X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=6fb584ca4774b3ec6a2ab2996d101d567d642af0;hb=f41f5deaf0c8c1bbfb3fe4ca8be208d27b8e11d7;hp=0655660e4ad9da84136ec807586e075da0c36e95;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 0655660..6fb584c 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,36 +1,49 @@
 /*
- * 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.
  * 
  * 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.
+ * 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/>.
+ * 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.datamodel;
 
-import java.util.*;
+import jalview.util.ShiftList;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * NOTE: Columns are zero based.
  */
 public class ColumnSelection
 {
-  Vector selected = new Vector();
+  /*
+   * list of selected columns (not ordered)
+   */
+  Vector<Integer> selected = new Vector<Integer>();
 
-  // Vector of int [] {startCol, endCol}
-  Vector hiddenColumns;
+  /*
+   * list of hidden column [start, end] ranges; the list is maintained in
+   * ascending start column order
+   */
+  Vector<int[]> hiddenColumns;
 
   /**
    * Add a column to the selection
@@ -56,7 +69,7 @@ public class ColumnSelection
   }
 
   /**
-   * removes col from selection
+   * Removes value 'col' from the selection (not the col'th item)
    * 
    * @param col
    *          index of column to be removed
@@ -67,6 +80,8 @@ public class ColumnSelection
 
     if (selected.contains(colInt))
     {
+      // 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
       selected.removeElement(colInt);
     }
   }
@@ -93,10 +108,10 @@ public class ColumnSelection
   }
 
   /**
-   * 
-   * @return Vector containing selected columns as Integers
+   * Returns a list of selected columns. The list contains no duplicates but is
+   * not necessarily ordered.
    */
-  public Vector getSelected()
+  public List<Integer> getSelected()
   {
     return selected;
   }
@@ -114,26 +129,11 @@ 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();
   }
 
   /**
@@ -145,11 +145,11 @@ public class ColumnSelection
   {
     int max = -1;
 
-    for (int i = 0; i < selected.size(); i++)
+    for (int sel : getSelected())
     {
-      if (columnAt(i) > max)
+      if (sel > max)
       {
-        max = columnAt(i);
+        max = sel;
       }
     }
 
@@ -165,11 +165,11 @@ public class ColumnSelection
   {
     int min = 1000000000;
 
-    for (int i = 0; i < selected.size(); i++)
+    for (int sel : getSelected())
     {
-      if (columnAt(i) < min)
+      if (sel < min)
       {
-        min = columnAt(i);
+        min = sel;
       }
     }
 
@@ -184,29 +184,30 @@ public class ColumnSelection
    * @param left
    *          shift in edit (+ve for removal, or -ve for inserts)
    */
-  public Vector compensateForEdit(int start, int change)
+  public List<int[]> compensateForEdit(int start, int change)
   {
-    Vector deletedHiddenColumns = null;
-    for (int i = 0; i < size(); i++)
+    List<int[]> deletedHiddenColumns = null;
+    for (int i = 0; i < selected.size(); i++)
     {
-      int temp = columnAt(i);
+      int temp = selected.get(i);
 
       if (temp >= start)
       {
+        // if this ever changes to List.set(), swap parameter order!!
         selected.setElementAt(new Integer(temp - change), i);
       }
     }
 
     if (hiddenColumns != null)
     {
-      deletedHiddenColumns = new Vector();
+      deletedHiddenColumns = new ArrayList<int[]>();
       int hSize = hiddenColumns.size();
       for (int i = 0; i < hSize; i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
-          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
+          deletedHiddenColumns.add(region);
 
           hiddenColumns.removeElementAt(i);
           i--;
@@ -244,12 +245,13 @@ public class ColumnSelection
    */
   private void compensateForDelEdits(int start, int change)
   {
-    for (int i = 0; i < size(); i++)
+    for (int i = 0; i < selected.size(); i++)
     {
-      int temp = columnAt(i);
+      int temp = selected.get(i);
 
