X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=700c2293a736a45c82b5c53937d6b80600e846c2;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=e03f2f4126b30b104e5d06d8800837163026b6f7;hpb=1c66dc9053356a709e9cd9d3282517b5221f1ba2;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e03f2f4..700c229 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/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
- * 
+ *
  * 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.appletgui;
@@ -35,6 +35,7 @@ import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
@@ -87,10 +88,12 @@ import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemListener, KeyListener
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+        ItemListener, KeyListener
 {
   public AlignmentPanel alignPanel;
 
@@ -101,9 +104,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   int DEFAULT_HEIGHT = 500;
 
   String jalviewServletURL;
-  
 
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
+          String title, boolean embedded)
   {
     if (applet != null)
     {
@@ -131,6 +134,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showGroupConservation.setState(viewport.isShowGroupConservation());
     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
     showSequenceLogo.setState(viewport.isShowSequenceLogo());
+    normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 
     seqLimits.setState(viewport.showJVSuffix);
 
@@ -194,10 +198,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       {
         RNAHelixColour.setEnabled(true);
       }
-      else {
+      else
+      {
         RNAHelixColour.setEnabled(false);
       }
-    } else {
+    }
+    else
+    {
       RNAHelixColour.setEnabled(false);
       purinePyrimidineColour.setEnabled(false);
     }
@@ -232,32 +239,44 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   /**
    * Load a features file onto the alignment
    * 
-   * @param file file URL, content, or other resolvable path
-   * @param type is protocol for accessing data referred to by file
+   * @param file
+   *          file URL, content, or other resolvable path
+   * @param type
+   *          is protocol for accessing data referred to by file
    */
 
-  public void parseFeaturesFile(String file, String type)
+  public boolean parseFeaturesFile(String file, String type)
   {
-    parseFeaturesFile(file, type, true);
+    return parseFeaturesFile(file, type, true);
   }
-  
+
   /**
    * Load a features file onto the alignment
    * 
-   * @param file file URL, content, or other resolvable path
-   * @param type is protocol for accessing data referred to by file
-   * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
+   * @param file
+   *          file URL, content, or other resolvable path
+   * @param type
+   *          is protocol for accessing data referred to by file
+   * @param autoenabledisplay
+   *          when true, display features flag will be automatically enabled if
+   *          features are loaded
+   * @return true if data parsed as a features file
    */
-  public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)
-  {    
+  public boolean parseFeaturesFile(String file, String type,
+          boolean autoenabledisplay)
+  {
+    // TODO: test if importing a features file onto an alignment which already
+    // has features with links overwrites the original links.
+
     Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
     try
     {
       featuresFile = new jalview.io.FeaturesFile(file, type)
-              .parse(viewport.getAlignment(),
-                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
-                      featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
+              .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
+                      .getFeatureRenderer().featureColours, featureLinks,
+                      true, viewport.applet.getDefaultParameter(
+                              "relaxedidmatch", false));
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -279,10 +298,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         viewport.featureSettings.refreshTable();
       }
       alignPanel.paintAlignment(true);
+      statusBar.setText("Successfully added features to alignment.");
     }
-
+    return featuresFile;
   }
 
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (viewport.cursorMode
@@ -296,8 +317,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
     case 27: // escape key
       deselectAllSequenceMenuItem_actionPerformed();
-      
-      alignPanel.alabels.cancelDrag(); 
+
+      alignPanel.alabels.cancelDrag();
       break;
     case KeyEvent.VK_X:
       if (evt.isControlDown() || evt.isMetaDown())
@@ -557,8 +578,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
-              .getSelected().size() > 0)
+      if ((viewport.getColumnSelection() != null
+              && viewport.getColumnSelection().getSelected() != null && viewport
+              .getColumnSelection().getSelected().size() > 0)
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -586,7 +608,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         hide = true;
         viewport.hideAllSelectedSeqs();
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
+      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+              .size() > 0))
       {
         viewport.showAllHiddenSeqs();
       }
@@ -609,14 +632,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }
   }
 
