X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=196242335a7bd7e80fa4d2f7b5606e154328f01a;hb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;hp=16f8fb892a29b34edddad6461d17a21ef79fe21a;hpb=4dac54360fdfecce521a1c63e75b4027219ac065;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 16f8fb8..1962423 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,40 +1,47 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * 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.
- *
- * 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 - 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 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/>.
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
+
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AlignmentAnnotation
 {
-  /** If true, this annotations is calculated every edit,
-   * eg consensus, quality or conservation graphs */
+  /**
+   * If true, this annotations is calculated every edit, eg consensus, quality
+   * or conservation graphs
+   */
   public boolean autoCalculated = false;
 
   public String annotationId;
-
+  
   public SequenceI sequenceRef;
 
   /** DOCUMENT ME!! */
@@ -45,7 +52,49 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
+  
+  
 
+  /**
+   * RNA secondary structure contact positions
+   */
+  public SequenceFeature[] _rnasecstr = null;
+  /**
+   * position of annotation resulting in invalid WUSS parsing or -1
+   */
+  private long invalidrnastruc=-1;
+  /**
+   * Updates the _rnasecstr field Determines the positions that base pair and
+   * the positions of helices based on secondary structure from a Stockholm file
+   * 
+   * @param RNAannot
+   */
+  private void _updateRnaSecStr(CharSequence RNAannot)
+  {
+    try {
+    _rnasecstr = Rna.GetBasePairs(RNAannot);
+    invalidrnastruc=-1;
+    }
+    catch (WUSSParseException px)
+    {
+      invalidrnastruc=px.getProblemPos();
+    }
+    if (invalidrnastruc>-1)
+    {
+      return;
+    }
+    Rna.HelixMap(_rnasecstr);
+    // setRNAStruc(RNAannot);
+    
+    if (_rnasecstr != null && _rnasecstr.length > 0)
+    {
+      // show all the RNA secondary structure annotation symbols.
+      isrna=true;
+      showAllColLabels = true;
+      scaleColLabel = true;
+    }
+    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+  }
   public java.util.Hashtable sequenceMapping;
 
   /** DOCUMENT ME!! */
@@ -54,34 +103,42 @@ public class AlignmentAnnotation
   /** DOCUMENT ME!! */
   public float graphMax;
 
-  public float score;
+  /**
+   * Score associated with label and description.
+   */
+  public double score = Double.NaN;
+
+  /**
+   * flag indicating if annotation has a score.
+   */
+  public boolean hasScore = false;
 
   public GraphLine threshold;
 
   // Graphical hints and tips
 
-  /** DOCUMENT ME!! */
+  /** Can this row be edited by the user ? */
   public boolean editable = false;
 
-  /** DOCUMENT ME!! */
+  /** Indicates if annotation has a graphical symbol track */
   public boolean hasIcons; //
 
-  /** DOCUMENT ME!! */
+  /** Indicates if annotation has a text character label */
   public boolean hasText;
 
-  /** DOCUMENT ME!! */
+  /** is the row visible */
   public boolean visible = true;
 
   public int graphGroup = -1;
 
-  /** DOCUMENT ME!! */
+  /** Displayed height of row in pixels */
   public int height = 0;
 
   public int graph = 0;
 
   public int graphHeight = 40;
 
-  public boolean padGaps = true;
+  public boolean padGaps = false;
 
   public static final int NO_GRAPH = 0;
 
@@ -89,6 +146,38 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
+  public boolean belowAlignment = true;
+
+  public SequenceGroup groupRef = null;
+
+  /**
+   * display every column label, even if there is a row of identical labels
+   */
+  public boolean showAllColLabels = false;
+
+  /**
+   * scale the column label to fit within the alignment column.
+   */
+  public boolean scaleColLabel = false;
+
+  /**
+   * centre the column labels relative to the alignment column
+   */
+  public boolean centreColLabels = false;
+
+  private boolean isrna;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable
+  {
+    sequenceRef = null;
+    groupRef = null;
+    super.finalize();
+  }
 
   public static int getGraphValueFromString(String string)
   {
@@ -108,13 +197,16 @@ public class AlignmentAnnotation
 