       if (temp >= start)
       {
+        // if this ever changes to List.set(), must swap parameter order!!!
         selected.setElementAt(new Integer(temp - change), i);
       }
     }
@@ -258,7 +260,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (region[0] >= start)
         {
           region[0] -= change;
@@ -295,13 +297,13 @@ 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];
@@ -316,16 +318,17 @@ 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];
@@ -333,7 +336,7 @@ public class ColumnSelection
       {
         if (i < j)
         {
-          hr = (int[]) intervals.elementAt(++i);
+          hr = intervals.elementAt(++i);
         }
         else
         {
@@ -346,7 +349,7 @@ public class ColumnSelection
       { // leadinghc disjoint or not a deletion
         if (s < t)
         {
-          sr = (int[]) deletions.elementAt(++s);
+          sr = shifts.get(++s);
         }
         else
         {
@@ -366,7 +369,7 @@ public class ColumnSelection
           j--;
           if (i <= j)
           {
-            hr = (int[]) intervals.elementAt(i);
+            hr = intervals.elementAt(i);
           }
           continue;
         }
@@ -392,7 +395,7 @@ public class ColumnSelection
           // sr contained in hr
           if (s < t)
           {
-            sr = (int[]) deletions.elementAt(++s);
+            sr = shifts.get(++s);
           }
           else
           {
@@ -406,15 +409,16 @@ public class ColumnSelection
     // operations.
   }
 
-  private boolean pruneColumnList(Vector deletion, Vector list)
+  private boolean pruneColumnList(final List<int[]> shifts,
+          Vector<Integer> list)
   {
-    int s = 0, t = deletion.size();
-    int[] sr = (int[]) list.elementAt(s++);
+    int s = 0, t = shifts.size();
+    int[] sr = shifts.get(s++);
     boolean pruned = false;
     int i = 0, j = list.size();
     while (i < j && s <= t)
     {
-      int c = ((Integer) list.elementAt(i++)).intValue();
+      int c = list.elementAt(i++).intValue();
       if (sr[0] <= c)
       {
         if (sr[1] + sr[0] >= c)
@@ -426,7 +430,7 @@ public class ColumnSelection
         {
           if (s < t)
           {
-            sr = (int[]) deletion.elementAt(s);
+            sr = shifts.get(s);
           }
           s++;
         }
@@ -445,7 +449,7 @@ 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.
@@ -472,16 +476,14 @@ 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 Vector getHiddenColumns()
+  public List<int[]> getHiddenColumns()
   {
-    return hiddenColumns;
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
   }
 
   /**
@@ -498,7 +500,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (result >= region[0])
         {
           result += region[1] - region[0] + 1;
@@ -526,7 +528,7 @@ public class ColumnSelection
       int[] region;
       do
       {
-        region = (int[]) hiddenColumns.elementAt(index++);
+        region = hiddenColumns.elementAt(index++);
         if (hiddenColumn > region[1])
         {
           result -= region[1] + 1 - region[0];
@@ -552,7 +554,7 @@ public class ColumnSelection
       int gaps = 0;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (hiddenRegion == 0)
         {
           return region[0];
@@ -583,7 +585,7 @@ public class ColumnSelection
       int index = 0;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (alPos < region[0])
         {
           return region[0];
@@ -611,7 +613,7 @@ public class ColumnSelection
       int index = hiddenColumns.size() - 1;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (alPos > region[1])
         {
           return region[1];
@@ -627,65 +629,89 @@ public class ColumnSelection
 
   public void hideSelectedColumns()
   {
-    while (size() > 0)
+    while (!selected.isEmpty())
     {
-      int column = ((Integer) getSelected().firstElement()).intValue();
+      int column = selected.get(0).intValue();
       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 = (int[]) hiddenColumns.elementAt(i);
-      if (start <= region[1] && end >= region[0])
+      int[] region = hiddenColumns.elementAt(i);
+
+      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);
@@ -698,6 +724,9 @@ public class ColumnSelection
       max++;
     }
 
+    /*
+     * min, max are now the closest unselected columns
+     */
     min++;
     max--;
     if (min > max)
@@ -708,13 +737,16 @@ public class ColumnSelection
     hideColumns(min, max);
   }
 