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == displayNonconservedMenuItem)
@@ -709,6 +735,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       showSequenceLogo_actionPerformed();
     }
+    else if (evt.getSource() == normSequenceLogo)
+    {
+      normSequenceLogo_actionPerformed();
+    }
     else if (evt.getSource() == showConsensusHistogram)
     {
       showConsensusHistogram_actionPerformed();
@@ -733,6 +763,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     this.alignPanel.annotationPanel.repaint();
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     Object source = evt.getSource();
@@ -753,9 +784,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       loadAnnotations();
     }
-    else if( source == loadScores ) {
-    	loadScores();
-    }
     else if (source == outputAnnotations)
     {
       outputAnnotations(true);
@@ -921,6 +949,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       showSequenceLogo_actionPerformed();
     }
+    else if (source == normSequenceLogo)
+    {
+      normSequenceLogo_actionPerformed();
+    }
     else if (source == showConsensusHistogram)
     {
       showConsensusHistogram_actionPerformed();
@@ -955,9 +987,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     else if (source == clustalColour)
     {
       abovePIDThreshold.setState(false);
-      changeColour(new ClustalxColourScheme(
-              viewport.getAlignment().getSequences(),
-              viewport.getAlignment().getWidth()));
+      changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
     }
     else if (source == zappoColour)
     {
@@ -1019,8 +1049,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       changeColour(new Blosum62ColourScheme());
     }
-    else if (source == tcoffeeColour) {
-        changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+    else if (source == tcoffeeColour)
+    {
+      changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
     }
     else if (source == annotationColour)
     {
@@ -1104,26 +1135,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   public void loadAnnotations()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-    cap.setText("Paste your features / annotations file here.");
+    cap.setText("Paste your features / annotations / T-coffee score file here.");
     cap.setAnnotationImport();
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
 
   }
-  
-  public void loadScores() {
-	  //TODO
-	  
-  }
 
   public String outputAnnotations(boolean displayTextbox)
   {
     String annotation = new AnnotationFile().printAnnotations(
             viewport.showAnnotation ? viewport.getAlignment()
-                    .getAlignmentAnnotation() : null, viewport.getAlignment()
-                    .getGroups(),
-            ((Alignment) viewport.getAlignment()).alignmentProperties);
+                    .getAlignmentAnnotation() : null, viewport
+                    .getAlignment().getGroups(), ((Alignment) viewport
+                    .getAlignment()).alignmentProperties);
 
     if (displayTextbox)
     {
@@ -1139,7 +1165,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   private Hashtable getDisplayedFeatureCols()
   {
-    if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
+    if (alignPanel.getFeatureRenderer() != null
+            && viewport.featuresDisplayed != null)
     {
       FeatureRenderer fr = alignPanel.getFeatureRenderer();
       Hashtable fcols = new Hashtable();
@@ -1159,26 +1186,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     String features;
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = new FeaturesFile().printJalviewFormat(
-              viewport.getAlignment().getSequencesArray(),
+      features = new FeaturesFile().printJalviewFormat(viewport
+              .getAlignment().getSequencesArray(),
               getDisplayedFeatureCols());
     }
     else
     {
-      features = new FeaturesFile().printGFFFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols());
     }
 
     if (displayTextbox)
     {
-      boolean frimport=false;
-      if (features==null || features.equals("No Features Visible"))
+      boolean frimport = false;
+      if (features == null || features.equals("No Features Visible"))
       {
         features = "# No features visible - paste some and import them here.";
-        frimport=true;
+        frimport = true;
       }
-      
+
       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
       if (frimport)
       {
@@ -1188,8 +1214,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
       cap.setText(features);
-    } else {
-      if (features==null)
+    }
+    else
+    {
+      if (features == null)
         features = "";
     }
 
@@ -1290,13 +1318,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.RemoveComponent(alignPanel);
-    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
-    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+    if (alignPanel.seqPanel != null
+            && alignPanel.seqPanel.seqCanvas != null)
+    {
+      PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+    }
+    if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
+    {
+      PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+    }
 
     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
     {
       System.exit(0);
-    } else {
+    }
+    else
+    {
     }
     viewport = null;
     alignPanel = null;
@@ -1350,8 +1387,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   }
 
