X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=bad78485fa0fe257bbc247c459f99981c4e5f3b2;hb=4fcca76a6c1460d492469ace09a728925b733bfe;hp=3e214b8e6bbfc899849f1d2b305a2c3865bbfdde;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3e214b8..bad7848 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,24 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * Jalview is free software: you can redistribute it and/or
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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;
 
-import java.io.*;
 import java.net.*;
 import java.util.*;
 
@@ -26,6 +24,8 @@ import java.awt.*;
 import java.awt.event.*;
 
 import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.JalviewLite;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
@@ -68,6 +68,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.updateConsensus(alignPanel);
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
+    displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+    followMouseOverFlag.setState(viewport.getFollowHighlight());
 
     seqLimits.setState(viewport.showJVSuffix);
 
@@ -84,6 +86,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           sortPairwiseMenuItem_actionPerformed();
         }
+        else if (param.equalsIgnoreCase("Length"))
+        {
+          sortLengthMenuItem_actionPerformed();
+        }
       }
 
       param = applet.getParameter("wrap");
@@ -101,7 +107,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         centreColumnLabelFlag.setState(true);
         centreColumnLabelFlag_stateChanged();
       }
-
       try
       {
         param = applet.getParameter("windowWidth");
@@ -149,7 +154,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * DOCUMENT ME!
    * 
    * @param String
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
 
   public void parseFeaturesFile(String file, String type)
@@ -158,10 +163,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type).parse(
-              viewport.alignment, alignPanel.seqPanel.seqCanvas
-                      .getFeatureRenderer().featureColours, featureLinks,
-              true);
+      featuresFile = new jalview.io.FeaturesFile(file, type)
+              .parse(viewport.alignment,
+                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
+                      featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -175,6 +180,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       viewport.showSequenceFeatures = true;
       sequenceFeatures.setState(true);
+      if (viewport.featureSettings != null)
+      {
+        viewport.featureSettings.refreshTable();
+      }
       alignPanel.paintAlignment(true);
     }
 
@@ -336,37 +345,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       boolean toggleSeqs = !evt.isControlDown();
       boolean toggleCols = !evt.isShiftDown();
-      boolean hide = false;
-      SequenceGroup sg = viewport.getSelectionGroup();
-
-      if (toggleSeqs)
-      {
-        if (sg != null && sg.getSize() != viewport.alignment.getHeight())
-        {
-          hide = true;
-          viewport.hideAllSelectedSeqs();
-        }
-        else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
-        {
-          viewport.showAllHiddenSeqs();
-        }
-      }
-
-      if (toggleCols)
-      {
-        if (viewport.colSel.getSelected().size() > 0)
-        {
-          viewport.hideSelectedColumns();
-          if (!toggleSeqs)
-          {
-            viewport.selectionGroup = sg;
-          }
-        }
-        else if (!hide)
-        {
-          viewport.showAllHiddenColumns();
-        }
-      }
+      toggleHiddenRegions(toggleSeqs, toggleCols);
       break;
     }
 
@@ -440,11 +419,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         if (evt.isAltDown())
         {
-          viewport.invertColumnSelection();
+          invertColSel_actionPerformed();
         }
         else
         {
-          this.invertSequenceMenuItem_actionPerformed();
+          invertSequenceMenuItem_actionPerformed();
         }
       }
       break;
@@ -467,6 +446,73 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.paintAlignment(true);
   }
 
