X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b45fa6b45e051704d94ca6e18ac02a550de7d9c3;hb=a822fc744dcc06e6a8d2399218da0d0dfd56cf2b;hp=0727b0cfe2c070638fb9e76f299032c493293f0c;hpb=fd026dead85b733e64fdc7c2e6c88d1adc10626a;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 0727b0c..b45fa6b 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.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.
  * 
@@ -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 +529,8 @@ 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);
-        }
+        int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+                sg.getEndRes() + 1);
 
         String description;
         int caseChange;
@@ -588,7 +552,7 @@ 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 +616,8 @@ 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 +799,8 @@ 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 +863,8 @@ 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 +893,8 @@ 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 +905,8 @@ 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();
   }
@@ -962,16 +928,11 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (conservationMenuItem.getState())
     {
 
-      Conservation c = new Conservation("Group",
+      sg.cs.setConservation(Conservation.calculateConservation("Group",
               ResidueProperties.propHash, 3,
-              sg.getSequences(ap.av.hiddenRepSequences), 0,
-              ap.av.alignment.getWidth());
-
-      c.calculate();
-      c.verdict(false, ap.av.ConsPercGaps);
-
-      sg.cs.setConservation(c);
-
+              sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+              ap.av.getAlignment().getWidth(),
+              false, ap.av.getConsPercGaps(),false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
@@ -991,7 +952,7 @@ 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;
@@ -1000,7 +961,7 @@ 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);
   }