   /**
-   * TODO: JAL-1104
-   * DOCUMENT ME!
+   * TODO: JAL-1104 DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
@@ -1369,18 +1405,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     AlignViewport originalSource = getOriginatingSource(command);
     // JBPNote Test
-    if (originalSource!=viewport) {
-      System.err.println("Warning: Viewport object mismatch whilst undoing");
+    if (originalSource != viewport)
+    {
+      System.err
+              .println("Warning: Viewport object mismatch whilst undoing");
     }
-    originalSource.updateHiddenColumns(); //    originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
+    originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
+                                          // viewport.getColumnSelection().getHiddenColumns()
+                                          // != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.firePropertyChange("alignment", null, originalSource
+            .getAlignment().getSequences());
   }
 
   /**
-   * TODO: JAL-1104
-   * DOCUMENT ME!
+   * TODO: JAL-1104 DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
@@ -1398,14 +1437,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     AlignViewport originalSource = getOriginatingSource(command);
     // JBPNote Test
-    if (originalSource!=viewport) {
-      System.err.println("Warning: Viewport object mismatch whilst re-doing");
+    if (originalSource != viewport)
+    {
+      System.err
+              .println("Warning: Viewport object mismatch whilst re-doing");
     }
-    originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
+    originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
+                                          // viewport.getColumnSelection().getHiddenColumns()
+                                          // != null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.firePropertyChange("alignment", null, originalSource
+            .getAlignment().getSequences());
   }
 
   AlignViewport getOriginatingSource(CommandI command)
@@ -1456,62 +1499,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       return;
     }
-
-    if (up)
-    {
-      for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-        if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-        if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,
+            up ? null : viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
   synchronized void slideSequences(boolean right, int size)
   {
-    Vector sg = new Vector();
+    List<SequenceI> sg = new Vector<SequenceI>();
     if (viewport.cursorMode)
     {
-      sg.addElement(viewport.getAlignment()
-              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+      sg.add(viewport.getAlignment().getSequenceAt(
+              alignPanel.seqPanel.seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
-                    .getHeight())
+            && viewport.getSelectionGroup().getSize() != viewport
+                    .getAlignment().getHeight())
     {
       sg = viewport.getSelectionGroup().getSequences(
               viewport.getHiddenRepSequences());
@@ -1522,7 +1525,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       return;
     }
 
-    Vector invertGroup = new Vector();
+    Vector<SequenceI> invertGroup = new Vector();
 
     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
     {
@@ -1530,13 +1533,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
     }
 
-    SequenceI[] seqs1 = new SequenceI[sg.size()];
-    for (int i = 0; i < sg.size(); i++)
-      seqs1[i] = (SequenceI) sg.elementAt(i);
+    SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
 
-    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
+            .size()]);
     for (int i = 0; i < invertGroup.size(); i++)
-      seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+      seqs2[i] = invertGroup.elementAt(i);
 
     SlideSequencesCommand ssc;
     if (right)
@@ -1761,12 +1763,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     // !newAlignment
     addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
-            seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
+            seqs, 0, viewport.getAlignment().getWidth(),
+            viewport.getAlignment()));
 
     viewport.setEndSeq(viewport.getAlignment().getHeight());
     viewport.getAlignment().getWidth();
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+            .getSequences());
 
   }
 
@@ -1858,6 +1861,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -1871,6 +1875,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
 
+  protected void normSequenceLogo_actionPerformed()
+  {
+    showSequenceLogo.setState(true);
+    viewport.setShowSequenceLogo(true);
+    viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
   protected void applyAutoAnnotationSettings_actionPerformed()
   {
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -1883,8 +1895,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
               viewport.getSequenceSelection(),
               viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()),
-              viewport.getAlignment().getGroups());
+                      viewport.getGapCharacter()), viewport.getAlignment()
+                      .getGroups());
       viewport.getAlignment().deleteAllGroups();
       viewport.sequenceColours = null;
       viewport.setSelectionGroup(null);
@@ -1897,10 +1909,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq
-                .hasMoreElements(); viewport.setSequenceColour(
-                (SequenceI) sq.nextElement(), col))
-          ;
+        for (SequenceI sq : gps[g].getSequences(null))
+          viewport.setSequenceColour(sq, col);
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
@@ -2016,12 +2026,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
       addHistoryItem(trimRegion);
 
-      Vector groups = viewport.getAlignment().getGroups();
-
-      for (int i = 0; i < groups.size(); i++)
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
@@ -2052,7 +2058,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }
 
     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
-            "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
+            "Remove Gapped Columns", seqs, start, end,
+            viewport.getAlignment());
 
     addHistoryItem(removeGapCols);
 
