X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=c2a6a9cdd1b294dade726b95237af449d429f182;hb=HEAD;hp=07abd538c186d2c8c33b4e1c56c75a6021dbc199;hpb=b46b15a5edcd1fa2cd670503287ec753e46245f3;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 07abd53..c2a6a9c 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,69 +1,127 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import jalview.analysis.*;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.util.MessageManager;
 import jalview.util.ShiftList;
-import java.util.Vector;
 
-public class SeqCigar
-    extends CigarSimple
+import java.util.Enumeration;
+import java.util.Hashtable;
+
+public class SeqCigar extends CigarSimple
 {
-    /**
-     * start(inclusive) and end(exclusive) of subsequence on refseq
-     */
-    private int start, end;
+  /**
+   * start(inclusive) and end(exclusive) of subsequence on refseq
+   */
+  private int start, end;
+
   private SequenceI refseq = null;
+
+  private Hashtable seqProps;
+
   /**
    * Reference dataset sequence for the cigar string
+   * 
    * @return SequenceI
    */
   public SequenceI getRefSeq()
   {
     return refseq;
   }
+
   /**
-   *
+   * 
    * @return int start index of cigar ops on refSeq
    */
-  public int getStart() {
+  public int getStart()
+  {
     return start;
   }
+
   /**
-   *
+   * 
    * @return int end index (exclusive) of cigar ops on refSeq
    */
-  public int getEnd() {
+  public int getEnd()
+  {
     return end;
   }
+
+  /**
+   * 
+   * @param column
+   * @return position in sequence for column (or -1 if no match state exists)
+   */
+  public int findPosition(int column)
+  {
+    int w = 0, ew, p = refseq.findPosition(start);
+    if (column < 0)
+    {
+      return -1;
+    }
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        if (operation[i] == M || operation[i] == D)
+        {
+          p += range[i];
+        }
+        if (operation[i] == M || operation[i] == I)
+        {
+          ew = w + range[i];
+          if (column < ew)
+          {
+            if (operation[i] == I)
+            {
+              return -1;
+            }
+            return p - (ew - column);
+          }
+          w = ew;
+        }
+      }
+    }
+    return -1;
+  }
+
   /**
    * Returns sequence as a string with cigar operations applied to it
+   * 
    * @return String
    */
+  @Override
   public String getSequenceString(char GapChar)
   {
-    return (length == 0) ? "" :
-        (String) getSequenceAndDeletions(refseq.getSequenceAsString(start, end), GapChar)[0];
+    return (length == 0) ? ""
+            : (String) getSequenceAndDeletions(
+                    refseq.getSequenceAsString(start, end), GapChar)[0];
   }
 
   /**
-   * recreates a gapped and edited version of RefSeq or null for an empty cigar string
+   * recreates a gapped and edited version of RefSeq or null for an empty cigar
+   * string
+   * 
    * @return SequenceI
    */
   public SequenceI getSeq(char GapChar)
@@ -73,62 +131,86 @@ public class SeqCigar
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq.getSequenceAsString(start,end),
-        GapChar);
+    Object[] edit_result = getSequenceAndDeletions(
+            refseq.getSequenceAsString(start, end), GapChar);
     if (edit_result == null)
     {
-      throw new Error(
-          "Implementation Error - unexpected null from getSequenceAndDeletions");
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
     }
     int bounds[] = (int[]) edit_result[1];
     seq = new Sequence(refseq.getName(), (String) edit_result[0],
-                       refseq.getStart() + start+bounds[0],
-                       refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
+            refseq.getStart() + start + bounds[0], refseq.getStart() + start
+                    + ((bounds[2] == 0) ? -1 : bounds[2]));
+    seq.setDescription(refseq.getDescription());
+    int sstart = seq.getStart(), send = seq.getEnd();
     // seq.checkValidRange(); probably not needed
+    // recover local properties if present
+    if (seqProps != null)
+    {
+      // this recovers dataset sequence reference as well as local features,
+      // names, start/end settings.
+      SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
+    }
+    // ensure dataset sequence is up to date from local reference
     seq.setDatasetSequence(refseq);
-    seq.setDescription(refseq.getDescription());
+    seq.setStart(sstart);
+    seq.setEnd(send);
     return seq;
   }
 
