formatAdapter.readFile

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8d747c2..3177bfc 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -42,6 +42,7 @@ public class PopupMenu extends JPopupMenu
   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
@@ -182,6 +183,14 @@ public class PopupMenu extends JPopupMenu
         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
@@ -196,6 +205,9 @@ public class PopupMenu extends JPopupMenu
     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
@@ -203,9 +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
@@ -231,7 +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
@@ -239,7 +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
@@ -247,7 +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
@@ -279,7 +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
@@ -287,7 +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
@@ -295,7 +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
@@ -311,7 +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
@@ -319,7 +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
@@ -392,39 +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
-    if(abovePIDColour.isSelected())\r
-{\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
-   Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
-   refresh();\r
-}\r
-else // remove PIDColouring\r
-{\r
-    ColourSchemeI cs = getGroup().cs;\r
-      ResidueColourScheme rcs = (ResidueColourScheme)cs;\r
-      rcs.setThreshold(0);\r
-      getGroup().cs = rcs;\r
-      refresh();\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
@@ -434,7 +454,13 @@ else // remove PIDColouring
 \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
@@ -458,13 +484,14 @@ else // remove PIDColouring
                                           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
@@ -539,7 +566,7 @@ else // remove PIDColouring
     if(s!=null)\r
     {\r
       sequence.setName(s);\r
-      ap.RefreshPanels();\r
+      ap.repaint();\r
     }\r
 \r
   }\r
@@ -549,7 +576,7 @@ else // remove PIDColouring
      SequenceGroup sg = ap.av.getSelectionGroup();\r
      ap.av.alignment.deleteGroup(sg);\r
      ap.av.setSelectionGroup(null);\r
-     ap.RefreshPanels();\r
+     ap.repaint();\r
   }\r
 \r
   void pdbMenuItem_actionPerformed(ActionEvent e)\r