X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5f605309ac1297d66b9eec58dab09129d506a905;hb=52c2c3879d5dc5e7b4ba7916f1ea964f83551f95;hp=338294b77bfab6ec444146bed2d39f3242c6e1a3;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 338294b..5f60530 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,726 +1,839 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import jalview.analysis.*;
-
-import jalview.util.*;
-
-import java.util.*;
-
-
-/** Data structure to hold and manipulate a multiple sequence alignment
- */
-public class Alignment implements AlignmentI
-{
-    protected Alignment dataset;
-    protected Vector sequences;
-    protected Vector groups = new Vector();
-    protected Vector superGroup = new Vector();
-    protected char gapCharacter = '-';
-    protected int type = NUCLEOTIDE;
-    public static final int PROTEIN = 0;
-    public static final int NUCLEOTIDE = 1;
-
-    /** DOCUMENT ME!! */
-    public AlignmentAnnotation[] annotations;
-
-    /** Make an alignment from an array of Sequences.
-     *
-     * @param sequences
-     */
-    public Alignment(SequenceI[] seqs)
-    {
-        int i=0;
-
-        if( jalview.util.Comparison.isNucleotide(seqs))
-          type = NUCLEOTIDE;
-        else
-          type = PROTEIN;
-
-        sequences = new Vector();
-
-        for (i = 0; i < seqs.length; i++)
-        {
-            sequences.addElement(seqs[i]);
-        }
-
-        getWidth();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getSequences()
-    {
-        return sequences;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
-    {
-        if (i < sequences.size())
-        {
-            return (SequenceI) sequences.elementAt(i);
-        }
-
-        return null;
-    }
-
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void addSequence(SequenceI snew)
-    {
-        sequences.addElement(snew);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void addSequence(SequenceI[] seq)
-    {
-        for (int i = 0; i < seq.length; i++)
-        {
-            addSequence(seq[i]);
-        }
-    }
-
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void setSequenceAt(int i, SequenceI snew)
-    {
-        SequenceI oldseq = getSequenceAt(i);
-        deleteSequence(oldseq);
-
-        sequences.setElementAt(snew, i);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getGroups()
-    {
-        return groups;
-    }
-
-    /** Takes out columns consisting entirely of gaps (-,.," ")
-     */
-    public void removeGaps()
-    {
-        SequenceI current;
-        int iSize = getWidth();
-
-        for (int i = 0; i < iSize; i++)
-        {
-            boolean delete = true;
-
-            for (int j = 0; j < getHeight(); j++)
-            {
-                current = getSequenceAt(j);
-
-                if (current.getLength() > i)
-                {
-                    /* MC Should move this to a method somewhere */
-                    if (!jalview.util.Comparison.isGap(current.getCharAt(i)))
-                    {
-                        delete = false;
-                    }
-                }
-            }
-
-            if (delete)
-            {
-                deleteColumns(i, i);
-                iSize--;
-                i--;
-            }
-        }
-    }
-
-    /** Removes a range of columns (start to end inclusive).
-     *
-     * @param start Start column in the alignment
-     * @param end End column in the alignment
-     */
-    public void deleteColumns(int start, int end)
-    {
-        deleteColumns(0, getHeight() - 1, start, end);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq1 DOCUMENT ME!
-     * @param seq2 DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public void deleteColumns(int seq1, int seq2, int start, int end)
-    {
-        for (int i = 0; i <= (end - start); i++)
-        {
-            for (int j = seq1; j <= seq2; j++)
-            {
-                getSequenceAt(j).deleteCharAt(start);
-            }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void trimLeft(int i)
-    {
-        for (int j = 0; j < getHeight(); j++)
-        {
-            SequenceI s = getSequenceAt(j);
-            int newstart = s.findPosition(i);
-
-            s.setStart(newstart);
-            s.setSequence(s.getSequence().substring(i));
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void trimRight(int i)
-    {
-        for (int j = 0; j < getHeight(); j++)
-        {
-            SequenceI s = getSequenceAt(j);
-            int newend = s.findPosition(i);
-
-            s.setEnd(newend);
-            s.setSequence(s.getSequence().substring(0, i + 1));
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     */
-    public void deleteSequence(SequenceI s)
-    {
-        for (int i = 0; i < getHeight(); i++)
-        {
-            if (getSequenceAt(i) == s)
-            {
-                deleteSequence(i);
-            }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteSequence(int i)
-    {
-        sequences.removeElementAt(i);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param threshold DOCUMENT ME!
