From 4484ac6bdcc92f0e0e430f64d3587f026fafb476 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 19 Mar 2007 15:41:54 +0000
Subject: [PATCH] translate aligned cDNA to aligned peptide

---
 src/jalview/analysis/Dna.java   |  227 ++++++++
 src/jalview/gui/AlignFrame.java | 1165 +++++++++++++++++++--------------------
 2 files changed, 804 insertions(+), 588 deletions(-)
 create mode 100644 src/jalview/analysis/Dna.java

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
new file mode 100644
index 0000000..836c39e
--- /dev/null
+++ b/src/jalview/analysis/Dna.java
@@ -0,0 +1,227 @@
+package jalview.analysis;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
+
+public class Dna {
+  /**
+   * 
+   * @param cdp1
+   * @param cdp2
+   * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is null, +1 if after cdp2
+   */
+  private static int compare_codonpos(int[] cdp1, int[] cdp2) {
+    if (cdp2==null || (cdp1[0]==cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
+      return 0;
+    if (cdp1[0]<cdp2[0] || cdp1[1]<cdp2[1] || cdp1[2]<cdp2[2])
+      return -1; // one base in cdp1 precedes the corresponding base in the other codon
+    return 1; // one base in cdp1 appears after the corresponding base in the other codon.
+  }
+  /**
+   * create a new alignment of protein sequences
+   * by an inframe translation of the provided NA sequences
+   * @param selection
+   * @param seqstring
+   * @param viscontigs
+   * @param gapCharacter
+   * @param annotations
+   * @param aWidth
+   * @return
+   */
+  public static AlignmentI CdnaTranslate(SequenceI[] selection, String[] seqstring, int viscontigs[], char gapCharacter, 
+      AlignmentAnnotation[] annotations, int aWidth) {
+    int s, sSize = selection.length;
+    SequenceI [] newSeq = new SequenceI[sSize];
+    int res, resSize;
+    StringBuffer protein;
+    String seq;
+
+    int[][] codons = new int[aWidth][]; // stores hash of subsequent positions for each codon start position in alignment
+
+    for (res=0;res<aWidth;res++)
+      codons[res]=null;
+    int aslen=0; // final width of aligned translated aa sequences
+    for(s=0; s<sSize; s++)
+    {
+      int vc,scontigs[]=new int[viscontigs.length];
+
+      for (vc=0;vc<scontigs.length; vc+=2)
+      {
+        scontigs[vc]=selection[s].findPosition(viscontigs[vc]); // not from 1!
+        scontigs[vc+1]=selection[s].findPosition(viscontigs[vc+1]-1); // exclusive
+        if (scontigs[vc+1]==selection[s].getEnd())
+          break;
+      }
+      if ((vc+2)<scontigs.length) {
+        int t[] = new int[vc+2];
+        System.arraycopy(scontigs, 0, t, 0, vc+2);
+        scontigs = t;
+      }
+      protein = new StringBuffer();
+      seq = seqstring[s].replace('U', 'T');
+      char codon[]=new char[3];
+      int cdp[]=new int[3],rf=0,gf=0,nend,npos;
+      int aspos=0;
+      resSize=0;
+      for (npos=0,nend=seq.length(); npos<nend; npos++) {
+        if (!jalview.util.Comparison.isGap(seq.charAt(npos))) { 
+          cdp[rf] = npos; // store position
+          codon[rf++]=seq.charAt(npos); // store base
+        }
+        // filled an RF yet ?
+        if (rf==3) {
+          String aa = ResidueProperties.codonTranslate(new String(codon));
+          rf=0;
+          if(aa==null)
+            aa=String.valueOf(gapCharacter);
+          else {
+            if(aa.equals("STOP"))
+            {
+              aa="X";
+            }
+            resSize++;
+          }
+          // insert/delete gaps prior to this codon - if necessary
+          boolean findpos=true;
+          while (findpos) 
+          {
+            // first ensure that the codons array is long enough.
+            if (codons.length<=aslen+1) {
+              // probably never have to do this ?
+              int[][] c = new int[codons.length+10][];
+              for (int i=0; i<codons.length; i++) {
+                c[i] = codons[i];
+                codons[i]=null;
+              }
+              codons = c;
+            }
+            // now check to see if we place the aa at the current aspos in the protein alignment
+            switch (Dna.compare_codonpos(cdp, codons[aspos])) 
+            {
+            case -1:
+              // this aa appears before the aligned codons at aspos - so shift them.
+              aslen++;
+              for (int sq=0;sq<s; sq++) {
+                newSeq[sq].insertCharAt(aspos, gapCharacter);
+              }
+              System.arraycopy(codons, aspos, codons, aspos+1, aslen-aspos);
+              findpos=false;
+              break;
+            case +1:
+              // this aa appears after the aligned codons at aspos, so prefix it with a gap
+              aa = ""+gapCharacter+aa;
+              aspos++;
+              if (aspos>=aslen)
+                aslen=aspos+1;
+              break; // check the next position for alignment
+            case 0:
+              // codon aligns at aspos position.
+              findpos = false;
+            }
+          }
+          // codon aligns with all other sequence residues found at aspos
+          protein.append(aa);
+          if (codons[aspos]==null) 
+          {
+            // mark this column as aligning to this aligned reading frame 
+            codons[aspos] = new int[] { cdp[0], cdp[1], cdp[2] };
+          }
+          aspos++;
+          if (aspos>=aslen)
+            aslen=aspos+1;
+        }
+      }
+      if (resSize>0) 
+      {
+        newSeq[s] = new Sequence(selection[s].getName(),
+            protein.toString());
+        if (rf!=0) 
+        {
+          jalview.bin.Cache.log.debug("trimming contigs for incomplete terminal codon.");
+          // trim contigs
+          vc=scontigs.length-1;
+          nend-=rf;
+          // incomplete ORF could be broken over one or two visible contig intervals.
+          while (vc>0 && scontigs[vc]>nend)
+          {
+            if (scontigs[vc-1]>nend) 
+            {
+              vc-=2;
+            } else {
+              // correct last interval in list.
+              scontigs[vc]=nend;
+            }
+          }
+          if ((vc+2)<scontigs.length) {
+            // truncate map list
+            int t[] = new int[vc+1];
+            System.arraycopy(scontigs,0,t,0,vc+1);
+            scontigs=t;
+          }
+        }
+        MapList map = new MapList(scontigs, new int[] { 1, resSize },3,1); // TODO: store mapping on newSeq for linked DNA/Protein viewing.
+      }
+      // register the mapping somehow
+      // 
+    }
+    if (aslen==0)
+      return null;
+    AlignmentI al = new Alignment(newSeq);
+    al.padGaps();  // ensure we look aligned.
+    al.setDataset(null);
+
+
+    ////////////////////////////////
+    // Copy annotations across
+    //
+    // Can only do this for columns with consecutive codons, or where
+    // annotation is sequence associated.
+    
+    int pos,a,aSize;
+    if(annotations!=null)
+    {
+      for (int i = 0; i < annotations.length; i++)
+      {
+        // Skip any autogenerated annotation
+        if (annotations[i].autoCalculated) {
+          continue;
+        }
+
+        aSize = aslen; // aa alignment width.
+        jalview.datamodel.Annotation[] anots =
+          new jalview.datamodel.Annotation[aSize];
+        
+        for (a = 0; a < aSize; a++)
+        {
+          // process through codon map.
+          if (codons[a]!=null && codons[a][0]==(codons[a][2]-2))
+          {
+            pos = codons[a][0];
+            if (annotations[i].annotations[pos] == null
+                || annotations[i].annotations[pos] == null)
+              continue;
+            
+            anots[a] = new Annotation(annotations[i].annotations[pos]);
+          }
+        }
+
+        jalview.datamodel.AlignmentAnnotation aa
+        = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+            annotations[i].description, anots);
+        al.addAnnotation(aa);
+      }
+    }
+    return al;
+  }
+}
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8c9246b..0756e2d 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -57,11 +57,13 @@ public class AlignFrame
 