+  /**
+   * called by key handler and the hide all/show all menu items
+   * 
+   * @param toggleSeqs
+   * @param toggleCols
+   */
+  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+  {
+    boolean hide = false;
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (!toggleSeqs && !toggleCols)
+    {
+      // 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.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
+              .getSelected().size() > 0)
+              || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+                      .getEndRes()))
+      {
+        // now invert the sequence set, if required - empty selection implies
+        // that no hiding is required.
+        if (sg != null)
+        {
+          invertSequenceMenuItem_actionPerformed();
+          sg = viewport.getSelectionGroup();
+          toggleSeqs = true;
+
+        }
+        viewport.expandColSelection(sg, true);
+        // finally invert the column selection and get the new sequence
+        // selection and indicate it should be hidden.
+        invertColSel_actionPerformed();
+        toggleCols = true;
+      }
+    }
+
+    if (toggleSeqs)
+    {
+      if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+      {
+        hide = true;
+        viewport.hideAllSelectedSeqs();
+      }
+      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+      {
+        viewport.showAllHiddenSeqs();
+      }
+    }
+
+    if (toggleCols)
+    {
+      if (viewport.colSel.getSelected().size() > 0)
+      {
+        viewport.hideSelectedColumns();
+        if (!toggleSeqs)
+        {
+          viewport.selectionGroup = sg;
+        }
+      }
+      else if (!hide)
+      {
+        viewport.showAllHiddenColumns();
+      }
+    }
+  }
+
   public void keyReleased(KeyEvent evt)
   {
   }
@@ -477,7 +523,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if (evt.getSource() == colourTextMenuItem)
+    if (evt.getSource() == displayNonconservedMenuItem)
+    {
+      displayNonconservedMenuItem_actionPerformed();
+    }
+    else if (evt.getSource() == colourTextMenuItem)
     {
       colourTextMenuItem_actionPerformed();
     }
@@ -543,10 +593,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       centreColumnLabelFlag_stateChanged();
     }
+    else if (evt.getSource() == this.followMouseOverFlag)
+    {
+      mouseOverFlag_stateChanged();
+    }
 
     alignPanel.paintAlignment(true);
   }
 
+  private void mouseOverFlag_stateChanged()
+  {
+    viewport.followHighlight = followMouseOverFlag.getState();
+    // TODO: could kick the scrollTo mechanism to reset view for current
+    // searchresults.
+  }
+
   private void centreColumnLabelFlag_stateChanged()
   {
     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
@@ -633,6 +694,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       delete_actionPerformed();
     }
+    else if (source == grpsFromSelection)
+    {
+      makeGrpsFromSelection_actionPerformed();
+    }
     else if (source == deleteGroups)
     {
       deleteGroups_actionPerformed();
@@ -690,6 +755,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
+      alignPanel.paintAlignment(true);
     }
     else if (source == hideColumns)
     {
@@ -700,6 +766,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
+      alignPanel.paintAlignment(true);
+    }
+    else if (source == hideAllButSelection)
+    {
+      toggleHiddenRegions(false, false);
+      alignPanel.paintAlignment(true);
+    }
+    else if (source == hideAllSelection)
+    {
+      SequenceGroup sg = viewport.getSelectionGroup();
+      viewport.expandColSelection(sg, false);
+      viewport.hideAllSelectedSeqs();
+      viewport.hideSelectedColumns();
+      alignPanel.paintAlignment(true);
+    }
+    else if (source == showAllHidden)
+    {
+      viewport.showAllHiddenColumns();
+      viewport.showAllHiddenSeqs();
+      alignPanel.paintAlignment(true);
     }
     else if (source == featureSettings)
     {
@@ -707,38 +793,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == alProperties)
     {
-      StringBuffer contents = new StringBuffer();
-
-      float avg = 0;
-      int min = Integer.MAX_VALUE, max = 0;
-      for (int i = 0; i < viewport.alignment.getHeight(); i++)
-      {
-        int size = viewport.alignment.getSequenceAt(i).getEnd()
-                - viewport.alignment.getSequenceAt(i).getStart();
-        avg += size;
-        if (size > max)
-          max = size;
-        if (size < min)
-          min = size;
-      }
-      avg = avg / (float) viewport.alignment.getHeight();
-
-      contents.append("\nSequences: " + viewport.alignment.getHeight());
-      contents.append("\nMinimum Sequence Length: " + min);
-      contents.append("\nMaximum Sequence Length: " + max);
-      contents.append("\nAverage Length: " + (int) avg);
-
-      if (((Alignment) viewport.alignment).alignmentProperties != null)
-      {
-        Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
-        Enumeration en = props.keys();
-        while (en.hasMoreElements())
-        {
-          String key = en.nextElement().toString();
-          contents.append("\n" + key + "\t" + props.get(key));
-        }
-      }
-
+      StringBuffer contents = new jalview.io.AlignmentProperties(
+              viewport.alignment).formatAsString();
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       cap.setText(contents.toString());
       Frame frame = new Frame();
@@ -757,8 +813,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == clustalColour)
     {
       abovePIDThreshold.setState(false);
-      changeColour(new ClustalxColourScheme(viewport.alignment
-              .getSequences(), viewport.alignment.getWidth()));
+      changeColour(new ClustalxColourScheme(
+              viewport.alignment.getSequences(),
+              viewport.alignment.getWidth()));
     }
     else if (source == zappoColour)
     {
@@ -824,6 +881,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       sortIDMenuItem_actionPerformed();
     }
+    else if (source == sortLengthMenuItem)
+    {
+      sortLengthMenuItem_actionPerformed();
+    }
     else if (source == sortGroupMenuItem)
     {
       sortGroupMenuItem_actionPerformed();
@@ -880,10 +941,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
-            + e.getActionCommand(), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(e
-            .getActionCommand(), viewport.getAlignment(),
+    jalview.bin.JalviewLite.addFrame(frame,
+            "Alignment output - " + e.getActionCommand(), 600, 500);
+    cap.setText(new AppletFormatAdapter().formatSequences(
+            e.getActionCommand(), viewport.getAlignment(),
             viewport.showJVSuffix));
   }
 
