X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;fp=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=2edb3f1d8905aa6a30854b146329200fcc5d72b8;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=0000000000000000000000000000000000000000;hpb=557859a3ea9a1e86899ef2033de90eadb6d87118;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
new file mode 100644
index 0000000..2edb3f1
--- /dev/null
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -0,0 +1,1264 @@
+package jalview.datamodel;
+
+import jalview.util.Comparison;
+import jalview.util.ShiftList;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Vector;
+
+public class HiddenColumns
+{
+  /*
+   * list of hidden column [start, end] ranges; the list is maintained in
+   * ascending start column order
+   */
+  private Vector<int[]> hiddenColumns;
+
+  /**
+   * This Method is used to return all the HiddenColumn regions
+   * 
+   * @return empty list or List of hidden column intervals
+   */
+  public List<int[]> getHiddenRegions()
+  {
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
+  }
+
+  /**
+   * Find the number of hidden columns
+   * 
+   * @return number of hidden columns
+   */
+  public int getSize()
+  {
+    int size = 0;
+    if (hasHidden())
+    {
+      for (int[] range : hiddenColumns)
+      {
+        size += range[1] - range[0] + 1;
+      }
+    }
+    return size;
+  }
+
+  /**
+   * Answers if there are any hidden columns
+   * 
+   * @return true if there are hidden columns
+   */
+  public boolean hasHidden()
+  {
+    return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+  }
+
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof HiddenColumns))
+    {
+      return false;
+    }
+    HiddenColumns that = (HiddenColumns) obj;
+
+    /*
+     * check hidden columns are either both null, or match
+     */
+    if (this.hiddenColumns == null)
+    {
+      return (that.hiddenColumns == null);
+    }
+    if (that.hiddenColumns == null
+            || that.hiddenColumns.size() != this.hiddenColumns.size())
+    {
+      return false;
+    }
+    int i = 0;
+    for (int[] thisRange : hiddenColumns)
+    {
+      int[] thatRange = that.hiddenColumns.get(i++);
+      if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Return absolute column index for a visible column index
+   * 
+   * @param column
+   *          int column index in alignment view (count from zero)
+   * @return alignment column index for column
+   */
+  public int adjustForHiddenColumns(int column)
+  {
+    int result = column;
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        if (result >= region[0])
+        {
+          result += region[1] - region[0] + 1;
+        }
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Use this method to find out where a column will appear in the visible
+   * alignment when hidden columns exist. If the column is not visible, then the
+   * left-most visible column will always be returned.
+   * 
+   * @param hiddenColumn
+   *          the column index in the full alignment including hidden columns
+   * @return the position of the column in the visible alignment
+   */
+  public int findColumnPosition(int hiddenColumn)
+  {
+    int result = hiddenColumn;
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      int[] region;
+      do
+      {
+        region = hiddenColumns.elementAt(index++);
+        if (hiddenColumn > region[1])
+        {
+          result -= region[1] + 1 - region[0];
+        }
+      } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+
+      if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+      {
+        // Here the hidden column is within a region, so
+        // we want to return the position of region[0]-1, adjusted for any
+        // earlier hidden columns.
+        // Calculate the difference between the actual hidden col position
+        // and region[0]-1, and then subtract from result to convert result from
+        // the adjusted hiddenColumn value to the adjusted region[0]-1 value
+
+        // However, if the region begins at 0 we cannot return region[0]-1
+        // just return 0
+        if (region[0] == 0)
+        {
+          return 0;
+        }
+        else
+        {
+          return result - (hiddenColumn - region[0] + 1);
+        }
+      }
+    }
+    return result; // return the shifted position after removing hidden columns.
+  }
+
+  /**
+   * Find the visible column which is a given visible number of columns to the
+   * left of another visible column. i.e. for a startColumn x, the column which
+   * is distance 1 away will be column x-1.