   Vector alignPanels = new Vector();
 
+
   /** DOCUMENT ME!! */
   String currentFileFormat = null;
 
   String fileName = null;
 
+
   /**
    * Creates a new AlignFrame object.
    *
@@ -72,6 +74,7 @@ public class AlignFrame
     this(al, null, width, height);
   }
 
+
   /**
    * new alignment window with hidden columns
    * @param al AlignmentI
@@ -85,7 +88,7 @@ public class AlignFrame
 
     alignPanel = new AlignmentPanel(this, viewport);
 
-    if (al.getDataset() == null)
+    if(al.getDataset()==null)
     {
       al.setDataset(null);
     }
@@ -116,9 +119,9 @@ public class AlignFrame
       BLOSUM62Colour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
       modifyConservation.setEnabled(false);
-      //  PIDColour.setEnabled(false);
-      //  abovePIDThreshold.setEnabled(false);
-      //  modifyPID.setEnabled(false);
+    //  PIDColour.setEnabled(false);
+    //  abovePIDThreshold.setEnabled(false);
+    //  modifyPID.setEnabled(false);
     }
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
@@ -133,246 +136,246 @@ public class AlignFrame
     }
 
     if (Desktop.desktop != null)
-    {
-      addServiceListeners();
-      setGUINucleotide(viewport.alignment.isNucleotide());
-    }
+   {
+     addServiceListeners();
+     setGUINucleotide(viewport.alignment.isNucleotide());
+   }
 
-    setMenusFromViewport(viewport);
+   setMenusFromViewport(viewport);
 
-    if (viewport.wrapAlignment)
-    {
-      wrapMenuItem_actionPerformed(null);
-    }
+   if (viewport.wrapAlignment)
+   {
+     wrapMenuItem_actionPerformed(null);
+   }
 
     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
 
-    addKeyListener();
+   addKeyListener();
 
   }
 
   public void setFileName(String file, String format)
   {
-    fileName = file;
-    currentFileFormat = format;
-    reload.setEnabled(true);
+     fileName = file;
+     currentFileFormat = format;
+     reload.setEnabled(true);
   }
 
   void addKeyListener()
   {
-    addKeyListener(new KeyAdapter()
-    {
-      public void keyPressed(KeyEvent evt)
+      addKeyListener(new KeyAdapter()
       {
-        if (viewport.cursorMode
-            && evt.getKeyCode() >= KeyEvent.VK_0
-            && evt.getKeyCode() <= KeyEvent.VK_9)
+        public void keyPressed(KeyEvent evt)
         {
-          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-        }
+          if (viewport.cursorMode
+              && evt.getKeyCode() >= KeyEvent.VK_0
+              && evt.getKeyCode() <= KeyEvent.VK_9)
+          {
+            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+          }
 
-        switch (evt.getKeyCode())
-        {
+          switch (evt.getKeyCode())
+          {
 
-          case 27: // escape key
-            deselectAllSequenceMenuItem_actionPerformed(null);
+            case 27: // escape key
+              deselectAllSequenceMenuItem_actionPerformed(null);
 
-            break;
+              break;
 
-          case KeyEvent.VK_DOWN:
+            case KeyEvent.VK_DOWN:
              if (evt.isAltDown() || !viewport.cursorMode)
               moveSelectedSequences(false);
-            if(viewport.cursorMode)
-              alignPanel.seqPanel.moveCursor(0, 1);
-            break;
+              if (viewport.cursorMode)
+                alignPanel.seqPanel.moveCursor(0, 1);
+              break;
 
-          case KeyEvent.VK_UP:
+            case KeyEvent.VK_UP:
             if (evt.isAltDown() || !viewport.cursorMode)
               moveSelectedSequences(true);
-            if(viewport.cursorMode)
-              alignPanel.seqPanel.moveCursor(0, -1);
+              if (viewport.cursorMode)
+                alignPanel.seqPanel.moveCursor(0, -1);
 
-            break;
+              break;
 
-          case KeyEvent.VK_LEFT:
+            case KeyEvent.VK_LEFT:
             if (evt.isAltDown() || !viewport.cursorMode)
               slideSequences(false,
                              alignPanel.seqPanel.getKeyboardNo1());
             else
-              alignPanel.seqPanel.moveCursor( -1, 0);
+                alignPanel.seqPanel.moveCursor( -1, 0);
 
 
-            break;
+              break;
 
-          case KeyEvent.VK_RIGHT:
+            case KeyEvent.VK_RIGHT:
             if (evt.isAltDown() || !viewport.cursorMode)
               slideSequences(true,
                              alignPanel.seqPanel.getKeyboardNo1());
             else
-              alignPanel.seqPanel.moveCursor( 1, 0);
-            break;
+                alignPanel.seqPanel.moveCursor(1, 0);
+              break;
 
-          case KeyEvent.VK_SPACE:
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
-                  || evt.isShiftDown()
-                  || evt.isAltDown());
-            }
-            break;
+            case KeyEvent.VK_SPACE:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                                           || evt.isShiftDown()
+                                           || evt.isAltDown());
+              }
+              break;
 
-          case KeyEvent.VK_DELETE:
-          case KeyEvent.VK_BACK_SPACE:
-            if (!viewport.cursorMode)
-            {
-              cut_actionPerformed(null);
-            }
-            else
+            case KeyEvent.VK_DELETE:
+            case KeyEvent.VK_BACK_SPACE:
+              if (!viewport.cursorMode)
+              {
+                cut_actionPerformed(null);
+              }
+              else
             {
-              alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
-                  || evt.isShiftDown()
-                  || evt.isAltDown());
+                alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                           || evt.isShiftDown()
+                                           || evt.isAltDown());
             }
 
-            break;
+              break;
 
-          case KeyEvent.VK_S:
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.setCursorRow();
-            }
-            break;
-          case KeyEvent.VK_C:
-            if (viewport.cursorMode && !evt.isControlDown())
-            {
-              alignPanel.seqPanel.setCursorColumn();
-            }
-            break;
-          case KeyEvent.VK_P:
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.setCursorPosition();
-            }
-            break;
+            case KeyEvent.VK_S:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorRow();
+              }
+              break;
+            case KeyEvent.VK_C:
+              if (viewport.cursorMode && !evt.isControlDown())
+              {
+                alignPanel.seqPanel.setCursorColumn();
+              }
+              break;
+            case KeyEvent.VK_P:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorPosition();
+              }
+              break;
 
-          case KeyEvent.VK_ENTER:
-          case KeyEvent.VK_COMMA:
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.setCursorRowAndColumn();
-            }
-            break;
+            case KeyEvent.VK_ENTER:
+            case KeyEvent.VK_COMMA:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorRowAndColumn();
+              }
+              break;
 
-          case KeyEvent.VK_Q:
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.setSelectionAreaAtCursor(true);
-            }
-            break;
-          case KeyEvent.VK_M:
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.setSelectionAreaAtCursor(false);
-            }
-            break;
+            case KeyEvent.VK_Q:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+              }
+              break;
+            case KeyEvent.VK_M:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+              }
+              break;
 