-     * @param sel DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector removeRedundancy(float threshold, Vector sel)
-    {
-        Vector del = new Vector();
-
-        for (int i = 1; i < sel.size(); i++)
-        {
-            for (int j = 0; j < i; j++)
-            {
-                // Only do the comparison if either have not been deleted
-                if (!del.contains((SequenceI) sel.elementAt(i)) ||
-                        !del.contains((SequenceI) sel.elementAt(j)))
-                {
-                    // use PID instead of Comparison (which is really not pleasant)
-                    float pid = Comparison.PID((SequenceI) sel.elementAt(j),
-                            (SequenceI) sel.elementAt(i));
-
-                    if (pid >= threshold)
-                    {
-                        // Delete the shortest one
-                        if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
-                                                                                         .elementAt(
-                                    i)).getSequence().length())
-                        {
-                            del.addElement(sel.elementAt(i));
-                        }
-                        else
-                        {
-                            del.addElement(sel.elementAt(i));
-                        }
-                    }
-                }
-            }
-        }
-
-        // Now delete the sequences
-        for (int i = 0; i < del.size(); i++)
-        {
-            deleteSequence((SequenceI) del.elementAt(i));
-        }
-
-        return del;
-    }
-
-    /**    */
-    public SequenceGroup findGroup(int i)
-    {
-        return findGroup(getSequenceAt(i));
-    }
-
-    /**    */
-    public SequenceGroup findGroup(SequenceI s)
-    {
-        for (int i = 0; i < this.groups.size(); i++)
-        {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-            if (sg.sequences.contains(s))
-            {
-                return sg;
-            }
-        }
-
-        return null;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup[] findAllGroups(SequenceI s)
-    {
-        Vector temp = new Vector();
-
-        int gSize = groups.size();
-        for (int i = 0; i < gSize; i++)
-        {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.sequences==null)
-            {
-              this.deleteGroup(sg);
-              gSize--;
-              continue;
-            }
-
-            if (sg.sequences.contains(s))
-            {
-                temp.addElement(sg);
-            }
-        }
-
-        SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
-        for (int i = 0; i < temp.size(); i++)
-        {
-            ret[i] = (SequenceGroup) temp.elementAt(i);
-        }
-
-        return ret;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void addSuperGroup(SuperGroup sg)
-    {
-        superGroup.addElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void removeSuperGroup(SuperGroup sg)
-    {
-        superGroup.removeElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg)
-    {
-        for (int i = 0; i < this.superGroup.size(); i++)
-        {
-            SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
-
-            if (temp.sequenceGroups.contains(sg))
-            {
-                return temp;
-            }
-        }
-
-        return null;
-    }
-
-    /**    */
-    public void addGroup(SequenceGroup sg)
-    {
-        if (!groups.contains(sg))
-        {
-            groups.addElement(sg);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void deleteAllGroups()
-    {
-        groups.removeAllElements();
-        superGroup.removeAllElements();
-
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI s = getSequenceAt(i);
-            s.setColor(java.awt.Color.white);
-            i++;
-        }
-    }
-
-    /**    */
-    public void deleteGroup(SequenceGroup g)
-    {
-        if (groups.contains(g))
-        {
-            groups.removeElement(g);
-        }
-    }
-
-    /**    */
-    public SequenceI findName(String name)
-    {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            if (getSequenceAt(i).getName().equals(name))
-            {
-                return getSequenceAt(i);
-            }
-
-            i++;
-        }
-
-        return null;
-    }
-
-
-    /**    */
-    public int findIndex(SequenceI s)
-    {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            if (s == getSequenceAt(i))
-            {
-                return i;
-            }
-
-            i++;
-        }
-
-        return -1;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getHeight()
-    {
-        return sequences.size();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWidth()
-    {
-        int maxLength = -1;
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() > maxLength)
-            {
-                maxLength = getSequenceAt(i).getLength();
-            }
-        }
-
-        return maxLength;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMaxIdLength()
-    {
-        int max = 0;
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI seq = getSequenceAt(i);
-            String tmp = seq.getName() + "/" + seq.getStart() + "-" +
-                seq.getEnd();
-
-            if (tmp.length() > max)
-            {
-                max = tmp.length();
-            }
-
-            i++;
-        }
-
-        return max;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gc DOCUMENT ME!
