X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=9af5ac2d3f89c01d24bc18ed236b4d7d16fdfcfa;hb=c564d188c1a8106d866651eba5c4cf60fbc0c232;hp=1b3af30457edc9f103bd93f1815d8c9c4d3e2089;hpb=14ff1fd59357c8967a6f6d673e48ff0516bce5d6;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
old mode 100755
new mode 100644
index 1b3af30..9af5ac2
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
 
@@ -23,11 +22,14 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
+import jalview.api.AlignViewportI;
 import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
 
-public class AlignViewport
+public class AlignViewport implements AlignViewportI, SelectionSource, VamsasSource
 {
   int startRes;
 
@@ -116,7 +118,9 @@ public class AlignViewport
   AlignmentAnnotation conservation;
 
   AlignmentAnnotation quality;
+
   AlignmentAnnotation[] groupConsensus;
+
   AlignmentAnnotation[] groupConservation;
 
   boolean autocalculateConsensus = true;
@@ -128,7 +132,7 @@ public class AlignViewport
 
   boolean ignoreGapsInConsensusCalculation = false;
 
-  jalview.bin.JalviewLite applet;
+  public jalview.bin.JalviewLite applet;
 
   Hashtable sequenceColours;
 
@@ -141,6 +145,13 @@ public class AlignViewport
   String sequenceSetID;
 
   Hashtable hiddenRepSequences;
+  
+  public void finalize() {
+    applet=null;
+    quality=null;
+    alignment=null;
+    colSel=null;
+  }
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
@@ -150,43 +161,53 @@ public class AlignViewport
     this.endRes = al.getWidth() - 1;
     this.startSeq = 0;
     this.endSeq = al.getHeight() - 1;
-    if (applet!=null)
+    if (applet != null)
     {
       // get the width and height scaling factors if they were specified
       String param = applet.getParameter("widthScale");
-      if (param!=null)
+      if (param != null)
       {
-        try {
+        try
+        {
           widthScale = new Float(param).floatValue();
         } catch (Exception e)
         {
         }
-        if (widthScale<=1.0)
+        if (widthScale <= 1.0)
         {
-          System.err.println("Invalid alignment character width scaling factor ("+widthScale+"). Ignoring.");
+          System.err
+                  .println("Invalid alignment character width scaling factor ("
+                          + widthScale + "). Ignoring.");
           widthScale = 1;
         }
         if (applet.debug)
         {
-          System.err.println("Alignment character width scaling factor is now "+widthScale);
+          System.err
+                  .println("Alignment character width scaling factor is now "
+                          + widthScale);
         }
       }
       param = applet.getParameter("heightScale");
-      if (param!=null)
+      if (param != null)
       {
-        try {
+        try
+        {
           heightScale = new Float(param).floatValue();
         } catch (Exception e)
         {
         }
-        if (heightScale<=1.0)
+        if (heightScale <= 1.0)
         {
-          System.err.println("Invalid alignment character height scaling factor ("+heightScale+"). Ignoring.");
+          System.err
+                  .println("Invalid alignment character height scaling factor ("
+                          + heightScale + "). Ignoring.");
           heightScale = 1;
         }
         if (applet.debug)
         {
-          System.err.println("Alignment character height scaling factor is now "+heightScale);
+          System.err
+                  .println("Alignment character height scaling factor is now "
+                          + heightScale);
         }
       }
     }
@@ -196,43 +217,19 @@ public class AlignViewport
 
     if (applet != null)
     {
-      String param = applet.getParameter("showFullId");
-      if (param != null)
-      {
-        showJVSuffix = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showAnnotation");
-      if (param != null)
-      {
-        showAnnotation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showConservation");
-      if (param != null)
-      {
-        showConservation = Boolean.valueOf(param).booleanValue();
-      }
+      showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
 
-      param = applet.getParameter("showQuality");
-      if (param != null)
-      {
-        showQuality = Boolean.valueOf(param).booleanValue();
-      }
+      showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
+      
+      showConservation = applet.getDefaultParameter("showConservation", showConservation);
+      
+      showQuality = applet.getDefaultParameter("showQuality", showQuality);
 
-      param = applet.getParameter("showConsensus");
-      if (param != null)
-      {
-        showConsensus = Boolean.valueOf(param).booleanValue();
-      }
+      showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
 
-      param = applet.getParameter("showUnconserved");
-      if (param != null)
-      {
-        this.showUnconserved = Boolean.valueOf(param).booleanValue();
-      }
+      showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
 
