X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=44ecf76ff963122941be68503119d9ef9e295cc6;hb=279af6f3b1803de7a1e467b83a7205df18e70d48;hp=fc96f62df9e4865a9f98ad184901cd6f49cf7007;hpb=f2b6ee8c1feb4f6a7e229ee94741ef93f0bd453d;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fc96f62..44ecf76 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,22 +1,24 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.viewmodel;
 
+import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
@@ -27,17 +29,24 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ClustalxColourScheme;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 /**
@@ -62,7 +71,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    */
   protected boolean isDataset = false;
 
-  private Hashtable hiddenRepSequences;
+  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
 
   protected ColumnSelection colSel = new ColumnSelection();
 
@@ -74,12 +83,196 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected ColourSchemeI globalColourScheme = null;
 
+  /**
+   * gui state - changes to colour scheme propagated to all groups
+   */
+  private boolean colourAppliesToAllGroups;
+
+  /**
+   * @param value
+   *          indicating if subsequent colourscheme changes will be propagated
+   *          to all groups
+   */
+  public void setColourAppliesToAllGroups(boolean b)
+  {
+    colourAppliesToAllGroups = b;
+  }
+
+  /**
+   * 
+   * 
+   * @return flag indicating if colourchanges propagated to all groups
+   */
+  public boolean getColourAppliesToAllGroups()
+  {
+    return colourAppliesToAllGroups;
+  }
+
+  boolean abovePIDThreshold = false;
+
+  /**
+   * GUI state
+   * 
+   * @return true if percent identity threshold is applied to shading
+   */
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
+
+  /**
+   * GUI state
+   * 
+   * 
+   * @param b
+   *          indicate if percent identity threshold is applied to shading
+   */
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
+
+  int threshold;
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param thresh
+   *          DOCUMENT ME!
+   */
+  public void setThreshold(int thresh)
+  {
+    threshold = thresh;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
+
+  int increment;
+
+  /**
+   * 
+   * @param inc
+   *          set the scalar for bleaching colourschemes according to degree of
+   *          conservation
+   */
+  public void setIncrement(int inc)
+  {
+    increment = inc;
+  }
+
+  /**
+   * GUI State
+   * 
+   * @return get scalar for bleaching colourschemes by conservation
+   */
+  public int getIncrement()
+  {
+    return increment;
+  }
+
+  boolean conservationColourSelected = false;
+
+  /**
+   * GUI state
+   * 
+   * @return true if conservation based shading is enabled
+   */
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
+
+  /**
+   * GUI state
+   * 
+   * @param b
+   *          enable conservation based shading
+   */
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
+  @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
+    // TODO: logic refactored from AlignFrame changeColour -
+    // autorecalc stuff should be changed to rely on the worker system
+    // check to see if we should implement a changeColour(cs) method rather than
+    // put th logic in here
+    // - means that caller decides if they want to just modify state and defer
+    // calculation till later or to do all calculations in thread.
+    // via changecolour
     globalColourScheme = cs;
+    boolean recalc=false;
+    if (cs!=null)
+    {
+      cs.setConservationApplied(recalc = getConservationSelected());
+      if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+      {
+        recalc = true;
+        cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+      } else {
+        cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+      }
+      if (recalc)
+      {
+        cs.setConsensus(hconsensus);
+        cs.setConservation(hconservation);
+      }
+      cs.alignmentChanged(alignment, hiddenRepSequences);
+    }
+    if (getColourAppliesToAllGroups())
+    {
+      for (SequenceGroup sg : getAlignment().getGroups())
+      {
+        if (cs == null)
+        {
+          sg.cs = null;
+          continue;
+        }
+        sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+        sg.setConsPercGaps(ConsPercGaps);
+        if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+                || cs instanceof Blosum62ColourScheme)
+        {
+          sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
+          recalc=true;
+        }
+        else
+        {
+          sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+        }
+
+        if (getConservationSelected())
+        {
+          sg.cs.setConservationApplied(true);
+          recalc=true;
+        }
+        else
+        {
+          sg.cs.setConservation(null);
+          // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+        }
+        if (recalc) {
+          sg.recalcConservation();
+        } else {
+          sg.cs.alignmentChanged(sg, hiddenRepSequences);
+        }
+      }
+    }
+
   }
 