   /**
    * Creates a new AlignmentAnnotation object.
-   *
-   * @param label DOCUMENT ME!
-   * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
+   * 
+   * @param label
+   *          short label shown under sequence labels
+   * @param description
+   *          text displayed on mouseover
+   * @param annotations
+   *          set of positional annotation elements
    */
   public AlignmentAnnotation(String label, String description,
-                             Annotation[] annotations)
+          Annotation[] annotations)
   {
     // always editable?
     editable = true;
@@ -122,83 +214,264 @@ public class AlignmentAnnotation
     this.description = description;
     this.annotations = annotations;
 
-     validateRangeAndDisplay();
+    validateRangeAndDisplay();
   }
 
+  /**
+   * Checks if annotation labels represent secondary structures
+   * 
+   */
   void areLabelsSecondaryStructure()
   {
     boolean nonSSLabel = false;
+    isrna = false;
+    StringBuffer rnastring = new StringBuffer();
+
+    char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
       if (annotations[i] == null)
       {
-        padGaps = false;
         continue;
       }
-      if (annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E')
+      if (annotations[i].secondaryStructure == 'H'
+              || annotations[i].secondaryStructure == 'E')
       {
-          hasIcons = true;
+        hasIcons |= true;
+      }
+      else
+      // Check for RNA secondary structure
+      {
+    	  //System.out.println(annotations[i].secondaryStructure);
+        if (annotations[i].secondaryStructure == '('
+        		|| annotations[i].secondaryStructure == '['
+        		|| annotations[i].secondaryStructure == '<'
+        		|| annotations[i].secondaryStructure == '{'
+        		|| annotations[i].secondaryStructure == 'A'
+        		|| annotations[i].secondaryStructure == 'B'
+        		|| annotations[i].secondaryStructure == 'C'
+        		|| annotations[i].secondaryStructure == 'D'
+        		|| annotations[i].secondaryStructure == '1'
+        		|| annotations[i].secondaryStructure == 'F'
+        		|| annotations[i].secondaryStructure == 'G'
+        		|| annotations[i].secondaryStructure == '2'
+        		|| annotations[i].secondaryStructure == 'I'
+        		|| annotations[i].secondaryStructure == 'J'
+        		|| annotations[i].secondaryStructure == 'K'
+        		|| annotations[i].secondaryStructure == 'L'
+        		|| annotations[i].secondaryStructure == 'M'
+        		|| annotations[i].secondaryStructure == 'N'
+        		|| annotations[i].secondaryStructure == 'O'
+        		|| annotations[i].secondaryStructure == 'P'
+        		|| annotations[i].secondaryStructure == 'Q'
+        		|| annotations[i].secondaryStructure == 'R'
+        		|| annotations[i].secondaryStructure == 'S'
+        		|| annotations[i].secondaryStructure == 'T'
+        		|| annotations[i].secondaryStructure == 'U'
+        		|| annotations[i].secondaryStructure == 'V'
+        		|| annotations[i].secondaryStructure == 'W'
+        		|| annotations[i].secondaryStructure == 'X'
+        		|| annotations[i].secondaryStructure == 'Y'
+        		|| annotations[i].secondaryStructure == 'Z')
+        {
+          hasIcons |= true;
+          isrna |= true;
+        }
       }
 
-      if(annotations[i].displayCharacter==null)
-        continue;
-
+      // System.out.println("displaychar " + annotations[i].displayCharacter);
 
