X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=a5d2dddddec50981973116f775a0a4441207a124;hb=254f06b3cfb98883a2ce8fb4a6350c597d52a8af;hp=f1c6cc4a2f6ca38e3c4febc9811f021d602a1d24;hpb=c1a4229bd662c4299301ee8827b36096d015c075;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index f1c6cc4..a5d2ddd 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,9 +21,12 @@
 package jalview.datamodel;
 
 import jalview.util.ShiftList;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
 import java.util.ArrayList;
-import java.util.Enumeration;
+import java.util.BitSet;
+import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
 
@@ -32,9 +35,157 @@ import java.util.Vector;
  */
 public class ColumnSelection
 {
-  Vector selected = new Vector();
+  private class IntList
+  {
+    /*
+     * list of selected columns (ordered by selection order, not column order)
+     */
+    private List<Integer> order = new ArrayList<Integer>();
+
+    /**
+     * bitfield for column selection - allows quick lookup
+     */
+    private BitSet selected = new BitSet();
+
+    /**
+     * adds a new column i to the selection - only if i is not already selected
+     * 
+     * @param i
+     */
+    public void add(int i)
+    {
+      if (!selected.get(i))
+      {
+        order.add(Integer.valueOf(i));
+        selected.set(i);
+      }
+    }
+
+    public void clear()
+    {
+      order.clear();
+      selected.clear();
+    }
+
+    public void remove(int col)
+    {
+
+      Integer colInt = new Integer(col);
+
+      if (selected.get(col))
+      {
+        // if this ever changes to List.remove(), ensure Integer not int
+        // argument
+        // as List.remove(int i) removes the i'th item which is wrong
+        order.remove(colInt);
+        selected.clear(col);
+      }
+    }
+
+    public boolean contains(Integer colInt)
+    {
+      return selected.get(colInt);
+    }
+
+    public boolean isEmpty()
+    {
+      return order.isEmpty();
+    }
+
+    public List<Integer> getList()
+    {
+      return order;
+    }
+
+    public int size()
+    {
+      return order.size();
+    }
+
+    /**
+     * gets the column that was selected first, second or i'th
+     * 
+     * @param i
+     * @return
+     */
+    public int elementAt(int i)
+    {
+      return order.get(i);
+    }
+
+    protected boolean pruneColumnList(final List<int[]> shifts)
+    {
+      int s = 0, t = shifts.size();
+      int[] sr = shifts.get(s++);
+      boolean pruned = false;
+      int i = 0, j = order.size();
+      while (i < j && s <= t)
+      {
+        int c = order.get(i++).intValue();
+        if (sr[0] <= c)
+        {
+          if (sr[1] + sr[0] >= c)
+          { // sr[1] -ve means inseriton.
+            order.remove(--i);
+            selected.clear(c);
+            j--;
+          }
+          else
+          {
+            if (s < t)
+            {
+              sr = shifts.get(s);
+            }
+            s++;
+          }
+        }
+      }
+      return pruned;
+    }
+
+    /**
+     * shift every selected column at or above start by change
+     * 
+     * @param start
+     *          - leftmost column to be shifted
+     * @param change
+     *          - delta for shift
+     */
+    public void compensateForEdits(int start, int change)
+    {
+      BitSet mask = new BitSet();
+      for (int i = 0; i < order.size(); i++)
+      {
+        int temp = order.get(i);
+
+        if (temp >= start)
+        {
+          // clear shifted bits and update List of selected columns
+          selected.clear(temp);
+          mask.set(temp - change);
+          order.set(i, new Integer(temp - change));
+        }
+      }
+      // lastly update the bitfield all at once
+      selected.or(mask);
+    }
 
-  // Vector of int [] {startCol, endCol}
+    public int getMaxColumn()
+    {
+      return selected.length() - 1;
+    }
+
+    public int getMinColumn()
+    {
+      return selected.get(0) ? 0 : selected.nextSetBit(0);
+    }
+  }
+
+  IntList selected = new IntList();
+  /*
+   * list of hidden column [start, end] ranges; the list is maintained in
+   * ascending start column order
+   */
   Vector<int[]> hiddenColumns;
 
   /**
@@ -45,11 +196,7 @@ public class ColumnSelection
    */
   public void addElement(int col)
   {
-    Integer column = new Integer(col);
-    if (!selected.contains(column))
-    {
-      selected.addElement(column);
-    }
+    selected.add(col);
   }
 
