X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=43831a247ac8504410961eab86aff4710372c95b;hb=d0b7395c10aec7c5da5a5662fc69783ec78fae8d;hp=88a0b0f6a528dfe41ab1489bbc702df33ba02b4d;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 88a0b0f..43831a2 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/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
@@ -36,7 +36,6 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-
   boolean cursorMode = false;
 
   boolean showJVSuffix = true;
@@ -79,15 +78,14 @@ public class AlignViewport
   boolean scaleRightWrapped = true;
 
   // The following vector holds the features which are
- // currently visible, in the correct order or rendering
+  // currently visible, in the correct order or rendering
   public Hashtable featuresDisplayed;
 
   boolean hasHiddenColumns = false;
   boolean hasHiddenRows = false;
   boolean showHiddenMarkers = true;
 
-
-  public Hashtable [] hconsensus;
+  public Hashtable[] hconsensus;
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
   AlignmentAnnotation quality;
@@ -96,7 +94,8 @@ public class AlignViewport
 
   public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+      PropertyChangeSupport(this);
 
   boolean ignoreGapsInConsensusCalculation = false;
 
@@ -123,8 +122,10 @@ public class AlignViewport
     this.endSeq = al.getHeight() - 1;
     setFont(font);
 
-    if(System.getProperty("os.name").startsWith("Mac"))
+    if (System.getProperty("os.name").startsWith("Mac"))
+    {
       MAC = true;
+    }
 
     if (applet != null)
     {
@@ -161,8 +162,10 @@ public class AlignViewport
       param = applet.getParameter("upperCase");
       if (param != null)
       {
-        if(param.equalsIgnoreCase("bold"))
+        if (param.equalsIgnoreCase("bold"))
+        {
           upperCasebold = true;
+        }
       }
 
     }
@@ -171,14 +174,16 @@ public class AlignViewport
     {
       String colour = applet.getParameter("defaultColour");
 
-      if(colour == null)
+      if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
-        if(colour !=null)
+        if (colour != null)
+        {
           colour = "User Defined";
+        }
       }
 
-      if(colour != null)
+      if (colour != null)
       {
         globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
         if (globalColourScheme != null)
@@ -187,24 +192,24 @@ public class AlignViewport
         }
       }
 
-      if(applet.getParameter("userDefinedColour")!=null)
+      if (applet.getParameter("userDefinedColour") != null)
       {
-        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+        ( (UserColourScheme) globalColourScheme).parseAppletParameter(
             applet.getParameter("userDefinedColour"));
       }
 
-      if(hconsensus==null)
+      if (hconsensus == null)
       {
-        if(!alignment.isNucleotide())
+        if (!alignment.isNucleotide())
         {
           conservation = new AlignmentAnnotation("Conservation",
-              "Conservation of total alignment less than " +
-              ConsPercGaps + "% gaps",
-              new Annotation[1], 0f,
-              11f,
-              AlignmentAnnotation.BAR_GRAPH);
+                                                 "Conservation of total alignment less than " +
+                                                 ConsPercGaps + "% gaps",
+                                                 new Annotation[1], 0f,
+                                                 11f,
+                                                 AlignmentAnnotation.BAR_GRAPH);
           conservation.hasText = true;
-
+          conservation.autoCalculated = true;
 
           if (showConservation)
           {
@@ -220,20 +225,22 @@ public class AlignViewport
                                               11f,
                                               AlignmentAnnotation.BAR_GRAPH);
             quality.hasText = true;
+            quality.autoCalculated = true;
 
             alignment.addAnnotation(quality);
           }
         }
 
         consensus = new AlignmentAnnotation("Consensus", "PID",
-                                             new Annotation[1], 0f, 100f,
-                                             AlignmentAnnotation.BAR_GRAPH);
+                                            new Annotation[1], 0f, 100f,
+                                            AlignmentAnnotation.BAR_GRAPH);
         consensus.hasText = true;
+        consensus.autoCalculated = true;
 
