X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b68008a0495a467e946fcd83b38e05ba11fb0052;hb=5c57814f95e73a63e012479651b919fdc4099f53;hp=ddb871e3e891f38cccb5cad4d4a8483d6f817f99;hpb=82cbe684b0afeb8a6a8c6014b9266cb90439dfe7;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ddb871e..b68008a 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,6 +1,6 @@
  /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,6 +18,10 @@
  */
 package jalview.gui;
 
+import java.util.*;
+
+import java.awt.*;
+
 import jalview.analysis.*;
 
 import jalview.bin.*;
@@ -26,11 +30,6 @@ import jalview.datamodel.*;
 
 import jalview.schemes.*;
 
-import java.awt.*;
-
-import java.util.*;
-
-
 /**
  * DOCUMENT ME!
  *
@@ -51,9 +50,6 @@ public class AlignViewport
     boolean renderGaps = true;
     boolean showSequenceFeatures = false;
     boolean showAnnotation = true;
-    boolean showConservation = true;
-    boolean showQuality = true;
-    boolean showIdentity = true;
     boolean colourAppliesToAllGroups = true;
     ColourSchemeI globalColourScheme = null;
     boolean conservationColourSelected = false;
@@ -64,6 +60,7 @@ public class AlignViewport
     boolean validCharWidth;
     int wrappedWidth;
     Font font;
+    boolean seqNameItalics;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -94,7 +91,8 @@ public class AlignViewport
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
     // JBPNote Prolly only need this in the applet version.
-    private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+      PropertyChangeSupport(this);
 
     boolean ignoreGapsInConsensusCalculation = false;
 
@@ -112,13 +110,20 @@ public class AlignViewport
 
     boolean gatherViewsHere = false;
 
+    Stack historyList = new Stack();
+    Stack redoList = new Stack();
+
+    Hashtable sequenceColours;
+
+    int thresholdTextColour = 0;
+    Color textColour = Color.black;
+    Color textColour2 = Color.white;
+
+    boolean rightAlignIds = false;
+
+    Hashtable hiddenRepSequences;
+
 
-    public AlignViewport(AlignmentI al, boolean dataset)
-    {
-      isDataset = dataset;
-      setAlignment(al);
-      init();
-    }
     /**
      * Creates a new AlignViewport object.
      *
@@ -134,13 +139,17 @@ public class AlignViewport
      * @param al AlignmentI
      * @param hiddenColumns ColumnSelection
      */
-    public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  {
       setAlignment(al);
-      if (hiddenColumns!=null) {
+    if (hiddenColumns != null)
+    {
         this.colSel = hiddenColumns;
         if (hiddenColumns.getHiddenColumns() != null)
+      {
           hasHiddenColumns = true;
       }
+    }
       init();
     }
 
@@ -155,19 +164,19 @@ public class AlignViewport
 
       showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
-      showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
 
-      showQuality = Cache.getDefault("SHOW_QUALITY", true);
-      showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
+      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
 
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-      padGaps = Cache.getDefault("PAD_GAPS", false);
+      padGaps = Cache.getDefault("PAD_GAPS", true);
 
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
        int style = 0;
 
        if (fontStyle.equals("bold"))
@@ -181,7 +190,6 @@ public class AlignViewport
 
        setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
 
-
        alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
 
 
@@ -198,13 +206,15 @@ public class AlignViewport
                 11f,
                 AlignmentAnnotation.BAR_GRAPH);
             conservation.hasText = true;
+            conservation.autoCalculated=true;
+
 
-            if (showConservation)
+            if (Cache.getDefault("SHOW_CONSERVATION", true))
             {
               alignment.addAnnotation(conservation);
             }
 
-            if (showQuality)
+            if (Cache.getDefault("SHOW_QUALITY", true))
             {
               quality = new AlignmentAnnotation("Quality",
                                                 "Alignment Quality based on Blosum62 scores",
@@ -212,6 +222,8 @@ public class AlignViewport
                                                 0f,
                                                 11f,
                                                 AlignmentAnnotation.BAR_GRAPH);
+              quality.hasText = true;
+              quality.autoCalculated=true;
 
               alignment.addAnnotation(quality);
             }
@@ -221,12 +233,12 @@ public class AlignViewport
                                                new Annotation[1], 0f, 100f,
                                                AlignmentAnnotation.BAR_GRAPH);
           consensus.hasText = true;
+          consensus.autoCalculated=true;
 