   /**
@@ -57,23 +204,18 @@ public class ColumnSelection
    */
   public void clear()
   {
-    selected.removeAllElements();
+    selected.clear();
   }
 
   /**
-   * removes col from selection
+   * Removes value 'col' from the selection (not the col'th item)
    * 
    * @param col
    *          index of column to be removed
    */
   public void removeElement(int col)
   {
-    Integer colInt = new Integer(col);
-
-    if (selected.contains(colInt))
-    {
-      selected.removeElement(colInt);
-    }
+    selected.remove(col);
   }
 
   /**
@@ -92,18 +234,19 @@ public class ColumnSelection
       colInt = new Integer(i);
       if (selected.contains(colInt))
       {
-        selected.removeElement(colInt);
+        selected.remove(colInt);
       }
     }
   }
 
   /**
-   * 
-   * @return Vector containing selected columns as Integers
+   * Returns a list of selected columns. The list contains no duplicates but is
+   * not necessarily ordered. It also may include columns hidden from the
+   * current view
    */
-  public Vector getSelected()
+  public List<Integer> getSelected()
   {
-    return selected;
+    return selected.getList();
   }
 
   /**
@@ -119,26 +262,11 @@ public class ColumnSelection
   }
 
   /**
-   * Column number at position i in selection
-   * 
-   * @param i
-   *          index into selected columns
-   * 
-   * @return column number in alignment
-   */
-  public int columnAt(int i)
-  {
-    return ((Integer) selected.elementAt(i)).intValue();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * Answers true if no columns are selected, else false
    */
-  public int size()
+  public boolean isEmpty()
   {
-    return selected.size();
+    return selected == null || selected.isEmpty();
   }
 
   /**
@@ -148,17 +276,11 @@ public class ColumnSelection
    */
   public int getMax()
   {
-    int max = -1;
-
-    for (int i = 0; i < selected.size(); i++)
+    if (selected.isEmpty())
     {
-      if (columnAt(i) > max)
-      {
-        max = columnAt(i);
-      }
+      return -1;
     }
-
-    return max;
+    return selected.getMaxColumn();
   }
 
   /**
@@ -168,17 +290,11 @@ public class ColumnSelection
    */
   public int getMin()
   {
-    int min = 1000000000;
-
-    for (int i = 0; i < selected.size(); i++)
+    if (selected.isEmpty())
     {
-      if (columnAt(i) < min)
-      {
-        min = columnAt(i);
-      }
+      return 1000000000;
     }
-
-    return min;
+    return selected.getMinColumn();
   }
 
   /**
@@ -192,15 +308,7 @@ public class ColumnSelection
   public List<int[]> compensateForEdit(int start, int change)
   {
     List<int[]> deletedHiddenColumns = null;
-    for (int i = 0; i < size(); i++)
-    {
-      int temp = columnAt(i);
-
-      if (temp >= start)
-      {
-        selected.setElementAt(new Integer(temp - change), i);
-      }
-    }
+    selected.compensateForEdits(start, change);
 
     if (hiddenColumns != null)
     {
@@ -249,15 +357,8 @@ public class ColumnSelection
    */
   private void compensateForDelEdits(int start, int change)
   {
-    for (int i = 0; i < size(); i++)
-    {
-      int temp = columnAt(i);
 
-      if (temp >= start)
-      {
-        selected.setElementAt(new Integer(temp - change), i);
-      }
-    }
+    selected.compensateForEdits(start, change);
 