+  @Override
   public ColourSchemeI getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -107,17 +300,25 @@ public abstract class AlignmentViewport implements AlignViewportI
    * view
    */
   protected Hashtable[] hStrucConsensus = null;
-
+  
+  protected Conservation hconservation = null;
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    hconservation = cons;
+  }
   /**
    * percentage gaps allowed in a column before all amino acid properties should
    * be considered unconserved
    */
   int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
+  @Override
   public int getConsPercGaps()
   {
     return ConsPercGaps;
   }
+
   @Override
   public void setSequenceConsensusHash(Hashtable[] hconsensus)
   {
@@ -181,8 +382,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (!calculator
-            .startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class))
+    if (calculator
+            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
     {
       calculator.registerWorker(new jalview.workers.ConservationThread(
               this, ap));
@@ -199,7 +400,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (!calculator.startRegisteredWorkersOfClass(ConsensusThread.class))
+    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -211,7 +412,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     if (autoCalculateStrucConsensus && strucConsensus == null
             && alignment.isNucleotide() && alignment.hasRNAStructure())
     {
-
+      // secondary structure has been added - so init the consensus line
+      initRNAStructure();
     }
 
     // see note in mantis : issue number 8585
@@ -219,8 +421,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       return;
     }
-    if (!calculator
-            .startRegisteredWorkersOfClass(StrucConsensusThread.class))
+    if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -231,6 +432,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     return calculator.isWorking();
   }
 
+  @Override
   public boolean isCalculationInProgress(
           AlignmentAnnotation alignmentAnnotation)
   {
@@ -272,10 +474,12 @@ public abstract class AlignmentViewport implements AlignViewportI
    * should consensus profile be rendered by default
    */
   protected boolean showSequenceLogo = false;
+
   /**
    * should consensus profile be rendered normalised to row height
    */
   protected boolean normaliseSequenceLogo = false;
+
   /**
    * should consensus histograms be rendered by default
    */
@@ -284,6 +488,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   /**
    * @return the showConsensusProfile
    */
+  @Override
   public boolean isShowSequenceLogo()
   {
     return showSequenceLogo;
@@ -354,6 +559,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * @return flag to indicate if the consensus histogram should be rendered by
    *         default
    */
+  @Override
   public boolean isShowConsensusHistogram()
   {
     return this.showConsensusHistogram;
@@ -364,7 +570,6 @@ public abstract class AlignmentViewport implements AlignViewportI
    */
   protected boolean showUnconserved = false;
 
-
   /**
    * when set, updateAlignment will always ensure sequences are of equal length
    */
@@ -399,6 +604,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return null or the currently selected sequence region
    */
+  @Override
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -411,6 +617,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          - group holding references to sequences in this alignment view
    * 
    */
+  @Override
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
@@ -425,6 +632,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return colSel;
@@ -434,14 +642,24 @@ public abstract class AlignmentViewport implements AlignViewportI
   {
     this.colSel = colSel;
   }
-  public Hashtable getHiddenRepSequences()
+
+  /**
+   * 
+   * @return
+   */
+  @Override
+  public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
   {
     return hiddenRepSequences;
   }
-  public void setHiddenRepSequences(Hashtable hiddenRepSequences)
+
+  @Override
+  public void setHiddenRepSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     this.hiddenRepSequences = hiddenRepSequences;
   }
+
   protected boolean hasHiddenColumns = false;
 
   public void updateHiddenColumns()
@@ -557,6 +775,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     return false;
   }
 
+  @Override
   public boolean getIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensusCalculation;
@@ -565,7 +784,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   // / property change stuff
 
   // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+  private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
           this);
 
   protected boolean showConservation = true;
@@ -574,6 +793,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
+  Hashtable sequenceColours;
 
   /**
    * Property change listener for changes in alignment
@@ -616,7 +836,6 @@ public abstract class AlignmentViewport implements AlignViewportI
   }
 
   // common hide/show column stuff
-  
 
   public void hideSelectedColumns()
   {
@@ -660,7 +879,6 @@ public abstract class AlignmentViewport implements AlignViewportI
     hasHiddenColumns = false;
   }
 
-  
   // common hide/show seq stuff
   public void showAllHiddenSeqs()
   {
@@ -715,8 +933,6 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
   }
 