   /*
-     We don't allow this - refseq is given at construction time only
-   public void setSeq(SequenceI seq) {
-    this.seq = seq;
-     }
+   * We don't allow this - refseq is given at construction time only public void
+   * setSeq(SequenceI seq) { this.seq = seq; }
    */
   /**
-   * internal constructor - sets seq to a gapless sequence derived from seq
-   * and prepends any 'D' operations needed to get to the first residue of seq.
-   * @param seq SequenceI
-   * @param initialDeletion true to mark initial dataset sequence residues as deleted in subsequence
-   * @param _s index of first position in seq
-   * @param _e index after last position in (possibly gapped) seq
+   * internal constructor - sets seq to a gapless sequence derived from seq and
+   * prepends any 'D' operations needed to get to the first residue of seq.
+   * 
+   * @param seq
+   *          SequenceI
+   * @param initialDeletion
+   *          true to mark initial dataset sequence residues as deleted in
+   *          subsequence
+   * @param _s
+   *          index of first position in seq
+   * @param _e
+   *          index after last position in (possibly gapped) seq
    * @return true if gaps are present in seq
    */
-  private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s, int _e)
+  private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
+          int _e)
   {
     boolean hasgaps = false;
     if (seq == null)
     {
-      throw new Error("Implementation Error - _setSeq(null,...)");
+      throw new Error(MessageManager
+              .getString("error.implementation_error_set_seq_null"));
+    }
+    if (_s < 0)
+    {
+      throw new Error(MessageManager
+              .formatMessage("error.implementation_error_s", new String[]
+              { Integer.valueOf(_s).toString() }));
     }
-    if (_s<0)
-      throw new Error("Implementation Error: _s="+_s);
     String seq_string = seq.getSequenceAsString();
-    if (_e==0 || _e<_s || _e>seq_string.length())
-      _e=seq_string.length();
+    if (_e == 0 || _e < _s || _e > seq_string.length())
+    {
+      _e = seq_string.length();
+    }
     // resolve start and end positions relative to ungapped reference sequence
-    start = seq.findPosition(_s)-seq.getStart();
-    end = seq.findPosition(_e)-seq.getStart();
-    int l_ungapped = end-start;
-    // Find correct sequence to reference and correct start and end - if necessary
+    start = seq.findPosition(_s) - seq.getStart();
+    end = seq.findPosition(_e) - seq.getStart();
+    int l_ungapped = end - start;
+    // Find correct sequence to reference and correct start and end - if
+    // necessary
     SequenceI ds = seq.getDatasetSequence();
     if (ds == null)
     {
       // make a new dataset sequence
-      String ungapped = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
-                                               new String(seq_string));
-      l_ungapped=ungapped.length();
+      String ungapped = AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(seq_string));
+      l_ungapped = ungapped.length();
       // check that we haven't just duplicated an ungapped sequence.
       if (l_ungapped == seq.getLength())
       {
@@ -136,63 +218,77 @@ public class SeqCigar
       }
       else
       {
-        ds = new Sequence(seq.getName(), ungapped,
-                          seq.getStart(),
-                          seq.getStart()+ungapped.length()-1);
+        ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
+                seq.getStart() + ungapped.length() - 1);
         // JBPNote: this would be consistent but may not be useful
-        //        seq.setDatasetSequence(ds);
+        // seq.setDatasetSequence(ds);
       }
     }
     // add in offset between seq and the dataset sequence
     if (ds.getStart() < seq.getStart())
     {
-      int offset=seq.getStart()-ds.getStart();
-      if (initialDeletion) {
-          // absolute cigar string
-          addDeleted(_s+offset);
-          start=0;
-          end+=offset;
-      } else {
-          // normal behaviour - just mark start and end subsequence
-          start+=offset;
-          end+=offset;
+      int offset = seq.getStart() - ds.getStart();
+      if (initialDeletion)
+      {
+        // absolute cigar string
+        addDeleted(_s + offset);
+        start = 0;
+        end += offset;
+      }
+      else
+      {
+        // normal behaviour - just mark start and end subsequence
+        start += offset;
+        end += offset;
 
       }
 
     }
 
     // any gaps to process ?
-    if (l_ungapped!=(_e-_s))
-      hasgaps=true;
-
-    this.refseq = ds;
+    if (l_ungapped != (_e - _s))
+    {
+      hasgaps = true;
+    }
 