     if (hiddenColumns != null)
     {
@@ -300,13 +401,13 @@ public class ColumnSelection
   {
     if (shiftrecord != null)
     {
-      Vector shifts = shiftrecord.shifts;
+      final List<int[]> shifts = shiftrecord.getShifts();
       if (shifts != null && shifts.size() > 0)
       {
         int shifted = 0;
         for (int i = 0, j = shifts.size(); i < j; i++)
         {
-          int[] sh = (int[]) shifts.elementAt(i);
+          int[] sh = shifts.get(i);
           // compensateForEdit(shifted+sh[0], sh[1]);
           compensateForDelEdits(shifted + sh[0], sh[1]);
           shifted -= sh[1];
@@ -321,16 +422,17 @@ public class ColumnSelection
    * removes intersection of position,length ranges in deletions from the
    * start,end regions marked in intervals.
    * 
-   * @param deletions
+   * @param shifts
    * @param intervals
    * @return
    */
-  private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+  private boolean pruneIntervalVector(final List<int[]> shifts,
+          Vector<int[]> intervals)
   {
     boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
-    int hr[] = (int[]) intervals.elementAt(i);
-    int sr[] = (int[]) deletions.elementAt(s);
+    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+    int hr[] = intervals.elementAt(i);
+    int sr[] = shifts.get(s);
     while (i <= j && s <= t)
     {
       boolean trailinghn = hr[1] >= sr[0];
@@ -338,7 +440,7 @@ public class ColumnSelection
       {
         if (i < j)
         {
-          hr = (int[]) intervals.elementAt(++i);
+          hr = intervals.elementAt(++i);
         }
         else
         {
@@ -351,7 +453,7 @@ public class ColumnSelection
       { // leadinghc disjoint or not a deletion
         if (s < t)
         {
-          sr = (int[]) deletions.elementAt(++s);
+          sr = shifts.get(++s);
         }
         else
         {
@@ -371,7 +473,7 @@ public class ColumnSelection
           j--;
           if (i <= j)
           {
-            hr = (int[]) intervals.elementAt(i);
+            hr = intervals.elementAt(i);
           }
           continue;
         }
@@ -397,7 +499,7 @@ public class ColumnSelection
           // sr contained in hr
           if (s < t)
           {
-            sr = (int[]) deletions.elementAt(++s);
+            sr = shifts.get(++s);
           }
           else
           {
@@ -411,35 +513,6 @@ public class ColumnSelection
     // operations.
   }
 
-  private boolean pruneColumnList(Vector deletion, Vector list)
-  {
-    int s = 0, t = deletion.size();
-    int[] sr = (int[]) list.elementAt(s++);
-    boolean pruned = false;
-    int i = 0, j = list.size();
-    while (i < j && s <= t)
-    {
-      int c = ((Integer) list.elementAt(i++)).intValue();
-      if (sr[0] <= c)
-      {
-        if (sr[1] + sr[0] >= c)
-        { // sr[1] -ve means inseriton.
-          list.removeElementAt(--i);
-          j--;
-        }
-        else
-        {
-          if (s < t)
-          {
-            sr = (int[]) deletion.elementAt(s);
-          }
-          s++;
-        }
-      }
-    }
-    return pruned;
-  }
-
   /**
    * remove any hiddenColumns or selected columns and shift remaining based on a
    * series of position, range deletions.
@@ -450,7 +523,7 @@ public class ColumnSelection
   {
     if (deletions != null)
     {
-      Vector shifts = deletions.shifts;
+      final List<int[]> shifts = deletions.getShifts();
       if (shifts != null && shifts.size() > 0)
       {
         // delete any intervals intersecting.
@@ -464,7 +537,7 @@ public class ColumnSelection
         }
         if (selected != null && selected.size() > 0)
         {
-          pruneColumnList(shifts, selected);
+          selected.pruneColumnList(shifts);
           if (selected != null && selected.size() == 0)
           {
             selected = null;
@@ -477,16 +550,14 @@ public class ColumnSelection
   }
 
   /**
-   * This Method is used to return all the HiddenColumn regions less than the
-   * given index.
+   * This Method is used to return all the HiddenColumn regions
    * 
-   * @param end
-   *          int
-   * @return Vector
+   * @return empty list or List of hidden column intervals
    */
   public List<int[]> getHiddenColumns()
   {
-    return hiddenColumns;
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
   }
 
   /**
@@ -632,65 +703,89 @@ public class ColumnSelection
 
   public void hideSelectedColumns()
   {
-    while (size() > 0)
+    while (!selected.isEmpty())
     {
-      int column = ((Integer) getSelected().firstElement()).intValue();
+      int column = selected.elementAt(0);
       hideColumns(column);
     }
 
   }
 
+  /**
+   * Adds the specified column range to the hidden columns
+   * 
+   * @param start
+   * @param end
+   */
   public void hideColumns(int start, int end)
   {
     if (hiddenColumns == null)
     {
-      hiddenColumns = new Vector();
+      hiddenColumns = new Vector<int[]>();
     }
 
-    boolean added = false;
-    boolean overlap = false;
-
+    /*
+     * traverse existing hidden ranges and insert / amend / append as
+     * appropriate
+     */
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
       int[] region = hiddenColumns.elementAt(i);
-      if (start <= region[1] && end >= region[0])
+
+      if (end < region[0] - 1)
       {
-        hiddenColumns.removeElementAt(i);
-        overlap = true;
-        break;
+        /*
+         * insert discontiguous preceding range
+         */
+        hiddenColumns.insertElementAt(new int[] { start, end }, i);
+        return;
       }
-      else if (end < region[0] && start < region[0])
+
+      if (end <= region[1])
       {
-        hiddenColumns.insertElementAt(new int[]
-        { start, end }, i);
-        added = true;
-        break;
+        /*
+         * new range overlaps existing, or is contiguous preceding it - adjust
+         * start column
+         */
+        region[0] = Math.min(region[0], start);
+        return;
       }
-    }
 