@@ -918,18 +979,37 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
+  private Hashtable getDisplayedFeatureCols()
+  {
+    if (alignPanel.getFeatureRenderer() != null)
+    {
+      FeatureRenderer fr = alignPanel.getFeatureRenderer();
+      Hashtable fcols = new Hashtable();
+      Enumeration en = viewport.featuresDisplayed.keys();
+      while (en.hasMoreElements())
+      {
+        Object col = en.nextElement();
+        fcols.put(col, fr.featureColours.get(col));
+      }
+      return fcols;
+    }
+    return null;
+  }
+
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = new FeaturesFile().printJalviewFormat(viewport.alignment
-              .getSequencesArray(), viewport.featuresDisplayed);
+      features = new FeaturesFile().printJalviewFormat(
+              viewport.alignment.getSequencesArray(),
+              getDisplayedFeatureCols());
     }
     else
     {
-      features = new FeaturesFile().printGFFFormat(viewport.alignment
-              .getSequencesArray(), viewport.featuresDisplayed);
+      features = new FeaturesFile().printGFFFormat(
+              viewport.alignment.getSequencesArray(),
+              getDisplayedFeatureCols());
     }
 
     if (displayTextbox)
@@ -961,9 +1041,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (viewport.applet.getParameter("annotations") != null)
     {
       url.append("&annotations=");
-      url
-              .append(appendProtocol(viewport.applet
-                      .getParameter("annotations")));
+      url.append(appendProtocol(viewport.applet.getParameter("annotations")));
     }
 
     if (viewport.applet.getParameter("jnetfile") != null)
@@ -1099,7 +1177,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void undoMenuItem_actionPerformed()
   {
@@ -1124,7 +1202,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void redoMenuItem_actionPerformed()
   {
@@ -1502,8 +1580,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     viewport.setEndSeq(viewport.alignment.getHeight());
     viewport.alignment.getWidth();
-    viewport.firePropertyChange("alignment", null, viewport.alignment
-            .getSequences());
+    viewport.firePropertyChange("alignment", null,
+            viewport.alignment.getSequences());
 
   }
 
@@ -1560,6 +1638,39 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       this.setVisible(false);
     }
+    viewport.sendSelection();
+  }
+
+  protected void makeGrpsFromSelection_actionPerformed()
+  {
+    if (viewport.getSelectionGroup() != null)
+    {
+      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+              viewport.getSequenceSelection(),
+              viewport.getAlignmentView(true).getSequenceStrings(
+                      viewport.getGapCharacter()),
+              viewport.alignment.getGroups());
+      viewport.alignment.deleteAllGroups();
+      viewport.sequenceColours = null;
+      viewport.setSelectionGroup(null);
+      // set view properties for each group
+      for (int g = 0; g < gps.length; g++)
+      {
+        // gps[g].setShowunconserved(viewport.getShowUnconserved());
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+        viewport.alignment.addGroup(gps[g]);
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        col = col.brighter();
+        for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+                .hasMoreElements(); viewport.setSequenceColour(
+                (SequenceI) sq.nextElement(), col))
+          ;
+      }
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+      // alignPanel.updateAnnotation();
+      alignPanel.paintAlignment(true);
+    }
   }
 
   protected void deleteGroups_actionPerformed()
@@ -1582,6 +1693,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(sg);
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    viewport.sendSelection();
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed()
@@ -1598,6 +1710,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    viewport.sendSelection();
   }
 