+   * 
+   * @param visibleDistance
+   *          the number of visible columns to offset by
+   * @param startColumn
+   *          the column to start from
+   * @return the position of the column in the visible alignment
+   */
+  public int subtractVisibleColumns(int visibleDistance, int startColumn)
+  {
+    int distance = visibleDistance;
+
+    // in case startColumn is in a hidden region, move it to the left
+    int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+
+    // get index of hidden region to left of start
+    int index = getHiddenIndexLeft(start);
+    if (index == -1)
+    {
+      // no hidden regions to left of startColumn
+      return start - distance;
+    }
+
+    // walk backwards through the alignment subtracting the counts of visible
+    // columns from distance
+    int[] region;
+    int gap = 0;
+    int nextstart = start;
+
+    while ((index > -1) && (distance - gap > 0))
+    {
+      // subtract the gap to right of region from distance
+      distance -= gap;
+      start = nextstart;
+
+      // calculate the next gap
+      region = hiddenColumns.get(index);
+      gap = start - region[1];
+
+      // set start to just to left of current region
+      nextstart = region[0] - 1;
+      index--;
+    }
+
+    if (distance - gap > 0)
+    {
+      // fell out of loop because there are no more hidden regions
+      distance -= gap;
+      return nextstart - distance;
+    }
+    return start - distance;
+
+  }
+
+  /**
+   * Use this method to determine where the next hiddenRegion starts
+   * 
+   * @param hiddenRegion
+   *          index of hidden region (counts from 0)
+   * @return column number in visible view
+   */
+  public int findHiddenRegionPosition(int hiddenRegion)
+  {
+    int result = 0;
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      int gaps = 0;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (hiddenRegion == 0)
+        {
+          return region[0];
+        }
+
+        gaps += region[1] + 1 - region[0];
+        result = region[1] + 1;
+        index++;
+      } while (index <= hiddenRegion);
+
+      result -= gaps;
+    }
+
+    return result;
+  }
+
+  /**
+   * This method returns the rightmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the next hidden column.
+   * 
+   * @param index
+   *          int
+   */
+  public int getHiddenBoundaryRight(int alPos)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = 0;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (alPos < region[0])
+        {
+          return region[0];
+        }
+
+        index++;
+      } while (index < hiddenColumns.size());
+    }
+
+    return alPos;
+
+  }
+
+  /**
+   * This method returns the leftmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the previous hidden column.
+   * 
+   * @param index
+   *          int
+   */
+  public int getHiddenBoundaryLeft(int alPos)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = hiddenColumns.size() - 1;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (alPos > region[1])
+        {
+          return region[1];
+        }
+
+        index--;
+      } while (index > -1);
+    }
+
+    return alPos;
+
+  }
+
+  /**
+   * This method returns the index of the hidden region to the left of a column
+   * position. If the column is in a hidden region it returns the index of the
+   * region to the left. If there is no hidden region to the left it returns -1.
+   * 
+   * @param pos
+   *          int
+   */
+  private int getHiddenIndexLeft(int pos)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = hiddenColumns.size() - 1;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (pos > region[1])
+        {
+          return index;
+        }
+
+        index--;
+      } while (index > -1);
+    }
+
+    return -1;
+
+  }
+
+  /**
+   * 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<int[]>();
+    }
+
+    /*
+     * traverse existing hidden ranges and insert / amend / append as
+     * appropriate
+     */
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = hiddenColumns.elementAt(i);
+
+      if (end < region[0] - 1)
+      {
+        /*
+         * insert discontiguous preceding range
+         */
+        hiddenColumns.insertElementAt(new int[] { start, end }, i);
+        return;
+      }
+
+      if (end <= region[1])
+      {
+        /*
+         * new range overlaps existing, or is contiguous preceding it - adjust
+         * start column
+         */
+        region[0] = Math.min(region[0], start);
+        return;
+      }
+
+      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);
+
+        /*
+         * also update or remove any subsequent ranges 
+         * that are overlapped
+         */
+        while (i < hiddenColumns.size() - 1)
+        {
+          int[] nextRegion = hiddenColumns.get(i + 1);
+          if (nextRegion[0] > end + 1)
+          {
+            /*
+             * gap to next hidden range - no more to update
+             */
+            break;
+          }
+          region[1] = Math.max(nextRegion[1], end);
+          hiddenColumns.remove(i + 1);
+        }
+        return;
+      }
+    }
+
+    /*
+     * remaining case is that the new range follows everything else
+     */
+    hiddenColumns.addElement(new int[] { start, end });
+  }
+
+  public boolean isVisible(int column)
+  {
+    if (hiddenColumns != null)
+    {
+      for (int[] region : hiddenColumns)
+      {
+        if (column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
+      }
+    }
+
+    return true;
+  }
+
+  /**
+   * ColumnSelection
+   */
+  public HiddenColumns()
+  {
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @param copy
+   */
+  public HiddenColumns(HiddenColumns copy)
+  {
