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[jalview.git] / src / jalview / gui / PopupMenu.java
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a1007bb..3177bfc 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -3,6 +3,7 @@ package jalview.gui;
 import jalview.datamodel.*;\r
 import jalview.analysis.*;\r
 import jalview.schemes.*;\r
+import java.awt.*;\r
 import javax.swing.*;\r
 import java.awt.event.*;\r
 import jalview.io.*;\r
@@ -11,9 +12,6 @@ import MCview.*;
 public class PopupMenu extends JPopupMenu\r
 {\r
   JMenu groupMenu = new JMenu();\r
-  JMenuItem copyGroup = new JMenuItem();\r
-  JMenuItem moveGroup = new JMenuItem();\r
-  JMenuItem deleteSequences = new JMenuItem();\r
   JMenuItem analyze = new JMenuItem();\r
   JMenu defineMenu = new JMenu();\r
   JMenuItem groupName = new JMenuItem();\r
@@ -43,6 +41,8 @@ public class PopupMenu extends JPopupMenu
   Sequence sequence;\r
   JMenuItem unGroupMenuItem = new JMenuItem();\r
   JMenuItem pdbMenuItem = new JMenuItem();\r
+  JMenuItem outline = new JMenuItem();\r
+  JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
 \r
   public PopupMenu(AlignmentPanel ap, Sequence seq)\r
   {\r
@@ -76,7 +76,7 @@ public class PopupMenu extends JPopupMenu
     catch(Exception e)\r
     {    e.printStackTrace();    }\r
 \r
-    SequenceGroup sg = ap.av.getRubberbandGroup();\r
+    SequenceGroup sg = ap.av.getSelectionGroup();\r
     if(sg!=null)\r
     {\r
       groupName.setText(sg.getName());\r
@@ -119,30 +119,6 @@ public class PopupMenu extends JPopupMenu
   private void jbInit() throws Exception\r
   {\r
     groupMenu.setText("Group");\r
-    copyGroup.setText("Copy region to new Alignment");\r
-    copyGroup.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        copyGroup_actionPerformed(e);\r
-      }\r
-    });\r
-    moveGroup.setText("Move sequences to new Alignment");\r
-    moveGroup.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        moveGroup_actionPerformed(e);\r
-      }\r
-    });\r
-    deleteSequences.setText("Delete sequences");\r
-    deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        deleteSequences_actionPerformed(e);\r
-      }\r
-    });\r
     analyze.setText("Analyze");\r
     analyze.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -160,6 +136,7 @@ public class PopupMenu extends JPopupMenu
         groupName_actionPerformed(e);\r
       }\r
     });\r
+    groupAnnotation.setEnabled(false);\r
     groupAnnotation.setText("Annotation");\r
     groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -178,6 +155,8 @@ public class PopupMenu extends JPopupMenu
       }\r
     });\r
     residueMenu.setText("Residue");\r
+    annotateResidue.setEnabled(false);\r
+    annotateResidue.setActionCommand("annotate residue");\r
     annotateResidue.setText("annotate residue???");\r
     PIDColour.setFocusPainted(false);\r
     unGroupMenuItem.setText("Remove Group");\r
@@ -196,22 +175,39 @@ public class PopupMenu extends JPopupMenu
         pdbMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    outline.setText("Border colour");\r
+    outline.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        outline_actionPerformed(e);\r
+      }\r
+    });\r
+    nucleotideMenuItem.setText("Nucleotide");\r
+    nucleotideMenuItem.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        nucleotideMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
     add(groupMenu);\r
     this.add(sequenceMenu);\r
     this.add(residueMenu);\r
     groupMenu.add(defineMenu);\r
     groupMenu.add(unGroupMenuItem);\r
     groupMenu.addSeparator();\r
-    groupMenu.add(copyGroup);\r
-    groupMenu.add(moveGroup);\r
-    groupMenu.add(deleteSequences);\r
-    groupMenu.addSeparator();\r
     groupMenu.add(analyze);\r
     defineMenu.add(groupName);\r
     defineMenu.add(groupAnnotation);\r
     defineMenu.addSeparator();\r
+    defineMenu.add(outline);\r
+    defineMenu.addSeparator();\r
     defineMenu.add(noColourmenuItem);\r
     defineMenu.add(clustalColour);\r
+    defineMenu.add(BLOSUM62Colour);\r
+    defineMenu.add(PIDColour);\r
+\r
     defineMenu.add(zappoColour);\r
     defineMenu.add(taylorColour);\r
     defineMenu.add(hydrophobicityColour);\r
@@ -219,9 +215,10 @@ public class PopupMenu extends JPopupMenu
     defineMenu.add(strandColour);\r
     defineMenu.add(turnColour);\r