-          case KeyEvent.VK_F2:
-            viewport.cursorMode = !viewport.cursorMode;
-            statusBar.setText("Keyboard editing mode is " +
-                              (viewport.cursorMode ? "on" : "off"));
-            if (viewport.cursorMode)
-            {
-              alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-              alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
-            }
-            alignPanel.seqPanel.seqCanvas.repaint();
-            break;
+            case KeyEvent.VK_F2:
+              viewport.cursorMode = !viewport.cursorMode;
+              statusBar.setText("Keyboard editing mode is " +
+                                           (viewport.cursorMode ? "on" : "off"));
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+                alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+              }
+              alignPanel.seqPanel.seqCanvas.repaint();
+              break;
 
-          case KeyEvent.VK_F1:
-            try
-            {
-              ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-              java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-              javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+            case KeyEvent.VK_F1:
+              try
+              {
+                ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+                java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+                javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 
-              javax.help.HelpBroker hb = hs.createHelpBroker();
-              hb.setCurrentID("home");
-              hb.setDisplayed(true);
-            }
-            catch (Exception ex)
+                javax.help.HelpBroker hb = hs.createHelpBroker();
+                hb.setCurrentID("home");
+                hb.setDisplayed(true);
+              }
+              catch (Exception ex)
+              {
+                ex.printStackTrace();
+              }
+              break
+                  ;
+            case KeyEvent.VK_H:
             {
-              ex.printStackTrace();
-            }
-            break
-                ;
-          case KeyEvent.VK_H:
-          {
-            boolean toggleSeqs = !evt.isControlDown();
-            boolean toggleCols = !evt.isShiftDown();
+              boolean toggleSeqs = !evt.isControlDown();
+              boolean toggleCols = !evt.isShiftDown();
 
-            boolean hide = false;
+              boolean hide = false;
 
-            SequenceGroup sg = viewport.getSelectionGroup();
-            if (toggleSeqs)
-            {
-              if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+              SequenceGroup sg = viewport.getSelectionGroup();
+              if (toggleSeqs)
               {
-                hideSelSequences_actionPerformed(null);
-                hide = true;
-              }
+                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+                {
+                  hideSelSequences_actionPerformed(null);
+                  hide = true;
+                }
               else if (! (toggleCols &&
                           viewport.colSel.getSelected().size() > 0))
               {
-                showAllSeqs_actionPerformed(null);
+                  showAllSeqs_actionPerformed(null);
               }
             }
 
-            if (toggleCols)
-            {
-              if (viewport.colSel.getSelected().size() > 0)
+              if (toggleCols)
               {
-                hideSelColumns_actionPerformed(null);
-                if (!toggleSeqs)
+                if (viewport.colSel.getSelected().size() > 0)
+                {
+                  hideSelColumns_actionPerformed(null);
+                  if (!toggleSeqs)
                 {
-                  viewport.selectionGroup = sg;
+                    viewport.selectionGroup = sg;
                 }
               }
-              else if (!hide)
+                else if (!hide)
               {
-                showAllColumns_actionPerformed(null);
+                  showAllColumns_actionPerformed(null);
               }
             }
-            break;
-          }
-          case KeyEvent.VK_PAGE_UP:
-            if (viewport.wrapAlignment)
+              break;
+            }
+            case KeyEvent.VK_PAGE_UP:
+              if (viewport.wrapAlignment)
             {
-              alignPanel.scrollUp(true);
+                alignPanel.scrollUp(true);
             }
-            else
+              else
             {
-              alignPanel.setScrollValues(viewport.startRes,
-                                         viewport.startSeq
-                                         - viewport.endSeq + viewport.startSeq);
+                alignPanel.setScrollValues(viewport.startRes,
+                                           viewport.startSeq
+                                           - viewport.endSeq + viewport.startSeq);
             }
-            break;
-          case KeyEvent.VK_PAGE_DOWN:
-            if (viewport.wrapAlignment)
+              break;
+            case KeyEvent.VK_PAGE_DOWN:
+              if (viewport.wrapAlignment)
             {
-              alignPanel.scrollUp(false);
+                alignPanel.scrollUp(false);
             }
-            else
+              else
             {
-              alignPanel.setScrollValues(viewport.startRes,
-                                         viewport.startSeq
-                                         + viewport.endSeq - viewport.startSeq);
+                alignPanel.setScrollValues(viewport.startRes,
+                                           viewport.startSeq
+                                           + viewport.endSeq - viewport.startSeq);
             }
-            break;
+              break;
+          }
         }
-      }
 
       public void keyReleased(KeyEvent evt)
       {
@@ -391,9 +394,10 @@ public class AlignFrame
             break;
         }
       }
-    });
+      });
   }
 
+
   public void addAlignmentPanel(final AlignmentPanel ap,
                                 boolean newPanel)
   {
@@ -405,9 +409,9 @@ public class AlignFrame
 
     int aSize = alignPanels.size();
 
-    tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+    tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
 
-    if (aSize == 1 && ap.av.viewName == null)
+    if (aSize == 1 && ap.av.viewName==null)
     {
       this.getContentPane().add(ap, BorderLayout.CENTER);
     }
@@ -425,7 +429,7 @@ public class AlignFrame
       ap.setVisible(false);
     }
 
-    if (newPanel)
+    if(newPanel)
     {
       if (ap.av.padGaps)
       {
@@ -442,10 +446,11 @@ public class AlignFrame
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
-    tabbedPane.addTab(first.av.viewName, first);
+    tabbedPane.addTab(first.av.viewName,first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
+
   public AlignViewport getViewport()
   {
     return viewport;
@@ -487,14 +492,14 @@ public class AlignFrame
 
   public void setGUINucleotide(boolean nucleotide)
   {
-    showTranslation.setVisible(nucleotide);
-    conservationMenuItem.setEnabled(!nucleotide);
-    modifyConservation.setEnabled(!nucleotide);
+    showTranslation.setVisible( nucleotide );
+    conservationMenuItem.setEnabled( !nucleotide );
+    modifyConservation.setEnabled(   !nucleotide );
 
     //Remember AlignFrame always starts as protein
-    if (!nucleotide)
+    if(!nucleotide)
     {
-      calculateMenu.remove(calculateMenu.getItemCount() - 2);
+      calculateMenu.remove(calculateMenu.getItemCount()-2);
     }
   }
 
@@ -530,29 +535,30 @@ public class AlignFrame
     updateEditMenuBar();
   }
 
+
   Hashtable progressBars;
   public void setProgressBar(String message, long id)
   {
-    if (progressBars == null)
+    if(progressBars == null)
     {
       progressBars = new Hashtable();
     }
 
     JPanel progressPanel;
     GridLayout layout = (GridLayout) statusPanel.getLayout();
-    if (progressBars.get(new Long(id)) != null)
-    {
-      progressPanel = (JPanel) progressBars.get(new Long(id));
-      statusPanel.remove(progressPanel);
-      progressBars.remove(progressPanel);
-      progressPanel = null;
-      if (message != null)
+    if(progressBars.get( new Long(id) )!=null)
+     {
+       progressPanel = (JPanel)progressBars.get( new Long(id) );
+       statusPanel.remove(progressPanel);
+       progressBars.remove( progressPanel );
+       progressPanel = null;
+       if(message!=null)
       {
-        statusBar.setText(message);
+         statusBar.setText(message);
       }
 
-      layout.setRows(layout.getRows() - 1);
-    }
+       layout.setRows(layout.getRows() - 1);
+     }
     else
     {
       progressPanel = new JPanel(new BorderLayout(10, 5));
@@ -572,12 +578,15 @@ public class AlignFrame
     validate();
   }
 