+    if (copy != null)
+    {
+      if (copy.hiddenColumns != null)
+      {
+        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
+        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+        {
+          int[] rh, cp;
+          rh = copy.hiddenColumns.elementAt(i);
+          if (rh != null)
+          {
+            cp = new int[rh.length];
+            System.arraycopy(rh, 0, cp, 0, rh.length);
+            hiddenColumns.addElement(cp);
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * propagate shift in alignment columns to column selection
+   * 
+   * @param start
+   *          beginning of edit
+   * @param left
+   *          shift in edit (+ve for removal, or -ve for inserts)
+   */
+  public List<int[]> compensateForEdit(int start, int change,
+          ColumnSelection sel)
+  {
+    List<int[]> deletedHiddenColumns = null;
+
+    if (hiddenColumns != null)
+    {
+      deletedHiddenColumns = new ArrayList<int[]>();
+      int hSize = hiddenColumns.size();
+      for (int i = 0; i < hSize; i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        if (region[0] > start && start + change > region[1])
+        {
+          deletedHiddenColumns.add(region);
+
+          hiddenColumns.removeElementAt(i);
+          i--;
+          hSize--;
+          continue;
+        }
+
+        if (region[0] > start)
+        {
+          region[0] -= change;
+          region[1] -= change;
+        }
+
+        if (region[0] < 0)
+        {
+          region[0] = 0;
+        }
+
+      }
+
+      this.revealHiddenColumns(0, sel);
+    }
+
+    return deletedHiddenColumns;
+  }
+
+  /**
+   * propagate shift in alignment columns to column selection special version of
+   * compensateForEdit - allowing for edits within hidden regions
+   * 
+   * @param start
+   *          beginning of edit
+   * @param left
+   *          shift in edit (+ve for removal, or -ve for inserts)
+   */
+  public void compensateForDelEdits(int start, int change)
+  {
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        if (region[0] >= start)
+        {
+          region[0] -= change;
+        }
+        if (region[1] >= start)
+        {
+          region[1] -= change;
+        }
+        if (region[1] < region[0])
+        {
+          hiddenColumns.removeElementAt(i--);
+        }
+
+        if (region[0] < 0)
+        {
+          region[0] = 0;
+        }
+        if (region[1] < 0)
+        {
+          region[1] = 0;
+        }
+      }
+    }
+  }
+
+  /**
+   * return all visible segments between the given start and end boundaries
+   * 
+   * @param start
+   *          (first column inclusive from 0)
+   * @param end
+   *          (last column - not inclusive)
+   * @return int[] {i_start, i_end, ..} where intervals lie in
+   *         start<=i_start<=i_end<end
+   */
+  public int[] getVisibleContigs(int start, int end)
+  {
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      List<int[]> visiblecontigs = new ArrayList<int[]>();
+      List<int[]> regions = getHiddenRegions();
+
+      int vstart = start;
+      int[] region;
+      int hideStart, hideEnd;
+
+      for (int j = 0; vstart < end && j < regions.size(); j++)
+      {
+        region = regions.get(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        if (hideEnd < vstart)
+        {
+          continue;
+        }
+        if (hideStart > vstart)
+        {
+          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+        }
+        vstart = hideEnd + 1;
+      }
+
+      if (vstart < end)
+      {
+        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 = visiblecontigs.get(i);
+        visiblecontigs.set(i, null);
+        vcontigs[i * 2] = vc[0];
+        vcontigs[i * 2 + 1] = vc[1];
+      }
+      visiblecontigs.clear();
+      return vcontigs;
+    }
+    else
+    {
+      return new int[] { start, end - 1 };
+    }
+  }
+
+  public String[] getVisibleSequenceStrings(int start, int end,
+          SequenceI[] seqs)
+  {
+    int i, iSize = seqs.length;
+    String selections[] = new String[iSize];
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        StringBuffer visibleSeq = new StringBuffer();
+        List<int[]> regions = getHiddenRegions();
+
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd;
+
+        for (int j = 0; j < regions.size(); j++)
+        {
+          region = regions.get(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+
+          if (hideStart < start)
+          {
+            continue;
+          }
+
+          blockStart = Math.min(blockStart, hideEnd + 1);
+          blockEnd = Math.min(blockEnd, hideStart);
+
+          if (blockStart > blockEnd)
+          {
+            break;
+          }
+
+          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
+
+        if (end > blockStart)
+        {
+          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
+
+        selections[i] = visibleSeq.toString();
+      }
+    }
+    else
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        selections[i] = seqs[i].getSequenceAsString(start, end);
+      }
+    }
+
+    return selections;
+  }
+
+  /**
+   * Locate the first and last position visible for this sequence. if seq isn't
+   * visible then return the position of the left and right of the hidden
+   * boundary region, and the corresponding alignment column indices for the
+   * extent of the sequence
+   * 
+   * @param seq
+   * @return int[] { visible start, visible end, first seqpos, last seqpos,
+   *         alignment index for seq start, alignment index for seq end }
+   */
+  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+  {
+    int fpos = seq.getStart(), lpos = seq.getEnd();
+    int start = 0;
+
