JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c751494..c1bbc8d 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -255,29 +255,29 @@ public class PopupMenu extends JPopupMenu
       }
       else
       {
-        if (ap.av.alignment.isNucleotide() == false)
+        if (ap.av.getAlignment().isNucleotide() == false)
         {
         structureMenu.remove(viewStructureMenu);
         }
         // structureMenu.remove(colStructureMenu);
       }
 
-      if (ap.av.alignment.isNucleotide() == true)
+      if (ap.av.getAlignment().isNucleotide() == true)
       {
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+        AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
         for (int i = 0; i < aa.length; i++)
         {
           if (aa[i].getRNAStruc() != null)
           {
             final String rnastruc = aa[i].getRNAStruc();
-            
+            final String structureLine=aa[i].label;
             menuItem = new JMenuItem();
-            menuItem.setText("RNA structure - consensus");
+            menuItem.setText("2D RNA "+structureLine);
             menuItem.addActionListener(new java.awt.event.ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
-                new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
                         .getName(), ap);
               }
             });
@@ -298,13 +298,13 @@ public class PopupMenu extends JPopupMenu
               
            // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
-              menuItem.setText("RNA structure - "+seq.getName());
+              menuItem.setText("2D RNA - "+seq.getName());
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-                  new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                  new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
                           .getName(), ap);
                 }
               });
@@ -340,9 +340,9 @@ public class PopupMenu extends JPopupMenu
         sequenceMenu.add(menuItem);
       }
 
-      if (ap.av.hasHiddenRows)
+      if (ap.av.hasHiddenRows())
       {
-        final int index = ap.av.alignment.findIndex(seq);
+        final int index = ap.av.getAlignment().findIndex(seq);
 
         if (ap.av.adjustForHiddenSeqs(index)
                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
@@ -364,7 +364,7 @@ public class PopupMenu extends JPopupMenu
       }
     }
     // for the case when no sequences are even visible
-    if (ap.av.hasHiddenRows) {
+    if (ap.av.hasHiddenRows()) {
       {
         menuItem = new JMenuItem("Reveal All");
         menuItem.addActionListener(new ActionListener()
@@ -506,7 +506,7 @@ public class PopupMenu extends JPopupMenu
       editMenu.setVisible(false);
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
+    if (!ap.av.getAlignment().getGroups().contains(sg))
     {
       unGroupMenuItem.setVisible(false);
     }
@@ -1289,8 +1289,7 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.hiddenRepSequences),
-            ap.av.alignment.getWidth());
+            sg,ap.av.getHiddenRepSequences());
     refresh();
   }
 
@@ -1417,7 +1416,7 @@ public class PopupMenu extends JPopupMenu
     if (abovePIDColour.isSelected())
     {
       sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1));
 
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
@@ -1471,7 +1470,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
     sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
             sg.getEndRes() + 1));
     refresh();
   }
@@ -1489,7 +1488,7 @@ public class PopupMenu extends JPopupMenu
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
             sg.getEndRes() + 1));
 
     refresh();
@@ -1525,11 +1524,11 @@ public class PopupMenu extends JPopupMenu
     {
       Conservation c = new Conservation("Group",
               ResidueProperties.propHash, 3,
-              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 
       c.calculate();
-      c.verdict(false, ap.av.ConsPercGaps);
+      c.verdict(false, ap.av.getConsPercGaps());
 
       sg.cs.setConservation(c);
 
@@ -1599,7 +1598,7 @@ public class PopupMenu extends JPopupMenu
     // this method won't add a new group if it already exists
     if (sg != null)
     {
-      ap.av.alignment.addGroup(sg);
+      ap.av.getAlignment().addGroup(sg);
     }
 
     return sg;
@@ -1653,7 +1652,7 @@ public class PopupMenu extends JPopupMenu
   void unGroupMenuItem_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    ap.av.alignment.deleteGroup(sg);
+    ap.av.getAlignment().deleteGroup(sg);
     ap.av.setSelectionGroup(null);
     refresh();
   }
@@ -1807,7 +1806,7 @@ public class PopupMenu extends JPopupMenu
       }
 
       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
-              sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+              sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
               caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
@@ -1834,7 +1833,7 @@ public class PopupMenu extends JPopupMenu
     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
-    AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation();
     if (nala != null)
     {
       for (int i = 0; i < nala.length; i++)
@@ -1883,9 +1882,9 @@ public class PopupMenu extends JPopupMenu
   public void discoverPDB_actionPerformed()
   {
 
-    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[]
+    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
     { sequence }
-            : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+            : ap.av.getSequenceSelection());
     Thread discpdb = new Thread(new Runnable()
     {
       public void run()
@@ -1954,10 +1953,10 @@ public class PopupMenu extends JPopupMenu
     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
             "Coloured by " + pdbid, anots);
 
-    ap.av.alignment.addAnnotation(an);
+    ap.av.getAlignment().addAnnotation(an);
     an.createSequenceMapping(sequence, 0, true);
     // an.adjustForAlignment();
-    ap.av.alignment.setAnnotationIndex(an, 0);
+    ap.av.getAlignment().setAnnotationIndex(an, 0);
 
     ap.adjustAnnotationHeight();
 
@@ -1984,8 +1983,8 @@ public class PopupMenu extends JPopupMenu
         EditCommand editCommand = new EditCommand("Edit Sequences",
                 EditCommand.REPLACE, dialog.getName().replace(' ',
                         ap.av.getGapCharacter()),
-                sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-                sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+                sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
 
         ap.alignFrame.addHistoryItem(editCommand);