X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=6e2d32b3c8f11a57ca244213b51b0bb043374a6c;hb=d429962a1e4d2413e0c18fd88227cffee8bfa502;hp=832f795114c887b62869ab2f1e0bf5b882f6a377;hpb=dc6d9b88b36c704faa61bcd3ed29a9e2f510bc83;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 832f795..6e2d32b 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -27,26 +27,21 @@ import jalview.io.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
+import java.io.InputStreamReader;
+import java.io.BufferedReader;
+import java.net.URL;
 
 public class AlignFrame
     extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
+  int NEW_WINDOW_WIDTH = 700;
+  int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
-  public AlignFrame(AlignmentI al)
-  {
-    this.applet = null;
-    viewport = new AlignViewport(al, null);
-    alignPanel = new AlignmentPanel(this, viewport);
-    add(alignPanel);
-    alignPanel.validate();
-  }
 
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
   {
     this.applet = applet;
     viewport = new AlignViewport(al, applet);
@@ -54,37 +49,184 @@ public class AlignFrame
     add(alignPanel);
     alignPanel.validate();
 
-    String treeFile = applet.getParameter("treeFile");
-    TreePanel treepanel = null;
-    if (treeFile != null)
+    if(applet!=null)
     {
-      try
+      String treeFile = applet.getParameter("treeFile");
+      if (treeFile != null)
       {
-        treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-            getCodeBase() + treeFile, "URL");
-        fin.parse();
+        try
+        {
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+              getCodeBase() + treeFile, "URL");
+          fin.parse();
 
-        if (fin.getTree() != null)
+          if (fin.getTree() != null)
+          {
+            TreePanel tp = null;
+            tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                               fin, "FromFile", applet.getCodeBase() + treeFile);
+            jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+            addTreeMenuItem(tp, treeFile);
+          }
+        }
+        catch (Exception ex)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase() + treeFile);
-          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
-          addTreeMenuItem(tp, treeFile);
+          ex.printStackTrace();
         }
       }
-      catch (Exception ex)
+
+      String param = applet.getParameter("sortBy");
+      if (param != null)
       {
-        ex.printStackTrace();
+        if (param.equalsIgnoreCase("Id"))
+          sortIDMenuItem_actionPerformed(null);
+        else if (param.equalsIgnoreCase("Pairwise Identity"))
+          sortPairwiseMenuItem_actionPerformed(null);
+      }
+
+      param = applet.getParameter("wrap");
+      if (param != null)
+      {
+        if (param.equalsIgnoreCase("true"))
+        {
+          wrapMenuItem.setState(true);
+          wrapMenuItem_actionPerformed(null);
+        }
+      }
+
+      try
+      {
+        param = applet.getParameter("windowWidth");
+        if (param != null)
+        {
+          int width = Integer.parseInt(param);
+          NEW_WINDOW_WIDTH = width;
+        }
+        param = applet.getParameter("windowHeight");
+        if (param != null)
+        {
+          int height = Integer.parseInt(param);
+          NEW_WINDOW_HEIGHT = height;
+        }
       }
+      catch (Exception ex)
+      {}
+
     }
 
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent e)
+          {
+            closeMenuItem_actionPerformed(null);
+          }
+    });
+
+    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+     public void propertyChange(java.beans.PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+   jalview.bin.JalviewLite.addFrame(this, title,
+                                    NEW_WINDOW_WIDTH,
+                                    NEW_WINDOW_HEIGHT);
+
+
   }
 
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param String DOCUMENT ME!
+   */
+
+  public void parseFeaturesFile(String file)
+  {
+    try
+    {
+      URL url = new URL(file);
+
+      BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));
+      SequenceI seq = null;
+      String line, type, desc, token;
+
+      int index, start, end;
+      StringTokenizer st;
+      SequenceFeature sf;
+      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+      int lineNo = 0;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() == 2)
+        {
+          type = st.nextToken();
+          UserColourScheme ucs = new UserColourScheme(st.nextToken());
+          fr.setColour(type, ucs.findColour("A"));
+          continue;
+        }
+
+        while (st.hasMoreElements())
+        {
+          desc = st.nextToken();
+          token = st.nextToken();
+          if (!token.equals("ID_NOT_SPECIFIED"))
+          {
+            index = viewport.alignment.findIndex(viewport.alignment.findName(
+                token));
+            st.nextToken();
+          }
+          else
+          {
+            index = Integer.parseInt(st.nextToken());
+          }
+
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+          start = seq.findIndex(start) - 1;
+          end = seq.findIndex(end) - 1;
+
+          type = st.nextToken();
+
+          if(fr.getColour(type)==null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            fr.setColour(type, ucs.findColour("A"));
+          }
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+
+          seq.addSequenceFeature(sf);
+        }
+      }
+
+      viewport.showSequenceFeatures = true;
+      ((Alignment)viewport.alignment).featuresAdded = true;
+
+      alignPanel.repaint();
+
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing groups file: " + ex);
+    }
+  }
+
+
   public void inputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
@@ -92,20 +234,24 @@ public class AlignFrame
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
+    cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
+                                              viewport.getAlignment().getSequences(),
+                                                      viewport.showDBPrefix,
+                                                      viewport.showJVSuffix));
   }
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
+    PaintRefresher.components.remove(viewport.alignment);
     dispose();
+    if(PaintRefresher.components.size()==0 && applet==null)
+      System.exit(0);
   }
 
