X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=71e76aff2f6835cc26c329b4a32c23c2cae4fa1c;hb=582d39cb05dfbb5f956f74d4a97a17d9f63b0786;hp=817472a322c2d1bafb8e4def94b8def09b9fb924;hpb=d80cb60cde197454e9b22e08f4861abfc61a25eb;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 817472a..71e76af 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,578 +1,686 @@
-/*
-* 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 Vector sequences;
-    protected Vector groups = new Vector();
-    protected Vector superGroup = new Vector();
-    protected char gapCharacter = '-';
-    public AlignmentAnnotation[] annotations;
-    public boolean featuresAdded = false;
-
-    /** Make an alignment from an array of Sequences.
-    *
-    * @param sequences
-    */
-    public Alignment(SequenceI[] seqs) {
-        sequences = new Vector();
-
-        for (int i = 0; i < seqs.length; i++)
-            sequences.addElement(seqs[i]);
-
-        getWidth();
-    }
-
-    public Vector getSequences() {
-        return sequences;
-    }
-
-    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);
-    }
-
-    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);
-    }
-
-    public Vector getGroups() {
-        return groups;
-    }
-
-    /** Sorts the sequences by sequence group size - largest to smallest.
-     * Uses QuickSort.
-     */
-    public void sortGroups() {
-        float[] arr = new float[groups.size()];
-        Object[] s = new Object[groups.size()];
-
-        for (int i = 0; i < groups.size(); i++) {
-            arr[i] = ((SequenceGroup) groups.elementAt(i)).sequences.size();
-            s[i] = groups.elementAt(i);
-        }
-
-        QuickSort.sort(arr, s);
-
-        Vector newg = new Vector(groups.size());
-
-        for (int i = groups.size() - 1; i >= 0; i--) {
-            newg.addElement(s[i]);
-        }
-
-        groups = newg;
-    }
-
-    /** 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--;
-            }
-        }
-    }
-
-    /** Returns an array of Sequences containing columns
-     * start to end (inclusive) only.
-     *
-     * @param start start column to fetch
-     * @param end end column to fetch
-     * @return Array of Sequences, ready to put into a new Alignment
-     */
-    public SequenceI[] getColumns(int start, int end) {
-        return getColumns(0, getHeight() - 1, start, end);
-    }
-
-    /** 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);
-    }
-
-    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);
-            }
-        }
-    }
-
-    public void insertColumns(SequenceI[] seqs, int pos) {
-        if (seqs.length == getHeight()) {
-            for (int i = 0; i < getHeight(); i++) {
-                String tmp = new String(getSequenceAt(i).getSequence());
-                getSequenceAt(i).setSequence(tmp.substring(0, pos) +
-                    seqs[i].getSequence() + tmp.substring(pos));
-            }
-        }
-    }
-
-    public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
-        SequenceI[] seqs = new Sequence[(seq2 - seq1) + 1];
-
-        for (int i = seq1; i <= seq2; i++) {
-            seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                    getSequenceAt(i).getSequence().substring(start, end),
-                    getSequenceAt(i).findPosition(start),
-                    getSequenceAt(i).findPosition(end));
-        }
-
-        return seqs;
-    }
-
-    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));
-        }
-    }
-
-    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));
-        }
-    }
-
-    public void deleteSequence(SequenceI s) {
-        for (int i = 0; i < getHeight(); i++)
-            if (getSequenceAt(i) == s) {
-                deleteSequence(i);
-            }
-    }
-
-    public void deleteSequence(int i) {
-        sequences.removeElementAt(i);
-    }
-
-    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 void sortByPID(SequenceI s) {
-        float[] scores = new float[getHeight()];
-        SequenceI[] seqs = new SequenceI[getHeight()];
-
-        for (int i = 0; i < getHeight(); i++) {
-            scores[i] = Comparison.compare(getSequenceAt(i), s);
-            seqs[i] = getSequenceAt(i);
-        }
-
-        QuickSort.sort(scores, 0, scores.length - 1, seqs);
-
-        int len = 0;
-
-        if ((getHeight() % 2) == 0) {
-            len = getHeight() / 2;
-        } else {
-            len = (getHeight() + 1) / 2;
-        }
-
-        for (int i = 0; i < len; i++) {
-            SequenceI tmp = seqs[i];
-            sequences.setElementAt(seqs[getHeight() - i - 1], i);
-            sequences.setElementAt(tmp, getHeight() - i - 1);
-        }
-    }
-
-    public void sortByID() {
-        String[] ids = new String[getHeight()];
-        SequenceI[] seqs = new SequenceI[getHeight()];
-
-        for (int i = 0; i < getHeight(); i++) {
-            ids[i] = getSequenceAt(i).getName();
-            seqs[i] = getSequenceAt(i);
-        }
-
-        QuickSort.sort(ids, seqs);
-
-        int len = 0;
-
-        if ((getHeight() % 2) == 0) {
-            len = getHeight() / 2;
-        } else {
-            len = (getHeight() + 1) / 2;
-            System.out.println("DEBUG:Sort len is odd = " + len); // log.