+
+
+
   /*
    Added so Castor Mapping file can obtain Jalview Version
-   */
+  */
   public String getVersion()
   {
-    return jalview.bin.Cache.getProperty("VERSION");
+    return  jalview.bin.Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -585,6 +594,7 @@ public class AlignFrame
     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
+
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
@@ -597,12 +607,12 @@ public class AlignFrame
 
   public void reload_actionPerformed(ActionEvent e)
   {
-    if (fileName != null)
+    if(fileName!=null)
     {
-      if (currentFileFormat.equals("Jalview"))
+      if(currentFileFormat.equals("Jalview"))
       {
-        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-        for (int i = 0; i < frames.length; i++)
+        JInternalFrame [] frames = Desktop.desktop.getAllFrames();
+        for(int i=0; i<frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame
               && frames[i] != this
@@ -612,7 +622,7 @@ public class AlignFrame
             {
               frames[i].setSelected(true);
               Desktop.instance.closeAssociatedWindows();
-            }
+          }
             catch (java.beans.PropertyVetoException ex)
             {}
           }
@@ -640,6 +650,7 @@ public class AlignFrame
     }
   }
 
+
   public void addFromText_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
@@ -650,11 +661,12 @@ public class AlignFrame
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
+
   public void save_actionPerformed(ActionEvent e)
   {
-    if (fileName == null
-        || currentFileFormat == null
-        || fileName.startsWith("http")
+    if(fileName==null
+       || currentFileFormat==null
+       || fileName.startsWith("http")
         )
     {
       saveAs_actionPerformed(null);
@@ -662,7 +674,7 @@ public class AlignFrame
     else
     {
       saveAlignment(fileName, currentFileFormat);
-    }
+  }
   }
 
   /**
@@ -673,14 +685,15 @@ public class AlignFrame
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty("LAST_DIRECTORY"),
+        getProperty( "LAST_DIRECTORY"),
         new String[]
-        {"fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar"},
+        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
         new String[]
-        {"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
+        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
         currentFileFormat,
         false);
 
+
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
@@ -689,18 +702,18 @@ public class AlignFrame
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      currentFileFormat = chooser.getSelectedFormat();
-      if (currentFileFormat == null)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              "You must select a file format before saving!",
-                                              "File format not specified",
-                                              JOptionPane.WARNING_MESSAGE);
-        value = chooser.showSaveDialog(this);
-        return;
-      }
+        currentFileFormat = chooser.getSelectedFormat();
+        if (currentFileFormat == null)
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "You must select a file format before saving!",
+                                                "File format not specified",
+                                                JOptionPane.WARNING_MESSAGE);
+          value = chooser.showSaveDialog(this);
+          return;
+        }
 
-      fileName = chooser.getSelectedFile().getPath();
+        fileName = chooser.getSelectedFile().getPath();
 
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
@@ -728,8 +741,8 @@ public class AlignFrame
       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
       statusBar.setText("Successfully saved to file: "
-                        + fileName + " in "
-                        + format + " format.");
+                          +fileName+" in "
+                          +format +" format.");
 
     }
     else
@@ -748,7 +761,7 @@ public class AlignFrame
         if (reply == JOptionPane.YES_OPTION)
         {
           omitHidden = viewport.getViewAsString(false);
-        }
+      }
       }
 
       String output = new FormatAdapter().formatSequences(
@@ -800,17 +813,17 @@ public class AlignFrame
    */
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    String[] omitHidden = null;
+    String [] omitHidden = null;
 
-    if (viewport.hasHiddenColumns)
+    if(viewport.hasHiddenColumns)
     {
       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
           "The Alignment contains hidden columns."
-          + "\nDo you want to output only the visible alignment?",
-          "Save / Omit Hidden Columns",
-          JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+      +"\nDo you want to output only the visible alignment?",
+      "Save / Omit Hidden Columns",
+      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
-      if (reply == JOptionPane.YES_OPTION)
+      if(reply==JOptionPane.YES_OPTION)
       {
         omitHidden = viewport.getViewAsString(false);
       }
@@ -822,6 +835,7 @@ public class AlignFrame
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
 
+
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment.getSequencesArray(),
@@ -837,7 +851,7 @@ public class AlignFrame
   {
     new HTMLOutput(viewport,
                    alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-                   alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
   public void createImageMap(File file, String image)
@@ -865,6 +879,7 @@ public class AlignFrame
     alignPanel.makeEPS(f);
   }
 
+
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -888,15 +903,17 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
-        alignPanel,
+      alignPanel,
         viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
-        viewport.alignment.getGroups()
+      viewport.alignment.getGroups()
         );
   }
 
+
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -918,6 +935,7 @@ public class AlignFrame
 
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -925,14 +943,14 @@ public class AlignFrame
    */
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
-    if (alignPanels != null && alignPanels.size() < 2)
+    if(alignPanels!=null && alignPanels.size()<2)
     {
       closeAllTabs = true;
     }
 
     try
     {
-      if (alignPanels != null)
+      if(alignPanels!=null)
       {
         if (closeAllTabs)
         {
@@ -958,9 +976,9 @@ public class AlignFrame
           tabbedPane.removeTabAt(index);
           tabbedPane.validate();
 
-          if (index == tabbedPane.getTabCount())
+          if(index==tabbedPane.getTabCount())
           {
-            index--;
+            index --;
           }
 
           this.tabSelectionChanged(index);
@@ -970,7 +988,7 @@ public class AlignFrame
       if (closeAllTabs)
       {
         this.setClosed(true);
-      }
+    }
     }
     catch (Exception ex)
     {
@@ -978,6 +996,7 @@ public class AlignFrame
     }
   }
 
+
   /**
    * DOCUMENT ME!
    */
@@ -1010,9 +1029,10 @@ public class AlignFrame
     }
   }
 
+
   public void addHistoryItem(CommandI command)
   {
-    if (command.getSize() > 0)
+    if(command.getSize()>0)
     {
       viewport.historyList.push(command);
       viewport.redoList.clear();
@@ -1021,6 +1041,8 @@ public class AlignFrame
     }
   }
 
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1028,14 +1050,14 @@ public class AlignFrame
    */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI) viewport.historyList.pop();
+    CommandI command = (CommandI)viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if (originalSource != null)
+    if(originalSource!=null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
       originalSource.firePropertyChange("alignment",
@@ -1051,7 +1073,7 @@ public class AlignFrame
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    if (viewport.redoList.size() < 1)
+    if(viewport.redoList.size()<1)
     {
       return;
     }
@@ -1063,7 +1085,7 @@ public class AlignFrame
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if (originalSource != null)
+    if(originalSource!=null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
       originalSource.firePropertyChange("alignment",
@@ -1076,9 +1098,9 @@ public class AlignFrame
   {
     AlignViewport originalSource = null;
     //For sequence removal and addition, we need to fire
-    //the property change event FROM the viewport where the
-    //original alignment was altered
-    AlignmentI al = null;
+   //the property change event FROM the viewport where the
+   //original alignment was altered
+    AlignmentI al=null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
@@ -1177,6 +1199,8 @@ public class AlignFrame
   }
 
 
+
+
   synchronized void slideSequences(boolean right, int size)
   {
     if(viewport.hasHiddenColumns)
@@ -1273,7 +1297,7 @@ public class AlignFrame
 
     repaint();
   }
-
+  
 
   /**
    * DOCUMENT ME!
@@ -1288,7 +1312,7 @@ public class AlignFrame
       return;
     }
 