+    if (hiddenColumns == null || hiddenColumns.size() == 0)
+    {
+      int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
+      return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+    }
+
+    // Simply walk along the sequence whilst watching for hidden column
+    // boundaries
+    List<int[]> regions = getHiddenRegions();
+    int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
+            .getLength(), hideEnd = -1;
+    int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+    boolean foundStart = false;
+    for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+            && p < pLen; p++)
+    {
+      if (!Comparison.isGap(seq.getCharAt(p)))
+      {
+        // keep track of first/last column
+        // containing sequence data regardless of visibility
+        if (firstP == -1)
+        {
+          firstP = p;
+        }
+        lastP = p;
+        // update hidden region start/end
+        while (hideEnd < p && rcount < regions.size())
+        {
+          int[] region = regions.get(rcount++);
+          visPrev = visNext;
+          visNext += region[0] - visPrev;
+          hideStart = region[0];
+          hideEnd = region[1];
+        }
+        if (hideEnd < p)
+        {
+          hideStart = seq.getLength();
+        }
+        // update visible boundary for sequence
+        if (p < hideStart)
+        {
+          if (!foundStart)
+          {
+            fpos = spos;
+            start = p;
+            foundStart = true;
+          }
+          lastvispos = p;
+          lpos = spos;
+        }
+        // look for next sequence position
+        spos++;
+      }
+    }
+    if (foundStart)
+    {
+      return new int[] { findColumnPosition(start),
+          findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+    }
+    // otherwise, sequence was completely hidden
+    return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param alignmentAnnotation
+   */
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param alignmentAnnotation
+   *          the annotation to operate on
+   */
+  public void makeVisibleAnnotation(int start, int end,
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    if (alignmentAnnotation.annotations == null)
+    {
+      return;
+    }
+    if (start == end && end == -1)
+    {
+      start = 0;
+      end = alignmentAnnotation.annotations.length;
+    }
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      // then mangle the alignmentAnnotation annotation array
+      Vector<Annotation[]> annels = new Vector<Annotation[]>();
+      Annotation[] els = null;
+      List<int[]> regions = getHiddenRegions();
+      int blockStart = start, blockEnd = end;
+      int[] region;
+      int hideStart, hideEnd, w = 0;
+
+      for (int j = 0; j < regions.size(); j++)
+      {
+        region = regions.get(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        if (hideStart < start)
+        {
+          continue;
+        }
+
+        blockStart = Math.min(blockStart, hideEnd + 1);
+        blockEnd = Math.min(blockEnd, hideStart);
+
+        if (blockStart > blockEnd)
+        {
+          break;
+        }
+
+        annels.addElement(els = new Annotation[blockEnd - blockStart]);
+        System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+                0, els.length);
+        w += els.length;
+        blockStart = hideEnd + 1;
+        blockEnd = end;
+      }
+
+      if (end > blockStart)
+      {
+        annels.addElement(els = new Annotation[end - blockStart + 1]);
+        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+        {
+          // copy just the visible segment of the annotation row
+          System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                  els, 0, els.length);
+        }
+        else
+        {
+          // copy to the end of the annotation row
+          System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                  els, 0,
+                  (alignmentAnnotation.annotations.length - blockStart));
+        }
+        w += els.length;
+      }
+      if (w == 0)
+      {
+        return;
+      }
+
+      alignmentAnnotation.annotations = new Annotation[w];
+      w = 0;
+
+      for (Annotation[] chnk : annels)
+      {
+        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                chnk.length);
+        w += chnk.length;
+      }
+    }
+    else
+    {
+      alignmentAnnotation.restrict(start, end);
+    }
+  }
+
+  /**
+   * 
+   * @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]);
+    }
+  }
+
+  /**
+   * Unhides, and adds to the selection list, all hidden columns
+   */
+  public void revealAllHiddenColumns(ColumnSelection sel)
+  {
+    if (hiddenColumns != null)
+    {
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = hiddenColumns.elementAt(i);
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          sel.addElement(j);
+        }
+      }
+    }
+
+    hiddenColumns = null;
+  }
+
+  /**
+   * Reveals, and marks as selected, the hidden column range with the given
+   * start column
+   * 
+   * @param start
+   */
+  public void revealHiddenColumns(int start, ColumnSelection sel)
+  {
+    for (int i = 0; i < hiddenColumns.size(); i++)
+    {
+      int[] region = hiddenColumns.elementAt(i);
+      if (start == region[0])
+      {
+        for (int j = region[0]; j < region[1] + 1; j++)
+        {
+          sel.addElement(j);
+        }
+
+        hiddenColumns.removeElement(region);
+        break;
+      }
+    }
+    if (hiddenColumns.size() == 0)
+    {
+      hiddenColumns = null;
+    }
+  }
+
+  /**
+   * removes intersection of position,length ranges in deletions from the
+   * start,end regions marked in intervals.
