X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=bd5bfcfcdfa260b7c1ff338bdf68c0d982e4f99c;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=04689cdead5eecd4d6fdfaf276abe465f227cf3b;hpb=80f46a9ba6bea3531ff6e59cf68f9f870e5af4da;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 04689cd..bd5bfcf 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,331 +1,820 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 java.util.Enumeration;
+import java.util.Hashtable;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AlignmentAnnotation
 {
-    public SequenceI sequenceRef;
+  /**
+   * 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!! */
+  public String label;
+
+  /** DOCUMENT ME!! */
+  public String description;
+
+  /** DOCUMENT ME!! */
+  public Annotation[] annotations;
+
+  public java.util.Hashtable sequenceMapping;
+
+  /** DOCUMENT ME!! */
+  public float graphMin;
+
+  /** DOCUMENT ME!! */
+  public float graphMax;
+
+  /**
+   * 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;
 
-    /** DOCUMENT ME!! */
-    public String label;
+  // Graphical hints and tips
 
-    /** DOCUMENT ME!! */
-    public String description;
+  /** Can this row be edited by the user ? */
+  public boolean editable = false;
 
-    /** DOCUMENT ME!! */
-    public Annotation[] annotations;
+  /** Indicates if annotation has a graphical symbol track */
+  public boolean hasIcons; //
 
-    public java.util.Hashtable sequenceMapping;
+  /** Indicates if annotation has a text character label */
+  public boolean hasText;
 
-    /** DOCUMENT ME!! */
-    public float graphMin;
+  /** is the row visible */
+  public boolean visible = true;
 
-    /** DOCUMENT ME!! */
-    public float graphMax;
+  public int graphGroup = -1;
 
-    public GraphLine threshold;
+  /** Displayed height of row in pixels */
+  public int height = 0;
 
-    // Graphical hints and tips
+  public int graph = 0;
 
-    /** DOCUMENT ME!! */
-    public boolean editable = false;
+  public int graphHeight = 40;
 
-    /** DOCUMENT ME!! */
-    public boolean hasIcons; //
+  public boolean padGaps = false;
 
-    /** DOCUMENT ME!! */
-    public boolean hasText;
+  public static final int NO_GRAPH = 0;
 
-    /** DOCUMENT ME!! */
-    public boolean visible = true;
+  public static final int BAR_GRAPH = 1;
 
-    public int graphGroup = -1;
+  public static final int LINE_GRAPH = 2;
 
-    /** DOCUMENT ME!! */
-    public int height = 0;
+  public boolean belowAlignment = true;
 
-    public int graph = 0;
+  public SequenceGroup groupRef = null;
 
-    public int graphHeight = 40;
+  /**
+   * display every column label, even if there is a row of identical labels
+   */
+  public boolean showAllColLabels = false;
 
-    public static final int NO_GRAPH = 0;
+  /**
+   * scale the column label to fit within the alignment column.
+   */
+  public boolean scaleColLabel = false;
 
-    public static final int BAR_GRAPH = 1;
+  /**
+   * centre the column labels relative to the alignment column
+   */
+  public boolean centreColLabels = false;
 
-    public static final int LINE_GRAPH = 2;
+  /*
+   * (non-Javadoc)
+   * 
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable
+  {
+    sequenceRef = null;
+    groupRef = null;
+    super.finalize();
+  }
 
-    public static int getGraphValueFromString(String string)
+  public static int getGraphValueFromString(String string)
+  {
+    if (string.equalsIgnoreCase("BAR_GRAPH"))
     {
-      if(string.equalsIgnoreCase("BAR_GRAPH"))
-        return BAR_GRAPH;
-      else if(string.equalsIgnoreCase("LINE_GRAPH"))
-        return LINE_GRAPH;
-      else
-        return NO_GRAPH;
+      return BAR_GRAPH;
     }
-
-    /**
-     * Creates a new AlignmentAnnotation object.
-     *
-     * @param label DOCUMENT ME!
-     * @param description DOCUMENT ME!
-     * @param annotations DOCUMENT ME!
-     */
-    public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations)
+    else if (string.equalsIgnoreCase("LINE_GRAPH"))
+    {
+      return LINE_GRAPH;
+    }
+    else
+    {
+      return NO_GRAPH;
+    }
+  }
+
+  /**
+   * Creates a new AlignmentAnnotation object.
+   * 
+   * @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)
+  {
+    // always editable?
+    editable = true;
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+
+    validateRangeAndDisplay();
+  }
+
+  void areLabelsSecondaryStructure()
+  {
+    boolean nonSSLabel = false;
+    char firstChar = 0;
+    for (int i = 0; i < annotations.length; i++)
     {
-        // always editable?
-        editable = true;
-        this.label = label;
-        this.description = description;
-        this.annotations = annotations;
+      if (annotations[i] == null)
+      {
+        continue;
+      }
+      if (annotations[i].secondaryStructure == 'H'
+              || annotations[i].secondaryStructure == 'E')
+      {
+        hasIcons |= true;
+      }
 