-     */
-    public void setGapCharacter(char gc)
-    {
-        gapCharacter = gc;
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.sequence = seq.sequence.replace('.', gc);
-            seq.sequence = seq.sequence.replace('-', gc);
-            seq.sequence = seq.sequence.replace(' ', gc);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return gapCharacter;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getAAFrequency()
-    {
-        return AAFrequency.calculate(sequences, 0, getWidth());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isAligned()
-    {
-        int width = getWidth();
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() != width)
-            {
-                return false;
-            }
-        }
-
-        return true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void deleteAnnotation(AlignmentAnnotation aa)
-    {
-        int aSize = 1;
-
-        if (annotations != null)
-        {
-            aSize = annotations.length;
-        }
-
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
-
-        int tIndex = 0;
-
-        for (int i = 0; i < aSize; i++)
-        {
-            if (annotations[i] == aa)
-            {
-                continue;
-            }
-
-            temp[tIndex] = annotations[i];
-            tIndex++;
-        }
-
-        annotations = temp;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void addAnnotation(AlignmentAnnotation aa)
-    {
-        int aSize = 1;
-
-        if (annotations != null)
-        {
-            aSize = annotations.length + 1;
-        }
-
-
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-        int i = 0;
-
-        if (aSize > 1)
-        {
-            for (i = 0; i < (aSize - 1); i++)
-            {
-                temp[i] = annotations[i];
-            }
-        }
-
-        temp[i] = aa;
-
-        annotations = temp;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentAnnotation[] getAlignmentAnnotation()
-    {
-        return annotations;
-    }
-
-    public void setNucleotide(boolean b)
-    {
-      if(b)
-        type = NUCLEOTIDE;
-      else
-        type = PROTEIN;
-    }
-
-    public boolean isNucleotide()
-    {
-      if(type==NUCLEOTIDE)
-        return true;
-      else
-        return false;
-    }
-
-    public void setDataset(Alignment data)
-    {
-      if(dataset==null && data==null)
-      {
-        // Create a new dataset for this alignment.
-        // Can only be done once, if dataset is not null
-        // This will not be performed
-        Sequence[] seqs = new Sequence[getHeight()];
-        for (int i = 0; i < getHeight(); i++)
-        {
-
-          seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                                 AlignSeq.extractGaps(
-                                     jalview.util.Comparison.GapChars,
-                                     getSequenceAt(i).getSequence()
-                                 ),
-                                 getSequenceAt(i).getStart(),
-                                 getSequenceAt(i).getEnd());
-
-          getSequenceAt(i).setDatasetSequence(seqs[i]);
-        }
-
-        dataset = new Alignment(seqs);
-      }
-      else if(dataset==null && data!=null)
-      {
-        dataset = data;
-      }
-    }
-
-    public Alignment getDataset()
-    {
-      return dataset;
-    }
-
-}
+/*
+ * 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
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import jalview.analysis.*;
+
+import jalview.util.*;
+
+import java.util.*;
+
+/** Data structure to hold and manipulate a multiple sequence alignment
+ */
+public class Alignment implements AlignmentI
+{
+    protected Alignment dataset;
+    protected Vector sequences;
+    protected Vector groups = new Vector();
+    protected char gapCharacter = '-';
+    protected int type = NUCLEOTIDE;
+    public static final int PROTEIN = 0;
+    public static final int NUCLEOTIDE = 1;
+
+    /** DOCUMENT ME!! */
+    public AlignmentAnnotation[] annotations;
+
+    HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+    private void initAlignment(SequenceI[] seqs) {
+      int i=0;
+
+      if( jalview.util.Comparison.isNucleotide(seqs))
+        type = NUCLEOTIDE;
+      else
+        type = PROTEIN;
+
+      sequences = new Vector();
+
+      for (i = 0; i < seqs.length; i++)
+      {
+        sequences.addElement(seqs[i]);
+      }
+
+    }
+    /** Make an alignment from an array of Sequences.