-         if (showConsensus)
-         {
-           alignment.addAnnotation(consensus);
-         }
+        if (showConsensus)
+        {
+          alignment.addAnnotation(consensus);
+        }
       }
     }
   }
@@ -248,8 +255,8 @@ public class AlignViewport
     return showSequenceFeatures;
   }
 
-
-  class ConservationThread extends Thread
+  class ConservationThread
+      extends Thread
   {
     AlignmentPanel ap;
     public ConservationThread(AlignmentPanel ap)
@@ -269,7 +276,7 @@ public class AlignViewport
           {
             if (ap != null)
             {
-              ap.repaint();
+              ap.paintAlignment(true);
             }
             Thread.sleep(200);
           }
@@ -281,24 +288,25 @@ public class AlignViewport
 
         UPDATING_CONSERVATION = true;
 
-
         int alWidth = alignment.getWidth();
-        if(alWidth<0)
+        if (alWidth < 0)
+        {
           return;
+        }
 
         Conservation cons = new jalview.analysis.Conservation("All",
             jalview.schemes.ResidueProperties.propHash, 3,
-            alignment.getSequences(), 0, alWidth -1);
+            alignment.getSequences(), 0, alWidth - 1);
 
         cons.calculate();
         cons.verdict(false, ConsPercGaps);
 
-        if (quality!=null)
+        if (quality != null)
         {
           cons.findQuality();
         }
 
-        char [] sequence = cons.getConsSequence().getSequence();
+        char[] sequence = cons.getConsSequence().getSequence();
         float minR;
         float minG;
         float minB;
@@ -321,7 +329,7 @@ public class AlignViewport
 
         conservation.annotations = new Annotation[alWidth];
 
-        if (quality!=null)
+        if (quality != null)
         {
           quality.graphMax = cons.qualityRange[1].floatValue();
           quality.annotations = new Annotation[alWidth];
@@ -336,11 +344,17 @@ public class AlignViewport
           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;
@@ -352,16 +366,17 @@ public class AlignViewport
                                        minB + (maxB * vprop)));
 
           // Quality calc
-          if (quality!=null)
+          if (quality != null)
           {
             value = ( (Double) cons.quality.elementAt(i)).floatValue();
             vprop = value - qmin;
             vprop /= qmax;
-            quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
-                                             value,
-                                             new Color(minR + (maxR * vprop),
-                minG + (maxG * vprop),
-                minB + (maxB * vprop)));
+            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+                ' ',
+                value,
+                new Color(minR + (maxR * vprop),
+                          minG + (maxG * vprop),
+                          minB + (maxB * vprop)));
           }
         }
       }
@@ -376,15 +391,14 @@ public class AlignViewport
       UPDATING_CONSERVATION = false;
       updatingConservation = false;
 
-      if(ap!=null)
+      if (ap != null)
       {
-        ap.repaint();
+        ap.paintAlignment(true);
       }
 
     }
   }
 
-
   ConservationThread conservationThread;
 
   ConsensusThread consensusThread;
@@ -404,8 +418,10 @@ public class AlignViewport
    */
   public void updateConservation(final AlignmentPanel ap)
   {
-    if (alignment.isNucleotide() || conservation==null)
+    if (alignment.isNucleotide() || conservation == null)
+    {
       return;
+    }
 
     conservationThread = new ConservationThread(ap);
     conservationThread.start();
@@ -420,14 +436,15 @@ public class AlignViewport
     consensusThread.start();
   }
 
-
-  class ConsensusThread extends Thread
+  class ConsensusThread
+      extends Thread
   {
     AlignmentPanel ap;
     public ConsensusThread(AlignmentPanel ap)
     {
       this.ap = ap;
     }
+
     public void run()
     {
       updatingConsensus = true;
@@ -437,7 +454,7 @@ public class AlignViewport
         {
           if (ap != null)
           {
-            ap.repaint();
+            ap.paintAlignment(true);
           }
 
           Thread.sleep(200);
@@ -448,19 +465,19 @@ public class AlignViewport
         }
       }
 
-
       UPDATING_CONSENSUS = true;
 
       try
       {
         int aWidth = alignment.getWidth();
-        if(aWidth<0)
+        if (aWidth < 0)
+        {
           return;
+        }
 
         consensus.annotations = null;
         consensus.annotations = new Annotation[aWidth];
 
