X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=398294b7cd9874d59c3d78a31c2adb7de99d81ca;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=38c32500838c229949292ba657e45a0ca79d3de3;hpb=c3c4dc54c7f7667de14e1dc797190a8e5b5699ae;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 38c3250..398294b 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -3,6 +3,7 @@ package jalview.gui;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.schemes.*;
+import java.awt.*;
 import javax.swing.*;
 import java.awt.event.*;
 import jalview.io.*;
@@ -40,6 +41,7 @@ public class PopupMenu extends JPopupMenu
   Sequence sequence;
   JMenuItem unGroupMenuItem = new JMenuItem();
   JMenuItem pdbMenuItem = new JMenuItem();
+  JMenuItem outline = new JMenuItem();
 
   public PopupMenu(AlignmentPanel ap, Sequence seq)
   {
@@ -73,7 +75,7 @@ public class PopupMenu extends JPopupMenu
     catch(Exception e)
     {    e.printStackTrace();    }
 
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
     if(sg!=null)
     {
       groupName.setText(sg.getName());
@@ -133,6 +135,7 @@ public class PopupMenu extends JPopupMenu
         groupName_actionPerformed(e);
       }
     });
+    groupAnnotation.setEnabled(false);
     groupAnnotation.setText("Annotation");
     groupAnnotation.addActionListener(new java.awt.event.ActionListener()
     {
@@ -151,6 +154,8 @@ public class PopupMenu extends JPopupMenu
       }
     });
     residueMenu.setText("Residue");
+    annotateResidue.setEnabled(false);
+    annotateResidue.setActionCommand("annotate residue");
     annotateResidue.setText("annotate residue???");
     PIDColour.setFocusPainted(false);
     unGroupMenuItem.setText("Remove Group");
@@ -169,6 +174,14 @@ public class PopupMenu extends JPopupMenu
         pdbMenuItem_actionPerformed(e);
       }
     });
+    outline.setText("Border colour");
+    outline.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outline_actionPerformed(e);
+      }
+    });
     add(groupMenu);
     this.add(sequenceMenu);
     this.add(residueMenu);
@@ -179,6 +192,8 @@ public class PopupMenu extends JPopupMenu
     defineMenu.add(groupName);
     defineMenu.add(groupAnnotation);
     defineMenu.addSeparator();
+    defineMenu.add(outline);
+    defineMenu.addSeparator();
     defineMenu.add(noColourmenuItem);
     defineMenu.add(clustalColour);
     defineMenu.add(zappoColour);
@@ -324,7 +339,6 @@ public class PopupMenu extends JPopupMenu
     if( superG !=null)
       superG.setSuperGroupProperties( sg );
 
-    ap.seqPanel.seqCanvas.paintFlag=true;
     ap.seqPanel.repaint();
   }
 
@@ -381,7 +395,30 @@ public class PopupMenu extends JPopupMenu
 
   protected void abovePIDColour_actionPerformed(ActionEvent e)
   {
-    Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
+    SequenceGroup sg = getGroup();
+    if (abovePIDColour.isSelected())
+    {
+      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                                               ap.av.alignment.getWidth()));
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+      if (sg.cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
+      else if (sg.cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+
+      SliderPanel.showPIDSlider();
+
+
+    }
+    else // remove PIDColouring
+    {
+      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
+      rcs.setThreshold(0);
+      sg.cs = rcs;
+    }
+
+    refresh();
+
   }
 
 
@@ -404,7 +441,13 @@ public class PopupMenu extends JPopupMenu
 
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = new Blosum62ColourScheme(ap.av);
+    SequenceGroup sg = getGroup();
+
+    sg.cs = new Blosum62ColourScheme();
+
+    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                                               ap.av.alignment.getWidth()));
+
     refresh();
   }
 
@@ -428,13 +471,14 @@ public class PopupMenu extends JPopupMenu
                                           ap.av.alignment.getWidth());
 
         c.calculate();
-        c.verdict(false, 100);
+        c.verdict(false, ap.av.ConsPercGaps);
         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
 
       sg.cs = ccs;
 
-      Desktop.setConservationSliderSource(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
@@ -486,10 +530,11 @@ public class PopupMenu extends JPopupMenu
 
   SequenceGroup getGroup()
   {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
     ap.av.alignment.addGroup(sg);
+
     return sg;
   }
 
@@ -508,17 +553,17 @@ public class PopupMenu extends JPopupMenu
     if(s!=null)
     {
       sequence.setName(s);
-      ap.RefreshPanels();
+      ap.repaint();
     }
 
   }
 
   void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-     SequenceGroup sg = ap.av.getRubberbandGroup();
+     SequenceGroup sg = ap.av.getSelectionGroup();
      ap.av.alignment.deleteGroup(sg);
-     ap.av.setRubberbandGroup(null);
-     ap.RefreshPanels();
+     ap.av.setSelectionGroup(null);
+     ap.repaint();
   }
 
   void pdbMenuItem_actionPerformed(ActionEvent e)
@@ -549,4 +594,12 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  protected void outline_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
+    if(col!=null)
+      sg.setOutlineColour(col);
+  }
+
 }