-    // Check  offsets
-    if (end>ds.getLength()) {
-      throw new Error("SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
-//      end = ds.getLength();
+    refseq = ds;
+    // copy over local properties for the sequence instance of the refseq
+    seqProps = SeqsetUtils.SeqCharacterHash(seq);
+    // Check offsets
+    if (end > ds.getLength())
+    {
+      throw new Error(MessageManager
+              .getString("error.implementation_error_seqcigar_possible"));
+      // end = ds.getLength();
     }
 
     return hasgaps;
   }
 
   /**
-   * directly initialise a cigar object with a sequence of range, operation pairs and a sequence to apply it to.
-   * operation and range should be relative to the seq.getStart()'th residue of the dataset seq resolved from seq.
-   * @param seq SequenceI
-   * @param operation char[]
-   * @param range int[]
+   * directly initialise a cigar object with a sequence of range, operation
+   * pairs and a sequence to apply it to. operation and range should be relative
+   * to the seq.getStart()'th residue of the dataset seq resolved from seq.
+   * 
+   * @param seq
+   *          SequenceI
+   * @param operation
+   *          char[]
+   * @param range
+   *          int[]
    */
   public SeqCigar(SequenceI seq, char operation[], int range[])
   {
     super();
     if (seq == null)
     {
-      throw new Error("Implementation Bug. Null seq !");
+      throw new Error(
+              MessageManager.getString("error.implmentation_bug_seq_null"));
     }
     if (operation.length != range.length)
     {
-      throw new Error("Implementation Bug. Cigar Operation list!= range list");
+      throw new Error(MessageManager.getString(
+              "error.implementation_bug_cigar_operation_list_range_list"));
     }
 
     if (operation != null)
@@ -202,16 +298,21 @@ public class SeqCigar
 
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error("NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+        throw new Error(MessageManager.getString(
+                "error.not_yet_implemented_cigar_object_from_cigar_string"));
       }
       for (int i = this.length, j = 0; j < operation.length; i++, j++)
       {
         char op = operation[j];
         if (op != M && op != I && op != D)
         {
-          throw new Error(
-              "Implementation Bug. Cigar Operation '" + j + "' '" + op +
-              "' not one of '" + M + "', '" + I + "', or '" + D + "'.");
+          throw new Error(MessageManager.formatMessage(
+                  "error.implementation_bug_cigar_operation", new String[]
+                  { Integer.valueOf(j).toString(),
+                      Integer.valueOf(op).toString(),
+                      Integer.valueOf(M).toString(),
+                      Integer.valueOf(I).toString(),
+                      Integer.valueOf(D).toString() }));
         }
         this.operation[i] = op;
         this.range[i] = range[j];
@@ -223,47 +324,59 @@ public class SeqCigar
       this.operation = null;
       this.range = null;
       this.length = 0;
-      if (_setSeq(seq, false,0, 0))
+      if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error("NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+        throw new Error(MessageManager.getString(
+                "error.not_yet_implemented_cigar_object_from_cigar_string"));
       }
     }
   }
 
   /**
    * add range matched residues to cigar string
-   * @param range int
+   * 
+   * @param range
+   *          int
    */
   public void addMatch(int range)
   {
     this.addOperation(M, range);
   }
+
   /**
-   * Adds
-   * insertion and match operations based on seq to the cigar up to
-   * the endpos column of seq.
-   *
-   * @param cigar CigarBase
-   * @param seq SequenceI
-   * @param startpos int
-   * @param endpos int
-   * @param initialDeletions if true then initial deletions will be added from start of seq to startpos
+   * Adds insertion and match operations based on seq to the cigar up to the
+   * endpos column of seq.
+   * 
+   * @param cigar
+   *          CigarBase
+   * @param seq
+   *          SequenceI
+   * @param startpos
+   *          int
+   * @param endpos
+   *          int
+   * @param initialDeletions
+   *          if true then initial deletions will be added from start of seq to
+   *          startpos
    */
   protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
-                                       int startpos, int endpos, boolean initialDeletions)
+          int startpos, int endpos, boolean initialDeletions)
   {
     char op = '\0';
     int range = 0;
     int p = 0, res = seq.getLength();
 
     if (!initialDeletions)
-      p=startpos;
-
+    {
+      p = startpos;
+    }
 
     while (p <= endpos)
     {
-      boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq.getCharAt(p)) : true;
-      if ( (startpos <= p) && (p <= endpos))
+      boolean isGap = (p < res)
+              ? jalview.util.Comparison.isGap(seq.getCharAt(p))
+              : true;
+      if ((startpos <= p) && (p <= endpos))
       {
         if (isGap)
         {
@@ -313,84 +426,111 @@ public class SeqCigar
 