   public void invertSequenceMenuItem_actionPerformed()
@@ -1609,6 +1722,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    viewport.sendSelection();
+  }
+
+  public void invertColSel_actionPerformed()
+  {
+    viewport.invertColumnSelection();
+    alignPanel.paintAlignment(true);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    viewport.sendSelection();
   }
 
   void trimAlignment(boolean trimLeft)
@@ -1779,9 +1901,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
         {
-          newal
-                  .addAnnotation(viewport.alignment
-                          .getAlignmentAnnotation()[i]);
+          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
         }
       }
     }
@@ -1790,8 +1910,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
-    PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
-            .getSequenceSetId());
+    PaintRefresher.Register(newaf.alignPanel,
+            newaf.alignPanel.av.getSequenceSetId());
 
     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
             newaf.alignPanel.av.getSequenceSetId());
@@ -1849,7 +1969,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * get sequence feature groups that are hidden or shown
    * 
    * @param visible
-   *                true is visible
+   *          true is visible
    * @return list
    */
   public String[] getFeatureGroupsOfState(boolean visible)
@@ -1867,9 +1987,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * Change the display state for the given feature groups
    * 
    * @param groups
-   *                list of group strings
+   *          list of group strings
    * @param state
-   *                visible or invisible
+   *          visible or invisible
    */
   public void setFeatureGroupState(String[] groups, boolean state)
   {
@@ -1901,6 +2021,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.paintAlignment(true);
   }
 
+  protected void displayNonconservedMenuItem_actionPerformed()
+  {
+    viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+    alignPanel.paintAlignment(true);
+  }
+
   protected void wrapMenuItem_actionPerformed()
   {
     viewport.setWrapAlignment(wrapMenuItem.getState());
@@ -1964,8 +2090,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
         Alignment al = (Alignment) viewport.alignment;
         Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0, al
-                        .getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
 
         c.calculate();
         c.verdict(false, viewport.ConsPercGaps);
@@ -2000,8 +2126,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg
-                  .getSequences(viewport.hiddenRepSequences), sg.getWidth());
+          sg.cs = new ClustalxColourScheme(
+                  sg.getSequences(viewport.hiddenRepSequences),
+                  sg.getWidth());
         }
         else
         {
@@ -2020,9 +2147,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                 || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(sg
-                  .getSequences(viewport.hiddenRepSequences), 0, sg
-                  .getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+                  sg.getSequences(viewport.hiddenRepSequences), 0,
+                  sg.getWidth()));
         }
         else
         {
@@ -2032,8 +2159,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg
-                          .getSequences(viewport.hiddenRepSequences), 0,
+                  ResidueProperties.propHash, 3,
+                  sg.getSequences(viewport.hiddenRepSequences), 0,
                   viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
@@ -2065,8 +2192,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (viewport.getAbovePIDThreshold()
             && viewport.globalColourScheme != null)
     {
-      SliderPanel.setPIDSliderSource(alignPanel, viewport
-              .getGlobalColourScheme(), "Background");
+      SliderPanel.setPIDSliderSource(alignPanel,
+              viewport.getGlobalColourScheme(), "Background");
       SliderPanel.showPIDSlider();
     }
   }
@@ -2111,6 +2238,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
             .getAlignment().getSequenceAt(0), null);
+
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.alignment));
     alignPanel.paintAlignment(true);
@@ -2118,17 +2246,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void sortIDMenuItem_actionPerformed()
   {
-    // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
-    // HistoryItem.SORT));
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+    alignPanel.paintAlignment(true);
+  }
+
+  public void sortLengthMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByLength(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+            viewport.alignment));
     alignPanel.paintAlignment(true);
   }
 
   public void sortGroupMenuItem_actionPerformed()
   {
-    // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
-    // HistoryItem.SORT));
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.alignment));
     alignPanel.paintAlignment(true);
 
   }
@@ -2153,7 +2291,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void PCAMenuItem_actionPerformed()
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
@@ -2210,7 +2348,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   void NewTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
@@ -2258,7 +2396,35 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     addTreeMenuItem(tp, treeFile);
   }
 