-    SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
     String[] omitHidden = null;
 
     if (viewport.hasHiddenColumns)
@@ -1318,25 +1342,25 @@ public class AlignFrame
     {
       er.printStackTrace();
       javax.swing.SwingUtilities.invokeLater(new Runnable()
-      {
-        public void run()
-        {
-          javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "Out of memory copying region!!"
-              +
-              "\nSee help files for increasing Java Virtual Machine memory."
-              , "Out of memory",
-              javax.swing.JOptionPane.WARNING_MESSAGE);
-        }
-      });
+          {
+            public void run()
+            {
+              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Out of memory copying region!!"
+                  +
+                  "\nSee help files for increasing Java Virtual Machine memory."
+                  , "Out of memory",
+                  javax.swing.JOptionPane.WARNING_MESSAGE);
+            }
+          });
 
       return;
     }
 
     Vector hiddenColumns = null;
-    if (viewport.hasHiddenColumns)
+    if(viewport.hasHiddenColumns)
     {
-      hiddenColumns = new Vector();
+      hiddenColumns =new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
            i++)
@@ -1346,7 +1370,7 @@ public class AlignFrame
 
         hiddenColumns.addElement(new int[]
                                  {region[0] - hiddenOffset,
-                                 region[1] - hiddenOffset});
+                          region[1]-hiddenOffset});
       }
     }
 
@@ -1355,7 +1379,7 @@ public class AlignFrame
         seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
-    statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
+    statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
   }
 
   /**
@@ -1428,45 +1452,46 @@ public class AlignFrame
 
       SequenceI[] sequences;
 
-      if (Desktop.jalviewClipboard != null)
-      {
-        // The clipboard was filled from within Jalview, we must use the sequences
-        // And dataset from the copied alignment
-        sequences = (SequenceI[]) Desktop.jalviewClipboard[0];
-      }
-      else
-      {
+
+     if(Desktop.jalviewClipboard!=null)
+     {
+       // The clipboard was filled from within Jalview, we must use the sequences
+       // And dataset from the copied alignment
+       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+     }
+     else
+     {
         sequences = new FormatAdapter().readFile(str, "Paste", format).
             getSequencesArray();
-      }
+     }
 
-      AlignmentI alignment = null;
+     AlignmentI alignment = null;
 
       if (newAlignment)
       {
-        alignment = new Alignment(sequences);
+          alignment = new Alignment(sequences);
 
-        if (Desktop.jalviewClipboard != null)
+          if (Desktop.jalviewClipboard != null)
         {
-          alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+            alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
         }
-        else
+          else
         {
-          alignment.setDataset(null);
-        }
+            alignment.setDataset(null);
+      }
       }
       else
       {
         alignment = viewport.getAlignment();
 
         //!newAlignment
-        SequenceI[] newseqs = new SequenceI[sequences.length];
+        SequenceI [] newseqs = new SequenceI[sequences.length];
         for (int i = 0; i < sequences.length; i++)
         {
           newseqs[i] = new Sequence(sequences[i].getName(),
                                     sequences[i].getSequence(),
                                     sequences[i].getStart(),
-                                    sequences[i].getEnd());
+              sequences[i].getEnd());
 
           alignment.addSequence(newseqs[i]);
         }
@@ -1483,81 +1508,88 @@ public class AlignFrame
             alignment)
             );
 
+
         viewport.setEndSeq(alignment.getHeight());
         alignment.getWidth();
         viewport.firePropertyChange("alignment", null, alignment.getSequences());
       }
 
+
+
       // Add any annotations attached to sequences
       for (int i = 0; i < sequences.length; i++)
-      {
-        if (sequences[i].getAnnotation() != null)
-        {
-          for (int a = 0; a < sequences[i].getAnnotation().length; a++)
-          {
-            AlignmentAnnotation newAnnot =
-                new AlignmentAnnotation(
-                    sequences[i].getAnnotation()[a].label,
-                    sequences[i].getAnnotation()[a].description,
-                    sequences[i].getAnnotation()[a].annotations,
-                    sequences[i].getAnnotation()[a].graphMin,
-                    sequences[i].getAnnotation()[a].graphMax,
-                    sequences[i].getAnnotation()[a].graph);
-
-            sequences[i].getAnnotation()[a] = newAnnot;
-            newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
-                sequenceMapping;
-            newAnnot.sequenceRef = sequences[i];
-            newAnnot.adjustForAlignment();
-            alignment.addAnnotation(newAnnot);
-            alignment.setAnnotationIndex(newAnnot, a);
-          }
+     {
+       if (sequences[i].getAnnotation() != null)
+       {
+         for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+         {
+           AlignmentAnnotation newAnnot =
+               new AlignmentAnnotation(
+                   sequences[i].getAnnotation()[a].label,
+                   sequences[i].getAnnotation()[a].description,
+                   sequences[i].getAnnotation()[a].annotations,
+                   sequences[i].getAnnotation()[a].graphMin,
+                   sequences[i].getAnnotation()[a].graphMax,
+                   sequences[i].getAnnotation()[a].graph);
+
+           sequences[i].getAnnotation()[a] = newAnnot;
+           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+               sequenceMapping;
+           newAnnot.sequenceRef = sequences[i];
+           newAnnot.adjustForAlignment();
+           alignment.addAnnotation(newAnnot);
+           alignment.setAnnotationIndex(newAnnot, a);
+         }
+
+         alignPanel.annotationPanel.adjustPanelHeight();
+       }
+     }
 
-          alignPanel.annotationPanel.adjustPanelHeight();
-        }
-      }
+     if(newAlignment)
+     {
+       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+       String newtitle = new String("Copied sequences");
 
-      if (newAlignment)
-      {
-        AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-        String newtitle = new String("Copied sequences");
+       if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
+         {
+           Vector hc = (Vector)Desktop.jalviewClipboard[2];
+           for(int i=0; i<hc.size(); i++)
+           {
+             int [] region = (int[]) hc.elementAt(i);
+             af.viewport.hideColumns(region[0], region[1]);
+           }
+         }
 
-        if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null)
-        {
-          Vector hc = (Vector) Desktop.jalviewClipboard[2];
-          for (int i = 0; i < hc.size(); i++)
-          {
-            int[] region = (int[]) hc.elementAt(i);
-            af.viewport.hideColumns(region[0], region[1]);
-          }
-        }
 
-        //>>>This is a fix for the moment, until a better solution is found!!<<<
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+       //>>>This is a fix for the moment, until a better solution is found!!<<<
+       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
 
-        if (title.startsWith("Copied sequences"))
-        {
-          newtitle = title;
-        }
-        else
-        {
-          newtitle = newtitle.concat("- from " + title);
-        }
 
-        Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
-                                 DEFAULT_HEIGHT);
+       if (title.startsWith("Copied sequences"))
+       {
+         newtitle = title;
+       }
+       else
+       {
+         newtitle = newtitle.concat("- from " + title);
+       }
+
+       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+                                DEFAULT_HEIGHT);
+
+     }
 
-      }
 
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
-      // could be anything being pasted in here
+        System.out.println("Exception whilst pasting: "+ex);
+        // could be anything being pasted in here
     }
 
+
   }
 
   /**
@@ -1593,34 +1625,38 @@ public class AlignFrame
       seqs.addElement(seq);
     }
 
-    // If the cut affects all sequences, remove highlighted columns
-    if (sg.getSize() == viewport.alignment.getHeight())
-    {
-      viewport.getColumnSelection().removeElements(sg.getStartRes(),
-          sg.getEndRes() + 1);
-    }
 
-    SequenceI[] cut = new SequenceI[seqs.size()];
-    for (int i = 0; i < seqs.size(); i++)
+   // If the cut affects all sequences, remove highlighted columns
+   if (sg.getSize() == viewport.alignment.getHeight())
+   {
+     viewport.getColumnSelection().removeElements(sg.getStartRes(),
+         sg.getEndRes() + 1);
+   }
+
+
+    SequenceI [] cut = new SequenceI[seqs.size()];
+    for(int i=0; i<seqs.size(); i++)
     {
-      cut[i] = (SequenceI) seqs.elementAt(i);
+      cut[i] = (SequenceI)seqs.elementAt(i);
     }
 