   /**
    * create a cigar string for given sequence
-   * @param seq SequenceI
+   * 
+   * @param seq
+   *          SequenceI
    */
   public SeqCigar(SequenceI seq)
   {
     super();
     if (seq == null)
     {
-      throw new Error("Implementation error for new Cigar(SequenceI)");
+      throw new Error(MessageManager
+              .getString("error.implementation_error_for_new_cigar"));
     }
     _setSeq(seq, false, 0, 0);
     // there is still work to do
-    addSequenceOps(this, seq, 0, seq.getLength()-1, false);
+    addSequenceOps(this, seq, 0, seq.getLength() - 1, false);
   }
 
   /**
    * Create Cigar from a range of gaps and residues on a sequence object
-   * @param seq SequenceI
-   * @param start int - first column in range
-   * @param end int - last column in range
+   * 
+   * @param seq
+   *          SequenceI
+   * @param start
+   *          int - first column in range
+   * @param end
+   *          int - last column in range
    */
   public SeqCigar(SequenceI seq, int start, int end)
   {
     super();
     if (seq == null)
     {
-      throw new Error("Implementation error for new Cigar(SequenceI)");
+      throw new Error(MessageManager
+              .getString("error.implementation_error_for_new_cigar"));
     }
-    _setSeq(seq, false, start, end+1);
+    _setSeq(seq, false, start, end + 1);
     // there is still work to do
     addSequenceOps(this, seq, start, end, false);
   }
 
   /**
-   * Create a cigar object from a cigar string like '[<I|D|M><range>]+'
-   * Will fail if the given seq already contains gaps (JBPNote: future implementation will fix)
-   * @param seq SequenceI object resolvable to a dataset sequence
-   * @param cigarString String
+   * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
+   * fail if the given seq already contains gaps (JBPNote: future implementation
+   * will fix)
+   * 
+   * @param seq
+   *          SequenceI object resolvable to a dataset sequence
+   * @param cigarString
+   *          String
    * @return Cigar
    */
   public static SeqCigar parseCigar(SequenceI seq, String cigarString)
-      throws Exception
+          throws Exception
   {
     Object[] opsandrange = parseCigarString(cigarString);
-    return new SeqCigar(seq, (char[]) opsandrange[0], (int[]) opsandrange[1]);
+    return new SeqCigar(seq, (char[]) opsandrange[0],
+            (int[]) opsandrange[1]);
   }
 
   /**
-   * createAlignment
-   *
-   * @param alseqs SeqCigar[]
-   * @param gapCharacter char
+   * create an alignment from the given array of cigar sequences and gap
+   * character, and marking the given segments as visible in the given
+   * hiddenColumns.
+   * 
+   * @param alseqs
+   * @param gapCharacter
+   * @param hidden
+   *          - hiddenColumns where hidden regions are marked
+   * @param segments
+   *          - visible regions of alignment
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
-      char gapCharacter, ColumnSelection colsel, int[] segments)
+          char gapCharacter, HiddenColumns hidden, int[] segments)
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
-    String[] alseqs_string=new String[alseqs.length];
+    String[] alseqs_string = new String[alseqs.length];
     Object[] gs_regions = new Object[alseqs.length];
     for (int i = 0; i < alseqs.length; i++)
     {
-      alseqs_string[i]=alseqs[i].getRefSeq().
-          getSequenceAsString(alseqs[i].start,alseqs[i].end);
-      gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
+      alseqs_string[i] = alseqs[i].getRefSeq()
+              .getSequenceAsString(alseqs[i].start, alseqs[i].end);
+      gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
+              gapCharacter); // gapped sequence, {start, start col, end.
+      // endcol}, hidden regions {{start, end, col}})
       if (gs_regions[i] == null)
       {
-        throw new Error("Implementation error: " + i +
-                        "'th sequence Cigar has no operations.");
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cigar_seq_no_operations",
+                new String[]
+                { Integer.valueOf(i).toString() }));
       }
-      g_seqs[i] = new StringBuffer( (String) ( (Object[]) gs_regions[i])[0]); // the visible gapped sequence
+      g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
+      // visible
+      // gapped
+      // sequence
     }
     // Now account for insertions. (well - deletions)
-    // this is complicated because we must keep track of shifted positions in each sequence
+    // this is complicated because we must keep track of shifted positions in
+    // each sequence
     ShiftList shifts = new ShiftList();
     for (int i = 0; i < alseqs.length; i++)
     {
-      Object[] gs_region = ( (Object[]) ( (Object[]) gs_regions[i])[2]);
+      Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
       if (gs_region != null)
 