+     *
+     * @param sequences
+     */
+    public Alignment(SequenceI[] seqs)
+    {
+      initAlignment(seqs);
+    }
+    /**
+     * Make a new alignment from an array of SeqCigars
+     * @param seqs SeqCigar[]
+     */
+    public Alignment(SeqCigar[] alseqs) {
+      SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection(), null);
+      initAlignment(seqs);
+    }
+    /**
+     * Make a new alignment from an CigarArray
+     * JBPNote - can only do this when compactAlignment does not contain hidden regions.
+     * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
+     * @param compactAlignment CigarArray
+     */
+    public static AlignmentI createAlignment(CigarArray compactAlignment) {
+      throw new Error("Alignment(CigarArray) not yet implemented");
+      // this(compactAlignment.refCigars);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequences()
+    {
+        return sequences;
+    }
+
+    public SequenceI [] getSequencesArray()
+    {
+      SequenceI [] reply = new SequenceI[sequences.size()];
+      for(int i=0; i<sequences.size(); i++)
+      {
+        reply[i] = (SequenceI)sequences.elementAt(i);
+      }
+      return reply;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
+    {
+        if (i < sequences.size())
+        {
+            return (SequenceI) sequences.elementAt(i);
+        }
+
+        return null;
+    }
+
+    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+     *
+     * @param snew
+     */
+    public void addSequence(SequenceI snew)
+    {
+      if(dataset!=null)
+      {
+        if(snew.getDatasetSequence()!=null)
+        {
+          System.out.println(snew.getName());
+          getDataset().addSequence(snew.getDatasetSequence());
+        }
+        else
+        {
+          Sequence ds = new Sequence(snew.getName(),
+                                     AlignSeq.extractGaps("-. ",
+              snew.getSequence()),
+                                     snew.getStart(),
+                                     snew.getEnd());
+
+          snew.setDatasetSequence(ds);
+          getDataset().addSequence(ds);
+        }
+      }
+      sequences.addElement(snew);
+
+      hiddenSequences.adjustHeightSequenceAdded();
+    }
+
+
+    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+     *
+     * @param snew
+     */
+    public void setSequenceAt(int i, SequenceI snew)
+    {
+        SequenceI oldseq = getSequenceAt(i);
+        deleteSequence(oldseq);
+
+        sequences.setElementAt(snew, i);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getGroups()
+    {
+        return groups;
+    }
+    /** Takes out columns consisting entirely of gaps (-,.," ")
+     */
+    public void removeGaps() {
+      removeGaps((ShiftList)null);
+    }
+    /**
+     * remove gaps in alignment - recording any frame shifts in shiftrecord
+     * intended to be passed to ColumnSelection.compensateForEdits(shiftrecord)
+     * @param shiftrecord
+     */
+    public void removeGaps(ShiftList shiftrecord) {
+        SequenceI[] seqs = getVisibleAndRepresentedSeqs();
+        int j, jSize = seqs.length;
+
+        int width = 0;
+        for (int i = 0; i < jSize; i++)
+        {
+          if (seqs[i].getLength() > width)
+          {
+            width = seqs[i].getLength();
+          }
+        }
+
+        int startCol = -1, endCol = -1;
+        boolean delete = true;
+        for (int i = 0; i < width; i++)
+        {
+            delete = true;
+
+            for (j = 0; j < jSize; j++)
+            {
+                if (seqs[j].getLength() > i)
+                {
+                    if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
+                    {
+                        if(delete)
+                          endCol = i;
+
+                        delete = false;
+                        break;
+                    }
+                }
+            }
+
+            if(delete && startCol==-1)
+            {
+              startCol = i;
+            }
+
+
+            if (!delete && startCol > -1)
+            {
+              deleteColumns(seqs, startCol, endCol);
+              if (shiftrecord!=null) {
+                shiftrecord.addShift(startCol, 1+endCol-startCol);
+              }
+              width -= (endCol - startCol);
+              i -= (endCol - startCol);
+              startCol = -1;
+              endCol = -1;
+            }
+        }
