/*
-* 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
-*/
+ * 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.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
-import jalview.datamodel.*;
-
-import jalview.io.NewickFile;
-
-import jalview.schemes.ResidueProperties;
-
-import jalview.util.*;
-
-import java.util.*;
-
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.SequenceNode;
+import jalview.viewmodel.AlignmentViewport;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * This class implements distance calculations used in constructing a Neighbour
+ * Joining tree
*/
-public class NJTree
+public class NJTree extends TreeBuilder
{
- Vector cluster;
- SequenceI[] sequence;
-
- //SequenceData is a string representation of what the user
- //sees. The display may contain hidden columns.
- public AlignmentView seqData=null;
-
- int[] done;
- int noseqs;
- int noClus;
- float[][] distance;
- int mini;
- int minj;
- float ri;
- float rj;
- Vector groups = new Vector();
- SequenceNode maxdist;
- SequenceNode top;
- float maxDistValue;
- float maxheight;
- int ycount;
- Vector node;
- String type;
- String pwtype;
- Object found = null;
- Object leaves = null;
-
- boolean hasDistances = true; // normal case for jalview trees
- boolean hasBootstrap = false; // normal case for jalview trees
-
- private boolean hasRootDistance = true;
-
- /**
- * Create a new NJTree object with leaves associated with sequences in seqs,
- * and original alignment data represented by Cigar strings.
- * @param seqs SequenceI[]
- * @param odata Cigar[]
- * @param treefile NewickFile
- */
- public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) {
- this(seqs, treefile);
- if (odata!=null)
- seqData = odata;
- /*
- sequenceString = new String[odata.length];
- char gapChar = jalview.util.Comparison.GapChars.charAt(0);
- for (int i = 0; i < odata.length; i++)
- {
- SequenceI oseq_aligned = odata[i].getSeq(gapChar);
- sequenceString[i] = oseq_aligned.getSequence();
- } */
- }
-
- /**
- * Creates a new NJTree object from a tree from an external source
- *
- * @param seqs SequenceI which should be associated with leafs of treefile
- * @param treefile A parsed tree
- */
- public NJTree(SequenceI[] seqs, NewickFile treefile)
- {
- this.sequence = seqs;
- top = treefile.getTree();
-
- /**
- * There is no dependent alignment to be recovered from an
- * imported tree.
- *
- if (sequenceString == null)
- {
- sequenceString = new String[seqs.length];
- for (int i = 0; i < seqs.length; i++)
- {
- sequenceString[i] = seqs[i].getSequence();
- }
- }
- */
-
- hasDistances = treefile.HasDistances();
- hasBootstrap = treefile.HasBootstrap();
- hasRootDistance = treefile.HasRootDistance();
-
- maxheight = findHeight(top);
-
- SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-
- Vector leaves = new Vector();
- findLeaves(top, leaves);
-
- int i = 0;
- int namesleft = seqs.length;
-
- SequenceNode j;
- SequenceI nam;
- String realnam;
- Vector one2many=new Vector();
- int countOne2Many=0;
- while (i < leaves.size())
- {
- j = (SequenceNode) leaves.elementAt(i++);
- realnam = j.getName();
- nam = null;
-
- if (namesleft > -1)
- {
- nam = algnIds.findIdMatch(realnam);
- }
-
- if (nam != null)
- {
- j.setElement(nam);
- if (one2many.contains(nam)) {
- countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
- } else {
- one2many.addElement(nam);
- namesleft--;
- }
- }
- else
- {
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
- j.setPlaceholder(true);
- }
- }
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment sequence ids (out of "+one2many.size()+" unique ids) linked to two or more leaves.");
- // }
- // one2many.clear();
- }
-
- /**
- * Creates a new NJTree object.
- *
- * @param sequence DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- */
- public NJTree(SequenceI[] sequence,
- AlignmentView seqData,
- String type,
- String pwtype,
- int start, int end)
- {
- this.sequence = sequence;
- this.node = new Vector();
- this.type = type;
- this.pwtype = pwtype;
- if (seqData!=null) {
- this.seqData = seqData;
- } else {
- SeqCigar[] seqs = new SeqCigar[sequence.length];
- for(int i=0; i<sequence.length; i++)
- {
- seqs[i] = new SeqCigar(sequence[i], start, end);
- }
- CigarArray sdata = new CigarArray(seqs);
- sdata.addOperation(CigarArray.M, end-start+1);
- this.seqData = new AlignmentView(sdata, start);
- }
-
- if (!(type.equals("NJ")))
- {
- type = "AV";
- }
-
- if (!(pwtype.equals("PID")))
- {
- type = "BL";
- }
-
- int i = 0;
-
- done = new int[sequence.length];
-
- while ((i < sequence.length) && (sequence[i] != null))
- {
- done[i] = 0;
- i++;
- }
-
- noseqs = i++;
-
- distance = findDistances(this.seqData.getSequenceStrings(Comparison.GapChars.charAt(0)));
-
- makeLeaves();
-
- noClus = cluster.size();
-
- cluster();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString()
- {
- jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
-
- return fout.print(false, true); // distances only
- }
-
- /**
- *
- * used when the alignment associated to a tree has changed.