   Stack historyList = new Stack();
@@ -150,6 +296,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
@@ -157,9 +304,7 @@ public class AlignFrame
     HistoryItem hi = (HistoryItem) redoList.pop();
     restoreHistoryItem(hi);
     updateEditMenuBar();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   // used by undo and redo
@@ -203,9 +348,7 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -278,30 +421,55 @@ public class AlignFrame
       orderedSeqs.put(index + "", seq);
     }
 
-    int index = 0;
+    int index = 0, startRes, endRes;
+    char ch;
+
     for (int i = 0; i < sg.getSize(); i++)
     {
-      SequenceI seq = null;
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
+        SequenceI seq = null;
+
+        while (seq == null)
         {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-          break;
+            if (orderedSeqs.containsKey(index + ""))
+            {
+                seq = (SequenceI) orderedSeqs.get(index + "");
+                index++;
+
+                break;
+            }
+            else
+            {
+                index++;
+            }
         }
-        else
+
+        //FIND START RES
+        //Returns residue following index if gap
+        startRes = seq.findPosition(sg.getStartRes());
+
+        //FIND END RES
+        //Need to find the residue preceeding index if gap
+        endRes = 0;
+
+        for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
         {
-          index++;
+          ch = seq.getCharAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+
+        if(endRes>0)
+        {
+          endRes += seq.getStart() -1;
         }
-      }
 
-      copiedSequences.append(seq.getName() + "\t" +
-                             seq.findPosition(sg.getStartRes()) + "\t"
-                             + seq.findPosition(sg.getEndRes()) + "\t"
-                             +
-                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+        copiedSequences.append(seq.getName() + "\t" +
+            startRes + "\t" +
+            endRes + "\t" +
+            seq.getSequence(sg.getStartRes(),
+                sg.getEndRes() + 1) + "\n");
     }
 
   }
@@ -354,7 +522,6 @@ public class AlignFrame
           newSeqs[i] = (SequenceI) seqs.elementAt(i);
         }
 
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
         String newtitle = new String("Copied sequences");
         if (getTitle().startsWith("Copied sequences"))
         {
@@ -364,6 +531,8 @@ public class AlignFrame
         {
           newtitle = newtitle.concat("- from " + getTitle());
         }
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
+
         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                          NEW_WINDOW_HEIGHT);
       }
@@ -371,9 +540,7 @@ public class AlignFrame
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
 
     }
@@ -397,13 +564,26 @@ public class AlignFrame
       return;
     }
 
+
     SequenceGroup sg = viewport.getSelectionGroup();
+    boolean allSequences = false;
+    if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+      // If the cut affects all sequences, remove highlighted columns
+      if (allSequences)
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+                                                     sg.getEndRes() + 1);
+      }
+
+
       if (seq.getSequence().length() < 1)
       {
         viewport.getAlignment().deleteSequence(seq);
@@ -426,9 +606,7 @@ public class AlignFrame
       catch (Exception ex)
       {}
     }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
   }
 
@@ -447,10 +625,10 @@ public class AlignFrame
     {
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
-    sg.setEndRes(viewport.alignment.getWidth());
+    sg.setEndRes(viewport.alignment.getWidth()-1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -458,7 +636,8 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
+    alignPanel.repaint();
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -469,7 +648,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
@@ -497,8 +676,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -525,8 +703,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
 
   }
@@ -536,10 +713,17 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment,
                                    HistoryItem.HIDE));
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -547,6 +731,11 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     SequenceI current;
     int jSize;
 
@@ -554,61 +743,142 @@ public class AlignFrame
 
     int start=0, end = viewport.alignment.getWidth();
 
-    if(viewport.getSelectionGroup()!=null)
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size()>0)
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
       seqs = viewport.alignment.getSequences();
 
-    for (int i = 0; i <seqs.size(); i++)
+    for (int i = 0; i < seqs.size(); i++)
     {
-      current = (SequenceI)seqs.elementAt(i);
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
+
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
         }
-        j++;
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
+        }
+      }
+      while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
       }
-      while(j < end);
     }
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
 
-    viewport.updateConservation();
+  public void alignmentChanged()
+  {
     viewport.updateConsensus();
+    viewport.updateConservation ();
+    resetAllColourSchemes();
+    if(alignPanel.overviewPanel!=null)
+      alignPanel.overviewPanel.updateOverviewImage();
     alignPanel.repaint();
   }
 
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
+
+      cs.setConsensus(viewport.vconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
+  }
+
+
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    Finder finder = new Finder(alignPanel);
+    new Finder(alignPanel);
   }
 
   public void font_actionPerformed(ActionEvent e)
   {
-    Frame frame = new Frame();
-    FontChooser fc = new FontChooser(alignPanel, frame);
-    frame.add(fc);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
+    new FontChooser(alignPanel);
+  }
 
