X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ceb08ee0daab7acda3a7a9ffe8ce6ccdfc8472a7;hb=28a4f823a8d3e6eae1a4569d8022c5a20fd0e3c7;hp=e71e64901d7c9a131bd1c3c12aa23db1f6efff6c;hpb=ed0fff390d4285dce71d8f66b33f1569af6469f6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e71e649..ceb08ee 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,18 +1,18 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
@@ -127,7 +127,7 @@ import javax.swing.SwingUtilities;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -159,7 +159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Creates a new AlignFrame object with specific width and height.
-   *
+   * 
    * @param al
    * @param width
    * @param height
@@ -172,7 +172,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Creates a new AlignFrame object with specific width, height and
    * sequenceSetId
-   *
+   * 
    * @param al
    * @param width
    * @param height
@@ -187,7 +187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Creates a new AlignFrame object with specific width, height and
    * sequenceSetId
-   *
+   * 
    * @param al
    * @param width
    * @param height
@@ -202,7 +202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * new alignment window with hidden columns
-   *
+   * 
    * @param al
    *          AlignmentI
    * @param hiddenColumns
@@ -221,7 +221,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
-   *
+   * 
    * @param al
    * @param hiddenColumns
    * @param width
@@ -238,7 +238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
-   *
+   * 
    * @param al
    * @param hiddenColumns
    * @param width
@@ -267,7 +267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Make a new AlignFrame from exisiting alignmentPanels
-   *
+   * 
    * @param ap
    *          AlignmentPanel
    * @param av
@@ -335,7 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Change the filename and format for the alignment, and enable the 'reload'
    * button functionality.
-   *
+   * 
    * @param file
    *          valid filename
    * @param format
@@ -691,7 +691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Need to call this method when tabs are selected for multiple views, or when
    * loading from Jalview2XML.java
-   *
+   * 
    * @param av
    *          AlignViewport
    */
@@ -737,13 +737,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     updateEditMenuBar();
   }
+
   // methods for implementing IProgressIndicator
   // need to refactor to a reusable stub class
   Hashtable progressBars, progressBarHandlers;
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   @Override
@@ -827,7 +828,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @return true if any progress bars are still active
    */
   @Override
@@ -880,6 +881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
+                  && ((AlignFrame) frames[i]).fileName != null
                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
           {
             try
@@ -961,7 +963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1057,8 +1059,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
       FormatAdapter f = new FormatAdapter();
-      String output = f.formatSequences(
-              format,
+      String output = f.formatSequences(format,
               viewport.getAlignment(), // class cast exceptions will
               // occur in the distant future
               omitHidden, f.getCacheSuffixDefault(format),
@@ -1114,7 +1115,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1160,7 +1161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1179,7 +1180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1191,7 +1192,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1210,7 +1211,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1262,7 +1263,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Close the current view or all views in the alignment frame. If the frame
    * only contains one view then the alignment will be removed from memory.
-   *
+   * 
    * @param closeAllTabs
    */
   @Override
@@ -1308,7 +1309,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * close alignPanel2 and shuffle tabs appropriately.
-   *
+   * 
    * @param alignPanel2
    */
   public void closeView(AlignmentPanel alignPanel2)
@@ -1384,7 +1385,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @return alignment objects for all views
    */
   AlignmentI[] getViewAlignments()
@@ -1409,7 +1410,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1445,7 +1446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1527,7 +1528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param up
    *          DOCUMENT ME!
    */
@@ -1539,7 +1540,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,
+            viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
@@ -1627,7 +1629,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1696,7 +1698,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1708,7 +1710,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1720,7 +1722,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Paste contents of Jalview clipboard
-   *
+   * 
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
    */
@@ -1781,6 +1783,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
+      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+      int fgroup = -1;
 
       if (newAlignment)
       {
@@ -1848,6 +1852,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           newDs.clear(); // tidy up
         }
+        if (alignment.getAlignmentAnnotation() != null)
+        {
+          for (AlignmentAnnotation alan : alignment
+                  .getAlignmentAnnotation())
+          {
+            if (alan.graphGroup > fgroup)
+            {
+              fgroup = alan.graphGroup;
+            }
+          }
+        }
         if (pastedal.getAlignmentAnnotation() != null)
         {
           // Add any annotation attached to alignment.