-           if (showIdentity)
+           if (Cache.getDefault("SHOW_IDENTITY", true))
            {
              alignment.addAnnotation(consensus);
            }
-
         }
 
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -237,7 +249,8 @@ public class AlignViewport
             if (globalColourScheme instanceof UserColourScheme)
             {
                 globalColourScheme = UserDefinedColours.loadDefaultColours();
-                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
+        ( (UserColourScheme) globalColourScheme).setThreshold(0,
+            getIgnoreGapsConsensus());
             }
 
             if (globalColourScheme != null)
@@ -245,6 +258,8 @@ public class AlignViewport
                 globalColourScheme.setConsensus(hconsensus);
             }
         }
+
+        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
     }
 
 
@@ -264,9 +279,8 @@ public class AlignViewport
       return showSequenceFeatures;
     }
 
-
-
-    class ConservationThread extends Thread
+  class ConservationThread
+      extends Thread
     {
       AlignmentPanel ap;
       public ConservationThread(AlignmentPanel ap)
@@ -278,25 +292,46 @@ public class AlignViewport
       {
         try
         {
-          long t = System.currentTimeMillis();
+          updatingConservation = true;
+
+          while (UPDATING_CONSERVATION)
+          {
+            try
+            {
+              if (ap != null)
+              {
+              ap.paintAlignment(true);
+              }
+              Thread.sleep(200);
+            }
+            catch (Exception ex)
+            {
+              ex.printStackTrace();
+            }
+          }
+
+          UPDATING_CONSERVATION = true;
+
+
+          int alWidth = alignment.getWidth();
+          if(alWidth<0)
+        {
+            return;
+        }
 
           Conservation cons = new jalview.analysis.Conservation("All",
               jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alignment.getWidth() - 1);
+              alignment.getSequences(), 0, alWidth -1);
 
           cons.calculate();
           cons.verdict(false, ConsPercGaps);
 
-          if (showQuality)
+          if (quality!=null)
           {
             cons.findQuality();
           }
 
-          System.out.println("Conservation took " + (System.currentTimeMillis() - t) +
-                             "ms");
-
-          int alWidth = alignment.getWidth();
-          String sequence = cons.getConsSequence().getSequence();
+          char [] sequence = cons.getConsSequence().getSequence();
           float minR;
           float minG;
           float minB;
@@ -319,8 +354,9 @@ public class AlignViewport
 
           conservation.annotations = new Annotation[alWidth];
 
-          if (showQuality)
+          if (quality!=null)
           {
+            quality.graphMax = cons.qualityRange[1].floatValue();
             quality.annotations = new Annotation[alWidth];
             qmin = cons.qualityRange[0].floatValue();
             qmax = cons.qualityRange[1].floatValue();
@@ -330,14 +366,20 @@ public class AlignViewport
           {
             float value = 0;
 
-            c = sequence.charAt(i);
+            c = sequence[i];
 
             if (Character.isDigit(c))
+          {
               value = (int) (c - '0');
+          }
             else if (c == '*')
+          {
               value = 11;
+          }
             else if (c == '+')
+          {
               value = 10;
+          }
 
             float vprop = value - min;
             vprop /= max;
@@ -349,28 +391,26 @@ public class AlignViewport
                                          minB + (maxB * vprop)));
 
             // Quality calc
-            if (showQuality)
+            if (quality!=null)
             {
               value = ( (Double) cons.quality.get(i)).floatValue();
               vprop = value - qmin;
               vprop /= qmax;
-              quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+                ' ',
                                                value,
                                                new Color(minR + (maxR * vprop),
                   minG + (maxG * vprop),
                   minB + (maxB * vprop)));
             }
           }
-
-          if (quality != null)
-          {
-            quality.graphMax = cons.qualityRange[1].floatValue();
-          }
         }
         catch (OutOfMemoryError error)
         {
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+
+
             public void run()
             {
               javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -382,16 +422,22 @@ public class AlignViewport
             }
           });
 
+          conservation = null;
+          quality = null;
+
           System.out.println("Conservation calculation: " + error);
           System.gc();
 
         }
 
+        UPDATING_CONSERVATION = false;
+        updatingConservation = false;
+
         if(ap!=null)
         {
-          ap.annotationPanel.repaint();
+        ap.paintAlignment(true);
         }
-        updatingConservation = false;
+
       }
     }
 