+  public void dbref_actionPerformed(ItemEvent e)
+  {
+    viewport.showDBPrefix = dbref.getState();
+    alignPanel.fontChanged();
+    alignPanel.repaint();
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void seqLimits_itemStateChanged(ItemEvent e)
   {
-    viewport.setShowFullId(fullSeqId.getState());
+    viewport.setShowJVSuffix(seqLimits.getState());
     alignPanel.fontChanged();
     alignPanel.repaint();
   }
 
+
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.getState());
@@ -663,11 +933,6 @@ public class AlignFrame
 
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
-    {
-      annotationPanelMenuItem.setState(false);
-      return;
-    }
     viewport.setShowAnnotation(annotationPanelMenuItem.getState());
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
@@ -761,53 +1026,48 @@ public class AlignFrame
   {
     int threshold = 0;
 
-    if (viewport.getAbovePIDThreshold())
+    if(cs!=null)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
-
-      if (cs instanceof ResidueColourScheme)
+      if (viewport.getAbovePIDThreshold())
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
-      }
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
-    {
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    }
+        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
 
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      ccs = new ConservationColourScheme(c, cs);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus(viewport.vconsensus);
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
 
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
-      viewport.setGlobalColourScheme(cs);
+
+      cs.setConsensus(viewport.vconsensus);
+
     }
+    viewport.setGlobalColourScheme(cs);
 
     if (viewport.getColourAppliesToAllGroups())
     {
@@ -823,9 +1083,7 @@ public class AlignFrame
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
-          sg.cs = cxs;
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
         else
         {
@@ -840,15 +1098,15 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
-          if (sg.cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          }
-
+          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 
         if (viewport.getConservationSelected())
         {
@@ -858,21 +1116,18 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
-          sg.cs = ccs;
+          sg.cs.setConservation(c);
         }
         else
         {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs.setConservation(null);
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
       }
     }
 
+
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
@@ -881,9 +1136,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+
+
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
                                      "Background");
@@ -893,7 +1150,7 @@ public class AlignFrame
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
@@ -908,15 +1165,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setState(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
@@ -928,23 +1177,14 @@ public class AlignFrame
     conservationMenuItem.setState(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
   }
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
+    new UserDefinedColours(alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -998,13 +1238,31 @@ public class AlignFrame
     if (viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
-      frame.add(new PairwiseAlignPanel(viewport));
+      frame.add(new PairwiseAlignPanel(alignPanel));
       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
     }
   }
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
+    //are the sequences aligned?
+    if (!viewport.alignment.isAligned())
+    {
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+    }
 
     if ( (viewport.getSelectionGroup() != null &&
           viewport.getSelectionGroup().getSize() < 4 &&
@@ -1016,11 +1274,7 @@ public class AlignFrame
 
     try
     {
-      PCAPanel pcaPanel = new PCAPanel(viewport, null);
-      Frame frame = new Frame();
-      frame.add(pcaPanel);
-      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
-                                       400, 400);
+      new PCAPanel(viewport);
     }
     catch (java.lang.OutOfMemoryError ex)
     {
@@ -1053,7 +1307,21 @@ public class AlignFrame
     //are the sequences aligned?
     if (!viewport.alignment.isAligned())
     {
-      return;
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+
     }
 
     final TreePanel tp;
@@ -1101,16 +1369,18 @@ public class AlignFrame
 
   protected void documentation_actionPerformed(ActionEvent e)
   {
-
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org");
-
+    showURL("http://www.jalview.org/help.html");
   }
 
   protected void about_actionPerformed(ActionEvent e)
   {
-    class AboutPanel
-        extends Canvas
+
+    class AboutPanel extends Canvas
     {
+      String version;
+      public AboutPanel(String version)
+      { this.version = version; }
+
       public void paint(Graphics g)
       {
         g.setColor(Color.white);
@@ -1121,7 +1391,7 @@ public class AlignFrame
         int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalView - Release 2.0", 200, y += fh);
+        g.drawString("Jalview - Release "+version, 200, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
                      x, y += fh * 2);
@@ -1137,9 +1407,65 @@ public class AlignFrame
       }
     }
 
+    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();
+      }
+    }
+
+
     Frame frame = new Frame();
-    frame.add(new AboutPanel());
+    frame.add(new AboutPanel(version));
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
 
   }
+
+  /**
+   * Displays the given URL in a new browser window
+   *
+   * @param url URL to display in browser window.
+   * <br>New window will be named "HELP_WINDOW"
+   */
+  public void showURL(String url)
+  {
+    showURL(url, "HELP");
+  }
+
+  public void showURL(String url, String target)
+  {
+    if (applet == null)
+    {
+      System.out.println("Not running as applet - no browser available.");
+    }
+    else
+    {
+      try
+      {
+        applet.getAppletContext().showDocument(new java.net.URL(url),
+                                               target);
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
 }