@@ -1858,6 +1873,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
             {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
@@ -1877,11 +1908,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (sequences[i].getAnnotation() != null)
         {
+          AlignmentAnnotation newann;
           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
           {
             annotationAdded = true;
-            sequences[i].getAnnotation()[a].adjustForAlignment();
-            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            newann = sequences[i].getAnnotation()[a];
+            newann.adjustForAlignment();
+            newann.padAnnotation(alwidth);
+            if (newann.graphGroup > -1)
+            {
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+            }
             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
             // was
             // duplicated
@@ -1921,6 +1972,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   newann.padAnnotation(avwidth);
                   alview[avnum].addAnnotation(newann); // annotation was
                   // duplicated earlier
+                  // TODO JAL-1145 graphGroups are not updated for sequence
+                  // annotation added to several views. This may cause
+                  // strangeness
                   alview[avnum].setAnnotationIndex(newann, a);
                 }
               }
@@ -1930,10 +1984,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         viewport.firePropertyChange("alignment", null,
                 alignment.getSequences());
-        if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector<AlignmentPanel>)alignPanels))
+        if (alignPanels != null)
+        {
+          for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+          {
+            ap.validateAnnotationDimensions(false);
+          }
+        }
+        else
         {
-          ap.validateAnnotationDimensions(false);
-        }} else { alignPanel.validateAnnotationDimensions(false);}
+          alignPanel.validateAnnotationDimensions(false);
+        }
 
       }
       else
@@ -1993,7 +2054,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2006,7 +2067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2067,7 +2128,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2084,7 +2145,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2107,7 +2168,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2131,7 +2192,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2167,7 +2228,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2179,7 +2240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2237,7 +2298,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       addHistoryItem(trimRegion);
 
-      for (SequenceGroup sg :viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
@@ -2253,7 +2314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2301,7 +2362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2340,7 +2401,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2364,7 +2425,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2381,7 +2442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @param copyAnnotation
    *          if true then duplicate all annnotation, groups and settings
    * @return new alignment panel, already displayed.
@@ -2392,7 +2453,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @param viewTitle
    *          title of newly created view
    * @return new alignment panel, already displayed.
@@ -2403,7 +2464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @param viewTitle
    *          title of newly created view
    * @param copyAnnotation
@@ -2499,7 +2560,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2511,7 +2572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2541,7 +2602,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
   @Override
@@ -2556,7 +2617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2569,7 +2630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2605,7 +2666,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * called by key handler and the hide all/show all menu items
-   *
+   * 
    * @param toggleSeqs
    * @param toggleCols
    */
@@ -2675,7 +2736,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
@@ -2688,7 +2749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
@@ -2705,7 +2766,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
@@ -2734,7 +2795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2747,7 +2808,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2760,7 +2821,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2773,7 +2834,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2786,7 +2847,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2799,7 +2860,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2831,7 +2892,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Set or clear 'Show Sequence Features'
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -2848,7 +2909,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Set or clear 'Show Sequence Features'
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -2872,7 +2933,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2900,7 +2961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2940,7 +3001,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2952,19 +3013,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
   @Override
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
+    changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+            viewport.getHiddenRepSequences()));
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2976,7 +3038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2988,7 +3050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3000,7 +3062,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3012,7 +3074,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3024,7 +3086,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3036,7 +3098,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3048,7 +3110,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3084,7 +3146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3096,7 +3158,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param cs
    *          DOCUMENT ME!