+
+        if (delete && startCol > -1)
+        {
+          deleteColumns(seqs, startCol, endCol);
+          if (shiftrecord!=null) {
+            shiftrecord.addShift(startCol, 1+endCol-startCol);
+          }
+        }
+    }
+
+    /** Removes a range of columns (start to end inclusive).
+     *
+     * @param seqs Sequences to remove columns from
+     * @param start Start column in the alignment
+     * @param end End column in the alignment
+     */
+    public void deleteColumns(SequenceI [] seqs, int start, int end)
+    {
+      for(int i=0; i<seqs.length; i++)
+        seqs[i].deleteChars(start, end);
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void trimLeft(int i)
+    {
+        SequenceI[] seqs = getVisibleAndRepresentedSeqs();
+        int j, jSize = seqs.length;
+        for (j = 0; j < jSize; j++)
+        {
+            int newstart = seqs[j].findPosition(i);
+
+            if(i>seqs[j].getLength())
+            {
+              sequences.removeElement(seqs[j]);
+              j--;
+              jSize--;
+            }
+            else
+            {
+              seqs[j].setStart(newstart);
+              seqs[j].setSequence(seqs[j].getSequence().substring(i));
+            }
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void trimRight(int i)
+    {
+        SequenceI[] seqs = getVisibleAndRepresentedSeqs();
+        int j, jSize = seqs.length;
+        for (j = 0; j < jSize; j++)
+        {
+            int newend = seqs[j].findPosition(i);
+
+            seqs[j].setEnd(newend);
+            if(seqs[j].getLength()>i)
+              seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s)
+    {
+      deleteSequence(findIndex(s));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteSequence(int i)
+    {
+        sequences.removeElementAt(i);
+        hiddenSequences.adjustHeightSequenceDeleted(i);
+    }
+
+
+    /**    */
+    public SequenceGroup findGroup(SequenceI s)
+    {
+        for (int i = 0; i < this.groups.size(); i++)
+        {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+            if (sg.getSequences(false).contains(s))
+            {
+                return sg;
+            }
+        }
+
+        return null;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup[] findAllGroups(SequenceI s)
+    {
+        Vector temp = new Vector();
+
+        int gSize = groups.size();
+        for (int i = 0; i < gSize; i++)
+        {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+            if(sg==null || sg.getSequences(false)==null)
+            {
+              this.deleteGroup(sg);
+              gSize--;
+              continue;
+            }
+
+            if (sg.getSequences(false).contains(s))
+            {
+                temp.addElement(sg);
+            }
+        }
+
+        SequenceGroup[] ret = new SequenceGroup[temp.size()];
+
+        for (int i = 0; i < temp.size(); i++)
+        {
+            ret[i] = (SequenceGroup) temp.elementAt(i);
+        }
+
+        return ret;
+    }
+
+
+
+    /**    */
+    public void addGroup(SequenceGroup sg)
+    {
+        if (!groups.contains(sg))
+        {
+            groups.addElement(sg);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void deleteAllGroups()
+    {
+        groups.removeAllElements();
+
+        int i = 0;
+
+        while (i < sequences.size())
+        {
+            SequenceI s = getSequenceAt(i);
+            s.setColor(java.awt.Color.white);
+            i++;
+        }
+    }
+
+    /**    */
+    public void deleteGroup(SequenceGroup g)
+    {
+        if (groups.contains(g))
+        {
+            groups.removeElement(g);
+        }
+    }
+
+    /**    */
+    public SequenceI findName(String name)
+    {
+        int i = 0;
+
+        while (i < sequences.size())
+        {
+            if (getSequenceAt(i).getName().equals(name))
+            {
+                return getSequenceAt(i);
+            }
+
+            i++;
+        }
+
+        return null;
+    }
+
+    public SequenceI [] findSequenceMatch(String name)
+    {
+      Vector matches = new Vector();
+      int i = 0;
+
+      while (i < sequences.size())
+      {
+          if (getSequenceAt(i).getName().equals(name))
+          {
+              matches.addElement(getSequenceAt(i));
+          }
+          i++;
+      }
+
+      SequenceI [] result = new SequenceI[matches.size()];
+      for(i=0; i<result.length; i++)