@@ -2136,7 +2143,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       {
         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
         {
-          newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
+          newal.addAnnotation(viewport.getAlignment()
+                  .getAlignmentAnnotation()[i]);
         }
       }
     }
@@ -2288,11 +2296,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
             overview.getPreferredSize().height + 50);
 
     frame.pack();
+    final AlignmentPanel ap = alignPanel;
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent e)
       {
-        alignPanel.setOverviewPanel(null);
+        if (ap != null)
+        {
+          ap.setOverviewPanel(null);
+        }
       };
     });
 
@@ -2344,71 +2357,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
       cs.setConsensus(viewport.getSequenceConsensusHash());
 
-    }             
-    viewport.setGlobalColourScheme(cs);
-
-    if (viewport.getColourAppliesToAllGroups())
-    {
-      Vector groups = viewport.getAlignment().getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-        if (cs == null)
-        {
-          sg.cs = null;
-          continue;
-        }
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(
-                  sg.getSequences(viewport.getHiddenRepSequences()),
-                  sg.getWidth());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = cs.getClass().newInstance();
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-            sg.cs = cs;
-          }
-        }
-
-        if (viewport.getAbovePIDThreshold()
-                || cs instanceof PIDColourScheme
-                || cs instanceof Blosum62ColourScheme)
-        {
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,
-                  sg.getWidth()));
-        }
-        else
-        {
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-        }
-
-        if (viewport.getConservationSelected())
-        {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3,
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,
-                  viewport.getAlignment().getWidth() - 1);
-          c.calculate();
-          c.verdict(false, viewport.getConsPercGaps());
-          sg.cs.setConservation(c);
-        }
-        else
-        {
-          sg.cs.setConservation(null);
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-        }
-
-      }
     }
+    viewport.setGlobalColourScheme(cs);
 
     if (alignPanel.getOverviewPanel() != null)
     {
@@ -2416,8 +2366,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }
 
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
-                    alignPanel);
+            .getStructureSelectionManager(viewport.applet)
+            .sequenceColoursChanged(alignPanel);
 
     alignPanel.paintAlignment(true);
   }
@@ -2483,7 +2433,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2603,8 +2554,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     if ((viewport.getSelectionGroup() != null && viewport
             .getSelectionGroup().getSize() > 1)
-            || (viewport.getSelectionGroup() == null && viewport.getAlignment()
-                    .getHeight() > 1))
+            || (viewport.getAlignment().getHeight() > 1))
     {
       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
 
@@ -2665,14 +2615,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     sortByTreeMenu.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         sortByTree(treePanel, title); // treePanel.getTitle());
       }
     });
-    
+
     treePanel.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowOpened(WindowEvent e)
       {
         if (viewport.sortByTree)
@@ -2682,24 +2634,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         super.windowOpened(e);
       }
 
+      @Override
       public void windowClosing(WindowEvent e)
       {
         sortByTreeMenu.remove(item);
       };
     });
   }
+
   public boolean sortBy(AlignmentOrder alorder, String undoname)
   {
-    SequenceI[] oldOrder = viewport.getAlignment()
-    .getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     if (viewport.applet.debug)
     {
-      System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
+      System.err.println("Sorting " + alorder.getOrder().size()
+              + " in alignment '" + getTitle() + "'");
     }
     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
-    if (undoname!=null)
+    if (undoname != null)
     {
-      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
+      addHistoryItem(new OrderCommand(undoname, oldOrder,
+              viewport.getAlignment()));
     }
     alignPanel.paintAlignment(true);
     return true;
@@ -2725,6 +2680,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         this.builddate = builddate;
       }
 
+      @Override
       public void paint(Graphics g)
       {
         g.setColor(Color.white);
@@ -2794,8 +2750,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   MenuItem loadTree = new MenuItem("Load Associated Tree ...");
 
   MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
-  
-  MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");
 
   MenuItem outputFeatures = new MenuItem("Export Features ...");
 
@@ -2870,14 +2824,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   MenuItem buriedColour = new MenuItem();
 
   MenuItem purinePyrimidineColour = new MenuItem();
+
   MenuItem RNAHelixColour = new MenuItem();
-  
+
   MenuItem userDefinedColour = new MenuItem();
 