-      param = applet.getParameter("upperCase");
+      String param = applet.getParameter("upperCase");
       if (param != null)
       {
         if (param.equalsIgnoreCase("bold"))
@@ -240,12 +237,21 @@ public class AlignViewport
           upperCasebold = true;
         }
       }
-      param = applet.getParameter("sortByTree");
-      if (param != null)
-      {
-        sortByTree=Boolean.valueOf(param).booleanValue();
-      }
+      sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+      followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
+      followSelection = followHighlight;
 
+      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+
+      normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+
+      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
+      
+      showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
+        
+      showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
+      
     }
 
     if (applet != null)
@@ -360,15 +366,17 @@ public class AlignViewport
 
         UPDATING_CONSERVATION = true;
 
-        int alWidth = alignment.getWidth();
+        int alWidth = (alignment==null) ? -1 : alignment.getWidth();
         if (alWidth < 0)
         {
+          updatingConservation = false;
+          UPDATING_CONSERVATION = false;
           return;
         }
 
         Conservation cons = new jalview.analysis.Conservation("All",
-                jalview.schemes.ResidueProperties.propHash, 3, alignment
-                        .getSequences(), 0, alWidth - 1);
+                jalview.schemes.ResidueProperties.propHash, 3,
+                alignment.getSequences(), 0, alWidth - 1);
 
         cons.calculate();
         cons.verdict(false, ConsPercGaps);
@@ -391,7 +399,7 @@ public class AlignViewport
         maxR = 1.0f - minR;
         maxG = 0.9f - minG;
         maxB = 0f - minB; // scalable range for colouring both Conservation and
-                          // Quality
+        // Quality
 
         float min = 0f;
         float max = 11f;
@@ -428,7 +436,8 @@ public class AlignViewport
           {
             value = 10;
           }
-          // TODO - refactor to use a graduatedColorScheme to calculate the histogram colors.
+          // TODO - refactor to use a graduatedColorScheme to calculate the
+          // histogram colors.
           float vprop = value - min;
           vprop /= max;
           conservation.annotations[i] = new Annotation(String.valueOf(c),
@@ -442,10 +451,10 @@ public class AlignViewport
             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)));
           }
         }
       } catch (OutOfMemoryError error)
@@ -470,15 +479,22 @@ public class AlignViewport
   ConservationThread conservationThread;
 
   ConsensusThread consensusThread;
+  
+//  StrucConsensusThread strucConsensusThread;
+
 
   boolean consUpdateNeeded = false;
 
   static boolean UPDATING_CONSENSUS = false;
 
+  static boolean UPDATING_STRUC_CONSENSUS = false;
+
   static boolean UPDATING_CONSERVATION = false;
 
   boolean updatingConsensus = false;
 
+  boolean updatingStrucConsensus = false;
+
   boolean updatingConservation = false;
 
   /**
@@ -536,9 +552,11 @@ public class AlignViewport
 
       try
       {
-        int aWidth = alignment.getWidth();
+        int aWidth = alignment==null ? -1 : alignment.getWidth();
         if (aWidth < 0)
         {
+          UPDATING_CONSENSUS = false;
+          updatingConsensus = false;
           return;
         }
 
@@ -546,9 +564,13 @@ public class AlignViewport
         consensus.annotations = new Annotation[aWidth];
 
         hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
-                .getWidth(), hconsensus, includeAllConsensusSymbols);
-        AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols);
+        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+                alignment.getWidth(), hconsensus, true); // always calculate the
+                                                         // full profile
+        updateAnnotation(true);
+        //AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
+        //        ignoreGapsInConsensusCalculation,
+        //        true);
         
         if (globalColourScheme != null)
         {
@@ -572,6 +594,28 @@ public class AlignViewport
         ap.paintAlignment(true);
       }
     }
+
+    /**
+     * update the consensus annotation from the sequence profile data using
+     * current visualization settings.
+     */
+    public void updateAnnotation()
+    {
+      updateAnnotation(false);
+    }
+
+    protected void updateAnnotation(boolean immediate)
+    {
+      // TODO: make calls thread-safe, so if another thread calls this method,
+      // it will either return or wait until one calculation is finished.
+      if (immediate
+              || (!updatingConsensus && consensus != null && hconsensus != null))
+      {
+        AAFrequency.completeConsensus(consensus, hconsensus, 0,
+                hconsensus.length, ignoreGapsInConsensusCalculation,
+                showSequenceLogo);
+      }
+    }
   }
 
