NPE in hashtable constructor

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2e6ea52..293948a 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -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);
   }
 
@@ -4638,9 +4640,8 @@ 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].setIncludeAllConsSymbols(viewport
-                .isIncludeAllConsensusSymbols());
+        gps[g].setShowNonconserved(viewport.getShowUnconserved());
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.alignment.addGroup(gps[g]);
         Color col = new Color((int) (Math.random() * 255), (int) (Math
                 .random() * 255), (int) (Math.random() * 255));