-    if (overlap)
-    {
-      hideColumns(start, end);
-    }
-    else if (!added)
-    {
-      hiddenColumns.addElement(new int[]
-      { start, end });
+      if (start <= region[1] + 1)
+      {
+        /*
+         * new range overlaps existing, or is contiguous following it - adjust
+         * start and end columns
+         */
+        region[0] = Math.min(region[0], start);
+        region[1] = Math.max(region[1], end);
+        return;
+      }
     }
 
+    /*
+     * remaining case is that the new range follows everything else
+     */
+      hiddenColumns.addElement(new int[] { start, end });
   }
 
   /**
-   * This method will find a range of selected columns around the column
-   * specified
+   * Hides the specified column and any adjacent selected columns
    * 
    * @param res
    *          int
    */
   public void hideColumns(int col)
   {
-    // First find out range of columns to hide
-    int min = col, max = col + 1;
+    /*
+     * deselect column (whether selected or not!)
+     */
+    removeElement(col);
+
+    /*
+     * find adjacent selected columns
+     */
+    int min = col - 1, max = col + 1;
     while (contains(min))
     {
       removeElement(min);
@@ -703,6 +798,9 @@ public class ColumnSelection
       max++;
     }
 
+    /*
+     * min, max are now the closest unselected columns
+     */
     min++;
     max--;
     if (min > max)
@@ -713,6 +811,9 @@ public class ColumnSelection
     hideColumns(min, max);
   }
 
+  /**
+   * Unhides, and adds to the selection list, all hidden columns
+   */
   public void revealAllHiddenColumns()
   {
     if (hiddenColumns != null)
@@ -730,12 +831,18 @@ public class ColumnSelection
     hiddenColumns = null;
   }
 
-  public void revealHiddenColumns(int res)
+  /**
+   * Reveals, and marks as selected, the hidden column range with the given
+   * start column
+   * 
+   * @param start
+   */
+  public void revealHiddenColumns(int start)
   {
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
       int[] region = hiddenColumns.elementAt(i);
-      if (res == region[0])
+      if (start == region[0])
       {
         for (int j = region[0]; j < region[1] + 1; j++)
         {
@@ -756,9 +863,8 @@ public class ColumnSelection
   {
     if (hiddenColumns != null)
     {
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      for (int[] region : hiddenColumns)
       {
-        int[] region = hiddenColumns.elementAt(i);
         if (column >= region[0] && column <= region[1])
         {
           return false;
@@ -780,15 +886,15 @@ public class ColumnSelection
     {
       if (copy.selected != null)
       {
-        selected = new Vector();
+        selected = new IntList();
         for (int i = 0, j = copy.selected.size(); i < j; i++)
         {
-          selected.addElement(copy.selected.elementAt(i));
+          selected.add(copy.selected.elementAt(i));
         }
       }
       if (copy.hiddenColumns != null)
       {
-        hiddenColumns = new Vector(copy.hiddenColumns.size());
+        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
         for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
         {
           int[] rh, cp;
@@ -885,7 +991,7 @@ public class ColumnSelection
   {
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      Vector visiblecontigs = new Vector();
+      List<int[]> visiblecontigs = new ArrayList<int[]>();
       List<int[]> regions = getHiddenColumns();
 
       int vstart = start;
@@ -904,32 +1010,29 @@ public class ColumnSelection
         }
         if (hideStart > vstart)
         {
-          visiblecontigs.addElement(new int[]
-          { vstart, hideStart - 1 });
+          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
 
       if (vstart < end)
       {
-        visiblecontigs.addElement(new int[]
-        { vstart, end - 1 });
+        visiblecontigs.add(new int[] { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
       {
-        int[] vc = (int[]) visiblecontigs.elementAt(i);
-        visiblecontigs.setElementAt(null, i);
+        int[] vc = visiblecontigs.get(i);
+        visiblecontigs.set(i, null);
         vcontigs[i * 2] = vc[0];
         vcontigs[i * 2 + 1] = vc[1];
       }
-      visiblecontigs.removeAllElements();
+      visiblecontigs.clear();
       return vcontigs;
     }
     else
     {
-      return new int[]
-      { start, end - 1 };
+      return new int[] { start, end - 1 };
     }
   }
 