-  void addTreeMenuItem(final TreePanel treePanel, String title)
+  /**
+   * sort the alignment using the given treePanel
+   * 
+   * @param treePanel
+   *          tree used to sort view
+   * @param title
+   *          string used for undo event name
+   */
+  public void sortByTree(TreePanel treePanel, String title)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter
+            .sortByTree(viewport.getAlignment(), treePanel.getTree());
+    // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+    // HistoryItem.SORT));
+    addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
+            viewport.alignment));
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * Do any automatic reordering of the alignment and add the necessary bits to
+   * the menu structure for the new tree
+   * 
+   * @param treePanel
+   * @param title
+   */
+  protected void addTreeMenuItem(final TreePanel treePanel,
+          final String title)
   {
     final MenuItem item = new MenuItem(title);
     sortByTreeMenu.add(item);
@@ -2266,23 +2432,43 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       public void actionPerformed(ActionEvent evt)
       {
-        // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-        // HistoryItem.SORT));
-        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
-                .getTree());
-        alignPanel.paintAlignment(true);
+        sortByTree(treePanel, title); // treePanel.getTitle());
       }
     });
 
     treePanel.addWindowListener(new WindowAdapter()
     {
+      public void windowOpened(WindowEvent e)
+      {
+        if (viewport.sortByTree)
+        {
+          sortByTree(treePanel, title);
+        }
+        super.windowOpened(e);
+      }
+
       public void windowClosing(WindowEvent e)
       {
         sortByTreeMenu.remove(item);
       };
     });
   }
-
+  public boolean sortBy(AlignmentOrder alorder, String undoname)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment()
+    .getSequencesArray();
+    if (viewport.applet.debug)
+    {
+      System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
+    }
+    AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+    if (undoname!=null)
+    {
+      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+    }
+    alignPanel.paintAlignment(true);
+    return true;
+  }
   protected void documentation_actionPerformed()
   {
     showURL("http://www.jalview.org/help.html", "HELP");
@@ -2295,9 +2481,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       String version;
 
-      public AboutPanel(String version)
+      String builddate;
+
+      public AboutPanel(String version, String builddate)
       {
         this.version = version;
+        this.builddate = builddate;
       }
 
       public void paint(Graphics g)
@@ -2313,53 +2502,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         // lite and application
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
         g.drawString("JalviewLite - Release " + version, x, y += fh);
+        g.setFont(new Font("Helvetica", Font.BOLD, 12));
+        g.drawString("Build date: " + builddate, x, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        g
-                .drawString(
-                        "Authors:  Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
-                        x, y += fh * 1.5);
+        g.drawString(
+                "Authors:  Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
+                x, y += fh * 1.5);
         g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
-        g
-                .drawString(
-                        "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
-                        x, y += fh);
-        g
-                .drawString(
-                        "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
-                        x, y += fh);
+        g.drawString(
+                "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+                x, y += fh);
+        g.drawString(
+                "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+                x, y += fh);
         g.drawString("If  you use Jalview, please cite:", x, y += fh + 8);
-        g
-                .drawString(
-                        "\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
-                        x, y += fh);
-        g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);
-      }
-    }
-
-    String version = "test";
-    java.net.URL url = getClass().getResource("/.build_properties");
-    if (url != null)
-    {
-      try
-      {
-        BufferedReader reader = new BufferedReader(new InputStreamReader(
-                url.openStream()));
-        String line;
-        while ((line = reader.readLine()) != null)
-        {
-          if (line.indexOf("VERSION") > -1)
-          {
-            version = line.substring(line.indexOf("=") + 1);
-          }
-        }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
+        g.drawString(
+                "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+                x, y += fh);
+        g.drawString(
+                "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+                x, y += fh);
+        g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+                x, y += fh);
       }
     }
 
     Frame frame = new Frame();
-    frame.add(new AboutPanel(version));
+    frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+            .getBuildDate()));
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
 