+
     /*
-         //ADD HISTORY ITEM
-     */
+    //ADD HISTORY ITEM
+    */
     addHistoryItem(new EditCommand("Cut Sequences",
-                                   EditCommand.CUT,
-                                   cut,
-                                   sg.getStartRes(),
-                                   sg.getEndRes() - sg.getStartRes() + 1,
-                                   viewport.alignment));
+                                      EditCommand.CUT,
+                                      cut,
+                                      sg.getStartRes(),
+                                      sg.getEndRes()-sg.getStartRes()+1,
+                                      viewport.alignment));
+
 
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
     viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+                                  viewport.getAlignment().getSequences());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -1676,7 +1712,7 @@ public class AlignFrame
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    if (viewport.cursorMode)
+    if(viewport.cursorMode)
     {
       alignPanel.seqPanel.keyboardNo1 = null;
       alignPanel.seqPanel.keyboardNo2 = null;
@@ -1723,6 +1759,7 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -1740,7 +1777,7 @@ public class AlignFrame
    */
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-    trimAlignment(false);
+      trimAlignment(false);
   }
 
   void trimAlignment(boolean trimLeft)
@@ -1750,7 +1787,7 @@ public class AlignFrame
 
     if (colSel.size() > 0)
     {
-      if (trimLeft)
+      if(trimLeft)
       {
         column = colSel.getMin();
       }
@@ -1759,8 +1796,8 @@ public class AlignFrame
         column = colSel.getMax();
       }
 
-      SequenceI[] seqs;
-      if (viewport.getSelectionGroup() != null)
+      SequenceI [] seqs;
+      if(viewport.getSelectionGroup()!=null)
       {
         seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
             hiddenRepSequences);
@@ -1770,30 +1807,32 @@ public class AlignFrame
         seqs = viewport.alignment.getSequencesArray();
       }
 
+
       TrimRegionCommand trimRegion;
-      if (trimLeft)
+      if(trimLeft)
       {
         trimRegion = new TrimRegionCommand("Remove Left",
-                                           TrimRegionCommand.TRIM_LEFT,
-                                           seqs,
-                                           column,
-                                           viewport.alignment,
-                                           viewport.colSel,
-                                           viewport.selectionGroup);
+                                    TrimRegionCommand.TRIM_LEFT,
+                                    seqs,
+                                    column,
+                                    viewport.alignment,
+                                    viewport.colSel,
+                                    viewport.selectionGroup);
         viewport.setStartRes(0);
       }
-      else
-      {
-        trimRegion = new TrimRegionCommand("Remove Right",
-                                           TrimRegionCommand.TRIM_RIGHT,
-                                           seqs,
-                                           column,
-                                           viewport.alignment,
-                                           viewport.colSel,
-                                           viewport.selectionGroup);
-      }
+     else
+     {
+       trimRegion = new TrimRegionCommand("Remove Right",
+                                   TrimRegionCommand.TRIM_RIGHT,
+                                   seqs,
+                                   column,
+                                   viewport.alignment,
+                                   viewport.colSel,
+                                   viewport.selectionGroup);
+     }
+
+     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
 
-      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 
       addHistoryItem(trimRegion);
 
@@ -1822,7 +1861,7 @@ public class AlignFrame
    */
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -1837,6 +1876,7 @@ public class AlignFrame
       seqs = viewport.alignment.getSequencesArray();
     }
 
+
     RemoveGapColCommand removeGapCols =
         new RemoveGapColCommand("Remove Gapped Columns",
                                 seqs,
@@ -1845,18 +1885,18 @@ public class AlignFrame
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
+    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
 
     //This is to maintain viewport position on first residue
     //of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
-    // ShiftList shifts;
-    // viewport.getAlignment().removeGaps(shifts=new ShiftList());
-    // edit.alColumnChanges=shifts.getInverse();
-    // if (viewport.hasHiddenColumns)
-    //   viewport.getColumnSelection().compensateForEdits(shifts);
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+   // ShiftList shifts;
+   // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+   // edit.alColumnChanges=shifts.getInverse();
+   // if (viewport.hasHiddenColumns)
+   //   viewport.getColumnSelection().compensateForEdits(shifts);
+   viewport.setStartRes(seq.findIndex(startRes)-1);
     viewport.firePropertyChange("alignment", null,
                                 viewport.getAlignment().getSequences());
 
@@ -1869,7 +1909,7 @@ public class AlignFrame
    */
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -1894,7 +1934,7 @@ public class AlignFrame
                                          start, end,
                                          viewport.alignment));
 
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.setStartRes(seq.findIndex(startRes)-1);
 
     viewport.firePropertyChange("alignment", null,
                                 viewport.getAlignment().getSequences());
@@ -1939,33 +1979,33 @@ public class AlignFrame
     newap.av.redoList = viewport.redoList;
 
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
-    String newViewName = "View " + index;
+    String newViewName = "View " +index;
 
     Vector comps = (Vector) PaintRefresher.components.get(viewport.
         getSequenceSetId());
     Vector existingNames = new Vector();
-    for (int i = 0; i < comps.size(); i++)
+    for(int i=0; i<comps.size(); i++)
     {
-      if (comps.elementAt(i) instanceof AlignmentPanel)
+      if(comps.elementAt(i) instanceof AlignmentPanel)
       {
-        AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
-        if (!existingNames.contains(ap.av.viewName))
+        AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
+        if(!existingNames.contains(ap.av.viewName))
         {
           existingNames.addElement(ap.av.viewName);
-        }
       }
     }
+    }
 
-    while (existingNames.contains(newViewName))
+    while(existingNames.contains(newViewName))
     {
-      newViewName = "View " + (++index);
+      newViewName = "View "+ (++index);
     }
 
     newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, false);
 
-    if (alignPanels.size() == 2)
+    if(alignPanels.size()==2)
     {
       viewport.gatherViewsHere = true;
     }
@@ -1974,7 +2014,7 @@ public class AlignFrame
 
   public void expandViews_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.explodeViews(this);
+        Desktop.instance.explodeViews(this);
   }
 
   public void gatherViews_actionPerformed(ActionEvent e)
@@ -1982,6 +2022,8 @@ public class AlignFrame
     Desktop.instance.gatherViews(this);
   }
 
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1992,6 +2034,7 @@ public class AlignFrame
     new FontChooser(alignPanel);
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -2011,6 +2054,8 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
+
+
   /**
    * DOCUMENT ME!
    *
@@ -2131,10 +2176,11 @@ public class AlignFrame
     alignPanel.paintAlignment(true);
   }
 
+
   public FeatureSettings featureSettings;
   public void featureSettings_actionPerformed(ActionEvent e)
   {
-    if (featureSettings != null)
+    if(featureSettings !=null )
     {
       featureSettings.close();
       featureSettings = null;
@@ -2311,6 +2357,7 @@ public class AlignFrame
     new AnnotationColourChooser(viewport, alignPanel);
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -2330,12 +2377,12 @@ public class AlignFrame
   {
     int threshold = 0;
 
-    if (cs != null)
+    if(cs!=null)
     {
       if (viewport.getAbovePIDThreshold())
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-            "Background");
+                                                   "Background");
 
         cs.setThreshold(threshold,
                         viewport.getIgnoreGapsConsensus());
@@ -2412,18 +2459,19 @@ public class AlignFrame
             || cs instanceof PIDColourScheme
             || cs instanceof Blosum62ColourScheme)
         {
-          sg.cs.setThreshold(threshold,
-                             viewport.getIgnoreGapsConsensus());
+         sg.cs.setThreshold(threshold,
+                viewport.getIgnoreGapsConsensus());
 