@@ -402,6 +448,10 @@ public class AlignViewport
 
     boolean consUpdateNeeded = false;
 
+    static boolean UPDATING_CONSENSUS = false;
+
+    static boolean UPDATING_CONSERVATION = false;
+
     boolean updatingConsensus = false;
 
     boolean updatingConservation = false;
@@ -409,46 +459,28 @@ public class AlignViewport
     /**
      * DOCUMENT ME!
      */
-    public void updateConservation(AlignmentPanel ap)
+    public void updateConservation(final AlignmentPanel ap)
+    {
+      if (alignment.isNucleotide() || conservation==null)
     {
-      if (alignment.isNucleotide())
         return;
+    }
 
-      updatingConservation = true;
-
-      if (conservationThread == null || !conservationThread.isAlive())
-      {
-        conservationThread = new ConservationThread(ap);
-        conservationThread.start();
-      }
-      else
-      {
-        consUpdateNeeded = true;
-        System.out.println("come back later");
-      }
+      conservationThread = new ConservationThread(ap);
+      conservationThread.start();
     }
 
     /**
      * DOCUMENT ME!
      */
-    public void updateConsensus(AlignmentPanel ap)
+    public void updateConsensus(final AlignmentPanel ap)
     {
-      updatingConsensus = true;
-
-      if (consensusThread == null || !consensusThread.isAlive())
-      {
-        consensusThread = new ConsensusThread(ap);
-        consensusThread.start();
-      }
-      else
-      {
-        consUpdateNeeded = true;
-        System.out.println("come back later");
-      }
+      consensusThread = new ConsensusThread(ap);
+      consensusThread.start();
     }
 
-
-    class ConsensusThread extends Thread
+  class ConsensusThread
+      extends Thread
     {
       AlignmentPanel ap;
       public ConsensusThread(AlignmentPanel ap)
@@ -457,32 +489,58 @@ public class AlignViewport
       }
       public void run()
       {
+        updatingConsensus = true;
+        while (UPDATING_CONSENSUS)
+        {
+          try
+          {
+            if (ap != null)
+            {
+            ap.paintAlignment(true);
+            }
+
+            Thread.sleep(200);
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
+        }
+
+
+        UPDATING_CONSENSUS = true;
+
         try
         {
           int aWidth = alignment.getWidth();
+          if(aWidth<0)
+        {
+            return;
+        }
 
           consensus.annotations = null;
           consensus.annotations = new Annotation[aWidth];
 
-          long t = System.currentTimeMillis();
+
           hconsensus = new Hashtable[aWidth];
           AAFrequency.calculate(alignment.getSequencesArray(),
                                 0,
                                 alignment.getWidth(),
                                 hconsensus);
 
-          System.out.println("Consensus took " +
-                             (System.currentTimeMillis() - t) + "ms");
-
           for (int i = 0; i < aWidth; i++)
           {
             float value = 0;
             if (ignoreGapsInConsensusCalculation)
+          {
               value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
                   floatValue();
+          }
             else
+          {
               value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
                   floatValue();
+          }
 
             String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
             String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
@@ -494,16 +552,23 @@ public class AlignViewport
             }
 
             mouseOver += ( (int) value + "%");
-            consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+              value);
           }
 
 
           if (globalColourScheme != null)
+        {
             globalColourScheme.setConsensus(hconsensus);
+        }
 
         }
         catch (OutOfMemoryError error)
         {
+          alignment.deleteAnnotation(consensus);
+
+          consensus = null;
+          hconsensus = null;
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
             public void run()
@@ -520,36 +585,49 @@ public class AlignViewport
           System.out.println("Consensus calculation: " + error);
           System.gc();
         }
+        UPDATING_CONSENSUS = false;
+        updatingConsensus = false;
 