       {
@@ -402,7 +542,9 @@ public class SeqCigar
           {
             insert[s] = gapCharacter;
           }
-          int inspos = shifts.shift(region[2]); // resolve insertion position in current alignment frame of reference
+          int inspos = shifts.shift(region[2]); // resolve insertion position in
+          // current alignment frame of
+          // reference
           for (int s = 0; s < alseqs.length; s++)
           {
             if (s != i)
@@ -412,7 +554,8 @@ public class SeqCigar
                 // prefix insertion with more gaps.
                 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
                 {
-                  g_seqs[s].append(gapCharacter); // to debug - use a diffferent gap character here
+                  g_seqs[s].append(gapCharacter); // to debug - use a diffferent
+                  // gap character here
                 }
               }
               g_seqs[s].insert(inspos, insert);
@@ -420,185 +563,115 @@ public class SeqCigar
             else
             {
               g_seqs[s].insert(inspos,
-                               alseqs_string[i].substring(region[0], region[1] + 1));
+                      alseqs_string[i].substring(region[0], region[1] + 1));
             }
           }
-          shifts.addShift(region[2], insert.length); // update shift in alignment frame of reference
-          if (segments==null)
+          shifts.addShift(region[2], insert.length); // update shift in
+          // alignment frame of
+          // reference
+          if (segments == null)
+          {
             // add a hidden column for this deletion
-            colsel.hideColumns(inspos, inspos+insert.length-1);
+            hidden.hideColumns(inspos, inspos + insert.length - 1);
+          }
         }
       }
     }
     for (int i = 0; i < alseqs.length; i++)
     {
-      int[] bounds = ( (int[]) ( (Object[]) gs_regions[i])[1]);
+      int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
       SequenceI ref = alseqs[i].getRefSeq();
       seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
-                             ref.getStart() + alseqs[i].start+bounds[0],
-                             ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
+              ref.getStart() + alseqs[i].start + bounds[0],
+              ref.getStart() + alseqs[i].start
+                      + (bounds[2] == 0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
       seqs[i].setDescription(ref.getDescription());
     }
-    if (segments!=null) {
-      for (int i=0; i<segments.length; i+=3) {
-        //int start=shifts.shift(segments[i]-1)+1;
-        //int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(segments[i+1], segments[i+1]+segments[i+2]-1);
+    if (segments != null)
+    {
+      for (int i = 0; i < segments.length; i += 3)
+      {
+        // int start=shifts.shift(segments[i]-1)+1;
+        // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
+        hidden.hideColumns(segments[i + 1],
+                segments[i + 1] + segments[i + 2] - 1);
       }
     }
     return seqs;
   }
 
   /**
-   * non rigorous testing
-   */
-  /**
-   *
-   * @param seq Sequence
-   * @param ex_cs_gapped String
-   * @return String
+   * references to entities that this sequence cigar is associated with.
    */
-  public static String testCigar_string(Sequence seq, String ex_cs_gapped)
+  private Hashtable selGroups = null;
+
+  public void setGroupMembership(Object group)
   {
-    SeqCigar c_sgapped = new SeqCigar(seq);
-    String cs_gapped = c_sgapped.getCigarstring();
-    if (!cs_gapped.equals(ex_cs_gapped))
+    if (selGroups == null)
     {
-      System.err.println("Failed getCigarstring: incorect string '" + cs_gapped +
-                         "' != " + ex_cs_gapped);
+      selGroups = new Hashtable();
     }
-    return cs_gapped;
+    selGroups.put(group, new int[0]);
   }
 
-  public static boolean testSeqRecovery(SeqCigar gen_sgapped,
-                                        SequenceI s_gapped)
+  /**
+   * Test for and if present remove association to group.
+   * 
+   * @param group
+   * @return true if group was associated and it was removed
+   */
+  public boolean removeGroupMembership(Object group)
   {
-      // this is non-rigorous - start and end  recovery is not tested.
-    SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
-    if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+    if (selGroups != null && selGroups.containsKey(group))
     {
-      System.err.println("Couldn't reconstruct sequence.\n" +
-                         gen_sgapped_s.getSequence() + "\n" +
-                         s_gapped.getSequence());
-      return false;
+      selGroups.remove(group);
+      return true;
     }
-    return true;
+    return false;
   }
 