    */
@@ -3150,8 +3212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.getColourAppliesToAllGroups())
     {
 
-
-      for (SequenceGroup sg:viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if (cs == null)
         {
@@ -3161,8 +3222,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg, viewport
-                  .getHiddenRepSequences());
+          sg.cs = new ClustalxColourScheme(sg,
+                  viewport.getHiddenRepSequences());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -3220,7 +3281,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3238,7 +3299,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3256,7 +3317,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3275,7 +3336,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3294,7 +3355,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3390,7 +3451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3402,7 +3463,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3414,7 +3475,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3431,7 +3492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3447,7 +3508,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3463,7 +3524,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3480,7 +3541,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3492,7 +3553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3516,7 +3577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3565,7 +3626,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3577,7 +3638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3589,7 +3650,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3601,7 +3662,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3613,7 +3674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param type
    *          DOCUMENT ME!
    * @param pwType
@@ -3625,7 +3686,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null)
+    if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() > 0)
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
@@ -3640,10 +3702,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      for (SequenceI _s:sg.getSequences())
+      for (SequenceI _s : sg.getSequences())
       {
-        if (_s.getLength() < sg
-                .getEndRes())
+        if (_s.getLength() < sg.getEndRes())
         {
           JOptionPane
                   .showMessageDialog(
@@ -3700,7 +3761,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param title
    *          DOCUMENT ME!
    * @param order
@@ -3732,7 +3793,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Add a new sort by annotation score menu item
-   *
+   * 
    * @param sort
    *          the menu to add the option to
    * @param scoreLabel
@@ -3769,7 +3830,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * search the alignment and rebuild the sort by annotation score submenu the
    * last alignment annotation vector hash is stored to minimize cost of
    * rebuilding in subsequence calls.
-   *
+   * 
    */
   @Override
   public void buildSortByAnnotationScoresMenu()
@@ -3785,7 +3846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // almost certainly a quicker way to do this - but we keep it simple
       Hashtable scoreSorts = new Hashtable();
       AlignmentAnnotation aann[];
-      for (SequenceI sqa:viewport.getAlignment().getSequences())
+      for (SequenceI sqa : viewport.getAlignment().getSequences())
       {
         aann = sqa.getAnnotation();
         for (int i = 0; aann != null && i < aann.length; i++)
@@ -3816,7 +3877,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * call. Listeners are added to remove the menu item when the treePanel is
    * closed, and adjust the tree leaf to sequence mapping when the alignment is
    * modified.
-   *
+   * 
    * @param treePanel
    *          Displayed tree window.
    * @param title
@@ -3885,7 +3946,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Work out whether the whole set of sequences or just the selected set will
    * be submitted for multiple alignment.
-   *
+   * 
    */
   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
@@ -3900,7 +3961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       /*
        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
        * SequenceI[sz = seqs.getSize(false)];
-       *
+       * 
        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
        * seqs.getSequenceAt(i); }
        */
@@ -3910,9 +3971,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       /*
        * Vector seqs = viewport.getAlignment().getSequences();
-       *
+       * 
        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       *
+       * 
        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
        * seqs.elementAt(i); } }
        */
@@ -3958,7 +4019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -4024,7 +4085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Add a treeviewer for the tree extracted from a newick file object to the
    * current alignment view
-   *
+   * 
    * @param nf
    *          the tree
    * @param title
@@ -4075,7 +4136,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Generates menu items and listener event actions for web service clients
-   *
+   * 
    */
   public void BuildWebServiceMenu()
   {
@@ -4246,7 +4307,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               } catch (Exception e)
               {
-                Cache.log.debug("Exception during web service menu building process.",e);
+                Cache.log
+                        .debug("Exception during web service menu building process.",
+                                e);
               }
               ;
             }
@@ -4264,7 +4327,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * construct any groupURL type service menu entries.
-   *
+   * 
    * @param webService
    */
   private void build_urlServiceMenu(JMenu webService)
@@ -4274,12 +4337,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
-     *
+     * 
      * @Override public void actionPerformed(ActionEvent e) {
      * jalview.datamodel.AlignmentView
      * .testSelectionViews(af.viewport.getAlignment(),
      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
-     *
+     * 
      * }); webService.add(testAlView);
      */
     // TODO: refactor to RestClient discoverer and merge menu entries for
@@ -4306,12 +4369,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
    * chooser = new JalviewFileChooser(jalview.bin.Cache.