-      if (annotations[i].displayCharacter.length() == 1
-          && !annotations[i].displayCharacter.equals("H")
-          && !annotations[i].displayCharacter.equals("E")
-          && !annotations[i].displayCharacter.equals("-")
-          && !annotations[i].displayCharacter.equals("."))
+      if (annotations[i].displayCharacter == null
+              || annotations[i].displayCharacter.length() == 0)
+      {
+        rnastring.append('.');
+        continue;
+      }
+      if (annotations[i].displayCharacter.length() == 1)
+      {
+        firstChar = annotations[i].displayCharacter.charAt(0);
+        // check to see if it looks like a sequence or is secondary structure
+        // labelling.
+        if (annotations[i].secondaryStructure != ' '
+                && !hasIcons
+                &&
+                // Uncomment to only catch case where
+                // displayCharacter==secondary
+                // Structure
+                // to correctly redisplay SS annotation imported from Stockholm,
+                // exported to JalviewXML and read back in again.
+                // &&
+                // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+                firstChar != ' '
+                && firstChar != 'H'
+                && firstChar != 'E'
+                && firstChar != '('
+                && firstChar != '['
+                && firstChar != '>'
+                && firstChar != '{'
+                && firstChar != 'A'
+                && firstChar != 'B'
+                && firstChar != 'C'
+                && firstChar != 'D'
+                && firstChar != '1'
+                && firstChar != 'F'
+                && firstChar != 'G'
+                && firstChar != '2'
+                && firstChar != 'I'
+                && firstChar != 'J'
+                && firstChar != 'K'
+                && firstChar != 'L'
+                && firstChar != 'M'
+                && firstChar != 'N'
+                && firstChar != 'O'
+                && firstChar != 'P'
+                && firstChar != 'Q'
+                && firstChar != 'R'
+                && firstChar != 'S'
+                && firstChar != 'T'
+                && firstChar != 'U'
+                && firstChar != 'V'
+                && firstChar != 'W'
+                && firstChar != 'X'
+                && firstChar != 'Y'
+                && firstChar != 'Z'
+                && firstChar != '-'
+                && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex
-                  [annotations[i].displayCharacter.charAt(0)] < 23)
+          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+                                                                         // parameterise
+                                                                         // to
+                                                                         // gap
+                                                                         // symbol
+                                                                         // number
           {
             nonSSLabel = true;
           }
         }
+      }
+      else
+      {
+        rnastring.append(annotations[i].displayCharacter.charAt(1));
+      }
 
-        if (annotations[i].displayCharacter.length() > 0)
-        {
-          hasText = true;
-        }
-        else
-          padGaps = false;
+      if (annotations[i].displayCharacter.length() > 0)
+      {
+        hasText = true;
       }
+    }
 
     if (nonSSLabel)
     {
       hasIcons = false;
       for (int j = 0; j < annotations.length; j++)
       {
-        if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
+        if (annotations[j] != null
+                && annotations[j].secondaryStructure != ' ')
         {
-          annotations[j].displayCharacter
-              = String.valueOf(annotations[j].secondaryStructure);
+          annotations[j].displayCharacter = String
+                  .valueOf(annotations[j].secondaryStructure);
           annotations[j].secondaryStructure = ' ';
         }
 
       }
     }
+    else
+    {
+      if (isrna)
+      {
+        _updateRnaSecStr(new AnnotCharSequence());
+      }
+    }
 