-  public static void main(String argv[])
-      throws Exception
+  /**
+   * forget all associations for this sequence.
+   */
+  public void clearMemberships()
   {
-    String o_seq;
-    Sequence s = new Sequence("MySeq",
-                              o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt",
-                              39, 80);
-    String orig_gapped;
-    Sequence s_gapped = new Sequence("MySeq",
-        orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
-                                     39, 80);
-    String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
-    s_gapped.setDatasetSequence(s);
-    String sub_gapped_s;
-    Sequence s_subsequence_gapped = new Sequence("MySeq",
-        sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
-                                                 43, 77);
-
-    s_subsequence_gapped.setDatasetSequence(s);
-    SeqCigar c_null = new SeqCigar(s);
-    String cs_null = c_null.getCigarstring();
-    if (!cs_null.equals("42M"))
-    {
-      System.err.println(
-          "Failed to recover ungapped sequence cigar operations:" +
-          ( (cs_null == "") ? "empty string" : cs_null));
-    }
-    testCigar_string(s_gapped, ex_cs_gapped);
-    SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
-    if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
-    {
-      System.err.println("Failed parseCigar(" + ex_cs_gapped +
-                         ")->getCigarString()->'" + gen_sgapped.getCigarstring() +
-                         "'");
-    }
-    testSeqRecovery(gen_sgapped, s_gapped);
-    // Test dataset resolution
-    SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
-    if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
-    {
-      System.err.println("Failed recovery for subsequence of dataset sequence");
-    }
-    // width functions
-    if (sub_gapped.getWidth() != sub_gapped_s.length())
+    if (selGroups != null)
     {
-      System.err.println("Failed getWidth()");
+      selGroups.clear();
     }
+    selGroups = null;
+  }
 
-    sub_gapped.getFullWidth();
-    if (sub_gapped.hasDeletedRegions())
-    {
-      System.err.println("hasDeletedRegions is incorrect.");
-    }
-    // Test start-end region SeqCigar
-    SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
-    if (sub_se_gp.getWidth() != 41)
-    {
-      System.err.println(
-          "SeqCigar(seq, start, end) not properly clipped alignsequence.");
-    }
-    System.out.println("Original sequence align:\n" + sub_gapped_s +
-                       "\nReconstructed window from 8 to 48\n"
-                       + "XXXXXXXX" + sub_se_gp.getSequenceString('-') + "..."
-                       + "\nCigar String:" + sub_se_gp.getCigarstring() + "\n"
-        );
-    SequenceI ssgp = sub_se_gp.getSeq('-');
-    System.out.println("\t " + ssgp.getSequence());
-    for (int r = 0; r < 10; r++)
-    {
-      sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
-      int sl = sub_se_gp.getWidth();
-      int st = sl - 1 - r;
-      for (int rs = 0; rs < 10; rs++)
-      {
-        int e = st + rs;
-        sub_se_gp.deleteRange(st, e);
-        String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
-        System.out.println(st + "," + e + "\t:" + ssgapedseq);
-        st -=3;
-      }
-    }
+  /**
+   * 
+   * @return null or array of all associated entities
+   */
+  public Object[] getAllMemberships()
+  {
+    if (selGroups == null)
     {
-      SeqCigar[] set = new SeqCigar[]
-          {
-          new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-          new SeqCigar(s_gapped)};
-      Alignment al = new Alignment(set);
-      for (int i = 0; i < al.getHeight(); i++)
-      {
-        System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
-                           al.getSequenceAt(i).getStart() + "\t" +
-                           al.getSequenceAt(i).getEnd() + "\t" +
-                           al.getSequenceAt(i).getSequence());
-      }
+      return null;
     }
+    Object[] mmbs = new Object[selGroups.size()];
+    Enumeration en = selGroups.keys();
+    for (int i = 0; en.hasMoreElements(); i++)
     {
-      System.out.println("Gapped.");
-      SeqCigar[] set = new SeqCigar[]
-          {
-          new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-          new SeqCigar(s_gapped)};
-      set[0].deleteRange(20, 25);
-      Alignment al = new Alignment(set);
-      for (int i = 0; i < al.getHeight(); i++)
-      {
-        System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
-                           al.getSequenceAt(i).getStart() + "\t" +
-                           al.getSequenceAt(i).getEnd() + "\t" +
-                           al.getSequenceAt(i).getSequence());
-      }
+      mmbs[i] = en.nextElement();
     }
-//    if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
-//      System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+    return mmbs;
   }
 
+  /**
+   * Test for group membership
+   * 
+   * @param sgr
+   *          - a selection group or some other object that may be associated
+   *          with seqCigar
+   * @return true if sgr is associated with this seqCigar
+   */
+  public boolean isMemberOf(Object sgr)
+  {
+    return (selGroups != null) && selGroups.get(sgr) != null;
+  }
 }