+   * 
+   * @param shifts
+   * @param intervals
+   * @return
+   */
+  private boolean pruneIntervalVector(final List<int[]> shifts,
+          Vector<int[]> intervals)
+  {
+    boolean pruned = false;
+    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];
+      if (!trailinghn)
+      {
+        if (i < j)
+        {
+          hr = intervals.elementAt(++i);
+        }
+        else
+        {
+          i++;
+        }
+        continue;
+      }
+      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
+      if (endshift < hr[0] || endshift < sr[0])
+      { // leadinghc disjoint or not a deletion
+        if (s < t)
+        {
+          sr = shifts.get(++s);
+        }
+        else
+        {
+          s++;
+        }
+        continue;
+      }
+      boolean leadinghn = hr[0] >= sr[0];
+      boolean leadinghc = hr[0] < endshift;
+      boolean trailinghc = hr[1] < endshift;
+      if (leadinghn)
+      {
+        if (trailinghc)
+        { // deleted hidden region.
+          intervals.removeElementAt(i);
+          pruned = true;
+          j--;
+          if (i <= j)
+          {
+            hr = intervals.elementAt(i);
+          }
+          continue;
+        }
+        if (leadinghc)
+        {
+          hr[0] = endshift; // clip c terminal region
+          leadinghn = !leadinghn;
+          pruned = true;
+        }
+      }
+      if (!leadinghn)
+      {
+        if (trailinghc)
+        {
+          if (trailinghn)
+          {
+            hr[1] = sr[0] - 1;
+            pruned = true;
+          }
+        }
+        else
+        {
+          // sr contained in hr
+          if (s < t)
+          {
+            sr = shifts.get(++s);
+          }
+          else
+          {
+            s++;
+          }
+          continue;
+        }
+      }
+    }
+    return pruned; // true if any interval was removed or modified by
+    // operations.
+  }
+
+  /**
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
+   * @param deletions
+   */
+  public void pruneDeletions(List<int[]> shifts)
+  {
+    // delete any intervals intersecting.
+    if (hiddenColumns != null)
+    {
+      pruneIntervalVector(shifts, hiddenColumns);
+      if (hiddenColumns != null && hiddenColumns.size() == 0)
+      {
+        hiddenColumns = null;
+      }
+    }
+  }
+
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   * @param al
+   *          - alignment to have gaps inserted into it
+   * @param input
+   *          - alignment view where sequence corresponding to profileseq is
+   *          first entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public static HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentI al, AlignmentView input)
+  {
+    int profsqpos = 0;
+
+    char gc = al.getGapCharacter();
+    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+    HiddenColumns nview = (HiddenColumns) alandhidden[1];
+    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+    nview.propagateInsertions(profileseq, al, origseq);
+    return nview;
+  }
+
+  /**
+   * 
+   * @param profileseq
+   *          - sequence in al which corresponds to origseq
+   * @param al
+   *          - alignment which is to have gaps inserted into it
+   * @param origseq
+   *          - sequence corresponding to profileseq which defines gap map for
+   *          modifying al
+   */
+  private void propagateInsertions(SequenceI profileseq, AlignmentI al,
+          SequenceI origseq)
+  {
+    char gc = al.getGapCharacter();
+    // recover mapping between sequence's non-gap positions and positions
+    // mapping to view.