+        result[i] = (SequenceI)matches.elementAt(i);
+
+      return result;
+
+    }
+
+
+    /**    */
+    public int findIndex(SequenceI s)
+    {
+        int i = 0;
+
+        while (i < sequences.size())
+        {
+            if (s == getSequenceAt(i))
+            {
+                return i;
+            }
+
+            i++;
+        }
+
+        return -1;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getHeight()
+    {
+        return sequences.size();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWidth()
+    {
+        int maxLength = -1;
+
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            if (getSequenceAt(i).getLength() > maxLength)
+            {
+                maxLength = getSequenceAt(i).getLength();
+            }
+        }
+
+        return maxLength;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMaxIdLength()
+    {
+        int max = 0;
+        int i = 0;
+
+        while (i < sequences.size())
+        {
+            SequenceI seq = getSequenceAt(i);
+            String tmp = seq.getName() + "/" + seq.getStart() + "-" +
+                seq.getEnd();
+
+            if (tmp.length() > max)
+            {
+                max = tmp.length();
+            }
+
+            i++;
+        }
+
+        return max;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gc DOCUMENT ME!
+     */
+    public void setGapCharacter(char gc)
+    {
+        gapCharacter = gc;
+
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            Sequence seq = (Sequence) sequences.elementAt(i);
+            seq.setSequence( seq.getSequence().replace('.', gc) );
+            seq.setSequence( seq.getSequence().replace('-', gc) );
+            seq.setSequence( seq.getSequence().replace(' ', gc) );
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
+        return gapCharacter;
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isAligned()
+    {
+        int width = getWidth();
+
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            if (getSequenceAt(i).getLength() != width)
+            {
+                return false;
+            }
+        }
+
+        return true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     */
+    public void deleteAnnotation(AlignmentAnnotation aa)
+    {
+        int aSize = 1;
+
+        if (annotations != null)
+        {
+            aSize = annotations.length;
+        }
+
+        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+        int tIndex = 0;
+
+        for (int i = 0; i < aSize; i++)
+        {
+            if (annotations[i] == aa)
+            {
+                continue;
+            }
+
+            temp[tIndex] = annotations[i];
+            tIndex++;
+        }
+
+        annotations = temp;
+    }
+
+
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     */
+    public void addAnnotation(AlignmentAnnotation aa)
+    {
+        int aSize = 1;
+        if (annotations != null)
+        {
+            aSize = annotations.length + 1;
+        }
+
+        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+        temp[aSize-1] = aa;
+
+        int i = 0;
+
+        if (aSize > 1)
+        {
+            for (i = 0; i < (aSize-1); i++)
+            {
+                temp[i] = annotations[i];
+            }
+        }
+
+        annotations = temp;
+    }
+
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+    {
+      if(aa==null || annotations==null || annotations.length-1<index)
+        return;
+
+      int aSize = annotations.length;
+      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+      temp[index] = aa;
+
+      for (int i = 0; i < aSize; i++)
+      {
+        if(i==index)
+          continue;
+
+        if(i<index)
+          temp[i] = annotations[i];
+        else
+          temp[i] = annotations[i-1];
+      }
+
+        annotations = temp;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public AlignmentAnnotation[] getAlignmentAnnotation()
+    {
+        return annotations;
+    }
+
+    public void setNucleotide(boolean b)
+    {
+      if(b)
+        type = NUCLEOTIDE;
+      else
+        type = PROTEIN;
+    }
+
+    public boolean isNucleotide()
+    {
+      if(type==NUCLEOTIDE)
+        return true;
+      else
+        return false;
+    }
+
+    public void setDataset(Alignment data)
+    {
+      if(dataset==null && data==null)
+      {
+        // Create a new dataset for this alignment.
