X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=6d3f073abfd2d5341407a02e30f777b9cac19894;hb=1a56a24b084eadd78387eabf71dc7114e356bd00;hp=e11830ccb0c15d1c290c006cc6d6ac4961294584;hpb=7749f0e593d610c517dfd6796cf6087191b189ad;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e11830c..6d3f073 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -21,11 +21,9 @@ package jalview.gui;
 import MCview.*;
 
 import jalview.analysis.*;
-
 import jalview.datamodel.*;
-
-
 import jalview.schemes.*;
+import jalview.commands.ChangeCaseCommand;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -144,8 +142,7 @@ public class PopupMenu extends JPopupMenu
 
         if (seq != null)
         {
-          int start = Math.max(sequence.getName().length()-15, 0);
-          sequenceMenu.setText(sequence.getName().substring(start));
+          sequenceMenu.setText(sequence.getName());
 
           JMenuItem menuItem;
           if( seq.getDatasetSequence().getPDBId() != null)
@@ -452,7 +449,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        upperCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     copy.setText("Copy");
@@ -468,7 +465,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        lowerCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     toggle.setText("Toggle Case");
@@ -476,7 +473,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        toggle_actionPerformed(e);
+        changeCase(e);
       }
     });
     pdbMenu.setText("Associate Structure with Sequence");
@@ -523,12 +520,12 @@ public class PopupMenu extends JPopupMenu
     groupMenu.addSeparator();
     groupMenu.add(groupName);
     groupMenu.add(unGroupMenuItem);
-        groupMenu.add(colourMenu);
+    groupMenu.add(colourMenu);
     groupMenu.add(showBoxes);
-        groupMenu.add(showText);
-        groupMenu.add(showColourText);
+    groupMenu.add(showText);
+    groupMenu.add(showColourText);
     groupMenu.add(outline);
-        sequenceMenu.add(sequenceName);
+    sequenceMenu.add(sequenceName);
     sequenceMenu.add(pdbMenu);
     colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
@@ -816,9 +813,9 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(true), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -864,8 +861,9 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -880,8 +878,9 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -912,8 +911,9 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth());
+                    sg.getSequences(true),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
@@ -1040,13 +1040,15 @@ public class PopupMenu extends JPopupMenu
             }
 
             s = s.replace(' ', '_');
-            sequence.getDatasetSequence().setName(s);
             sequence.setName(s);
             ap.repaint();
         }
 
-        sequence.getDatasetSequence().setDescription(description.getText());
         sequence.setDescription(description.getText());
+
+        ap.av.firePropertyChange("alignment", null,
+                                  ap.av.getAlignment().getSequences());
+
     }
 
     /**
@@ -1176,59 +1178,77 @@ public class PopupMenu extends JPopupMenu
     ap.alignFrame.cut_actionPerformed(null);
   }
 
-  public void upperCase_actionPerformed(ActionEvent e)
-  {
-    changeCase(e.getSource());
-  }
-
-  public void lowerCase_actionPerformed(ActionEvent e)
-  {
-    changeCase(e.getSource());
-  }
-
-  public void toggle_actionPerformed(ActionEvent e)
-  {
-    changeCase(e.getSource());
-  }
-
-  void changeCase(Object source)
+  void changeCase(ActionEvent e)
   {
+    Object source = e.getSource();
     SequenceGroup sg = ap.av.getSelectionGroup();
+    Vector regions = new Vector();
     if (sg != null)
     {
-      for (int g = 0; g < sg.getSize(true); g++)
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
+
+      do
       {
-        int start = sg.getStartRes();
-        int end = sg.getEndRes() + 1;
+        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});
 
-        do
+        if (ap.av.hasHiddenColumns)
         {
-          if (ap.av.hasHiddenColumns)
-          {
-            end = ap.av.colSel.getHiddenBoundaryRight(start);
-            if (start == end)
-              end = sg.getEndRes() + 1;
-            if (end > sg.getEndRes())
-              end = sg.getEndRes() + 1;
-          }
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+        }
+      }
+      while (end < sg.getEndRes());
 
-          if (source == toggle)
-            ( (SequenceI) sg.getSequences(true).elementAt(g))
-                .toggleCase(start, end);
-          else
-            ( (SequenceI) sg.getSequences(true).elementAt(g))
-                .changeCase(source == upperCase, start, end);
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
 
-          if (ap.av.hasHiddenColumns)
-          {
-            start = ap.av.colSel.adjustForHiddenColumns(end);
-            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
-          }
 
-        }
-        while (end < sg.getEndRes());
+      String description;
+      int caseChange;
+
+      if(source==toggle)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
       }
-      PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+      else if(source==upperCase)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(true), startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
+
     }
   }