     defineMenu.add(buriedColour);\r
+    defineMenu.add(nucleotideMenuItem);\r
+\r
     defineMenu.add(userDefinedColour);\r
-    defineMenu.add(PIDColour);\r
-    defineMenu.add(BLOSUM62Colour);\r
+\r
     defineMenu.addSeparator();\r
     defineMenu.add(abovePIDColour);\r
     defineMenu.add(conservationMenuItem);\r
@@ -247,7 +244,7 @@ public class PopupMenu extends JPopupMenu
         clustalColour_actionPerformed(e);\r
       }\r
     });\r
-    zappoColour.setText("Zappo colour scheme");\r
+    zappoColour.setText("Zappo");\r
     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -255,7 +252,7 @@ public class PopupMenu extends JPopupMenu
         zappoColour_actionPerformed(e);\r
       }\r
     });\r
-    taylorColour.setText("Taylor colour scheme");\r
+    taylorColour.setText("Taylor");\r
     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -263,7 +260,7 @@ public class PopupMenu extends JPopupMenu
         taylorColour_actionPerformed(e);\r
       }\r
     });\r
-    hydrophobicityColour.setText("By hydrophobicity");\r
+    hydrophobicityColour.setText("Hydrophobicity");\r
     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -295,7 +292,7 @@ public class PopupMenu extends JPopupMenu
         turnColour_actionPerformed(e);\r
       }\r
     });\r
-    buriedColour.setText("Buried index");\r
+    buriedColour.setText("Buried Index");\r
     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -303,7 +300,7 @@ public class PopupMenu extends JPopupMenu
         buriedColour_actionPerformed(e);\r
       }\r
     });\r
-    abovePIDColour.setText("Above PID threshold only");\r
+    abovePIDColour.setText("Above % Identity");\r
     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -311,7 +308,7 @@ public class PopupMenu extends JPopupMenu
         abovePIDColour_actionPerformed(e);\r
       }\r
     });\r
-    userDefinedColour.setText("User defined colours");\r
+    userDefinedColour.setText("User Defined");\r
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -327,7 +324,7 @@ public class PopupMenu extends JPopupMenu
         PIDColour_actionPerformed(e);\r
       }\r
     });\r
-    BLOSUM62Colour.setText("BLOSUM62 score");\r
+    BLOSUM62Colour.setText("BLOSUM62");\r
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -335,7 +332,7 @@ public class PopupMenu extends JPopupMenu
         BLOSUM62Colour_actionPerformed(e);\r
       }\r
     });\r
-    conservationMenuItem.setText("By conservation");\r
+    conservationMenuItem.setText("Conservation");\r
    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
    {\r
      public void actionPerformed(ActionEvent e)\r
@@ -355,7 +352,6 @@ public class PopupMenu extends JPopupMenu
     if( superG !=null)\r
       superG.setSuperGroupProperties( sg );\r
 \r
-    ap.seqPanel.seqCanvas.paintFlag=true;\r
     ap.seqPanel.repaint();\r
   }\r
 \r
@@ -409,23 +405,46 @@ public class PopupMenu extends JPopupMenu
     refresh();\r
   }\r
 \r
+  public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    getGroup().cs = new NucleotideColourScheme();\r
+    refresh();\r
+  }\r
+\r
+\r
 \r
   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
   {\r
-    Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
+    SequenceGroup sg = getGroup();\r
+    if (abovePIDColour.isSelected())\r
+    {\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+                                               ap.av.alignment.getWidth()));\r
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
+      if (sg.cs instanceof ResidueColourScheme)\r
+        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
+      else if (sg.cs instanceof ScoreColourScheme)\r
+        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+\r
+      SliderPanel.showPIDSlider();\r
+\r
+\r
+    }\r
+    else // remove PIDColouring\r
+    {\r
+      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
+      rcs.setThreshold(0);\r
+      sg.cs = rcs;\r
+    }\r
+\r
+    refresh();\r
+\r
   }\r
 \r
 \r
   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
-    JInternalFrame frame = new JInternalFrame();\r
-    UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
-    frame.setContentPane(chooser);\r
-    Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
-    frame.setResizable(false);\r
-    frame.setIconifiable(false);\r
-    frame.setMaximizable(false);\r