+    pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
+    int[] viscontigs = al.getHiddenColumns().getVisibleContigs(0,
+            profileseq.getLength());
+    int spos = 0;
+    int offset = 0;
+
+    // add profile to visible contigs
+    for (int v = 0; v < viscontigs.length; v += 2)
+    {
+      if (viscontigs[v] > spos)
+      {
+        StringBuffer sb = new StringBuffer();
+        for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+        {
+          sb.append(gc);
+        }
+        for (int s = 0, ns = al.getHeight(); s < ns; s++)
+        {
+          SequenceI sqobj = al.getSequenceAt(s);
+          if (sqobj != profileseq)
+          {
+            String sq = al.getSequenceAt(s).getSequenceAsString();
+            if (sq.length() <= spos + offset)
+            {
+              // pad sequence
+              int diff = spos + offset - sq.length() - 1;
+              if (diff > 0)
+              {
+                // pad gaps
+                sq = sq + sb;
+                while ((diff = spos + offset - sq.length() - 1) > 0)
+                {
+                  // sq = sq
+                  // + ((diff >= sb.length()) ? sb.toString() : sb
+                  // .substring(0, diff));
+                  if (diff >= sb.length())
+                  {
+                    sq += sb.toString();
+                  }
+                  else
+                  {
+                    char[] buf = new char[diff];
+                    sb.getChars(0, diff, buf, 0);
+                    sq += buf.toString();
+                  }
+                }
+              }
+              sq += sb.toString();
+            }
+            else
+            {
+              al.getSequenceAt(s).setSequence(
+                      sq.substring(0, spos + offset) + sb.toString()
+                              + sq.substring(spos + offset));
+            }
+          }
+        }
+        // offset+=sb.length();
+      }
+      spos = viscontigs[v + 1] + 1;
+    }
+    if ((offset + spos) < profileseq.getLength())
+    {
+      // pad the final region with gaps.
+      StringBuffer sb = new StringBuffer();
+      for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+      {
+        sb.append(gc);
+      }
+      for (int s = 0, ns = al.getHeight(); s < ns; s++)
+      {
+        SequenceI sqobj = al.getSequenceAt(s);
+        if (sqobj == profileseq)
+        {
+          continue;
+        }
+        String sq = sqobj.getSequenceAsString();
+        // pad sequence
+        int diff = origseq.getLength() - sq.length();
+        while (diff > 0)
+        {
+          // sq = sq
+          // + ((diff >= sb.length()) ? sb.toString() : sb
+          // .substring(0, diff));
+          if (diff >= sb.length())
+          {
+            sq += sb.toString();
+          }
+          else
+          {
+            char[] buf = new char[diff];
+            sb.getChars(0, diff, buf, 0);
+            sq += buf.toString();
+          }
+          diff = origseq.getLength() - sq.length();
+        }
+      }
+    }
+  }
+
+  /**
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
+   * @param deletions
+   */
+  private void pruneDeletions(ShiftList deletions)
+  {
+    if (deletions != null)
+    {
+      final List<int[]> shifts = deletions.getShifts();
+      if (shifts != null && shifts.size() > 0)
+      {
+        pruneDeletions(shifts);
+
+        // and shift the rest.
+        this.compensateForEdits(deletions);
+      }
+    }
+  }
+
+  /**
+   * Adjust hidden column boundaries based on a series of column additions or
+   * deletions in visible regions.
+   * 
+   * @param shiftrecord
+   * @return
+   */
+  private ShiftList compensateForEdits(ShiftList shiftrecord)
+  {
+    if (shiftrecord != null)
+    {
+      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 = shifts.get(i);
+          compensateForDelEdits(shifted + sh[0], sh[1]);
+          shifted -= sh[1];
+        }
+      }
+      return shiftrecord.getInverse();
+    }
+    return null;
+  }
+
+  /**
+   * Returns a hashCode built from hidden column ranges
+   */
+  public int hashCode(int hc)
+  {
+    int hashCode = hc;
+    if (hiddenColumns != null)
+    {
+      for (int[] hidden : hiddenColumns)
+      {
+        hashCode = 31 * hashCode + hidden[0];
+        hashCode = 31 * hashCode + hidden[1];
+      }
+    }
+    return hashCode;
+  }
+
+}