     annotationId = this.hashCode() + "";
   }
   /**
-   * Creates a new AlignmentAnnotation object.
+   * flyweight access to positions in the alignment annotation row for RNA processing
+   * @author jimp
    *
-   * @param label DOCUMENT ME!
-   * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
-   * @param min DOCUMENT ME!
-   * @param max DOCUMENT ME!
-   * @param winLength DOCUMENT ME!
+   */
+  private class AnnotCharSequence  implements CharSequence 
+  {
+    int offset=0;
+    int max=0;
+    
+    public AnnotCharSequence() {
+      this(0,annotations.length);
+    }
+    public AnnotCharSequence(int start, int end) {
+      offset=start;
+      max=end;
+    }
+    @Override
+    public CharSequence subSequence(int start, int end)
+    {
+      return new AnnotCharSequence(offset+start, offset+end);
+    }
+    
+    @Override
+    public int length()
+    {
+      return max-offset;
+    }
+    
+    @Override
+    public char charAt(int index)
+    {
+      String dc;
+      return ((index+offset<0) || (index+offset)>=max || annotations[index+offset]==null || (dc=annotations[index+offset].displayCharacter.trim()).length()<1)
+              ? '.' : dc.charAt(0);
+    }
+    public String toString()
+    {
+      char[] string=new char[max-offset];
+      int mx=annotations.length;
+        
+      for (int i=offset;i<mx;i++)
+      {
+        String dc;
+        string[i]=(annotations[i]==null || (dc=annotations[i].displayCharacter.trim()).length()<1 )? '.' : dc.charAt(0);
+      }
+      return new String(string);
+    }
+  };
+  
+  private long _lastrnaannot=-1;
+  public String getRNAStruc(){
+    if (isrna)
+    {
+      String rnastruc = new AnnotCharSequence().toString();
+      if (_lastrnaannot!=rnastruc.hashCode())
+      {
+        // ensure rna structure contacts are up to date
+        _lastrnaannot=rnastruc.hashCode();
+        _updateRnaSecStr(rnastruc);
+      }
+      return rnastruc;
+    }
+    return null;
+  }
+
+/**
+   * Creates a new AlignmentAnnotation object.
+   * 
+   * @param label
+   *          DOCUMENT ME!
+   * @param description
+   *          DOCUMENT ME!
+   * @param annotations
+   *          DOCUMENT ME!
+   * @param min
+   *          DOCUMENT ME!
+   * @param max
+   *          DOCUMENT ME!
+   * @param winLength
+   *          DOCUMENT ME!
    */
   public AlignmentAnnotation(String label, String description,
-                             Annotation[] annotations, float min, float max,
-                             int graphType)
+          Annotation[] annotations, float min, float max, int graphType)
   {
     // graphs are not editable
-    editable = graphType==0;
+    editable = graphType == 0;
 
     this.label = label;
     this.description = description;
@@ -208,14 +481,20 @@ public class AlignmentAnnotation
     graphMax = max;
     validateRangeAndDisplay();
   }
+
   /**
-   * checks graphMin and graphMax,
-   * secondary structure symbols,
-   * sets graphType appropriately,
-   * sets null labels to the empty string
-   * if appropriate.
+   * checks graphMin and graphMax, secondary structure symbols, sets graphType
+   * appropriately, sets null labels to the empty string if appropriate.
    */
-  private void validateRangeAndDisplay() {
+  public void validateRangeAndDisplay()
+  {
+
+    if (annotations == null)
+    {
+      visible = false; // try to prevent renderer from displaying.
+      return; // this is a non-annotation row annotation - ie a sequence score.
+    }
+
     int graphType = graph;
     float min = graphMin;
     float max = graphMax;
@@ -231,9 +510,8 @@ public class AlignmentAnnotation
           continue;
         }
 
-        if (drawValues
-            && annotations[i].displayCharacter!=null
-            && annotations[i].displayCharacter.length() > 1)
+        if (drawValues && annotations[i].displayCharacter != null
+                && annotations[i].displayCharacter.length() > 1)
         {
           drawValues = false;
         }
@@ -248,6 +526,18 @@ public class AlignmentAnnotation
           min = annotations[i].value;
         }
       }
+      // ensure zero is origin for min/max ranges on only one side of zero
+      if (min > 0)
+      {
+        min = 0;
+      }
+      else
+      {
+        if (max < 0)
+        {
+          max = 0;
+        }
+      }
     }
 
     graphMin = min;
@@ -261,15 +551,16 @@ public class AlignmentAnnotation
       {
         if (annotations[i] != null)
         {
-          annotations[i].displayCharacter = "";
+          annotations[i].displayCharacter = "X";
         }
       }
     }
   }
 