         if (ap != null)
         {
-          ap.annotationPanel.repaint();
+        ap.paintAlignment(true);
         }
-
-
-        updatingConsensus = false;
       }
     }
     /**
      * get the consensus sequence as displayed under the PID consensus annotation row.
      * @return consensus sequence as a new sequence object
      */
-    public SequenceI getConsensusSeq() {
+  public SequenceI getConsensusSeq()
+  {
       if (consensus==null)
+    {
         updateConsensus(null);
+    }
       if (consensus==null)
+    {
         return null;
+    }
       StringBuffer seqs=new StringBuffer();
-      for (int i=0; i<consensus.annotations.length; i++) {
-        if (consensus.annotations[i]!=null) {
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      if (consensus.annotations[i] != null)
+      {
           if (consensus.annotations[i].description.charAt(0) == '[')
+        {
             seqs.append(consensus.annotations[i].description.charAt(1));
+        }
           else
+        {
             seqs.append(consensus.annotations[i].displayCharacter);
         }
       }
+    }
+
       SequenceI sq = new Sequence("Consensus", seqs.toString());
-      sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    sq.setDescription("Percentage Identity Consensus " +
+                      ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
+                       ""));
       return sq;
     }
     /**
@@ -1187,7 +1265,8 @@ public class AlignViewport
       updateConsensus(ap);
       if(globalColourScheme!=null)
       {
-        globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+                                      ignoreGapsInConsensusCalculation);
       }
     }
 
@@ -1210,7 +1289,9 @@ public class AlignViewport
     public void hideSelectedColumns()
     {
       if (colSel.size() < 1)
+    {
         return;
+    }
 
       colSel.hideSelectedColumns();
       setSelectionGroup(null);
@@ -1222,17 +1303,58 @@ public class AlignViewport
     public void hideColumns(int start, int end)
     {
       if(start==end)
+    {
         colSel.hideColumns(start);
+    }
       else
+    {
         colSel.hideColumns(start, end);
+    }
 
       hasHiddenColumns = true;
     }
 
+    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+    {
+      int sSize = sg.getSize();
+      if(sSize < 2)
+    {
+        return;
+    }
+
+      if(hiddenRepSequences==null)
+    {
+        hiddenRepSequences = new Hashtable();
+    }
+
+       hiddenRepSequences.put(repSequence, sg);
+
+      //Hide all sequences except the repSequence
+      SequenceI [] seqs = new SequenceI[sSize-1];
+      int index = 0;
+      for(int i=0; i<sSize; i++)
+    {
+        if(sg.getSequenceAt(i)!=repSequence)
+        {
+          if(index==sSize-1)
+        {
+            return;
+        }
+
+          seqs[index++] = sg.getSequenceAt(i);
+        }
+    }
+
+      hideSequence(seqs);
+
+    }
+
     public void hideAllSelectedSeqs()
     {
-      if (selectionGroup == null)
+    if (selectionGroup == null || selectionGroup.getSize()<1)
+    {
         return;
+    }
 
       SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
@@ -1246,8 +1368,9 @@ public class AlignViewport
       if(seq!=null)
       {
         for (int i = 0; i < seq.length; i++)
+        {
           alignment.getHiddenSequences().hideSequence(seq[i]);
-
+        }
         hasHiddenRows = true;
         firePropertyChange("alignment", null, alignment.getSequences());
       }
@@ -1255,7 +1378,8 @@ public class AlignViewport
 
     public void showSequence(int index)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index
+          , hiddenRepSequences);
       if(tmp.size()>0)
       {
         if(selectionGroup==null)
@@ -1274,15 +1398,19 @@ public class AlignViewport
       }
 
       if(alignment.getHiddenSequences().getSize()<1)
+    {
         hasHiddenRows = false;
     }
+  }
 
     public void showColumn(int col)
     {
       colSel.revealHiddenColumns(col);
       if(colSel.getHiddenColumns()==null)
+    {
         hasHiddenColumns = false;
     }
+  }
 
     public void showAllHiddenColumns()
     {
@@ -1299,7 +1427,7 @@ public class AlignViewport
           selectionGroup = new SequenceGroup();
           selectionGroup.setEndRes(alignment.getWidth()-1);
         }
-        Vector tmp = alignment.getHiddenSequences().showAll();
+        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
         for(int t=0; t<tmp.size(); t++)
         {
           selectionGroup.addSequence(
@@ -1308,23 +1436,28 @@ public class AlignViewport
         }
         firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
+        hiddenRepSequences = null;
       }
     }
 
+
+
     public void invertColumnSelection()
     {
-      int column;
       for(int i=0; i<alignment.getWidth(); i++)
       {
-        column = i;
-
-        if(colSel.contains(column))
-          colSel.removeElement(column);
+        if(colSel.contains(i))
+      {
+          colSel.removeElement(i);
+      }
         else
-          colSel.addElement(column);
-
+        {
+          if (!hasHiddenColumns || colSel.isVisible(i))
+          {
+            colSel.addElement(i);
+          }
+        }
       }
-
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1333,8 +1466,10 @@ public class AlignViewport
     }
 