    * getProperty("LAST_DIRECTORY"));
-   *
+   * 
    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
    * to Vamsas file"); chooser.setToolTipText("Export");
-   *
+   * 
    * int value = chooser.showSaveDialog(this);
-   *
+   * 
    * if (value == JalviewFileChooser.APPROVE_OPTION) {
    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
@@ -4319,7 +4382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   /**
    * prototype of an automatically enabled/disabled analysis function
-   *
+   * 
    */
   protected void setShowProductsEnabled()
   {
@@ -4339,7 +4402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * search selection for sequence xRef products and build the show products
    * menu.
-   *
+   * 
    * @param selection
    * @param dataset
    * @return true if showProducts menu should be enabled.
@@ -4540,7 +4603,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       al = null;
-      jalview.bin.Cache.log.debug("Exception during translation.", ex);
+      jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+      JOptionPane
+      .showMessageDialog(
+              Desktop.desktop,
+              "Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.",
+              "Implementation error: Translation Failed", JOptionPane.ERROR_MESSAGE);
+      return;
     }
     if (al == null)
     {
@@ -4560,7 +4629,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Try to load a features file onto the alignment.
-   *
+   * 
    * @param file
    *          contents or path to retrieve file
    * @param type
@@ -4809,7 +4878,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * it's and Annotation file, then a JNet file, and finally a features file. If
    * all are false then the user may have dropped an alignment file onto this
    * AlignFrame.
-   *
+   * 
    * @param file
    *          either a filename or a URL string.
    */
@@ -4850,11 +4919,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             }
             else
             {
-              // some problem - if no warning its probable that the ID matching process didn't work
-              JOptionPane.showMessageDialog(Desktop.desktop,
-                      tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
-                      "Problem reading T-COFFEE score file",
-                      JOptionPane.WARNING_MESSAGE);
+              // some problem - if no warning its probable that the ID matching
+              // process didn't work
+              JOptionPane
+                      .showMessageDialog(
+                              Desktop.desktop,
+                              tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+                                      : tcf.getWarningMessage(),
+                              "Problem reading T-COFFEE score file",
+                              JOptionPane.WARNING_MESSAGE);
             }
           }
           else
@@ -4863,7 +4936,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception x)
         {
-          Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+          Cache.log
+                  .debug("Exception when processing data source as T-COFFEE score file",
+                          x);
           tcf = null;
         }
         if (tcf == null)
@@ -4887,7 +4962,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             /*
              * if (format.equalsIgnoreCase("PDB")) {
-             *
+             * 
              * String pdbfn = ""; // try to match up filename with sequence id
              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
@@ -4932,6 +5007,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
+    } catch (OutOfMemoryError oom)
+    {
+      try
+      {
+        System.gc();
+      } catch (Exception x)
+      {
+      }
+      ;
+      new OOMWarning(
+              "loading data "
+                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+                              : "using " + protocol + " from " + file)
+                              : ".")
+                      + (format != null ? "(parsing as '" + format
+                              + "' file)" : ""), oom, Desktop.desktop);
     }
   }
 
@@ -4989,7 +5080,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
@@ -5002,7 +5093,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
@@ -5015,7 +5106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * find the viewport amongst the tabs in this alignment frame and close that
    * tab
-   *
+   * 
    * @param av
    */
   public boolean closeView(AlignViewport av)
@@ -5288,7 +5379,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
@@ -5302,7 +5393,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
@@ -5317,7 +5408,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5331,7 +5422,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5345,7 +5436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5360,6 +5451,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
   {
+    showSequenceLogo.setState(true);
+    viewport.setShowSequenceLogo(true);
     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
@@ -5372,7 +5465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5399,10 +5492,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
-        for (SequenceI s:gps[g].getSequences())
-          viewport.setSequenceColour(
-                s, col)
-          ;
+        for (SequenceI s : gps[g].getSequences())
+          viewport.setSequenceColour(s, col);
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
@@ -5412,7 +5503,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * make the given alignmentPanel the currently selected tab
-   *
+   * 
    * @param alignmentPanel
    */
   public void setDisplayedView(AlignmentPanel alignmentPanel)