+  /**
+   * Unhides, and adds to the selection list, all hidden columns
+   */
   public void revealAllHiddenColumns()
   {
     if (hiddenColumns != null)
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         for (int j = region[0]; j < region[1] + 1; j++)
         {
           addElement(j);
@@ -725,12 +757,18 @@ 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 = (int[]) hiddenColumns.elementAt(i);
-      if (res == region[0])
+      int[] region = hiddenColumns.elementAt(i);
+      if (start == region[0])
       {
         for (int j = region[0]; j < region[1] + 1; j++)
         {
@@ -750,14 +788,15 @@ public class ColumnSelection
   public boolean isVisible(int column)
   {
     if (hiddenColumns != null)
-      for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      for (int[] region : hiddenColumns)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
         if (column >= region[0] && column <= region[1])
         {
           return false;
         }
       }
+    }
 
     return true;
   }
@@ -773,7 +812,7 @@ public class ColumnSelection
     {
       if (copy.selected != null)
       {
-        selected = new Vector();
+        selected = new Vector<Integer>();
         for (int i = 0, j = copy.selected.size(); i < j; i++)
         {
           selected.addElement(copy.selected.elementAt(i));
@@ -781,11 +820,11 @@ public class ColumnSelection
       }
       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;
-          rh = (int[]) copy.hiddenColumns.elementAt(i);
+          rh = copy.hiddenColumns.elementAt(i);
           if (rh != null)
           {
             cp = new int[rh.length];
@@ -814,7 +853,7 @@ public class ColumnSelection
       for (i = 0; i < iSize; i++)
       {
         StringBuffer visibleSeq = new StringBuffer();
-        Vector regions = getHiddenColumns();
+        List<int[]> regions = getHiddenColumns();
 
         int blockStart = start, blockEnd = end;
         int[] region;
@@ -822,7 +861,7 @@ public class ColumnSelection
 
         for (int j = 0; j < regions.size(); j++)
         {
-          region = (int[]) regions.elementAt(j);
+          region = regions.get(j);
           hideStart = region[0];
           hideEnd = region[1];
 
@@ -878,8 +917,8 @@ public class ColumnSelection
   {
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      Vector visiblecontigs = new Vector();
-      Vector regions = getHiddenColumns();
+      List<int[]> visiblecontigs = new ArrayList<int[]>();
+      List<int[]> regions = getHiddenColumns();
 
       int vstart = start;
       int[] region;
@@ -887,7 +926,7 @@ public class ColumnSelection
 
       for (int j = 0; vstart < end && j < regions.size(); j++)
       {
-        region = (int[]) regions.elementAt(j);
+        region = regions.get(j);
         hideStart = region[0];
         hideEnd = region[1];
 
@@ -897,32 +936,29 @@ 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 };
     }
   }
 
@@ -963,16 +999,16 @@ 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;
-      Vector regions = getHiddenColumns();
+      List<int[]> regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
       int[] region;
       int hideStart, hideEnd, w = 0;
 
       for (int j = 0; j < regions.size(); j++)
       {
-        region = (int[]) regions.elementAt(j);
+        region = regions.get(j);
         hideStart = region[0];
         hideEnd = region[1];
 
@@ -1016,13 +1052,15 @@ public class ColumnSelection
         w += els.length;
       }
       if (w == 0)
+      {
         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;
@@ -1068,17 +1106,15 @@ 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))
+          if (!selected.contains(col))
           {
-            selected.addElement(eo);
+            selected.addElement(col);
           }
         }
       }
@@ -1093,22 +1129,20 @@ public class ColumnSelection
    */
   public void setElementsFrom(ColumnSelection colsel)
   {
-    selected = new Vector();
+    selected = new Vector<Integer>();
     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);
         }
       }
     }
@@ -1128,7 +1162,7 @@ public class ColumnSelection
    *         profileseq marked as hidden.
    */
   public static ColumnSelection propagateInsertions(SequenceI profileseq,
-          Alignment al, AlignmentView input)
+          AlignmentI al, AlignmentView input)
   {
     int profsqpos = 0;
 
@@ -1256,4 +1290,131 @@ public class ColumnSelection
       }
     }
   }
+
+  /**
+   * 
+   * @return true if there are columns marked
+   */
+  public boolean hasSelectedColumns()
+  {
+    return (selected != null && selected.size() > 0);
+  }
+
+  /**
+   * 
+   * @return true if there are columns hidden
+   */
+  public boolean hasHiddenColumns()
+  {
+    return hiddenColumns != null && hiddenColumns.size() > 0;
+  }
+
+  /**
+   * 
+   * @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
+   * 
+   * @param sr
+   */
+  public void hideInsertionsFor(SequenceI sr)
+  {
+    List<int[]> inserts = sr.getInsertions();
+    for (int[] r : inserts)
+    {
+      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;
+  }
 }