trim hidden regions outside selection when copying selected region to clipboard ...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 18465e1..2d1fc1e 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -531,10 +531,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     @Override
                     public void run()
                     {
-                      System.err.println("Change support: build services again.");
+                      System.err
+                              .println("Change support JWS1: build services again.");
                       BuildWebServiceMenu();
                     }
-                    
+
                   });
                 }
               }
@@ -545,18 +546,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     {
                       public void propertyChange(PropertyChangeEvent evt)
                       {
-                        SwingUtilities.invokeLater(new Runnable()
-                        {
-
-                          @Override
-                          public void run()
-                          {
-                            System.err.println("Change support: build services again.");
-                            BuildWebServiceMenu();
-                          }
-                          
-                        });
-                        }
+                        System.err
+                                .println("Change support JWS2: build services again.");
+                        BuildWebServiceMenu();
+                      }
                     });
     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
@@ -619,7 +612,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     annotationPanelMenuItem.setState(av.showAnnotation);
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
-    showUnconservedMenuItem.setSelected(av.showUnconserved);
+    showNonconservedMenuItem.setSelected(av.showUnconserved);
     showGroupConsensus.setSelected(av.showGroupConsensus);
     showGroupConservation.setSelected(av.showGroupConservation);
     showConsensusHistogram.setSelected(av.showConsensusHistogram);
@@ -1561,15 +1554,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.hasHiddenColumns)
     {
       hiddenColumns = new Vector();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+              .getSelectionGroup().getEndRes();
       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
               .size(); i++)
       {
         int[] region = (int[]) viewport.getColumnSelection()
                 .getHiddenColumns().elementAt(i);
-
-        hiddenColumns.addElement(new int[]
-        { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+        {
+          hiddenColumns.addElement(new int[]
+          { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        }
       }
     }
 
@@ -4634,7 +4630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+    viewport.setShowUnconserved(showNonconservedMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -4717,7 +4713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
-        gps[g].setShowunconserved(viewport.getShowUnconserved());
+        gps[g].setShowNonconserved(viewport.getShowUnconserved());
         gps[g].setIncludeAllConsSymbols(viewport
                 .isIncludeAllConsensusSymbols());
         viewport.alignment.addGroup(gps[g]);