   /**
-   * Copy constructor
-   * creates a new independent annotation row with the same associated sequenceRef
+   * Copy constructor creates a new independent annotation row with the same
+   * associated sequenceRef
+   * 
    * @param annotation
    */
   public AlignmentAnnotation(AlignmentAnnotation annotation)
@@ -282,6 +573,7 @@ public class AlignmentAnnotation
     this.graph = annotation.graph;
     this.graphHeight = annotation.graphHeight;
     this.graphGroup = annotation.graphGroup;
+    this.groupRef = annotation.groupRef;
     this.editable = annotation.editable;
     this.autoCalculated = annotation.autoCalculated;
     this.hasIcons = annotation.hasIcons;
@@ -289,71 +581,109 @@ public class AlignmentAnnotation
     this.height = annotation.height;
     this.label = annotation.label;
     this.padGaps = annotation.padGaps;
-    if (threshold!=null) {
+    this.visible = annotation.visible;
+    this.centreColLabels=annotation.centreColLabels;
+    this.scaleColLabel=annotation.scaleColLabel;
+    this.showAllColLabels=annotation.showAllColLabels;
+    this.calcId = annotation.calcId;
+    if (this.hasScore = annotation.hasScore)
+    {
+      this.score = annotation.score;
+    }
+    if (annotation.threshold != null)
+    {
       threshold = new GraphLine(annotation.threshold);
     }
-    if (annotation.annotations!=null) {
+    if (annotation.annotations != null)
+    {
       Annotation[] ann = annotation.annotations;
       this.annotations = new Annotation[ann.length];
-      for (int i=0; i<ann.length; i++) {
+      for (int i = 0; i < ann.length; i++)
+      {
         annotations[i] = new Annotation(ann[i]);
-      };
-      if (annotation.sequenceRef!=null) {
+      }
+      ;
+      if (annotation.sequenceRef != null)
+      {
         this.sequenceRef = annotation.sequenceRef;
-        if (annotation.sequenceMapping!=null)
+        if (annotation.sequenceMapping != null)
         {
-          Integer p=null;
+          Integer p = null;
           sequenceMapping = new Hashtable();
-          Enumeration pos=annotation.sequenceMapping.keys();
-          while (pos.hasMoreElements()) {
+          Enumeration pos = annotation.sequenceMapping.keys();
+          while (pos.hasMoreElements())
+          {
             // could optimise this!
             p = (Integer) pos.nextElement();
             Annotation a = (Annotation) annotation.sequenceMapping.get(p);
-            if (a==null)
+            if (a == null)
             {
               continue;
             }
-            for (int i=0; i<ann.length; i++)
+            for (int i = 0; i < ann.length; i++)
             {
-              if (ann[i]==a)
+              if (ann[i] == a)
               {
                 sequenceMapping.put(p, annotations[i]);
               }
             }
           }
-        } else {
+        }
+        else
+        {
           this.sequenceMapping = null;
         }
       }
     }
+    // TODO: check if we need to do this: JAL-952
+    //if (this.isrna=annotation.isrna)
+    {
+      // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+    }
     validateRangeAndDisplay(); // construct hashcodes, etc.
   }
 
   /**
    * clip the annotation to the columns given by startRes and endRes (inclusive)
    * and prune any existing sequenceMapping to just those columns.
+   * 
    * @param startRes
    * @param endRes
    */
   public void restrict(int startRes, int endRes)
   {
-    Annotation[] temp = new Annotation[endRes-startRes+1];
-    if (startRes<annotations.length)
+    if (annotations == null)
     {
-      System.arraycopy(annotations, startRes, temp, 0, Math.min(endRes, annotations.length-1)-startRes+1);
+      // non-positional
+      return;
     }
-    if (sequenceRef!=null) {
+    if (startRes < 0)
+      startRes = 0;
+    if (startRes >= annotations.length)
+      startRes = annotations.length - 1;
+    if (endRes >= annotations.length)
+      endRes = annotations.length - 1;
+    if (annotations == null)
+      return;
+    Annotation[] temp = new Annotation[endRes - startRes + 1];
+    if (startRes < annotations.length)
+    {
+      System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
+              + 1);
+    }
+    if (sequenceRef != null)
+    {
       // Clip the mapping, if it exists.
       int spos = sequenceRef.findPosition(startRes);
       int epos = sequenceRef.findPosition(endRes);
-      if (sequenceMapping!=null)
+      if (sequenceMapping != null)
       {
         Hashtable newmapping = new Hashtable();
         Enumeration e = sequenceMapping.keys();
         while (e.hasMoreElements())
         {
           Integer pos = (Integer) e.nextElement();
-          if (pos.intValue()>=spos && pos.intValue()<=epos)
+          if (pos.intValue() >= spos && pos.intValue() <= epos)
           {
             newmapping.put(pos, sequenceMapping.get(pos));
           }
@@ -362,33 +692,37 @@ public class AlignmentAnnotation
         sequenceMapping = newmapping;
       }
     }
-    annotations=temp;
+    annotations = temp;
   }
+
   /**
    * set the annotation row to be at least length Annotations
-   * @param length minimum number of columns required in the annotation row
+   * 
+   * @param length
+   *          minimum number of columns required in the annotation row
    * @return false if the annotation row is greater than length
    */
-  public boolean padAnnotation(int length) {
-    if (annotations==null)
+  public boolean padAnnotation(int length)
+  {
+    if (annotations == null)
     {
-      annotations = new Annotation[length];
-      return true;
+      return true; // annotation row is correct - null == not visible and
+      // undefined length
     }
-    if (annotations.length<length)
+    if (annotations.length < length)
     {
       Annotation[] na = new Annotation[length];
       System.arraycopy(annotations, 0, na, 0, annotations.length);
       annotations = na;
       return true;
     }
-    return annotations.length>length;
+    return annotations.length > length;
 
