(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 17bc65f..7a99a20 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -157,7 +157,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
       displayNonconserved.setState(sg.getShowNonconserved());
-      if (!ap.av.alignment.getGroups().contains(sg))
+      if (!ap.av.getAlignment().getGroups().contains(sg))
       {
         groupMenu.remove(unGroupMenuItem);
       }
@@ -300,12 +300,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
       remove(seqMenu);
     }
 
-    if (!ap.av.hasHiddenRows)
+    if (!ap.av.hasHiddenRows())
     {
       remove(revealAll);
       remove(revealSeq);
     } else {
-      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)
@@ -513,8 +513,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
           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);
 
@@ -529,44 +529,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
       Vector regions = new Vector();
       if (sg != null)
       {
-        int start = sg.getStartRes();
-        int end = sg.getEndRes() + 1;
-
-        do
-        {
-          if (ap.av.hasHiddenColumns)
-          {
-            if (start == 0)
-            {
-              start = ap.av.colSel.adjustForHiddenColumns(start);
-            }
-
-            end = ap.av.colSel.getHiddenBoundaryRight(start);
-            if (start == end)
-            {
-              end = sg.getEndRes() + 1;
-            }
-            if (end > sg.getEndRes())
-            {
-              end = sg.getEndRes() + 1;
-            }
-          }
-
-          regions.addElement(new int[]
-          { start, end });
-
-          if (ap.av.hasHiddenColumns)
-          {
-            start = ap.av.colSel.adjustForHiddenColumns(end);
-            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
-          }
-        } while (end < sg.getEndRes());
-
-        int[][] startEnd = new int[regions.size()][2];
-        for (int i = 0; i < regions.size(); i++)
-        {
-          startEnd[i] = (int[]) regions.elementAt(i);
-        }
+        // TODO test change case behaves identically in JvLite
+        int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+                sg.getEndRes() + 1);
 
         String description;
         int caseChange;
@@ -588,7 +553,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         }
 
         ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
-                sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
                 caseChange);
 
         ap.alignFrame.addHistoryItem(caseCommand);
@@ -652,6 +617,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
             "Selection output - " + e.getActionCommand(), 600, 500);
+    // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
+    // TODO consider using getSequenceSelection instead here
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
             e.getActionCommand(),
@@ -833,8 +800,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.hiddenRepSequences),
-            ap.av.alignment.getWidth());
+            sg.getSequences(ap.av.getHiddenRepSequences()),
+            ap.av.getAlignment().getWidth());
     refresh();
   }
 
@@ -897,8 +864,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (abovePIDColour.getState())
     {
       sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(ap.av.hiddenRepSequences), 0,
-              ap.av.alignment.getWidth()));
+              sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+              ap.av.getAlignment().getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
@@ -927,8 +894,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
     sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.hiddenRepSequences), 0,
-            ap.av.alignment.getWidth()));
+            sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+            ap.av.getAlignment().getWidth()));
     refresh();
   }
 
@@ -939,8 +906,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.hiddenRepSequences), 0,
-            ap.av.alignment.getWidth()));
+            sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+            ap.av.getAlignment().getWidth()));
 
     refresh();
   }
@@ -964,8 +931,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
       sg.cs.setConservation(Conservation.calculateConservation("Group",
               ResidueProperties.propHash, 3,
-              sg.getSequences(ap.av.hiddenRepSequences), 0,
-              ap.av.alignment.getWidth(),
+              sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+              ap.av.getAlignment().getWidth(),
               false, ap.av.getConsPercGaps(),false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
@@ -986,7 +953,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     // 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;
@@ -995,7 +962,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   void unGroupMenuItem_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    ap.av.alignment.deleteGroup(sg);
+    ap.av.getAlignment().deleteGroup(sg);
     ap.av.setSelectionGroup(null);
     ap.paintAlignment(true);
   }