@@ -970,7 +1073,7 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       // then mangle the alignmentAnnotation annotation array
-      Vector annels = new Vector();
+      Vector<Annotation[]> annels = new Vector<Annotation[]>();
       Annotation[] els = null;
       List<int[]> regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
@@ -1026,12 +1129,12 @@ public class ColumnSelection
       {
         return;
       }
-      Enumeration e = annels.elements();
+
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;
-      while (e.hasMoreElements())
+
+      for (Annotation[] chnk : annels)
       {
-        Annotation[] chnk = (Annotation[]) e.nextElement();
         System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
                 chnk.length);
         w += chnk.length;
@@ -1077,18 +1180,13 @@ public class ColumnSelection
    */
   public void addElementsFrom(ColumnSelection colsel)
   {
-    if (colsel != null && colsel.size() > 0)
+    if (colsel != null && !colsel.isEmpty())
     {
-      Enumeration e = colsel.getSelected().elements();
-      while (e.hasMoreElements())
+      for (Integer col : colsel.getSelected())
       {
-        Object eo = e.nextElement();
-        if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+        if (hiddenColumns != null && isVisible(col.intValue()))
         {
-          if (!selected.contains(eo))
-          {
-            selected.addElement(eo);
-          }
+          selected.add(col);
         }
       }
     }
@@ -1102,22 +1200,20 @@ public class ColumnSelection
    */
   public void setElementsFrom(ColumnSelection colsel)
   {
-    selected = new Vector();
+    selected = new IntList();
     if (colsel.selected != null && colsel.selected.size() > 0)
     {
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
         // only select visible columns in this columns selection
-        selected = new Vector();
         addElementsFrom(colsel);
       }
       else
       {
         // add everything regardless
-        Enumeration en = colsel.selected.elements();
-        while (en.hasMoreElements())
+        for (Integer col : colsel.getSelected())
         {
-          selected.addElement(en.nextElement());
+          addElement(col);
         }
       }
     }
@@ -1137,7 +1233,7 @@ public class ColumnSelection
    *         profileseq marked as hidden.
    */
   public static ColumnSelection propagateInsertions(SequenceI profileseq,
-          Alignment al, AlignmentView input)
+          AlignmentI al, AlignmentView input)
   {
     int profsqpos = 0;
 
@@ -1285,6 +1381,15 @@ public class ColumnSelection
   }
 
   /**
+   * 
+   * @return true if there are more than one set of columns hidden
+   */
+  public boolean hasManyHiddenColumns()
+  {
+    return hiddenColumns != null && hiddenColumns.size() > 1;
+  }
+
+  /**
    * mark the columns corresponding to gap characters as hidden in the column
    * selection
    * 
@@ -1298,4 +1403,89 @@ public class ColumnSelection
       hideColumns(r[0], r[1]);
     }
   }
+
+  public boolean filterAnnotations(Annotation[] annotations,
+          AnnotationFilterParameter filterParams)
+  {
+    this.revealAllHiddenColumns();
+    this.clear();
+    int count = 0;
+    do
+    {
+      if (annotations[count] != null)
+      {
+
+        boolean itemMatched = false;
+
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+                && annotations[count].value >= filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+                && annotations[count].value <= filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterAlphaHelix()
+                && annotations[count].secondaryStructure == 'H')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterBetaSheet()
+                && annotations[count].secondaryStructure == 'E')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterTurn()
+                && annotations[count].secondaryStructure == 'S')
+        {
+          itemMatched = true;
+        }
+
+        String regexSearchString = filterParams.getRegexString();
+        if (regexSearchString != null
+                && !filterParams.getRegexSearchFields().isEmpty())
+        {
+          List<SearchableAnnotationField> fields = filterParams
+                  .getRegexSearchFields();
+          try
+          {
+            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
+                    && annotations[count].displayCharacter
+                            .matches(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          } catch (java.util.regex.PatternSyntaxException pse)
+          {
+            if (annotations[count].displayCharacter
+                    .equals(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          }
+          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
+                  && annotations[count].description != null
+                  && annotations[count].description
+                          .matches(regexSearchString))
+          {
+            itemMatched = true;
+          }
+        }
+
+        if (itemMatched)
+        {
+          this.addElement(count);
+        }
+      }
+      count++;
+    } while (count < annotations.length);
+    return false;
+  }
 }