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String toString()
@@ -415,8 +749,8 @@ public class AlignmentAnnotation
 
       buffer.append(", ");
     }
-
-    if (label.equals("Consensus"))
+    // TODO: remove disgusting hack for 'special' treatment of consensus line.
+    if (label.indexOf("Consensus") == 0)
     {
       buffer.append("\n");
 
@@ -445,24 +779,29 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
+   * Attach the annotation to seqRef, starting from startRes position. If
+   * alreadyMapped is true then the indices of the annotation[] array are
+   * sequence positions rather than alignment column positions.
+   * 
    * @param seqRef
    * @param startRes
    * @param alreadyMapped
    */
-  public void createSequenceMapping(SequenceI seqRef,
-                                    int startRes,
-                                    boolean alreadyMapped)
+  public void createSequenceMapping(SequenceI seqRef, int startRes,
+          boolean alreadyMapped)
   {
 
     if (seqRef == null)
     {
       return;
     }
-
+    sequenceRef = seqRef;
+    if (annotations == null)
+    {
+      return;
+    }
     sequenceMapping = new java.util.Hashtable();
 
-    sequenceRef = seqRef;
     int seqPos;
 
     for (int i = 0; i < annotations.length; i++)
@@ -486,14 +825,19 @@ public class AlignmentAnnotation
 
   public void adjustForAlignment()
   {
-    if (sequenceRef==null)
+    if (sequenceRef == null)
+      return;
+
+    if (annotations == null)
+    {
       return;
+    }
 
     int a = 0, aSize = sequenceRef.getLength();
 
     if (aSize == 0)
     {
-      //Its been deleted
+      // Its been deleted
       return;
     }
 
@@ -514,31 +858,45 @@ public class AlignmentAnnotation
 
     annotations = temp;
   }
+
   /**
-   * remove any null entries in annotation row and return the
-   * number of non-null annotation elements.
+   * remove any null entries in annotation row and return the number of non-null
+   * annotation elements.
+   * 
    * @return
    */
-  private int compactAnnotationArray() {
-    int j=0;
-    for (int i=0;i<annotations.length; i++) {
-      if (annotations[i]!=null && j!=i) {
-        annotations[j++] = annotations[i];
+  public int compactAnnotationArray()
+  {
+    int i = 0, iSize = annotations.length;
+    while (i < iSize)
+    {
+      if (annotations[i] == null)
+      {
+        if (i + 1 < iSize)
+          System.arraycopy(annotations, i + 1, annotations, i, iSize - i
+                  - 1);
+        iSize--;
+      }
+      else
+      {
+        i++;
       }
     }
     Annotation[] ann = annotations;
-    annotations = new Annotation[j];
-    System.arraycopy(ann, 0, annotations, 0, j);
+    annotations = new Annotation[i];
+    System.arraycopy(ann, 0, annotations, 0, i);
     ann = null;
-    return j;
+    return iSize;
   }
 