   }
@@ -2374,22 +2544,38 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       try
       {
-        if (url.indexOf(":")==-1)
+        if (url.indexOf(":") == -1)
         {
-          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
-          if (url.indexOf("/")==0)
+          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+          // form valid URL
+          if (url.indexOf("/") == 0)
           {
             String codebase = viewport.applet.getCodeBase().toString();
-            url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
-          } else {
-            url = viewport.applet.getCodeBase()+url;
+            url = codebase.substring(0, codebase.length()
+                    - viewport.applet.getCodeBase().getFile().length())
+                    + url;
+          }
+          else
+          {
+            url = viewport.applet.getCodeBase() + url;
           }
           System.out.println("Show url (prepended codebase): " + url);
-        } else {
+        }
+        else
+        {
           System.out.println("Show url: " + url);
         }
-        viewport.applet.getAppletContext().showDocument(
-                new java.net.URL(url), target);
+        if (url.indexOf("javascript:") == 0)
+        {
+          // no target for the javascript context
+          viewport.applet.getAppletContext().showDocument(
+                  new java.net.URL(url));
+        }
+        else
+        {
+          viewport.applet.getAppletContext().showDocument(
+                  new java.net.URL(url), target);
+        }
       } catch (Exception ex)
       {
         ex.printStackTrace();
@@ -2446,6 +2632,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem sortIDMenuItem = new MenuItem();
 
+  MenuItem sortLengthMenuItem = new MenuItem();
+
   MenuItem sortGroupMenuItem = new MenuItem();
 
   MenuItem removeRedundancyMenuItem = new MenuItem();
@@ -2494,6 +2682,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
 
+  CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
+
   MenuItem alProperties = new MenuItem("Alignment Properties...");
 
   MenuItem overviewMenuItem = new MenuItem();
@@ -2518,6 +2708,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem deleteGroups = new MenuItem();
 
+  MenuItem grpsFromSelection = new MenuItem();
+
   MenuItem delete = new MenuItem();
 
   MenuItem copy = new MenuItem();
@@ -2565,6 +2757,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
 
+  CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+
   private void jbInit() throws Exception
   {
 
@@ -2617,6 +2811,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sortPairwiseMenuItem.addActionListener(this);
     sortIDMenuItem.setLabel("by ID");
     sortIDMenuItem.addActionListener(this);
+    sortLengthMenuItem.setLabel("by Length");
+    sortLengthMenuItem.addActionListener(this);
     sortGroupMenuItem.setLabel("by Group");
     sortGroupMenuItem.addActionListener(this);
     removeRedundancyMenuItem.setLabel("Remove Redundancy...");
@@ -2666,6 +2862,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     annotationPanelMenuItem.addItemListener(this);
     colourTextMenuItem.setLabel("Colour Text");
     colourTextMenuItem.addItemListener(this);
+    displayNonconservedMenuItem.setLabel("Show nonconserved");
+    displayNonconservedMenuItem.addItemListener(this);
     alProperties.addActionListener(this);
     overviewMenuItem.setLabel("Overview Window");
     overviewMenuItem.addActionListener(this);
@@ -2692,6 +2890,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.addActionListener(this);
     deleteGroups.setLabel("Undefine Groups");
     deleteGroups.addActionListener(this);
+    grpsFromSelection.setLabel("Make Groups for selection");
+    grpsFromSelection.addActionListener(this);
     copy.setLabel("Copy");
     copy.addActionListener(this);
     cut.setLabel("Cut");
@@ -2732,7 +2932,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     centreColumnLabelFlag.setLabel("Centre column labels");
     centreColumnLabelFlag.addItemListener(this);
-
+    followMouseOverFlag.setLabel("Automatic Scrolling");
+    followMouseOverFlag.addItemListener(this);
     helpMenu.setLabel("Help");
     documentation.setLabel("Documentation");
     documentation.addActionListener(this);
@@ -2757,11 +2958,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     menu2.setLabel("Hide");
     hideColumns.setLabel("Selected Columns");
     hideSequences.setLabel("Selected Sequences");
+    hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
+    hideAllSelection.setLabel("Selected Region");
+    showAllHidden.setLabel("All Sequences and Columns");
     invertColSel.addActionListener(this);
     showColumns.addActionListener(this);
     showSeqs.addActionListener(this);
     hideColumns.addActionListener(this);
     hideSequences.addActionListener(this);
+    hideAllButSelection.addActionListener(this);
+    hideAllSelection.addActionListener(this);
+    showAllHidden.addActionListener(this);
     formatMenu.setLabel("Format");
     selectMenu.setLabel("Select");
     newView.setLabel("New View");
@@ -2809,6 +3016,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewMenu.add(menu1);
     viewMenu.add(menu2);
     viewMenu.addSeparator();
+    viewMenu.add(followMouseOverFlag);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
     viewMenu.add(sequenceFeatures);
@@ -2848,6 +3056,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
+    sort.add(sortLengthMenuItem);
     sort.add(sortByTreeMenu);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
@@ -2859,8 +3068,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     helpMenu.add(about);
     menu1.add(showColumns);
     menu1.add(showSeqs);
+    menu1.add(showAllHidden);
     menu2.add(hideColumns);
     menu2.add(hideSequences);
+    menu2.add(hideAllSelection);
+    menu2.add(hideAllButSelection);
     formatMenu.add(font);
     formatMenu.add(seqLimits);
     formatMenu.add(wrapMenuItem);
@@ -2870,6 +3082,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     formatMenu.add(viewBoxesMenuItem);
     formatMenu.add(viewTextMenuItem);
     formatMenu.add(colourTextMenuItem);
+    formatMenu.add(displayNonconservedMenuItem);
     formatMenu.add(renderGapsMenuItem);
     formatMenu.add(centreColumnLabelFlag);
     selectMenu.add(findMenuItem);
@@ -2878,7 +3091,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     selectMenu.add(deselectAllSequenceMenuItem);
     selectMenu.add(invertSequenceMenuItem);
     selectMenu.add(invertColSel);
+    selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
+
   }
 