   /**
@@ -584,6 +628,10 @@ public class AlignViewport
   {
     if (consensus == null)
     {
+      updateConsensus(null);
+    }
+    if (consensus == null)
+    {
       return null;
     }
     StringBuffer seqs = new StringBuffer();
@@ -709,7 +757,7 @@ public class AlignViewport
 
   protected FeatureSettings featureSettings = null;
 
-  private float heightScale=1,widthScale=1;
+  private float heightScale = 1, widthScale = 1;
 
   public void setFont(Font f)
   {
@@ -721,14 +769,14 @@ public class AlignViewport
     }
 
     java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
-    setCharHeight((int)(heightScale*fm.getHeight()));
-    charWidth = (int)(widthScale*fm.charWidth('M'));
+    setCharHeight((int) (heightScale * fm.getHeight()));
+    charWidth = (int) (widthScale * fm.charWidth('M'));
 
     if (upperCasebold)
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
       fm = nullFrame.getGraphics().getFontMetrics(f2);
-      charWidth = (int)(widthScale*(fm.stringWidth("MMMMMMMMMMM") / 10));
+      charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
     }
   }
 
@@ -955,7 +1003,7 @@ public class AlignViewport
    * Property change listener for changes in alignment
    * 
    * @param listener
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void addPropertyChangeListener(
           java.beans.PropertyChangeListener listener)
@@ -967,7 +1015,7 @@ public class AlignViewport
    * DOCUMENT ME!
    * 
    * @param listener
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
@@ -979,11 +1027,11 @@ public class AlignViewport
    * Property change listener for changes in alignment
    * 
    * @param prop
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param oldvalue
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param newvalue
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void firePropertyChange(String prop, Object oldvalue,
           Object newvalue)
@@ -1103,7 +1151,31 @@ public class AlignViewport
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
+  public void showSequence(int index)
+  {
+    Vector tmp = alignment.getHiddenSequences().showSequence(index,
+            hiddenRepSequences);
+    if (tmp.size() > 0)
+    {
+      if (selectionGroup == null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
+      }
 
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      sendSelection();
+    }
+
+    if (alignment.getHiddenSequences().getSize() < 1)
+    {
+      hasHiddenRows = false;
+    }
+  }
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
@@ -1137,6 +1209,7 @@ public class AlignViewport
       firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
       hiddenRepSequences = null;
+      sendSelection();
     }
   }
 
@@ -1167,6 +1240,7 @@ public class AlignViewport
 
     return sequences;
   }
+
   /**
    * get the currently selected sequence objects or all the sequences in the
    * alignment.
@@ -1175,8 +1249,8 @@ public class AlignViewport
    */
   public SequenceI[] getSequenceSelection()
   {
-    SequenceI[] sequences=null;
-    if (selectionGroup!=null)
+    SequenceI[] sequences = null;
+    if (selectionGroup != null)
     {
       sequences = selectionGroup.getSequencesInOrder(alignment);
     }
@@ -1186,6 +1260,7 @@ public class AlignViewport
     }
     return sequences;
   }
+
   /**
    * This method returns the visible alignment as text, as seen on the GUI, ie
    * if columns are hidden they will not be returned in the result. Use this for
@@ -1197,90 +1272,7 @@ public class AlignViewport
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
-    CigarArray selection = null;
-    SequenceI[] seqs = null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if (selectedRegionOnly && selectionGroup != null)
-    {
-      iSize = selectionGroup.getSize();
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes(); // inclusive for start and end in
-                                        // SeqCigar constructor
-    }
-    else
-    {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth() - 1;
-    }
-    SeqCigar[] selseqs = new SeqCigar[iSize];
-    for (i = 0; i < iSize; i++)
-    {
-      selseqs[i] = new SeqCigar(seqs[i], start, end);
-    }
-    selection = new CigarArray(selseqs);
-    // now construct the CigarArray operations
-    if (hasHiddenColumns)
-    {
-      Vector regions = colSel.getHiddenColumns();
-      int[] region;
-      int hideStart, hideEnd;
-      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 (hideEnd > last)
-          {
-            hideStart = last;
-          }
-          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
-    {
-      selection.addOperation(CigarArray.M, end - start + 1);
-    }
-    return selection;
+    return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
   }
 