   /**
    * Associate this annotion with the aligned residues of a particular sequence.
-   * sequenceMapping will be updated in the following way:
-   *   null sequenceI - existing mapping will be discarded but annotations left in mapped positions.
-   *   valid sequenceI not equal to current sequenceRef: mapping is discarded and rebuilt assuming 1:1 correspondence
-   *   TODO: overload with parameter to specify correspondence between current and new sequenceRef
+   * sequenceMapping will be updated in the following way: null sequenceI -
+   * existing mapping will be discarded but annotations left in mapped
+   * positions. valid sequenceI not equal to current sequenceRef: mapping is
+   * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+   * parameter to specify correspondence between current and new sequenceRef
+   * 
    * @param sequenceI
    */
   public void setSequenceRef(SequenceI sequenceI)
@@ -547,7 +905,10 @@ public class AlignmentAnnotation
     {
       if (sequenceRef != null)
       {
-        if (sequenceRef != sequenceI && !sequenceRef.equals(sequenceI) && sequenceRef.getDatasetSequence()!=sequenceI.getDatasetSequence())
+        if (sequenceRef != sequenceI
+                && !sequenceRef.equals(sequenceI)
+                && sequenceRef.getDatasetSequence() != sequenceI
+                        .getDatasetSequence())
         {
           // if sequenceRef isn't intersecting with sequenceI
           // throw away old mapping and reconstruct.
@@ -580,4 +941,127 @@ public class AlignmentAnnotation
       sequenceRef = null;
     }
   }
+
+  /**
+   * @return the score
+   */
+  public double getScore()
+  {
+    return score;
+  }
+
+  /**
+   * @param score
+   *          the score to set
+   */
+  public void setScore(double score)
+  {
+    hasScore = true;
+    this.score = score;
+  }
+
+  /**
+   * 
+   * @return true if annotation has an associated score
+   */
+  public boolean hasScore()
+  {
+    return hasScore || !Double.isNaN(score);
+  }
+
+  /**
+   * Score only annotation
+   * 
+   * @param label
+   * @param description
+   * @param score
+   */
+  public AlignmentAnnotation(String label, String description, double score)
+  {
+    this(label, description, null);
+    setScore(score);
+  }
+
+  /**
+   * copy constructor with edit based on the hidden columns marked in colSel
+   * 
+   * @param alignmentAnnotation
+   * @param colSel
+   */
+  public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+          ColumnSelection colSel)
+  {
+    this(alignmentAnnotation);
+    if (annotations == null)
+    {
+      return;
+    }
+    colSel.makeVisibleAnnotation(this);
+  }
+
+  public void setPadGaps(boolean padgaps, char gapchar)
+  {
+    this.padGaps = padgaps;
+    if (padgaps)
+    {
+      hasText = true;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] == null)
+          annotations[i] = new Annotation(String.valueOf(gapchar), null,
+                  ' ', 0f,null);
+        else if (annotations[i].displayCharacter == null
+                || annotations[i].displayCharacter.equals(" "))
+          annotations[i].displayCharacter = String.valueOf(gapchar);
+      }
+    }
+  }
+
+  /**
+   * format description string for display
+   * 
+   * @param seqname
+   * @return Get the annotation description string optionally prefixed by
+   *         associated sequence name (if any)
+   */
+  public String getDescription(boolean seqname)
+  {
+    if (seqname && this.sequenceRef != null)
+    {
+      int i=description.toLowerCase().indexOf("<html>");
+      if (i>-1)
+      {
+        // move the html tag to before the sequence reference.
+        return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+      }
+      return sequenceRef.getName() + " : " + description;
+    }
+    return description;
+  }
+
+  public boolean isValidStruc()
+  {
+    return invalidrnastruc==-1;
+  }
+  public long getInvalidStrucPos()
+  {
+    return invalidrnastruc;
+  }
+
+  /**
+   * machine readable ID string indicating what generated this annotation
+   */
+  protected String calcId="";
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  public void setCalcId(String calcId)
+  {
+    this.calcId = calcId;
+  }
+  
+ 
+  
 }