     /**
-     * This method returns the a new SequenceI [] with
-     * the selection sequence and start and end points adjusted
+     * This method returns an array of new SequenceI objects 
+     * derived from the whole alignment or just the current
+     * selection with start and end points adjusted
+     * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
      * @return String[]
      */
     public SequenceI[] getSelectionAsNewSequence()
@@ -1342,13 +1477,38 @@ public class AlignViewport
       SequenceI[] sequences;
 
       if (selectionGroup == null)
+    {
         sequences = alignment.getSequencesArray();
+        AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); 
+        for (int i=0; i<sequences.length; i++)
+        {
+          sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
+        }
+    }
       else
+    {
         sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    }
 
       return sequences;
     }
-
+    /**
+     * get the currently selected sequence objects or all the sequences in the alignment.
+     * @return array of references to sequence objects
+     */
+    public SequenceI[] getSequenceSelection()
+    {
+      SequenceI[] sequences;
+      if (selectionGroup==null)
+      {
+        sequences = alignment.getSequencesArray();
+      }
+      else
+      {
+        sequences = selectionGroup.getSequencesInOrder(alignment);
+      }
+      return sequences;
+    }
     /**
      * This method returns the visible alignment as text, as
      * seen on the GUI, ie if columns are hidden they will not
@@ -1357,7 +1517,8 @@ public class AlignViewport
      * which contain hidden columns.
      * @return String[]
      */
-    public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+  public jalview.datamodel.CigarArray getViewAsCigars(boolean
+      selectedRegionOnly)
     {
       CigarArray selection=null;
       SequenceI [] seqs= null;
@@ -1365,7 +1526,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
@@ -1383,7 +1544,8 @@ public class AlignViewport
       }
       selection=new CigarArray(selseqs);
       // now construct the CigarArray operations
-      if (hasHiddenColumns) {
+    if (hasHiddenColumns)
+    {
         Vector regions = colSel.getHiddenColumns();
         int [] region;
         int hideStart, hideEnd;
@@ -1394,34 +1556,50 @@ public class AlignViewport
           hideStart = region[0];
           hideEnd = region[1];
           // edit hidden regions to selection range
-          if(hideStart<last) {
+        if (hideStart < last)
+        {
             if (hideEnd > last)
             {
               hideStart = last;
-            } else
+          }
+          else
+          {
               continue;
           }
+        }
 
           if (hideStart>end)
+        {
             break;
+        }
 
           if (hideEnd>end)
+        {
             hideEnd=end;
+        }
 
           if (hideStart>hideEnd)
+        {
             break;
+        }
           /**
            * form operations...
            */
           if (last<hideStart)
+        {
             selection.addOperation(CigarArray.M, hideStart-last);
+        }
           selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
           last = hideEnd+1;
         }
         // Final match if necessary.
         if (last<end)
+      {
           selection.addOperation(CigarArray.M, end-last+1);
-      } else {
+      }
+    }
+    else
+    {
         selection.addOperation(CigarArray.M, end-start+1);
       }
       return selection;
@@ -1432,15 +1610,18 @@ public class AlignViewport
      * @param selectedOnly boolean true to just return the selected view
      * @return AlignmentView
      */
-    jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  {
       // JBPNote:
       // this is here because the AlignmentView constructor modifies the CigarArray
       // object. Refactoring of Cigar and alignment view representation should
       // be done to remove redundancy.
       CigarArray aligview = getViewAsCigars(selectedOnly);
-      if (aligview!=null) {
-        return new AlignmentView(aligview, 
-            (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
+    if (aligview != null)
+    {
+        return new AlignmentView(aligview,
+                               (selectedOnly && selectionGroup != null) ?
+                               selectionGroup.getStartRes() : 0);
       }
       return null;
     }
@@ -1460,7 +1641,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes()+1;
@@ -1473,18 +1654,66 @@ public class AlignViewport
       }
 
       selection = new String[iSize];
-      if (hasHiddenColumns) {
+    if (hasHiddenColumns)
+    {
         selection = colSel.getVisibleSequenceStrings(start, end, seqs);
-      } else {
+    }
+    else
+    {
         for(i=0; i<iSize; i++)
         {
-          selection[i] = seqs[i].getSequence(start, end);
+          selection[i] = seqs[i].getSequenceAsString(start, end);
         }
 