   /**
@@ -1288,26 +1280,28 @@ public class AlignViewport
    * to an analysis function
    * 
    * @param selectedOnly
-   *                boolean true to just return the selected view
+   *          boolean true to just return the selected view
    * @return AlignmentView
    */
   jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  {    
+    return getAlignmentView(selectedOnly, false);
+  }
+  
+  /**
+   * 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
+   * @param markGroups
+   *          boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true) 
+   * @return AlignmentView
+   */
+  public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
   {
-    // 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);
-    }
-    return null;
+    return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
   }
-
   /**
    * This method returns the visible alignment as text, as seen on the GUI, ie
    * if columns are hidden they will not be returned in the result. Use this for
@@ -1438,6 +1432,20 @@ public class AlignViewport
 
     return sequenceSetID;
   }
+  /**
+   * unique viewId for synchronizing state (e.g. with stored Jalview Project)
+   * 
+   */
+  private String viewId = null;
+
+  public String getViewId()
+  {
+    if (viewId == null)
+    {
+      viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
+    }
+    return viewId;
+  }
 
   public void alignmentChanged(AlignmentPanel ap)
   {
@@ -1490,8 +1498,8 @@ public class AlignViewport
       {
         Alignment al = (Alignment) alignment;
         Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0, al
-                        .getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
         c.calculate();
         c.verdict(false, ConsPercGaps);
 
@@ -1505,8 +1513,8 @@ public class AlignViewport
       SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
       if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
-                .getSequences(hiddenRepSequences), sg.getWidth());
+        ((ClustalxColourScheme) sg.cs).resetClustalX(
+                sg.getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }
@@ -1514,7 +1522,6 @@ public class AlignViewport
 
   boolean centreColumnLabels;
 
-  
   public boolean getCentreColumnLabels()
   {
     return centreColumnLabels;
@@ -1536,19 +1543,80 @@ public class AlignViewport
       }
     }
   }
-  public boolean followHighlight=false;
-  public boolean getFollowHighlight() {
+
+  public boolean followHighlight = true;
+
+  public boolean getFollowHighlight()
+  {
     return followHighlight;
   }
+
+  public boolean followSelection = true;
+
+  /**
+   * @return true if view selection should always follow the selections
+   *         broadcast by other selection sources
+   */
+  public boolean getFollowSelection()
+  {
+    return followSelection;
+  }
+
+  private long sgrouphash = -1, colselhash = -1;
+
+  /**
+   * checks current SelectionGroup against record of last hash value, and
+   * updates record.
+   * 
+   * @return true if SelectionGroup changed since last call
+   */
+  boolean isSelectionGroupChanged()
+  {
+    int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
+    if (hc != sgrouphash)
+    {
+      sgrouphash = hc;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * checks current colsel against record of last hash value, and updates
+   * record.
+   * 
+   * @return true if colsel changed since last call
+   */
+  boolean isColSelChanged()
+  {
+    int hc = (colSel == null) ? -1 : colSel.hashCode();
+    if (hc != colselhash)
+    {
+      colselhash = hc;
+      return true;
+    }
+    return false;
+  }
+  public void sendSelection()
+  {
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(applet).sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
+  }
+
+
+
+
   /**
    * show non-conserved residues only
    */
-  public boolean showUnconserved=false;
+  public boolean showUnconserved = false;
 
   /**
    * when set, alignment should be reordered according to a newly opened tree
    */
-  public boolean sortByTree=false;
+  public boolean sortByTree = false;
 
   /**
    * @return the showUnconserved
@@ -1559,7 +1627,8 @@ public class AlignViewport
   }
 
   /**
-   * @param showUnconserved the showUnconserved to set
+   * @param showNonconserved
+   *          the showUnconserved to set
    */
   public void setShowunconserved(boolean displayNonconserved)
   {
@@ -1567,30 +1636,29 @@ public class AlignViewport
   }
 