-
-  
   public void hideAllSelectedSeqs()
   {
     if (selectionGroup == null || selectionGroup.getSize() < 1)
@@ -730,7 +946,6 @@ public abstract class AlignmentViewport implements AlignViewportI
 
     setSelectionGroup(null);
   }
-  
 
   public void hideSequence(SequenceI[] seq)
   {
@@ -804,7 +1019,6 @@ public abstract class AlignmentViewport implements AlignViewportI
    * broadcast selection to any interested parties
    */
   public abstract void sendSelection();
-  
 
   public void invertColumnSelection()
   {
@@ -828,7 +1042,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     // JBPNote: in applet, this method returned references to the alignment
     // sequences, and it did not honour the presence/absence of annotation
     // attached to the alignment (probably!)
-    if (selectionGroup == null)
+    if (selectionGroup == null || selectionGroup.getSize() == 0)
     {
       sequences = alignment.getSequencesArray();
       AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
@@ -854,6 +1068,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return array of references to sequence objects
    */
+  @Override
   public SequenceI[] getSequenceSelection()
   {
     SequenceI[] sequences = null;
@@ -868,7 +1083,6 @@ public abstract class AlignmentViewport implements AlignViewportI
     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
@@ -877,6 +1091,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
@@ -893,6 +1108,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          boolean true to just return the selected view
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -911,6 +1127,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          is true)
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
@@ -918,7 +1135,6 @@ public abstract class AlignmentViewport implements AlignViewportI
             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
@@ -927,6 +1143,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
     String[] selection = null;
@@ -1015,6 +1232,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     return startEnd;
 
   }
+
   /**
    * @return the padGaps
    */
@@ -1059,12 +1277,11 @@ public abstract class AlignmentViewport implements AlignViewportI
 
     // Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
-    Vector groups = alignment.getGroups();
+    List<SequenceGroup> groups = alignment.getGroups();
     if (groups != null)
     {
-      for (int i = 0; i < groups.size(); i++)
+      for (SequenceGroup sg : groups)
       {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
         if (sg.getEndRes() > alWidth)
         {
           sg.setEndRes(alWidth - 1);
@@ -1082,7 +1299,6 @@ public abstract class AlignmentViewport implements AlignViewportI
     // alignment.adjustSequenceAnnotations();
   }
 
-  
   /**
    * reset scope and do calculations for all applied colourschemes on alignment
    */
@@ -1091,13 +1307,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     ColourSchemeI cs = globalColourScheme;
     if (cs != null)
     {
-      cs.alignmentChanged(alignment);
-      // TODO: fold all recalc events for clustalX into alignmentChanged
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
-                alignment.getWidth());
-      }
+      cs.alignmentChanged(alignment, hiddenRepSequences);
 
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())
@@ -1108,14 +1318,11 @@ public abstract class AlignmentViewport implements AlignViewportI
       }
     }
 