-\r
+    UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
   }\r
 \r
   protected void PIDColour_actionPerformed(ActionEvent e)\r
@@ -435,7 +454,13 @@ public class PopupMenu extends JPopupMenu
 \r
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
   {\r
-    getGroup().cs = new Blosum62ColourScheme(ap.av);\r
+    SequenceGroup sg = getGroup();\r
+\r
+    sg.cs = new Blosum62ColourScheme();\r
+\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+                                               ap.av.alignment.getWidth()));\r
+\r
     refresh();\r
   }\r
 \r
@@ -459,13 +484,14 @@ public class PopupMenu extends JPopupMenu
                                           ap.av.alignment.getWidth());\r
 \r
         c.calculate();\r
-        c.verdict(false, 100);\r
+        c.verdict(false, ap.av.ConsPercGaps);\r
         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
 \r
       sg.cs = ccs;\r
 \r
-      Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
+      SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+      SliderPanel.showConservationSlider();\r
     }\r
     else // remove ConservationColouring\r
     {\r
@@ -492,60 +518,6 @@ public class PopupMenu extends JPopupMenu
     groupName.setText(reply);\r
   }\r
 \r
-  protected void copyGroup_actionPerformed(ActionEvent e)\r
-  {\r
-    SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
-    SequenceI[] s = new Sequence[sg.sequences.size()];\r
-     for (int i=0; i < sg.sequences.size(); i++)\r
-     {\r
-       s[i] = new Sequence( sg.getSequenceAt(i));\r
-       s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
-     }\r
-     AlignFrame af = new AlignFrame(new Alignment(s));\r
-     int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
-     if (newHeight > 500)\r
-       newHeight = 500;\r
-     Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
-   }\r
-\r
-  protected  void moveGroup_actionPerformed(ActionEvent e)\r
-  {\r
-    SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
-    SequenceI[] s = new Sequence[sg.sequences.size()];\r
-\r
-     for (int i=0; i < sg.sequences.size(); i++)\r
-       s[i] = new Sequence( sg.getSequenceAt(i));\r
-\r
-     AlignFrame af = new AlignFrame(new Alignment(s));\r
-     int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
-     if(newHeight>500)\r
-       newHeight=500;\r
-     Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
-\r
-\r
-     for (int i=0; i < sg.sequences.size(); i++)\r
-       ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
-\r
-\r
-     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
-     ap.RefreshPanels();\r
-\r
-\r
-  }\r
-\r
-  protected void deleteSequences_actionPerformed(ActionEvent e)\r
-  {\r
-    SequenceGroup sg = ap.av.getRubberbandGroup();\r
-    for (int i=0;i < sg.sequences.size(); i++)\r
-            ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
-\r
-    ap.av.alignment.deleteGroup(sg);\r
-    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
-    ap.RefreshPanels();\r
-\r
-  }\r
 \r
   protected void analyze_actionPerformed(ActionEvent e)\r
   {\r
@@ -571,10 +543,11 @@ public class PopupMenu extends JPopupMenu
 \r
   SequenceGroup getGroup()\r
   {\r
-    SequenceGroup sg = ap.av.getRubberbandGroup();\r
+    SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
     // this method won't add a new group if it already exists\r
     ap.av.alignment.addGroup(sg);\r
+\r
     return sg;\r
   }\r
 \r
@@ -593,17 +566,17 @@ public class PopupMenu extends JPopupMenu
     if(s!=null)\r
     {\r
       sequence.setName(s);\r
-      ap.RefreshPanels();\r
+      ap.repaint();\r
     }\r
 \r
   }\r
 \r
   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-     SequenceGroup sg = ap.av.getRubberbandGroup();\r
+     SequenceGroup sg = ap.av.getSelectionGroup();\r
      ap.av.alignment.deleteGroup(sg);\r
-     ap.av.setRubberbandGroup(null);\r
-     ap.RefreshPanels();\r
+     ap.av.setSelectionGroup(null);\r
+     ap.repaint();\r
   }\r
 \r
   void pdbMenuItem_actionPerformed(ActionEvent e)\r
@@ -634,4 +607,12 @@ public class PopupMenu extends JPopupMenu
     }\r
   }\r
 \r
+  protected void outline_actionPerformed(ActionEvent e)\r
+  {\r
+    SequenceGroup sg = getGroup();\r
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
+    if(col!=null)\r
+      sg.setOutlineColour(col);\r
+  }\r
+\r
 }\r