-          sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
-              sg.getEndRes() + 1));
-        }
+         sg.cs.setConsensus(AAFrequency.calculate(
+             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
+             sg.getEndRes()+1));
+       }
         else
         {
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
+
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
@@ -2431,7 +2479,7 @@ public class AlignFrame
                                             sg.getSequences(viewport.
               hiddenRepSequences),
                                             sg.getStartRes(),
-                                            sg.getEndRes() + 1);
+                                            sg.getEndRes()+1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
@@ -2439,9 +2487,9 @@ public class AlignFrame
         else
         {
           sg.cs.setConservation(null);
-        }
       }
     }
+    }
 
     if (alignPanel.getOverviewPanel() != null)
     {
@@ -2461,7 +2509,7 @@ public class AlignFrame
    */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
                                      viewport.getGlobalColourScheme(),
@@ -2477,7 +2525,7 @@ public class AlignFrame
    */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel,
                                         viewport.globalColourScheme,
@@ -2566,37 +2614,37 @@ public class AlignFrame
             nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
-        {
-          public void mousePressed(MouseEvent evt)
-          {
-            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
             {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
                   Desktop.desktop,
-                  "Remove from default list?",
-                  "Remove user defined colour",
-                  JOptionPane.YES_NO_OPTION);
-              if (option == JOptionPane.YES_OPTION)
-              {
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
                 jalview.gui.UserDefinedColours.removeColourFromDefaults(
                     radioItem.getText());
-                colourMenu.remove(radioItem);
-              }
-              else
-              {
-                radioItem.addActionListener(new ActionListener()
-                {
-                  public void actionPerformed(ActionEvent evt)
-                  {
-                    userDefinedColour_actionPerformed(evt);
+                    colourMenu.remove(radioItem);
                   }
-                });
+                  else
+              {
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
               }
-            }
           }
-        });
+            });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -2638,7 +2686,7 @@ public class AlignFrame
    */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
@@ -2653,7 +2701,7 @@ public class AlignFrame
    */
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
     alignPanel.paintAlignment(true);
@@ -2666,7 +2714,7 @@ public class AlignFrame
    */
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
 
@@ -2683,6 +2731,7 @@ public class AlignFrame
     new RedundancyPanel(alignPanel, this);
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -2727,13 +2776,14 @@ public class AlignFrame
       return;
     }
 
-    new PCAPanel(alignPanel);
+     new PCAPanel(alignPanel);
   }
 
+
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if (viewport.autoCalculateConsensus)
+    if(viewport.autoCalculateConsensus)
     {
       viewport.firePropertyChange("alignment",
                                   null,
@@ -2741,6 +2791,7 @@ public class AlignFrame
     }
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -2841,7 +2892,7 @@ public class AlignFrame
         return;
       }
 
-      if (viewport.alignment.getHeight() < 2)
+      if(viewport.alignment.getHeight()<2)
       {
         return;
       }
@@ -2851,9 +2902,9 @@ public class AlignFrame
 
     title += " from ";
 
-    if (viewport.viewName != null)
+    if(viewport.viewName!=null)
     {
-      title += viewport.viewName + " of ";
+      title+= viewport.viewName+" of ";
     }
 
     title += this.title;
@@ -2875,7 +2926,7 @@ public class AlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+        SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
 
         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
@@ -2905,9 +2956,9 @@ public class AlignFrame
         getSequenceSetId());
     Vector treePanels = new Vector();
     int i, iSize = comps.size();
-    for (i = 0; i < iSize; i++)
+    for(i=0; i<iSize; i++)
     {
-      if (comps.elementAt(i) instanceof TreePanel)
+      if(comps.elementAt(i) instanceof TreePanel)
       {
         treePanels.add(comps.elementAt(i));
       }
@@ -2915,7 +2966,7 @@ public class AlignFrame
 
     iSize = treePanels.size();
 
-    if (iSize < 1)
+    if(iSize<1)
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -2923,11 +2974,11 @@ public class AlignFrame
 
     sortByTreeMenu.setVisible(true);
 
-    for (i = 0; i < treePanels.size(); i++)
+    for(i=0; i<treePanels.size(); i++)
     {
-      TreePanel tp = (TreePanel) treePanels.elementAt(i);
+      TreePanel tp = (TreePanel)treePanels.elementAt(i);
       final JMenuItem item = new JMenuItem(tp.getTitle());
-      final NJTree tree = ( (TreePanel) treePanels.elementAt(i)).getTree();
+      final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
       item.addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(ActionEvent e)
@@ -2962,27 +3013,28 @@ public class AlignFrame
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       /*SequenceGroup seqs = viewport.getSelectionGroup();
-             int sz;
-             msa = new SequenceI[sz = seqs.getSize(false)];
+      int sz;
+      msa = new SequenceI[sz = seqs.getSize(false)];
 
-             for (int i = 0; i < sz; i++)
-             {
+      for (int i = 0; i < sz; i++)
+      {
         msa[i] = (SequenceI) seqs.getSequenceAt(i);
-             } */
+      } */
       msa = viewport.getAlignmentView(true);
     }
     else
     {
       /*Vector seqs = viewport.getAlignment().getSequences();
-             if (seqs.size() > 1)
-             {
+
+      if (seqs.size() > 1)
+      {
         msa = new SequenceI[seqs.size()];
 
         for (int i = 0; i < seqs.size(); i++)
         {
           msa[i] = (SequenceI) seqs.elementAt(i);
         }
-             }*/
+      }*/
       msa = viewport.getAlignmentView(false);
     }
     return msa;
@@ -2996,7 +3048,7 @@ public class AlignFrame
    */
   AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
-    AlignmentView seqs = null;
+   AlignmentView seqs = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 0))
@@ -3016,7 +3068,6 @@ public class AlignFrame
     }
     return seqs;
   }
-
   /**
    * DOCUMENT ME!
    *
@@ -3056,15 +3107,16 @@ public class AlignFrame
     }
   }
 
+
   public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
-    return ShowNewickTree(nf, title, 600, 500, 4, 5);
+    return ShowNewickTree(nf,title,600,500,4,5);
   }
 
   public TreePanel ShowNewickTree(NewickFile nf, String title,
                                   AlignmentView input)
   {
-    return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
+    return ShowNewickTree(nf,title, input, 600,500,4,5);
   }
 
   public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
@@ -3072,7 +3124,6 @@ public class AlignFrame
   {
     return ShowNewickTree(nf, title, null, w, h, x, y);
   }
-
   /**
    * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
    *
@@ -3102,13 +3153,14 @@ public class AlignFrame
                            title,
                            nf, input);
 
-        tp.setSize(w, h);
+        tp.setSize(w,h);
 
-        if (x > 0 && y > 0)
+        if(x>0 && y>0)
         {
-          tp.setLocation(x, y);
+          tp.setLocation(x,y);
         }
 
+
         Desktop.addInternalFrame(tp, title, w, h);
       }
     }
@@ -3120,6 +3172,7 @@ public class AlignFrame
     return tp;
   }
 
+
   /**
    * Generates menu items and listener event actions for web service clients
    *
@@ -3160,7 +3213,7 @@ public class AlignFrame
           if (sh.getName().indexOf("lustal") > -1)
           {
             // We know that ClustalWS can accept partial alignments for refinement.
-            final JMenuItem methodR = new JMenuItem(sh.getName() + " Realign");
+            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
             methodR.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)
@@ -3205,7 +3258,7 @@ public class AlignFrame
                 {
                   // Sequence profile based prediction
                   new jalview.ws.JPredClient(sh,
-                                             title, true, msa, af, true);
+                      title, true, msa, af, true);
                 }
               }
             }
@@ -3230,144 +3283,80 @@ public class AlignFrame
     // TODO: group services by location as well as function.
   }
 
