X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=700c2293a736a45c82b5c53937d6b80600e846c2;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=bcb518f08a4c8b74e9935f6c485043efba6fe543;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index bcb518f..700c229 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -92,7 +92,8 @@ 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;
 
@@ -104,8 +105,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   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)
     {
@@ -197,10 +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);
     }
@@ -234,9 +238,11 @@ 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 boolean parseFeaturesFile(String file, String type)
@@ -246,24 +252,31 @@ 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 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 boolean 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.
+    // 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();
@@ -552,7 +565,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /**
    * called by key handler and the hide all/show all menu items
-   *
+   * 
    * @param toggleSeqs
    * @param toggleCols
    */
@@ -565,8 +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()))
       {
@@ -594,7 +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();
       }
@@ -972,7 +987,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     else if (source == clustalColour)
     {
       abovePIDThreshold.setState(false);
-      changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
+      changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
     }
     else if (source == zappoColour)
     {
@@ -1034,8 +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)
     {
@@ -1131,9 +1147,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   {
     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)
     {
@@ -1149,7 +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();
@@ -1169,24 +1186,23 @@ 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);
@@ -1198,8 +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 = "";
     }
 
@@ -1300,18 +1318,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.RemoveComponent(alignPanel);
-    if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
+    if (alignPanel.seqPanel != null
+            && alignPanel.seqPanel.seqCanvas != null)
     {
       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
     }
-    if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
+    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;
@@ -1365,9 +1387,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   }
 
   /**
-   * TODO: JAL-1104
-   * DOCUMENT ME!
-   *
+   * TODO: JAL-1104 DOCUMENT ME!
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1384,19 +1405,22 @@ 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!
    */
@@ -1413,14 +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)
@@ -1471,21 +1499,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       return;
     }
-    viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,
+            up ? null : viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
   synchronized void slideSequences(boolean right, int size)
   {
-    List<SequenceI>sg = new Vector<SequenceI>();
+    List<SequenceI> sg = new Vector<SequenceI>();
     if (viewport.cursorMode)
     {
-      sg.add(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());
@@ -1506,7 +1535,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
 
-    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
+    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
+            .size()]);
     for (int i = 0; i < invertGroup.size(); i++)
       seqs2[i] = invertGroup.elementAt(i);
 
@@ -1733,12 +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());
 
   }
 
@@ -1800,7 +1831,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /**
    * group consensus toggled
-   *
+   * 
    */
   protected void showGroupConsensus_actionPerformed()
   {
@@ -1820,7 +1851,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -1830,9 +1861,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
+
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -1842,6 +1874,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     viewport.setShowSequenceLogo(showSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
+
   protected void normSequenceLogo_actionPerformed()
   {
     showSequenceLogo.setState(true);
@@ -1862,8 +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);
@@ -1877,9 +1910,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
         for (SequenceI sq : gps[g].getSequences(null))
-          viewport.setSequenceColour(
-                sq, col)
-          ;
+          viewport.setSequenceColour(sq, col);
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
@@ -1995,9 +2026,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
       addHistoryItem(trimRegion);
 
-
-
-      for (SequenceGroup sg:viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
@@ -2029,7 +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);
 
@@ -2090,7 +2120,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /**
    * create a new view derived from the current view
-   *
+   * 
    * @param viewtitle
    * @return frame for the new view
    */
@@ -2113,7 +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]);
         }
       }
     }
@@ -2163,7 +2194,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   }
 
   /**
-   *
+   * 
    * @return list of feature groups on the view
    */
   public String[] getFeatureGroups()
@@ -2179,7 +2210,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /**
    * get sequence feature groups that are hidden or shown
-   *
+   * 
    * @param visible
    *          true is visible
    * @return list
@@ -2197,7 +2228,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /**
    * Change the display state for the given feature groups
-   *
+   * 
    * @param groups
    *          list of group strings
    * @param state
@@ -2265,13 +2296,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
             overview.getPreferredSize().height + 50);
 
     frame.pack();
-    final AlignmentPanel ap=alignPanel;
+    final AlignmentPanel ap = alignPanel;
     frame.addWindowListener(new WindowAdapter()
     {
       @Override
       public void windowClosing(WindowEvent e)
       {
-        if (ap!=null) {
+        if (ap != null)
+        {
           ap.setOverviewPanel(null);
         }
       };
@@ -2328,15 +2360,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }
     viewport.setGlobalColourScheme(cs);
 
-
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
 
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
-                    alignPanel);
+            .getStructureSelectionManager(viewport.applet)
+            .sequenceColoursChanged(alignPanel);
 
     alignPanel.paintAlignment(true);
   }
@@ -2402,7 +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);
   }
 
@@ -2522,8 +2554,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
     if ((viewport.getSelectionGroup() != null && viewport
             .getSelectionGroup().getSize() > 1)
-            || (viewport.getAlignment()
-                    .getHeight() > 1))
+            || (viewport.getAlignment().getHeight() > 1))
     {
       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
 
@@ -2552,7 +2583,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   /**
    * sort the alignment using the given treePanel
-   *
+   * 
    * @param treePanel
    *          tree used to sort view
    * @param title
@@ -2573,7 +2604,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   /**
    * Do any automatic reordering of the alignment and add the necessary bits to
    * the menu structure for the new tree
-   *
+   * 
    * @param treePanel
    * @param title
    */
@@ -2610,18 +2641,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       };
     });
   }
+
   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;
@@ -2791,6 +2824,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   MenuItem buriedColour = new MenuItem();
 
   MenuItem purinePyrimidineColour = new MenuItem();
+
   MenuItem RNAHelixColour = new MenuItem();
 
   MenuItem userDefinedColour = new MenuItem();
@@ -2888,12 +2922,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   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
@@ -2996,9 +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);
@@ -3128,7 +3171,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showConsensusHistogram.addItemListener(this);
     showSequenceLogo.addItemListener(this);
     normSequenceLogo.addItemListener(this);
-    
+
     applyAutoAnnotationSettings.addItemListener(this);
     formatMenu.setLabel("Format");
     selectMenu.setLabel("Select");
@@ -3305,7 +3348,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
    * Attach the alignFrame panels after embedding menus, if necessary. This used
    * to be called setEmbedded, but is now creates the dropdown menus in a
    * platform independent manner to avoid OSX/Mac menu appendage daftness.
-   *
+   * 
    * @param reallyEmbedded
    *          true to attach the view to the applet area on the page rather than
    *          in a new window
@@ -3337,9 +3380,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         @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)
@@ -3375,7 +3420,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
    * structures in the original jmol window. Note This method doesn't work
    * without an additional javascript library to exchange messages between the
    * distinct applets. See http://issues.jalview.org/browse/JAL-621
-   *
+   * 
    * @param viewer
    *          JmolViewer instance
    * @param sequenceIds
@@ -3433,14 +3478,16 @@ 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
-   *
+   * 
    * @param sequenceId
    *          - sequenceId within the dataset.
    * @param pdbEntryString
@@ -3558,8 +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;
     }
@@ -3611,9 +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)
   {
@@ -3624,65 +3678,79 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   {
     alignPanel.seqPanel.scrollTo(row, column);
   }
+
   public void scrollToRow(int row)
   {
     alignPanel.seqPanel.scrollToRow(row);
   }
+
   public void scrollToColumn(int 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
-   *
-   * @param source File/URL/T-COFFEE score file contents
+   * 
+   * @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;
+  }
 
 }