       }
 
-      int gsize = sg.getSize(false);
-      SequenceI [] hseqs;
+      ap.av.setSelectionGroup(null);
 
-      hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
+      if (representGroup)
+      {
+        ap.av.hideRepSequences(sequence, sg);
 
-        int index = 0;
-        for(int i=0; i<gsize; i++)
-        {
-          if(representGroup && sg.getSequenceAt(i)!=sequence)
-          {
-            sequence.addHiddenSequence(sg.getSequenceAt(i));
-            hseqs[index++] = sg.getSequenceAt(i);
-          }
-          else if(!representGroup)
-          {
-            hseqs[index++] = sg.getSequenceAt(i);
-          }
-        }
+        return;
+      }
 
-        ap.av.hideSequence(hseqs);
+      int gsize = sg.getSize();
+      SequenceI[] hseqs;
 
-        ap.av.setSelectionGroup(null);
+      hseqs = new SequenceI[gsize];
+
+      int index = 0;
+      for (int i = 0; i < gsize; i++)
+      {
+        hseqs[index++] = sg.getSequenceAt(i);
+      }
+
+      ap.av.hideSequence(hseqs);
     }
 
   public void copy_actionPerformed(ActionEvent e)
@@ -1238,7 +1225,8 @@ public class PopupMenu extends JPopupMenu
       }
 
       ChangeCaseCommand caseCommand = new ChangeCaseCommand(
-          description, sg.getSequencesAsArray(true), startEnd, caseChange
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+          startEnd, caseChange
           );
 
       ap.alignFrame.addHistoryItem(caseCommand);
@@ -1253,6 +1241,7 @@ public class PopupMenu extends JPopupMenu
   public void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
@@ -1346,7 +1335,7 @@ public class PopupMenu extends JPopupMenu
     if(sg==null)
       return;
 
-    int gSize= sg.getSize(false);
+    int gSize= sg.getSize();
     SequenceI [] seqs = new SequenceI[gSize];
     SequenceFeature [] features = new SequenceFeature[gSize];
 
@@ -1366,4 +1355,11 @@ public class PopupMenu extends JPopupMenu
       ap.highlightSearchResults(null);
     }
   }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg != null)
+      new TextColourChooser().chooseColour(ap, sg);
+  }
 }