-        for (int i = 0; i < annotations.length; i++)
+      if (annotations[i].displayCharacter == null)
+      {
+        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 < jalview.schemes.ResidueProperties.aaIndex.length)
         {
-            if ((annotations[i] != null) &&
-                    ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E')))
-            {
-                hasIcons = true;
-            }
+          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+                                                                         // parameterise
+                                                                         // to
+                                                                         // gap
+                                                                         // symbol
+                                                                         // number
+          {
+            nonSSLabel = true;
+          }
+        }
+      }
 
-            if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0))
-            {
-                hasText = true;
-            }
+      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 != ' ')
+        {
+          annotations[j].displayCharacter = String
+                  .valueOf(annotations[j].secondaryStructure);
+          annotations[j].secondaryStructure = ' ';
         }
+
+      }
     }
 
-    /**
-     * 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)
+    annotationId = this.hashCode() + "";
+  }
+
+  /**
+   * 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)
+  {
+    // graphs are not editable
+    editable = graphType == 0;
+
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+    graph = graphType;
+    graphMin = min;
+    graphMax = max;
+    validateRangeAndDisplay();
+  }
+
+  /**
+   * checks graphMin and graphMax, secondary structure symbols, sets graphType
+   * appropriately, sets null labels to the empty string if appropriate.
+   */
+  private void validateRangeAndDisplay()
+  {
+
+    if (annotations == null)
     {
-        // graphs are not editable
-        this.label = label;
-        this.description = description;
-        this.annotations = annotations;
-        graph = graphType;
+      visible = false; // try to prevent renderer from displaying.
+      return; // this is a non-annotation row annotation - ie a sequence score.
+    }
 
-        boolean drawValues = true;
+    int graphType = graph;
+    float min = graphMin;
+    float max = graphMax;
+    boolean drawValues = true;
 
-        if (min == max)
+    if (min == max)
+    {
+      min = 999999999;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] == null)
         {
-            min = 999999999;
-            for (int i = 0; i < annotations.length; i++)
-            {
-                if (annotations[i] == null)
-                {
-                    continue;
-                }
-
-                if(drawValues && annotations[i].displayCharacter.length() > 1 )
-                {
-                  drawValues = false;
-                }
-
-                if (annotations[i].value > max)
-                {
-                    max = annotations[i].value;
-                }
-
-                if (annotations[i].value < min)
-                {
-                    min = annotations[i].value;
-                }
-            }
+          continue;
         }
 
-        graphMin = min;
-        graphMax = max;
+        if (drawValues && annotations[i].displayCharacter != null
+                && annotations[i].displayCharacter.length() > 1)
+        {
+          drawValues = false;
+        }
+
+        if (annotations[i].value > max)
+        {
+          max = annotations[i].value;
+        }
+
+        if (annotations[i].value < min)
+        {
+          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;
+    graphMax = max;
 