-        }
-
-        for (int i = 0; i < len; i++) {
-            System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " +
-                seqs[getHeight() - i - 1].getName()); // log.
-
-            SequenceI tmp = seqs[i];
-            sequences.setElementAt(seqs[getHeight() - i - 1], i);
-            sequences.setElementAt(tmp, getHeight() - i - 1);
-        }
-    }
-
-    /**    */
-    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;
-    }
-
-    public SequenceGroup[] findAllGroups(SequenceI s) {
-        Vector temp = new Vector();
-
-        for (int i = 0; i < this.groups.size(); i++) {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-            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;
-    }
-
-    /**    */
-    public void addToGroup(SequenceGroup g, SequenceI s) {
-        if (!(g.sequences.contains(s))) {
-            g.sequences.addElement(s);
-        }
-    }
-
-    /**    */
-    public void removeFromGroup(SequenceGroup g, SequenceI s) {
-        if ((g != null) && (g.sequences != null)) {
-            if (g.sequences.contains(s)) {
-                g.sequences.removeElement(s);
-
-                if (g.sequences.size() == 0) {
-                    groups.removeElement(g);
-                }
-            }
-        }
-    }
-
-    public void addSuperGroup(SuperGroup sg) {
-        superGroup.addElement(sg);
-    }
-
-    public void removeSuperGroup(SuperGroup sg) {
-        superGroup.removeElement(sg);
-    }
-
-    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);
-        }
-    }
-
-    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()) {
-            SequenceI s = getSequenceAt(i);
-
-            if (s.getName().equals(name)) {
-                return s;
-            }
-
-            i++;
-        }
-
-        return null;
-    }
-
-    /**    */
-    public SequenceI findbyDisplayId(String name) {
-        int i = 0;
-
-        while (i < sequences.size()) {
-            SequenceI s = getSequenceAt(i);
-
-            if (s.getDisplayId().equals(name)) {
-                return s;
-            }
-
-            i++;
-        }
-
-        return null;
-    }
-
-    /**    */
-    public int findIndex(SequenceI s) {
-        int i = 0;
-
-        while (i < sequences.size()) {
-            if (s == getSequenceAt(i)) {
-                return i;
-            }
-
-            i++;
-        }
-
-        return -1;
-    }
-
-    public int getHeight() {
-        return sequences.size();
-    }
-
-    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;
-    }
-
-    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;
-    }
-
-    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);
-        }
-    }
-
-    public char getGapCharacter() {
-        return gapCharacter;
-    }
-
-    public Vector getAAFrequency() {
-        return AAFrequency.calculate(sequences, 0, getWidth());
-    }
-
-    public boolean isAligned() {
-        int width = getWidth();
-
-        for (int i = 0; i < sequences.size(); i++)
-            if (getSequenceAt(i).getLength() != width) {
-                return false;
-            }
-
-        return true;
-    }
-
-    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 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;
-    }
-
-    public AlignmentAnnotation[] getAlignmentAnnotation() {
-        return annotations;
-    }
-}
+/*
+ * 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)
+        {
+          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;
+    }
+
+    /**
+     * 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)
+    {
+      if(i>-1 && i<getHeight())
+      {
+        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();
+    }
+
+    /**    */
+    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!
+     *
+     * @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;
+        }
+
+        if(aSize<1)
+          return;
+
+        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()];
+        SequenceI currentSeq;
+        for (int i = 0; i < getHeight(); i++)
+        {
+          currentSeq = getSequenceAt(i);
+          if(currentSeq.getDatasetSequence()!=null)
+          {
+            seqs[i] = (Sequence)currentSeq.getDatasetSequence();
+          }
+          else
+          {
+            seqs[i] = new Sequence(currentSeq.getName(),
+                                   AlignSeq.extractGaps(
+                                       jalview.util.Comparison.GapChars,
+                                       currentSeq.getSequence()
+                                   ),
+                                   currentSeq.getStart(),
+                                   currentSeq.getEnd());
+            seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+            seqs[i].setDescription(currentSeq.getDescription());
+            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++;
+
+      int cLength;
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
+        cLength = current.getLength();
+
+        if (cLength < maxLength)
+        {
+          current.insertCharAt(cLength,
+                              maxLength-cLength, 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;
+  }
+
+}