-    int s, sSize = alignment.getGroups().size();
-    for (s = 0; s < sSize; s++)
+    for (SequenceGroup sg : alignment.getGroups())
     {
-      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
-      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+      if (sg.cs != null)
       {
-        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
-                .getSequences(hiddenRepSequences), sg.getWidth());
+        sg.cs.alignmentChanged(sg, hiddenRepSequences);
       }
       sg.recalcConservation();
     }
@@ -1131,60 +1338,271 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       if (!alignment.isNucleotide())
       {
-        if (showConservation)
+        initConservation();
+        initQuality();
+      }
+      else
+      {
+        initRNAStructure();
+      }
+      initConsensus();
+    }
+  }
+
+  private void initConsensus()
+  {
+
+    consensus = new AlignmentAnnotation("Consensus", "PID",
+            new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+    consensus.hasText = true;
+    consensus.autoCalculated = true;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(consensus);
+    }
+  }
+
+  private void initConservation()
+  {
+    if (showConservation)
+    {
+      if (conservation == null)
+      {
+        conservation = new AlignmentAnnotation("Conservation",
+                "Conservation of total alignment less than "
+                        + getConsPercGaps() + "% gaps",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
+        alignment.addAnnotation(conservation);
+      }
+    }
+  }
+  private void initQuality()
+  {
+    if (showQuality)
+    {
+      if (quality == null)
+      {
+        quality = new AlignmentAnnotation("Quality",
+                "Alignment Quality based on Blosum62 scores",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        quality.hasText = true;
+        quality.autoCalculated = true;
+        alignment.addAnnotation(quality);
+      }
+    }
+  }
+  private void initRNAStructure()
+  {
+    if (alignment.hasRNAStructure() && strucConsensus==null)
+    {
+      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+              new Annotation[1], 0f, 100f,
+              AlignmentAnnotation.BAR_GRAPH);
+      strucConsensus.hasText = true;
+      strucConsensus.autoCalculated = true;
+
+      if (showConsensus)
+      {
+        alignment.addAnnotation(strucConsensus);
+      }
+    }
+  }
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.api.AlignViewportI#calcPanelHeight()
+   */
+  public int calcPanelHeight()
+  {
+    // setHeight of panels
+    AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
+    int height = 0;
+    int charHeight = getCharHeight();
+    if (aa != null)
+    {
+      BitSet graphgrp = new BitSet();
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (aa[i] == null)
         {
-          if (conservation == null)
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                    "Conservation of total alignment less than "
-                            + getConsPercGaps() + "% gaps",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated = true;
-            alignment.addAnnotation(conservation);
-          }
+          System.err.println("Null annotation row: ignoring.");
+          continue;
         }
-        if (showQuality)
+        if (!aa[i].visible)
         {
-          if (quality == null)
+          continue;
+        }
+        if (aa[i].graphGroup > -1)
+        {
+          if (graphgrp.get(aa[i].graphGroup))
+          {
+            continue;
+          }
+          else
           {
-            quality = new AlignmentAnnotation("Quality",
-                    "Alignment Quality based on Blosum62 scores",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            quality.hasText = true;
-            quality.autoCalculated = true;
-            alignment.addAnnotation(quality);
+            graphgrp.set(aa[i].graphGroup);
           }
         }
+        aa[i].height = 0;
+
+        if (aa[i].hasText)
+        {
+          aa[i].height += charHeight;
+        }
+
+        if (aa[i].hasIcons)
+        {
+          aa[i].height += 16;
+        }
+
+        if (aa[i].graph > 0)
+        {
+          aa[i].height += aa[i].graphHeight;
+        }
+
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
+
+        height += aa[i].height;
       }
-      else
+    }
+    if (height == 0)
+    {
+      // set minimum
+      height = 20;
+    }
+    return height;
+  }
+
+  @Override
+  public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    boolean updateCalcs = false;
+    boolean conv = isShowGroupConservation();
+    boolean cons = isShowGroupConsensus();
+    boolean showprf = isShowSequenceLogo();
+    boolean showConsHist = isShowConsensusHistogram();
+    boolean normLogo = isNormaliseSequenceLogo();
+
+    /**
+     * TODO reorder the annotation rows according to group/sequence ordering on
+     * alignment
+     */
+    boolean sortg = true;
+
+    // remove old automatic annotation
+    // add any new annotation
+
+    // intersect alignment annotation with alignment groups
+
+    AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
+    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    if (aan != null)
+    {
+      for (int an = 0; an < aan.length; an++)
       {
-        if (alignment.hasRNAStructure())
+        if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
-          strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-                  new Annotation[1], 0f, 100f,
-                  AlignmentAnnotation.BAR_GRAPH);
-          strucConsensus.hasText = true;
-          strucConsensus.autoCalculated = true;
+          oldrfs.add(aan[an].groupRef);
+          alignment.deleteAnnotation(aan[an],false);
         }
       }
+    }
+    if (alignment.getGroups() != null)
+    {
+      for (SequenceGroup sg : alignment.getGroups())
+      {
+        updateCalcs = false;
+        if (applyGlobalSettings
+                || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setshowSequenceLogo(showprf);
+          sg.setShowConsensusHistogram(showConsHist);
+          sg.setNormaliseSequenceLogo(normLogo);
+        }
+        if (conv)
+        {
+          updateCalcs = true;
+          alignment.addAnnotation(sg.getConservationRow(), 0);
+        }
+        if (cons)
+        {
+          updateCalcs = true;
+          alignment.addAnnotation(sg.getConsensus(), 0);
+        }
+        // refresh the annotation rows
+        if (updateCalcs)
+        {
+          sg.recalcConservation();
+        }
+      }
+    }
+    oldrfs.clear();
+  }
 
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
+  @Override
+  public Color getSequenceColour(SequenceI seq)
+  {
+    Color sqc=Color.white;
+    if (sequenceColours != null)
+    {
+      sqc = (Color) sequenceColours.get(seq);
+      if (sqc == null) {
+        sqc = Color.white;
+      }
+    }
+    return sqc;
+  }
 
-      if (showConsensus)
+  @Override
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+  @Override
+  public void updateSequenceIdColours()
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+    for (SequenceGroup sg : alignment.getGroups())
+    {
+      if (sg.idColour != null)
       {
-        alignment.addAnnotation(consensus);
-        if (strucConsensus != null)
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
         {
-          alignment.addAnnotation(strucConsensus);
+          sequenceColours.put(s, sg.idColour);
         }
       }
     }
   }
 
+  @Override
+  public void clearSequenceColours()
+  {
+    sequenceColours = null;
+  };
 }