-
         hconsensus = new Hashtable[aWidth];
         AAFrequency.calculate(alignment.getSequencesArray(),
                               0,
@@ -471,11 +488,15 @@ public class AlignViewport
         {
           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) + " ";
@@ -487,12 +508,14 @@ 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)
@@ -509,7 +532,7 @@ public class AlignViewport
 
       if (ap != null)
       {
-        ap.repaint();
+        ap.paintAlignment(true);
       }
     }
   }
@@ -524,21 +547,32 @@ public class AlignViewport
    */
   public SequenceI getConsensusSeq()
   {
-    if (consensus==null)
+    if (consensus == null)
+    {
       return null;
-    StringBuffer seqs=new StringBuffer();
-    for (int i=0; i<consensus.annotations.length; i++) {
-      if (consensus.annotations[i]!=null) {
+    }
+    StringBuffer seqs = new StringBuffer();
+    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;
   }
+
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -640,7 +674,7 @@ public class AlignViewport
   public void setFont(Font f)
   {
     font = f;
-    if(nullFrame == null)
+    if (nullFrame == null)
     {
       nullFrame = new java.awt.Frame();
       nullFrame.addNotify();
@@ -650,7 +684,7 @@ public class AlignViewport
     setCharHeight(fm.getHeight());
     charWidth = fm.charWidth('M');
 
-    if(upperCasebold)
+    if (upperCasebold)
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
       fm = nullFrame.getGraphics().getFontMetrics(f2);
@@ -779,8 +813,10 @@ public class AlignViewport
   public void setHiddenColumns(ColumnSelection colsel)
   {
     this.colSel = colsel;
-    if(colSel.getHiddenColumns()!=null)
+    if (colSel.getHiddenColumns() != null)
+    {
       hasHiddenColumns = true;
+    }
   }
 
   public ColumnSelection getColumnSelection()
@@ -867,10 +903,10 @@ public class AlignViewport
   {
     ignoreGapsInConsensusCalculation = b;
     updateConsensus(null);
-    if (globalColourScheme!=null)
+    if (globalColourScheme != null)
     {
       globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-          ignoreGapsInConsensusCalculation);
+                                      ignoreGapsInConsensusCalculation);
 
     }
   }
@@ -883,7 +919,7 @@ public class AlignViewport
   public void addPropertyChangeListener(
       java.beans.PropertyChangeListener listener)
   {
-      changeSupport.addPropertyChangeListener(listener);
+    changeSupport.addPropertyChangeListener(listener);
   }
 
   /**
@@ -894,7 +930,7 @@ public class AlignViewport
   public void removePropertyChangeListener(
       java.beans.PropertyChangeListener listener)
   {
-      changeSupport.removePropertyChangeListener(listener);
+    changeSupport.removePropertyChangeListener(listener);
   }
 
   /**
@@ -906,19 +942,20 @@ public class AlignViewport
    */
   public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
   {
-      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 
-
-
   public boolean getIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensusCalculation;
   }
+
   public void hideSelectedColumns()
   {
     if (colSel.size() < 1)
+    {
       return;
+    }
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
@@ -931,7 +968,9 @@ public class AlignViewport
     for (int i = 0; i < alignment.getWidth(); i++)
     {
       if (colSel.contains(i))
+      {
         colSel.removeElement(i);
+      }
       else
       {
         if (!hasHiddenColumns || colSel.isVisible(i))
@@ -942,13 +981,16 @@ public class AlignViewport
     }
   }
 
-
   public void hideColumns(int start, int end)
   {
-    if(start==end)
+    if (start == end)
+    {
       colSel.hideColumns(start);
+    }
     else
+    {
       colSel.hideColumns(start, end);
+    }
 
     hasHiddenColumns = true;
   }
@@ -956,34 +998,44 @@ public class AlignViewport
   public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
   {
     int sSize = sg.getSize();
-    if(sSize < 2)
+    if (sSize < 2)
+    {
       return;
+    }
 