   /**
-   * consensus annotation includes all percentage for all symbols in column
-   * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible)  
-   */
-  private boolean includeAllConsensusSymbols=false;
-  
-  /**
    * should conservation rows be shown for groups
-   * DISABLED FOR 2.5 RELEASE (bug 62446)
    */
   boolean showGroupConservation = false;
+
   /**
    * should consensus rows be shown for groups
-   * DISABLED FOR 2.5 RELEASE (bug 62446)
    */
   boolean showGroupConsensus = false;
+
   /**
    * should consensus profile be rendered by default
-   * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible)  
    */
   public boolean showSequenceLogo = false;
   /**
+   * should consensus profile be rendered normalised to row height
+   */
+  public  boolean normaliseSequenceLogo = false;
+
+  /**
    * should consensus histograms be rendered by default
    */
   public boolean showConsensusHistogram = true;
+
   /**
    * @return the showConsensusProfile
    */
@@ -1598,34 +1666,167 @@ public class AlignViewport
   {
     return showSequenceLogo;
   }
+
   /**
-   * @param showSequenceLogo the new value
+   * @param showSequenceLogo
+   *          the new value
+   */
   public void setShowSequenceLogo(boolean showSequenceLogo)
   {
+    if (showSequenceLogo != this.showSequenceLogo)
+    {
+      // TODO: decouple settings setting from calculation when refactoring
+      // annotation update method from alignframe to viewport
+      this.showSequenceLogo = showSequenceLogo;
+      if (consensusThread != null)
+      {
+        consensusThread.updateAnnotation();
+      }
+    }
     this.showSequenceLogo = showSequenceLogo;
   }
+
+  /**
+   * @param showConsensusHistogram
+   *          the showConsensusHistogram to set
+   */
+  public void setShowConsensusHistogram(boolean showConsensusHistogram)
+  {
+    this.showConsensusHistogram = showConsensusHistogram;
+  }
+
+  /**
+   * @return the showGroupConservation
+   */
+  public boolean isShowGroupConservation()
+  {
+    return showGroupConservation;
+  }
+
+  /**
+   * @param showGroupConservation
+   *          the showGroupConservation to set
+   */
+  public void setShowGroupConservation(boolean showGroupConservation)
+  {
+    this.showGroupConservation = showGroupConservation;
+  }
+
+  /**
+   * @return the showGroupConsensus
    */
+  public boolean isShowGroupConsensus()
+  {
+    return showGroupConsensus;
+  }
+
   /**
-   * @param showGroupConsensus the showGroupConsensus to set
+   * @param showGroupConsensus
+   *          the showGroupConsensus to set
    */
   public void setShowGroupConsensus(boolean showGroupConsensus)
   {
     this.showGroupConsensus = showGroupConsensus;
   }
+
   /**
-   * @return the includeAllConsensusSymbols
+   * 
+   * @return flag to indicate if the consensus histogram should be rendered by
+   *         default
    */
-  public boolean isIncludeAllConsensusSymbols()
+  public boolean isShowConsensusHistogram()
   {
-    return false;
+    return this.showConsensusHistogram;
+  }
+
+  /**
+   * synthesize a column selection if none exists so it covers the given
+   * selection group. if wholewidth is false, no column selection is made if the
+   * selection group covers the whole alignment width.
+   * 
+   * @param sg
+   * @param wholewidth
+   */
+  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+  {
+    int sgs, sge;
+    if (sg != null
+            && (sgs = sg.getStartRes()) >= 0
+            && sg.getStartRes() <= (sge = sg.getEndRes())
+            && (colSel == null || colSel.getSelected() == null || colSel
+                    .getSelected().size() == 0))
+    {
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+      {
+        // do nothing
+        return;
+      }
+      if (colSel == null)
+      {
+        colSel = new ColumnSelection();
+      }
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+      {
+        colSel.addElement(cspos);
+      }
+    }
+  }
+
+  @Override
+  public boolean hasHiddenColumns()
+  {
+    return hasHiddenColumns;
   }
   
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  public boolean isCalcInProgress()
+  {
+    // TODO generalise to iterate over all calculators associated with av
+    return updatingConsensus || updatingConservation || updatingStrucConsensus;
+  }
+
+  public boolean isCalculationInProgress(
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    if (!alignmentAnnotation.autoCalculated)
+      return false;
+    if ((updatingConsensus && consensus==alignmentAnnotation)
+            || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
+            // || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
+            )
+    {
+      return true;
+    }
+    return false;
+  }
+
   /**
    * 
-   * @return flag to indicate if the consensus histogram should be rendered by default
+   * @return true if alignment characters should be displayed 
    */
-  public boolean isShowConsensusHistogram()
+  public boolean isValidCharWidth()
   {
-    return this.showConsensusHistogram;
+    return validCharWidth;
+  }
+
+  @Override
+  public Hashtable[] getSequenceConsensusHash()
+  {
+    return hconsensus;
+  }
+
+  @Override
+  public Hashtable[] getRnaStructureConsensusHash()
+  {
+    return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus;
   }
 }