+        // Can only be done once, if dataset is not null
+        // This will not be performed
+        Sequence[] seqs = new Sequence[getHeight()];
+        for (int i = 0; i < getHeight(); i++)
+        {
+          if(getSequenceAt(i).getDatasetSequence()!=null)
+          {
+            seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+          }
+          else
+          {
+            seqs[i] = new Sequence(getSequenceAt(i).getName(),
+                                   AlignSeq.extractGaps(
+                                       jalview.util.Comparison.GapChars,
+                                       getSequenceAt(i).getSequence()
+                                   ),
+                                   getSequenceAt(i).getStart(),
+                                   getSequenceAt(i).getEnd());
+            seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures();
+            getSequenceAt(i).setSequenceFeatures(null);
+            getSequenceAt(i).setDatasetSequence(seqs[i]);
+          }
+        }
+
+        dataset = new Alignment(seqs);
+      }
+      else if(dataset==null && data!=null)
+      {
+        dataset = data;
+      }
+    }
+
+    public Alignment getDataset()
+    {
+      return dataset;
+    }
+
+    public boolean padGaps() {
+      boolean modified=false;
+
+      //Remove excess gaps from the end of alignment
+      int maxLength = -1;
+
+      SequenceI current;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        current = getSequenceAt(i);
+        for (int j = current.getLength(); j > maxLength; j--)
+        {
+          if (j > maxLength && !jalview.util.Comparison.isGap(
+              current.getCharAt(j)))
+          {
+            maxLength = j;
+            break;
+          }
+        }
+      }
+
+      maxLength++;
+
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
+
+        if (current.getLength() < maxLength)
+        {
+          current.insertCharAt(maxLength - 1, gapCharacter);
+          modified=true;
+        }
+        else if(current.getLength() > maxLength)
+        {
+          current.deleteChars(maxLength, current.getLength());
+        }
+      }
+      return modified;
+    }
+
+    public HiddenSequences getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+    SequenceI [] getVisibleAndRepresentedSeqs()
+    {
+      if(hiddenSequences==null || hiddenSequences.getSize()<1)
+        return getSequencesArray();
+
+      Vector seqs = new Vector();
+      SequenceI seq;
+      SequenceGroup hidden;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        seq = (SequenceI) sequences.elementAt(i);
+        seqs.addElement(seq);
+        hidden = seq.getHiddenSequences();
+        if(hidden!=null)
+        {
+          for(int j=0; j<hidden.getSize(false); j++)
+          {
+            seqs.addElement(hidden.getSequenceAt(j));
+          }
+        }
+      }
+      SequenceI [] result = new SequenceI[seqs.size()];
+      for(int i=0; i<seqs.size(); i++)
+        result[i] = (SequenceI)seqs.elementAt(i);
+
+      return result;
+
+    }
+
+  public CigarArray getCompactAlignment()
+  {
+    SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+    for (int i=0; i<sequences.size(); i++) {
+      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+    }
+    CigarArray cal = new CigarArray(alseqs);
+    cal.addOperation(CigarArray.M, getWidth());
+    return cal;
+  }
+
+}