-    if(hiddenRepSequences==null)
+    if (hiddenRepSequences == null)
+    {
       hiddenRepSequences = new Hashtable();
+    }
 
-     hiddenRepSequences.put(repSequence, sg);
+    hiddenRepSequences.put(repSequence, sg);
 
     //Hide all sequences except the repSequence
-    SequenceI [] seqs = new SequenceI[sSize-1];
+    SequenceI[] seqs = new SequenceI[sSize - 1];
     int index = 0;
-    for(int i=0; i<sSize; i++)
-      if(sg.getSequenceAt(i)!=repSequence)
+    for (int i = 0; i < sSize; i++)
+    {
+      if (sg.getSequenceAt(i) != repSequence)
       {
-        if(index==sSize-1)
+        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);
 
@@ -992,12 +1044,14 @@ public class AlignViewport
     setSelectionGroup(null);
   }
 
-  public void hideSequence(SequenceI [] seq)
+  public void hideSequence(SequenceI[] seq)
   {
-    if(seq!=null)
+    if (seq != null)
     {
       for (int i = 0; i < seq.length; i++)
+      {
         alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
 
       hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
@@ -1007,8 +1061,10 @@ public class AlignViewport
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-    if(colSel.getHiddenColumns()==null)
+    if (colSel.getHiddenColumns() == null)
+    {
       hasHiddenColumns = false;
+    }
   }
 
   public void showAllHiddenColumns()
@@ -1019,24 +1075,24 @@ public class AlignViewport
 
   public void showAllHiddenSeqs()
   {
-    if(alignment.getHiddenSequences().getSize()>0)
+    if (alignment.getHiddenSequences().getSize() > 0)
     {
-      if(selectionGroup==null)
+      if (selectionGroup == null)
       {
         selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth()-1);
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
       Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
-      for(int t=0; t<tmp.size(); t++)
+      for (int t = 0; t < tmp.size(); t++)
       {
         selectionGroup.addSequence(
-            (SequenceI)tmp.elementAt(t), false
+            (SequenceI) tmp.elementAt(t), false
             );
       }
       firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
       hiddenRepSequences = null;
-      }
+    }
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1054,9 +1110,13 @@ public class AlignViewport
     SequenceI[] sequences;
 
     if (selectionGroup == null)
+    {
       sequences = alignment.getSequencesArray();
+    }
     else
+    {
       sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    }
 
     return sequences;
   }
@@ -1069,13 +1129,14 @@ 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;
+    CigarArray selection = null;
+    SequenceI[] seqs = null;
     int i, iSize;
     int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
+    if (selectedRegionOnly && selectionGroup != null)
     {
       iSize = selectionGroup.getSize();
       seqs = selectionGroup.getSequencesInOrder(alignment);
@@ -1086,76 +1147,98 @@ public class AlignViewport
     {
       iSize = alignment.getHeight();
       seqs = alignment.getSequencesArray();
-      end = alignment.getWidth()-1;
+      end = alignment.getWidth() - 1;
     }
     SeqCigar[] selseqs = new SeqCigar[iSize];
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
       selseqs[i] = new SeqCigar(seqs[i], start, end);
     }
-    selection=new CigarArray(selseqs);
+    selection = new CigarArray(selseqs);
     // now construct the CigarArray operations
-    if (hasHiddenColumns) {
+    if (hasHiddenColumns)
+    {
       Vector regions = colSel.getHiddenColumns();
-      int [] region;
+      int[] region;
       int hideStart, hideEnd;
-      int last=start;
-      for (int j = 0; last<end & j < regions.size(); j++)
+      int last = start;
+      for (int j = 0; last < end & j < regions.size(); j++)
       {
         region = (int[]) regions.elementAt(j);
         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)
+        if (hideStart > end)
+        {
           break;
+        }
 
-        if (hideEnd>end)
-          hideEnd=end;
+        if (hideEnd > end)
+        {
+          hideEnd = end;
+        }
 
