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 2e6ea52..0e607c7 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -588,7 +588,7 @@ 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);
@@ -1530,15 +1530,17 @@ 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[]
+        if (region[0]>=hiddenOffset && region[1]<=hiddenCutoff)
+        {
+          hiddenColumns.addElement(new int[]
         { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        }
       }
     }
 
@@ -4555,7 +4557,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+    viewport.setShowUnconserved(showNonconservedMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -4638,7 +4640,7 @@ 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]);