DEFAULT_FILE_FORMAT added

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 398294b..66b29a0 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -12,10 +12,7 @@ import MCview.*;
 public class PopupMenu extends JPopupMenu\r
 {\r
   JMenu groupMenu = new JMenu();\r
-  JMenuItem analyze = new JMenuItem();\r
-  JMenu defineMenu = new JMenu();\r
   JMenuItem groupName = new JMenuItem();\r
-  JMenuItem groupAnnotation = new JMenuItem();\r
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
@@ -35,13 +32,11 @@ public class PopupMenu extends JPopupMenu
   AlignmentPanel ap;\r
   JMenu sequenceMenu = new JMenu();\r
   JMenuItem sequenceName = new JMenuItem();\r
-  JMenu residueMenu = new JMenu();\r
-  JMenuItem annotateResidue = new JMenuItem();\r
-\r
   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
@@ -108,25 +103,17 @@ public class PopupMenu extends JPopupMenu
         conservationMenuItem.setSelected(true);\r
     }\r
 \r
+    if( !ap.av.alignment.getGroups().contains(sg))\r
+        unGroupMenuItem.setVisible(false);\r
 \r
-    if(seq!=null)\r
-      residueMenu.setVisible(false);\r
-    else\r
-      sequenceMenu.setVisible(false);\r
+    if(seq==null)\r
+       sequenceMenu.setVisible(false);\r
 \r
   }\r
   private void jbInit() throws Exception\r
   {\r
     groupMenu.setText("Group");\r
-    analyze.setText("Analyze");\r
-    analyze.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        analyze_actionPerformed(e);\r
-      }\r
-    });\r
-    defineMenu.setText("Define");\r
+    groupMenu.setText("Define");\r
     groupName.setText("Name");\r
     groupName.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -135,15 +122,6 @@ 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
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        groupAnnotation_actionPerformed(e);\r
-      }\r
-    });\r
     sequenceMenu.setText("Sequence");\r
     sequenceName.setText("Edit name");\r
     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
@@ -153,10 +131,6 @@ public class PopupMenu extends JPopupMenu
         sequenceName_actionPerformed(e);\r
       }\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
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -182,38 +156,44 @@ 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
-    groupMenu.add(defineMenu);\r
+    add(sequenceMenu);\r
+    groupMenu.add(groupName);\r
+    groupMenu.addSeparator();\r
     groupMenu.add(unGroupMenuItem);\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(zappoColour);\r
-    defineMenu.add(taylorColour);\r
-    defineMenu.add(hydrophobicityColour);\r
-    defineMenu.add(helixColour);\r
-    defineMenu.add(strandColour);\r
-    defineMenu.add(turnColour);\r
-    defineMenu.add(buriedColour);\r
-    defineMenu.add(userDefinedColour);\r
-    defineMenu.add(PIDColour);\r
-    defineMenu.add(BLOSUM62Colour);\r
-    defineMenu.addSeparator();\r
-    defineMenu.add(abovePIDColour);\r
-    defineMenu.add(conservationMenuItem);\r
+    groupMenu.add(outline);\r
+    groupMenu.addSeparator();\r
+    groupMenu.add(noColourmenuItem);\r
+    groupMenu.add(clustalColour);\r
+    groupMenu.add(BLOSUM62Colour);\r
+    groupMenu.add(PIDColour);\r
+\r
+    groupMenu.add(zappoColour);\r
+    groupMenu.add(taylorColour);\r
+    groupMenu.add(hydrophobicityColour);\r
+    groupMenu.add(helixColour);\r
+    groupMenu.add(strandColour);\r
+    groupMenu.add(turnColour);\r
+    groupMenu.add(buriedColour);\r
+    groupMenu.add(nucleotideMenuItem);\r
+\r
+    groupMenu.add(userDefinedColour);\r
+\r
+    groupMenu.addSeparator();\r
+    groupMenu.add(abovePIDColour);\r
+    groupMenu.add(conservationMenuItem);\r
 \r
     sequenceMenu.add(sequenceName);\r
     sequenceMenu.add(pdbMenuItem);\r
-    residueMenu.add(annotateResidue);\r
-\r
     noColourmenuItem.setText("None");\r
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -231,7 +211,7 @@ 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 +219,7 @@ 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 +227,7 @@ 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 +259,7 @@ 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 +267,7 @@ 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 +275,7 @@ 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 +291,7 @@ 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 +299,7 @@ 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
@@ -392,6 +372,13 @@ 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
@@ -424,14 +411,7 @@ public class PopupMenu extends JPopupMenu
 \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
@@ -576,14 +556,10 @@ public class PopupMenu extends JPopupMenu
       EBIFetchClient ebi = new EBIFetchClient();\r
       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
 \r
+      System.out.println("Got "+ sequence.getPDBId() );\r
       PDBfile pdb = new PDBfile(result);\r
-      sequence.setPDBfile(pdb);\r
-\r
-      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
-      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
-    //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
 \r
-      rotCanvas rc = new rotCanvas(pdb);\r
+      rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
       JInternalFrame frame = new JInternalFrame();\r
       frame.setContentPane(rc);\r
       Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
@@ -600,6 +576,7 @@ public class PopupMenu extends JPopupMenu
     Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
     if(col!=null)\r
       sg.setOutlineColour(col);\r
+    ap.repaint();\r
   }\r
 \r
 }\r