   MenuItem featureSettings = new MenuItem();
@@ -2901,6 +3116,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem hideSequences = new MenuItem();
 
+  MenuItem hideAllButSelection = new MenuItem();
+
+  MenuItem hideAllSelection = new MenuItem();
+
+  MenuItem showAllHidden = new MenuItem();
+
   Menu formatMenu = new Menu();
 
   Menu selectMenu = new Menu();
@@ -2913,8 +3134,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * 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
+   *          true to attach the view to the applet area on the page rather than
+   *          in a new window
    */
   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
   {
@@ -2932,10 +3153,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.applet.setLayout(new BorderLayout());
       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
       viewport.applet.add(statusBar, BorderLayout.SOUTH);
-      alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
-              .getSize().height
-              - embeddedMenu.HEIGHT - statusBar.HEIGHT);
+      alignPanel.setSize(viewport.applet.getSize().width,
+              viewport.applet.getSize().height - embeddedMenu.HEIGHT
+                      - statusBar.HEIGHT);
       viewport.applet.add(alignPanel, BorderLayout.CENTER);
+      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;
+        }}
+        
+        @Override
+        public void focusGained(FocusEvent e)
+        {
+          me.viewport.applet.currentAlignFrame = me;
+        }
+      });
       viewport.applet.validate();
     }
     else
@@ -2956,4 +3194,236 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               DEFAULT_HEIGHT);
     }
   }
+
+  /**
+   * create a new binding between structures in an existing jmol viewer instance
+   * and an alignpanel with sequences that have existing PDBFile entries. Note,
+   * this does not open a new Jmol window, or modify the display of the
+   * 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
+   *          - sequence Ids to search for associations
+   */
+  public SequenceStructureBinding addStructureViewInstance(
+          Object jmolviewer, String[] sequenceIds)
+  {
+    org.jmol.api.JmolViewer viewer = null;
+    try
+    {
+      viewer = (org.jmol.api.JmolViewer) jmolviewer;
+    } catch (ClassCastException ex)
+    {
+      System.err.println("Unsupported viewer object :"
+              + jmolviewer.getClass());
+    }
+    if (viewer == null)
+    {
+      System.err.println("Can't use this object as a structure viewer:"
+              + jmolviewer.getClass());
+      return null;
+    }
+    SequenceI[] seqs = null;
+    if (sequenceIds == null || sequenceIds.length == 0)
+    {
+      seqs = viewport.getAlignment().getSequencesArray();
+    }
+    else
+    {
+      Vector sqi = new Vector();
+      AlignmentI al = viewport.getAlignment();
+      for (int sid = 0; sid < sequenceIds.length; sid++)
+      {
+        SequenceI sq = al.findName(sequenceIds[sid]);
+        if (sq != null)
+        {
+          sqi.addElement(sq);
+        }
+      }
+      if (sqi.size() > 0)
+      {
+        seqs = new SequenceI[sqi.size()];
+        for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
+        {
+          seqs[sid] = (SequenceI) sqi.elementAt(sid);
+        }
+      }
+      else
+      {
+        return null;
+      }
+    }
+    ExtJmol jmv = null;
+    // 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});
+    }
+    return jmv;
+
+  }
+
+  public boolean addPdbFile(String sequenceId, String pdbEntryString,
+          String pdbFile)
+  {
+    SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+    boolean needtoadd = false;
+    if (toaddpdb != null)
+    {
+      Vector pdbe = toaddpdb.getPDBId();
+      PDBEntry pdbentry = null;
+      if (pdbe != null && pdbe.size() > 0)
+      {
+        for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+        {
+          pdbentry = (PDBEntry) pdbe.elementAt(pe);
+          if (!pdbentry.getId().equals(pdbEntryString)