   MenuItem PIDColour = new MenuItem();
 
   MenuItem BLOSUM62Colour = new MenuItem();
-  
+
   MenuItem tcoffeeColour = new MenuItem();
 
   MenuItem njTreeBlosumMenuItem = new MenuItem();
@@ -2965,15 +2920,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
 
   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-  
+
   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
-  Menu autoAnnMenu=new Menu();
-  CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
+
+  Menu autoAnnMenu = new Menu();
+
+  CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
+
   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+
   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+
   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+
   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
 
+  CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+
   private void jbInit() throws Exception
   {
 
@@ -2990,6 +2953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           outputText_actionPerformed(e);
@@ -3003,7 +2967,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     loadTree.addActionListener(this);
     loadAnnotations.addActionListener(this);
-    loadScores.addActionListener(this);
     outputFeatures.addActionListener(this);
     outputAnnotations.addActionListener(this);
     selectAllSequenceMenuItem.addActionListener(this);
@@ -3074,9 +3037,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     BLOSUM62Colour.setLabel("BLOSUM62 Score");
     BLOSUM62Colour.addActionListener(this);
     tcoffeeColour.setLabel("T-Coffee Scores");
-    tcoffeeColour.setEnabled(false);	// it will enabled only if a score file is provided
+    tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
+                                     // provided
     tcoffeeColour.addActionListener(this);
-    avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem
+            .setLabel("Average Distance Using BLOSUM62");
     avDistanceTreeBlosumMenuItem.addActionListener(this);
     njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
     njTreeBlosumMenuItem.addActionListener(this);
@@ -3188,10 +3153,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showGroupConservation.setLabel("Group Conservation");
     showConsensusHistogram.setLabel("Show Consensus Histogram");
     showSequenceLogo.setLabel("Show Consensus Logo");
+    normSequenceLogo.setLabel("Normalise Consensus Logo");
     applyAutoAnnotationSettings.setLabel("Apply to all groups");
     applyAutoAnnotationSettings.setState(true);
     autoAnnMenu.setLabel("Autocalculated Annotation");
-    
+
     invertColSel.addActionListener(this);
     showColumns.addActionListener(this);
     showSeqs.addActionListener(this);
@@ -3204,6 +3170,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showGroupConservation.addItemListener(this);
     showConsensusHistogram.addItemListener(this);
     showSequenceLogo.addItemListener(this);
+    normSequenceLogo.addItemListener(this);
+
     applyAutoAnnotationSettings.addItemListener(this);
     formatMenu.setLabel("Format");
     selectMenu.setLabel("Select");
@@ -3221,8 +3189,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     fileMenu.add(inputText);
     fileMenu.add(loadTree);
     fileMenu.add(loadAnnotations);
-    fileMenu.add(loadScores);
-    
+
     fileMenu.addSeparator();
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(outputFeatures);
@@ -3258,6 +3225,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     autoAnnMenu.add(applyAutoAnnotationSettings);
     autoAnnMenu.add(showConsensusHistogram);
     autoAnnMenu.add(showSequenceLogo);
+    autoAnnMenu.add(normSequenceLogo);
     autoAnnMenu.addSeparator();
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
@@ -3408,14 +3376,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       final AlignFrame me = this;
       viewport.applet.addFocusListener(new FocusListener()
       {
-        
+
         @Override
         public void focusLost(FocusEvent e)
         {
-          if (me.viewport.applet.currentAlignFrame==me) {
-                  me.viewport.applet.currentAlignFrame = null;
-        }}
-        
+          if (me.viewport.applet.currentAlignFrame == me)
+          {
+            me.viewport.applet.currentAlignFrame = null;
+          }
+        }
+
         @Override
         public void focusGained(FocusEvent e)
         {
@@ -3508,11 +3478,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     // TODO: search for a jmv that involves viewer
     if (jmv == null)
     { // create a new viewer/jalview binding.
-      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
+      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
+      { seqs });
     }
     return jmv;
 
   }
+
   /**
    * bind a pdb file to a sequence in the current view
    * 
@@ -3633,8 +3605,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     if (applet.useXtrnalSviewer)
     {
       // register the association(s) and quit, don't create any windows.
-      if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
-        System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
+      if (StructureSelectionManager.getStructureSelectionManager(applet)
+              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+      {
+        System.err.println("Failed to map " + pdb.getFile() + " ("
+                + protocol + ") to any sequences");
       }
       return;
     }
@@ -3686,9 +3661,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   }
 