-        if (hideStart>hideEnd)
+        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;
+        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 {
-      selection.addOperation(CigarArray.M, end-start+1);
+      if (last < end)
+      {
+        selection.addOperation(CigarArray.M, end - last + 1);
+      }
+    }
+    else
+    {
+      selection.addOperation(CigarArray.M, end - start + 1);
     }
     return selection;
   }
+
   /**
    * return a compact representation of the current alignment selection to
    * pass to an analysis function
    * @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) {
+    if (aligview != null)
+    {
       return new AlignmentView(aligview,
-          (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
+                               (selectedOnly && selectionGroup != null) ?
+                               selectionGroup.getStartRes() : 0);
     }
     return null;
   }
+
   /**
    * This method returns the visible alignment as text, as
    * seen on the GUI, ie if columns are hidden they will not
@@ -1164,18 +1247,18 @@ public class AlignViewport
    * which contain hidden columns.
    * @return String[]
    */
-  public String [] getViewAsString(boolean selectedRegionOnly)
+  public String[] getViewAsString(boolean selectedRegionOnly)
   {
-    String [] selection = null;
-    SequenceI [] seqs= null;
+    String[] selection = null;
+    SequenceI[] seqs = null;
     int i, iSize;
     int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
+    if (selectedRegionOnly && selectionGroup != null)
     {
       iSize = selectionGroup.getSize();
       seqs = selectionGroup.getSequencesInOrder(alignment);
       start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes()+1;
+      end = selectionGroup.getEndRes() + 1;
     }
     else
     {
@@ -1186,48 +1269,48 @@ public class AlignViewport
 
     selection = new String[iSize];
 
-
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
       if (hasHiddenColumns)
       {
-           StringBuffer visibleSeq = new StringBuffer();
-           Vector regions = colSel.getHiddenColumns();
-
-           int blockStart = start, blockEnd=end;
-           int [] region;
-           int hideStart, hideEnd;
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = colSel.getHiddenColumns();
 
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd;
 
-             if(hideStart < start)
-             {
-               continue;
-             }
+        for (int j = 0; j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
 
-             blockStart = Math.min(blockStart, hideEnd+1);
-             blockEnd = Math.min(blockEnd, hideStart);
+          if (hideStart < start)
+          {
+            continue;
+          }
 
-             if(blockStart>blockEnd)
-             {
-                break;
-             }
+          blockStart = Math.min(blockStart, hideEnd + 1);
+          blockEnd = Math.min(blockEnd, hideStart);
 
+          if (blockStart > blockEnd)
+          {
+            break;
+          }
 
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
 
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
 
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        if (end > blockStart)
+        {
+          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
 
-           selection[i] = visibleSeq.toString();
+        selection[i] = visibleSeq.toString();
       }
       else
       {
@@ -1251,26 +1334,38 @@ public class AlignViewport
   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);
+    }
   }
 
   public String getSequenceSetId()
   {
     if (sequenceSetID == null)
+    {
       sequenceSetID = alignment.hashCode() + "";
+    }
 
     return sequenceSetID;
   }
@@ -1288,28 +1383,32 @@ public class AlignViewport
     //Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
     Vector groups = alignment.getGroups();
-    if(groups!=null)
+    if (groups != null)
     {
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        if(sg.getEndRes()>alWidth)
-          sg.setEndRes(alWidth-1);
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
+        {
+          sg.setEndRes(alWidth - 1);
+        }
       }
     }
 
-    if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
-      selectionGroup.setEndRes(alWidth-1);
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+    {
+      selectionGroup.setEndRes(alWidth - 1);
+    }
 
     resetAllColourSchemes();
 
-    alignment.adjustSequenceAnnotations();
+    //AW  alignment.adjustSequenceAnnotations();
   }
 
   void resetAllColourSchemes()
   {
     ColourSchemeI cs = globalColourScheme;
-    if(cs!=null)
+    if (cs != null)
     {
       if (cs instanceof ClustalxColourScheme)
       {
@@ -1334,17 +1433,16 @@ public class AlignViewport
     }
 
     int s, sSize = alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
+    for (s = 0; s < sSize; s++)
     {
-      SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
-      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(
+        ( (ClustalxColourScheme) sg.cs).resetClustalX(
             sg.getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }
   }
 
-
 }