-        for (int i = 0; i < annotations.length; i++)
+    areLabelsSecondaryStructure();
+
+    if (!drawValues && graphType != NO_GRAPH)
+    {
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
         {
-            if (!hasIcons
-                && annotations[i] != null
-                && ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E')))
+          annotations[i].displayCharacter = "";
+        }
+      }
+    }
+  }
+
+  /**
+   * Copy constructor creates a new independent annotation row with the same
+   * associated sequenceRef
+   * 
+   * @param annotation
+   */
+  public AlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    this.label = new String(annotation.label);
+    if (annotation.description != null)
+      this.description = new String(annotation.description);
+    this.graphMin = annotation.graphMin;
+    this.graphMax = annotation.graphMax;
+    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;
+    this.hasText = annotation.hasText;
+    this.height = annotation.height;
+    this.label = annotation.label;
+    this.padGaps = annotation.padGaps;
+    this.visible = annotation.visible;
+    if (this.hasScore = annotation.hasScore)
+    {
+      this.score = annotation.score;
+    }
+    if (threshold != null)
+    {
+      threshold = new GraphLine(annotation.threshold);
+    }
+    if (annotation.annotations != null)
+    {
+      Annotation[] ann = annotation.annotations;
+      this.annotations = new Annotation[ann.length];
+      for (int i = 0; i < ann.length; i++)
+      {
+        annotations[i] = new Annotation(ann[i]);
+      }
+      ;
+      if (annotation.sequenceRef != null)
+      {
+        this.sequenceRef = annotation.sequenceRef;
+        if (annotation.sequenceMapping != null)
+        {
+          Integer p = null;
+          sequenceMapping = new Hashtable();
+          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)
             {
-                hasIcons = true;
+              continue;
             }
-
-            if (!hasText
-                && annotations[i]!=null
-                && annotations[i].displayCharacter.length() > 0)
+            for (int i = 0; i < ann.length; i++)
             {
-                hasText = true;
+              if (ann[i] == a)
+              {
+                sequenceMapping.put(p, annotations[i]);
+              }
             }
+          }
         }
-
-        if(!drawValues && graphType!=NO_GRAPH)
+        else
+        {
+          this.sequenceMapping = null;
+        }
+      }
+    }
+    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)
+  {
+    if (annotations == null)
+    {
+      // non-positional
+      return;
+    }
+    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)
+      {
+        Hashtable newmapping = new Hashtable();
+        Enumeration e = sequenceMapping.keys();
+        while (e.hasMoreElements())
         {
-          for (int i = 0; i < annotations.length; i++)
+          Integer pos = (Integer) e.nextElement();
+          if (pos.intValue() >= spos && pos.intValue() <= epos)
           {
-            if (annotations[i] != null)
-              annotations[i].displayCharacter = "";
+            newmapping.put(pos, sequenceMapping.get(pos));
           }
         }
+        sequenceMapping.clear();
+        sequenceMapping = newmapping;
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String toString()
+    annotations = temp;
+  }
+
+  /**
+   * set the annotation row to be at least length Annotations
+   * 
+   * @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)
+    {
+      return true; // annotation row is correct - null == not visible and
+      // undefined length
+    }
+    if (annotations.length < length)
     {
-        StringBuffer buffer = new StringBuffer();
+      Annotation[] na = new Annotation[length];
+      System.arraycopy(annotations, 0, na, 0, annotations.length);
+      annotations = na;
+      return true;
+    }
+    return annotations.length > length;
 
-        for (int i = 0; i < annotations.length; i++)
-        {
-            if (annotations[i] != null)
-            {
-                if (graph!=0)
-                {
-                    buffer.append(annotations[i].value);
-                }
-                else if (hasIcons)
-                {
-                    buffer.append(annotations[i].secondaryStructure);
-                }
-                else
-                {
-                    buffer.append(annotations[i].displayCharacter);
-                }
-            }
+  }
 
-            buffer.append(", ");
-        }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String toString()
+  {
+    StringBuffer buffer = new StringBuffer();
 
-        if (label.equals("Consensus"))
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] != null)
+      {
+        if (graph != 0)
+        {
+          buffer.append(annotations[i].value);
+        }
+        else if (hasIcons)
         {
-            buffer.append("\n");
+          buffer.append(annotations[i].secondaryStructure);
+        }
+        else
+        {
+          buffer.append(annotations[i].displayCharacter);
+        }
+      }
 
-            for (int i = 0; i < annotations.length; i++)
-            {
-                if (annotations[i] != null)
-                {
-                    buffer.append(annotations[i].description);
-                }
+      buffer.append(", ");
+    }
+    // TODO: remove disgusting hack for 'special' treatment of consensus line.
+    if (label.indexOf("Consensus") == 0)
+    {
+      buffer.append("\n");
 
-                buffer.append(", ");
-            }
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
+        {
+          buffer.append(annotations[i].description);
         }
 
-        return buffer.toString();
+        buffer.append(", ");
       }
+    }
 
-      public void setThreshold(GraphLine line)
-      {
-        threshold = line;
-      }
+    return buffer.toString();
+  }
+
+  public void setThreshold(GraphLine line)
+  {
+    threshold = line;
+  }
+
+  public GraphLine getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * 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)
+  {
+
+    if (seqRef == null)
+    {
+      return;
+    }
+    sequenceRef = seqRef;
+    if (annotations == null)
+    {
+      return;
+    }
+    sequenceMapping = new java.util.Hashtable();
 