   /**
-   * modify the current selection, providing the user has not made a selection already.
-   * @param sel - sequences from this alignment 
-   * @param csel - columns to be selected on the alignment
+   * modify the current selection, providing the user has not made a selection
+   * already.
+   * 
+   * @param sel
+   *          - sequences from this alignment
+   * @param csel
+   *          - columns to be selected on the alignment
    */
   public void select(SequenceGroup sel, ColumnSelection csel)
   {
@@ -3697,67 +3676,81 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   public void scrollTo(int row, int column)
   {
-    alignPanel.seqPanel.scrollTo(row, column);    
+    alignPanel.seqPanel.scrollTo(row, column);
   }
+
   public void scrollToRow(int row)
   {
-    alignPanel.seqPanel.scrollToRow(row);    
+    alignPanel.seqPanel.scrollToRow(row);
   }
+
   public void scrollToColumn(int column)
   {
-    alignPanel.seqPanel.scrollToColumn(column);    
+    alignPanel.seqPanel.scrollToColumn(column);
   }
+
   /**
    * @return the alignments unique ID.
    */
-  public String getSequenceSetId() {
+  public String getSequenceSetId()
+  {
     return viewport.getSequenceSetId();
   }
-  
-  
+
   /**
-   * Load the (T-Coffee) score file from the specified url 
+   * Load the (T-Coffee) score file from the specified url
    * 
-   * @param source File/URL/T-COFFEE score file contents
-   * @throws IOException 
+   * @param source
+   *          File/URL/T-COFFEE score file contents
+   * @throws IOException
    * @return true if alignment was annotated with data from source
    */
-  public boolean loadScoreFile( String source ) throws IOException {
-
-    TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
-	  if( !file.isValid()) {
-	    // TODO: raise dialog for gui
-	    System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
-	    System.err.println("Origin was:\n"+source);
-	    return false;
-	  }
-	  
-	  /*
-	   * check that the score matrix matches the alignment dimensions
-	   */
-	  AlignmentI aln; 
-	  if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
-	    // TODO: raise a dialog box here rather than bomb out.
-	    System.err.println("The scores matrix does not match the alignment dimensions");
-		  
-	  }
-	  
-	   // TODO add parameter to indicate if matching should be done
-	  if (file.annotateAlignment(alignPanel.getAlignment(), false))
-	  {
-	    alignPanel.fontChanged();
-	    tcoffeeColour.setEnabled(true);
-	          // switch to this color
-	          changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
-	          return true;
-          } else {
-            System.err.println("Problems resolving T-Coffee scores:");
-            if (file.getWarningMessage()!=null) {
-              System.err.println(file.getWarningMessage());
-            }
-          }
-	  return false;
+  public boolean loadScoreFile(String source) throws IOException
+  {
+
+    TCoffeeScoreFile file = new TCoffeeScoreFile(source,
+            AppletFormatAdapter.checkProtocol(source));
+    if (!file.isValid())
+    {
+      // TODO: raise dialog for gui
+      System.err.println("Problems parsing T-Coffee scores: "
+              + file.getWarningMessage());
+      System.err.println("Origin was:\n" + source);
+      return false;
+    }
+
+    /*
+     * check that the score matrix matches the alignment dimensions
+     */
+    AlignmentI aln;
+    if ((aln = viewport.getAlignment()) != null
+            && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
+                    .getWidth()))
+    {
+      // TODO: raise a dialog box here rather than bomb out.
+      System.err
+              .println("The scores matrix does not match the alignment dimensions");
+
+    }
+
+    // TODO add parameter to indicate if matching should be done
+    if (file.annotateAlignment(alignPanel.getAlignment(), false))
+    {
+      alignPanel.fontChanged();
+      tcoffeeColour.setEnabled(true);
+      // switch to this color
+      changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+      return true;
+    }
+    else
+    {
+      System.err.println("Problems resolving T-Coffee scores:");
+      if (file.getWarningMessage() != null)
+      {
+        System.err.println(file.getWarningMessage());
+      }
+    }
+    return false;
   }
-  
-  
+
 }