X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=5292de9792060d12ffd757f5e6f2cd3fa99a38f3;hb=7cf75b5b379dd71b3480726419c7dc55d8e01f0e;hp=339a47058b3800e29d03a1d1421033a3a1c6e00c;hpb=ddb541d14e7e192655b2b5c57d30af6f9d83007e;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 339a470..5292de9 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -142,8 +142,7 @@ public class PopupMenu extends JPopupMenu
 
         if (seq != null)
         {
-          int start = Math.max(sequence.getName().length()-15, 0);
-          sequenceMenu.setText(sequence.getName().substring(start));
+          sequenceMenu.setText(sequence.getName());
 
           JMenuItem menuItem;
           if( seq.getDatasetSequence().getPDBId() != null)
@@ -814,9 +813,9 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(true), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -862,8 +861,9 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -878,8 +878,9 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -910,8 +911,9 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth());
+                    sg.getSequences(true),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
@@ -950,31 +952,6 @@ 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!
@@ -1038,13 +1015,15 @@ 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());
+
     }
 
     /**
@@ -1245,14 +1224,13 @@ public class PopupMenu extends JPopupMenu
       ap.av.firePropertyChange("alignment", null,
                                 ap.av.getAlignment().getSequences());
 
-
-  //    PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
   }
 
   public void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);