-      public GraphLine getThreshold()
-      {
-          return threshold;
-      }
+    int seqPos;
 
-      /**
-       * Attach the annotation to seqRef, starting from startRes position.
-       * @param seqRef
-       * @param startRes
-       */
-      public void createSequenceMapping(SequenceI seqRef, int startRes)
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] != null)
       {
-        if(seqRef == null)
-          return;
-
-        sequenceMapping = new java.util.Hashtable();
+        if (alreadyMapped)
+        {
+          seqPos = seqRef.findPosition(i);
+        }
+        else
+        {
+          seqPos = i + startRes;
+        }
 
-        sequenceRef = seqRef;
+        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+      }
+    }
 
-        if(startRes < sequenceRef.getStart())
-          startRes = sequenceRef.getStart();
+  }
 
-        int seqPos;
+  public void adjustForAlignment()
+  {
+    if (sequenceRef == null)
+      return;
 
-        int fileOffset = 0;
-        if(startRes > sequenceRef.getStart())
-        {
-          fileOffset = startRes - sequenceRef.getStart();
-        }
+    if (annotations == null)
+    {
+      return;
+    }
 
-        for(int i = 0; i < annotations.length; i++)
-        {
-            seqPos = sequenceRef.findPosition(i + fileOffset);
-            if(seqPos<annotations.length)
-            {
-              if (annotations[i] != null)
-              {
-                  sequenceMapping.put(new Integer(seqPos),
-                                      annotations[i]);
-              }
-            }
-         }
+    int a = 0, aSize = sequenceRef.getLength();
 
-        adjustForAlignment();
+    if (aSize == 0)
+    {
+      // Its been deleted
+      return;
+    }
 
-      }
+    int position;
+    Annotation[] temp = new Annotation[aSize];
+    Integer index;
 
-      public void adjustForAlignment()
+    for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    {
+      index = new Integer(a);
+      if (sequenceMapping.containsKey(index))
       {
-          int a=0, aSize = sequenceRef.getLength();
-
-          if(aSize == 0)
-          {
-            //Its been deleted
-            return;
-          }
+        position = sequenceRef.findIndex(a) - 1;
 
-          int position;
-          Annotation[] temp = new Annotation[aSize];
-          Integer index;
+        temp[position] = (Annotation) sequenceMapping.get(index);
+      }
+    }
 
-          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    annotations = temp;
+  }
+
+  /**
+   * remove any null entries in annotation row and return the number of non-null
+   * annotation elements.
+   * 
+   * @return
+   */
+  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[i];
+    System.arraycopy(ann, 0, annotations, 0, i);
+    ann = null;
+    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
+   * 
+   * @param sequenceI
+   */
+  public void setSequenceRef(SequenceI sequenceI)
+  {
+    if (sequenceI != null)
+    {
+      if (sequenceRef != null)
+      {
+        if (sequenceRef != sequenceI
+                && !sequenceRef.equals(sequenceI)
+                && sequenceRef.getDatasetSequence() != sequenceI
+                        .getDatasetSequence())
+        {
+          // if sequenceRef isn't intersecting with sequenceI
+          // throw away old mapping and reconstruct.
+          sequenceRef = null;
+          if (sequenceMapping != null)
           {
-              index = new Integer(a);
-              if(sequenceMapping.containsKey(index))
-              {
-                position = sequenceRef.findIndex(a)-1;
-
-                temp[position] = (Annotation)sequenceMapping.get(index);
-              }
+            sequenceMapping = null;
+            // compactAnnotationArray();
           }
+          createSequenceMapping(sequenceI, 1, true);
+          adjustForAlignment();
+        }
+        else
+        {
+          // Mapping carried over
+          sequenceRef = sequenceI;
+        }
+      }
+      else
+      {
+        // No mapping exists
+        createSequenceMapping(sequenceI, 1, true);
+        adjustForAlignment();
+      }
+    }
+    else
+    {
+      // throw away the mapping without compacting.
+      sequenceMapping = null;
+      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);
+  }
 
-          annotations = temp;
+  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);
+        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)
+    {
+      return sequenceRef.getName() + " : " + description;
+    }
+    return description;
+  }
 }
-
-