-  /* public void vamsasStore_actionPerformed(ActionEvent e)
-   {
-     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-         getProperty("LAST_DIRECTORY"));
-
-     chooser.setFileView(new JalviewFileView());
-     chooser.setDialogTitle("Export to Vamsas file");
-     chooser.setToolTipText("Export");
-
-     int value = chooser.showSaveDialog(this);
-
-     if (value == JalviewFileChooser.APPROVE_OPTION)
-     {
-   jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
-       //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
-       vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
-     }
-   }*/
-
-
-
-
-  public void showTranslation_actionPerformed(ActionEvent e)
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
   {
-    SequenceI[] selection = viewport.getSelectionAsNewSequence();
-    String[] seqstring = viewport.getViewAsString(true);
-
-    int s, sSize = selection.length;
-    SequenceI[] newSeq = new SequenceI[sSize];
-
-    int res, resSize;
-    StringBuffer protein;
-    String seq;
-    for (s = 0; s < sSize; s++)
-    {
-      protein = new StringBuffer();
-      seq = AlignSeq.extractGaps("-. ", seqstring[s]);
-      resSize = seq.length();
-      resSize -= resSize % 3;
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
 
-      for (res = 0; res < resSize; res += 3)
-      {
-        String codon = seq.substring(res, res + 3);
-        codon = codon.replace('U', 'T');
-        String aa = ResidueProperties.codonTranslate(codon);
-        if (aa == null)
-        {
-          protein.append(viewport.getGapCharacter());
-        }
-        else if (aa.equals("STOP"))
-        {
-          protein.append("X");
-        }
-        else
-        {
-          protein.append(aa);
-        }
-      }
-      newSeq[s] = new Sequence(selection[s].getName(),
-                               protein.toString());
-    }
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Export to Vamsas file");
+    chooser.setToolTipText("Export");
 
-    AlignmentI al = new Alignment(newSeq);
-    al.setDataset(null);
+    int value = chooser.showSaveDialog(this);
 
-    ////////////////////////////////
-    // Copy annotations across
-    jalview.datamodel.AlignmentAnnotation[] annotations
-        = viewport.alignment.getAlignmentAnnotation();
-    int a, aSize;
-    if (annotations != null)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      for (int i = 0; i < annotations.length; i++)
-      {
-        if (annotations[i] == viewport.quality ||
-            annotations[i] == viewport.conservation ||
-            annotations[i] == viewport.consensus)
-        {
-          System.out.println("COPT HERE");
-          continue;
-        }
-
-        aSize = viewport.alignment.getWidth() / 3;
-        jalview.datamodel.Annotation[] anots =
-            new jalview.datamodel.Annotation[aSize];
+      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+    }
+  }*/
 
-        for (a = 0; a < viewport.alignment.getWidth(); a++)
-        {
-          if (annotations[i].annotations[a] == null
-              || annotations[i].annotations[a] == null)
-          {
-            continue;
-          }
 
-          anots[a / 3] = new Annotation(
-              annotations[i].annotations[a].displayCharacter,
-              annotations[i].annotations[a].description,
-              annotations[i].annotations[a].secondaryStructure,
-              annotations[i].annotations[a].value,
-              annotations[i].annotations[a].colour);
-        }
 
-        jalview.datamodel.AlignmentAnnotation aa
-            = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-            annotations[i].description, anots);
-        al.addAnnotation(aa);
-      }
-    }
 
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+  ///////////////////////////////
+  // Collect Data to be translated/transferred
+    
+  SequenceI [] selection = viewport.getSelectionAsNewSequence();
+  String [] seqstring = viewport.getViewAsString(true);
+  AlignmentI al  = null;
+  try {
+    al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true), 
+        viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(), 
+        viewport.alignment.getWidth());
+  } catch (Exception ex) {
+    al = null;
+    jalview.bin.Cache.log.debug("Exception during translation.",ex);
+  }
+  if (al==null)   
+  {
+    JOptionPane.showMessageDialog(Desktop.desktop,
+        "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+        "Translation Failed",
+        JOptionPane.WARNING_MESSAGE);
+  } else {
     AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              DEFAULT_WIDTH,
                              DEFAULT_HEIGHT);
-
   }
+}
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param String DOCUMENT ME!
-   */
-  public boolean parseFeaturesFile(String file, String type)
-  {
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseFeaturesFile(String file, String type)
+{
     boolean featuresFile = false;
     try
     {
       featuresFile = new FeaturesFile(file,
           type).parse(viewport.alignment.getDataset(),
-                      alignPanel.seqPanel.seqCanvas.
-                      getFeatureRenderer().featureColours,
-                      false);
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours,
+                                         false);
     }
-    catch (Exception ex)
+    catch(Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if(featuresFile)
     {
       viewport.showSequenceFeatures = true;
       showSeqFeatures.setSelected(true);
@@ -3375,22 +3364,22 @@ public class AlignFrame
     }
 
     return featuresFile;
-  }
+}
 
-  public void dragEnter(DropTargetDragEvent evt)
-  {}
+public void dragEnter(DropTargetDragEvent evt)
+{}
 
-  public void dragExit(DropTargetEvent evt)
-  {}
+public void dragExit(DropTargetEvent evt)
+{}
 
-  public void dragOver(DropTargetDragEvent evt)
-  {}
+public void dragOver(DropTargetDragEvent evt)
+{}
 
-  public void dropActionChanged(DropTargetDragEvent evt)
-  {}
+public void dropActionChanged(DropTargetDragEvent evt)
+{}
 
-  public void drop(DropTargetDropEvent evt)
-  {
+public void drop(DropTargetDropEvent evt)
+{
     Transferable t = evt.getTransferable();
     java.util.List files = null;
 
@@ -3448,13 +3437,13 @@ public class AlignFrame
         ex.printStackTrace();
       }
     }
-  }
+}
 
   // This method will attempt to load a "dropped" file first by testing
   // whether its and Annotation file, then features file. If both are
   // false then the user may have dropped an alignment file onto this
   // AlignFrame
-  public void loadJalviewDataFile(String file)
+   public void loadJalviewDataFile(String file)
   {
     try
     {
@@ -3470,12 +3459,12 @@ public class AlignFrame
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file, protocol);
+        boolean isGroupsFile = parseFeaturesFile(file,protocol);
         if (!isGroupsFile)
         {
           String format = new IdentifyFile().Identify(file, protocol);
 
-          if (format.equalsIgnoreCase("JnetFile"))
+          if(format.equalsIgnoreCase("JnetFile"))
           {
             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                 file, protocol);
@@ -3488,9 +3477,9 @@ public class AlignFrame
           else
           {
             new FileLoader().LoadFile(viewport, file, protocol, format);
-          }
         }
       }
+      }
       else
       {
         // (isAnnotation)
@@ -3516,7 +3505,7 @@ public class AlignFrame
 
   public void tabbedPane_mousePressed(MouseEvent e)
   {
-    if (SwingUtilities.isRightMouseButton(e))
+    if(SwingUtilities.isRightMouseButton(e))
     {
       String reply = JOptionPane.showInternalInputDialog(this,
           "Enter View Name",
@@ -3526,11 +3515,12 @@ public class AlignFrame
       if (reply != null)
       {
         viewport.viewName = reply;
-        tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
+        tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
       }
     }
   }
 
+
   public AlignViewport getCurrentView()
   {
     return viewport;
@@ -3543,9 +3533,8 @@ class PrintThread
   AlignmentPanel ap;
   public PrintThread(AlignmentPanel ap)
   {
-    this.ap = ap;
+   this.ap = ap;
   }
-
   static PageFormat pf;
   public void run()
   {
-- 
1.7.10.2