       }
       return selection;
     }
 
+  public int [][] getVisibleRegionBoundaries(int min, int max)
+  {
+    Vector regions = new Vector();
+    int start = min;
+    int end = max;
+
+    do
+    {
+      if (hasHiddenColumns)
+      {
+        if (start == 0)
+        {
+          start = colSel.adjustForHiddenColumns(start);
+        }
+
+        end = colSel.getHiddenBoundaryRight(start);
+        if (start == end)
+        {
+          end = max;
+        }
+        if (end > max)
+        {
+          end = max;
+        }
+      }
+
+      regions.addElement(new int[]
+                         {start, end});
+
+      if (hasHiddenColumns)
+      {
+        start = colSel.adjustForHiddenColumns(end);
+        start = colSel.getHiddenBoundaryLeft(start) + 1;
+      }
+    }
+    while (end < max);
+
+    int[][] startEnd = new int[regions.size()][2];
+
+    regions.copyInto(startEnd);
+
+    return startEnd;
+
+  }
+
     public boolean getShowHiddenMarkers()
     {
       return showHiddenMarkers;
@@ -1498,9 +1727,141 @@ public class AlignViewport
     public String getSequenceSetId()
     {
       if(sequenceSetID==null)
+    {
         sequenceSetID =  alignment.hashCode()+"";
+    }
 
       return sequenceSetID;
     }
 
+    public void alignmentChanged(AlignmentPanel ap)
+    {
+        if (padGaps)
+    {
+          alignment.padGaps();
+    }
+
+        if (hconsensus != null && autoCalculateConsensus)
+        {
+          updateConsensus(ap);
+          updateConservation(ap);
+        }
+
+        //Reset endRes of groups if beyond alignment width
+        int alWidth = alignment.getWidth();
+        Vector groups = alignment.getGroups();
+        if(groups!=null)
+        {
+          for(int i=0; i<groups.size(); i++)
+          {
+            SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+            if(sg.getEndRes()>alWidth)
+        {
+              sg.setEndRes(alWidth-1);
+          }
+        }
+    }
+
+        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+    {
+          selectionGroup.setEndRes(alWidth-1);
+    }
+
+        resetAllColourSchemes();
+
+       // alignment.adjustSequenceAnnotations();
+    }
+
+
+    void resetAllColourSchemes()
+    {
+      ColourSchemeI cs = globalColourScheme;
+      if(cs!=null)
+      {
+        if (cs instanceof ClustalxColourScheme)
+        {
+          ( (ClustalxColourScheme) cs).
+              resetClustalX(alignment.getSequences(),
+                            alignment.getWidth());
+        }
+
+        cs.setConsensus(hconsensus);
+        if (cs.conservationApplied())
+        {
+          Alignment al = (Alignment) alignment;
+          Conservation c = new Conservation("All",
+                                            ResidueProperties.propHash, 3,
+                                            al.getSequences(), 0,
+                                            al.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, ConsPercGaps);
+
+          cs.setConservation(c);
+        }
+      }
+
+      int s, sSize = alignment.getGroups().size();
+      for(s=0; s<sSize; s++)
+      {
+        SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
+        if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+        {
+          ((ClustalxColourScheme)sg.cs).resetClustalX(
+              sg.getSequences(hiddenRepSequences), sg.getWidth());
+        }
+        sg.recalcConservation();
+      }
+    }
+
+
+    public Color getSequenceColour(SequenceI seq)
+    {
+      if(sequenceColours==null || !sequenceColours.containsKey(seq))
+    {
+        return Color.white;
+    }
+      else
+    {
+        return (Color)sequenceColours.get(seq);
+    }
+  }
+
+    public void setSequenceColour(SequenceI seq, Color col)
+    {
+      if(sequenceColours==null)
+    {
+        sequenceColours = new Hashtable();
+    }
+
+      if(col == null)
+    {
+        sequenceColours.remove(seq);
+    }
+      else
+    {
+        sequenceColours.put(seq, col);
+    }
+    }
+    /**
+     * returns the visible column regions of the alignment
+     * @param selectedRegionOnly true to just return the contigs intersecting with the selected area
+     * @return
+     */
+    public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
+      int[] viscontigs=null;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        end = alignment.getWidth();
+      }
+      viscontigs = colSel.getVisibleContigs(start, end);
+      return viscontigs;
+    }
+
+
 }