+                  && !pdbentry.getFile().equals(pdbFile))
+          {
+            pdbentry = null;
+          }
+          else
+          {
+            continue;
+          }
+        }
+      }
+      if (pdbentry == null)
+      {
+        pdbentry = new PDBEntry();
+        pdbentry.setId(pdbEntryString);
+        pdbentry.setFile(pdbFile);
+        needtoadd = true; // add this new entry to sequence.
+      }
+      // resolve data source
+      // TODO: this code should be a refactored to an io package
+      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+      if (protocol == null)
+      {
+        return false;
+      }
+      if (needtoadd)
+      {
+        // make a note of the access mode and add
+        if (pdbentry.getProperty() == null)
+        {
+          pdbentry.setProperty(new Hashtable());
+        }
+        pdbentry.getProperty().put("protocol", protocol);
+        toaddpdb.addPDBId(pdbentry);
+      }
+    }
+    return true;
+  }
+
+  private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+  {
+    if (seqs != null)
+    {
+      Vector sequences = new Vector();
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i] != null)
+        {
+          sequences.addElement(new Object[]
+          { seqs[i], (chains != null) ? chains[i] : null });
+        }
+      }
+      seqs = new SequenceI[sequences.size()];
+      chains = new String[sequences.size()];
+      for (int i = 0, isize = sequences.size(); i < isize; i++)
+      {
+        Object[] oj = (Object[]) sequences.elementAt(i);
+
+        seqs[i] = (SequenceI) oj[0];
+        chains[i] = (String) oj[1];
+      }
+    }
+    return new Object[]
+    { seqs, chains };
+
+  }
+
+  public void newStructureView(JalviewLite applet, PDBEntry pdb,
+          SequenceI[] seqs, String[] chains, String protocol)
+  {
+    // Scrub any null sequences from the array
+    Object[] sqch = cleanSeqChainArrays(seqs, chains);
+    seqs = (SequenceI[]) sqch[0];
+    chains = (String[]) sqch[1];
+    if (seqs == null || seqs.length == 0)
+    {
+      System.err
+              .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+    }
+    if (protocol == null || protocol.trim().length() == 0
+            || protocol.equals("null"))
+    {
+      protocol = (String) pdb.getProperty().get("protocol");
+      if (protocol == null)
+      {
+        System.err.println("Couldn't work out protocol to open structure: "
+                + pdb.getId());
+        return;
+      }
+    }
+    if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+    {
+      // can only do alignments with Jmol
+      // find the last jmol window assigned to this alignment
+      jalview.appletgui.AppletJmol ajm = null, tajm;
+      Vector jmols = applet
+              .getAppletWindow(jalview.appletgui.AppletJmol.class);
+      for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+      {
+        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+        if (tajm.ap.alignFrame == this)
+        {
+          ajm = tajm;
+          break;
+        }
+      }
+      if (ajm != null)
+      {
+        System.err
+                .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+        // try and add the pdb structure
+        // ajm.addS
+        ajm = null;
+      }
+    }
+    // otherwise, create a new window
+    if (applet.jmolAvailable)
+    {
+      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+              protocol);
+      applet.lastFrameX += 40;
+      applet.lastFrameY += 40;
+    }
+    else
+    {
+      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+    }
+
+  }
+
+  public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+          SequenceI[][] seqs, String[][] chains, String[] protocols)
+  {
+    // TODO Auto-generated method stub
+    System.err.println("Aligned Structure View: Not yet implemented.");
+  }
+
+  /**
+   * 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)
+  {
+    alignPanel.seqPanel.selection(sel, csel, null);
+  }
 }