- *
- * @param alignment Vector
- */
- public void UpdatePlaceHolders(Vector alignment)
- {
- Vector leaves = new Vector();
- findLeaves(top, leaves);
-
- int sz = leaves.size();
- SequenceIdMatcher seqmatcher = null;
- int i = 0;
-
- while (i < sz)
- {
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
-
- if (alignment.contains(leaf.element()))
- {
- leaf.setPlaceholder(false);
- }
- else
- {
- if (seqmatcher == null)
- {
- // Only create this the first time we need it
- SequenceI[] seqs = new SequenceI[alignment.size()];
-
- for (int j = 0; j < seqs.length; j++)
- seqs[j] = (SequenceI) alignment.elementAt(j);
-
- seqmatcher = new SequenceIdMatcher(seqs);
- }
-
- SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
-
- if (nam != null)
- {
- leaf.setPlaceholder(false);
- leaf.setElement(nam);
- }
- else
- {
- leaf.setPlaceholder(true);
- }
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void cluster()
- {
- while (noClus > 2)
- {
- if (type.equals("NJ"))
- {
- findMinNJDistance();
- }
- else
- {
- findMinDistance();
- }
-
- Cluster c = joinClusters(mini, minj);
-
- done[minj] = 1;
-
- cluster.setElementAt(null, minj);
- cluster.setElementAt(c, mini);
-
- noClus--;
- }
-
- boolean onefound = false;
-
- int one = -1;
- int two = -1;
-
- for (int i = 0; i < noseqs; i++)
- {
- if (done[i] != 1)
- {
- if (onefound == false)
- {
- two = i;
- onefound = true;
- }
- else
- {
- one = i;
- }
- }
- }
-
- joinClusters(one, two);
- top = (SequenceNode) (node.elementAt(one));
-
- reCount(top);
- findHeight(top);
- findMaxDist(top);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Cluster joinClusters(int i, int j)
- {
- float dist = distance[i][j];
-
- int noi = ((Cluster) cluster.elementAt(i)).value.length;
- int noj = ((Cluster) cluster.elementAt(j)).value.length;
-
- int[] value = new int[noi + noj];
-
- for (int ii = 0; ii < noi; ii++)
- {
- value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
- }
-
- for (int ii = noi; ii < (noi + noj); ii++)
- {
- value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
- }
-
- Cluster c = new Cluster(value);
-
- ri = findr(i, j);
- rj = findr(j, i);
-
- if (type.equals("NJ"))
- {
- findClusterNJDistance(i, j);
- }
- else
- {
- findClusterDistance(i, j);
- }
-
- SequenceNode sn = new SequenceNode();
-
- sn.setLeft((SequenceNode) (node.elementAt(i)));
- sn.setRight((SequenceNode) (node.elementAt(j)));
-
- SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
- SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
-
- if (type.equals("NJ"))
- {
- findNewNJDistances(tmpi, tmpj, dist);
- }
- else
- {
- findNewDistances(tmpi, tmpj, dist);
- }
-
- tmpi.setParent(sn);
- tmpj.setParent(sn);
-
- node.setElementAt(sn, i);
-
- return c;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tmpi DOCUMENT ME!
- * @param tmpj DOCUMENT ME!
- * @param dist DOCUMENT ME!
- */
- public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
- {
-
- tmpi.dist = ((dist + ri) - rj) / 2;
- tmpj.dist = (dist - tmpi.dist);
-
- if (tmpi.dist < 0)
- {
- tmpi.dist = 0;
- }
-
- if (tmpj.dist < 0)
- {
- tmpj.dist = 0;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tmpi DOCUMENT ME!
- * @param tmpj DOCUMENT ME!
- * @param dist DOCUMENT ME!
- */
- public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
- {
- float ih = 0;
- float jh = 0;
-
- SequenceNode sni = tmpi;
- SequenceNode snj = tmpj;
-
- while (sni != null)
- {
- ih = ih + sni.dist;
- sni = (SequenceNode) sni.left();
- }
-
- while (snj != null)
- {
- jh = jh + snj.dist;
- snj = (SequenceNode) snj.left();
- }
-
- tmpi.dist = ((dist / 2) - ih);
- tmpj.dist = ((dist / 2) - jh);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void findClusterDistance(int i, int j)
- {
- int noi = ((Cluster) cluster.elementAt(i)).value.length;
- int noj = ((Cluster) cluster.elementAt(j)).value.length;
-
- // New distances from cluster to others
- float[] newdist = new float[noseqs];
-
- for (int l = 0; l < noseqs; l++)
- {
- if ((l != i) && (l != j))
- {
- newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
- noj);
- }
- else
- {
- newdist[l] = 0;
- }
- }
-
- for (int ii = 0; ii < noseqs; ii++)
- {
- distance[i][ii] = newdist[ii];
- distance[ii][i] = newdist[ii];
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void findClusterNJDistance(int i, int j)
- {
-
- // New distances from cluster to others
- float[] newdist = new float[noseqs];
-
- for (int l = 0; l < noseqs; l++)
- {
- if ((l != i) && (l != j))
- {
- newdist[l] = ((distance[i][l] + distance[j][l]) -
- distance[i][j]) / 2;
- }
- else
- {
- newdist[l] = 0;
- }
- }
-
- for (int ii = 0; ii < noseqs; ii++)
- {
- distance[i][ii] = newdist[ii];
- distance[ii][i] = newdist[ii];
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findr(int i, int j)
- {
- float tmp = 1;
-
- for (int k = 0; k < noseqs; k++)
- {
- if ((k != i) && (k != j) && (done[k] != 1))
- {
- tmp = tmp + distance[i][k];
- }
- }
-
- if (noClus > 2)
- {
- tmp = tmp / (noClus - 2);
- }
-
- return tmp;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findMinNJDistance()
- {
- float min = 100000;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i + 1; j < noseqs; j++)
- {
- if ((done[i] != 1) && (done[j] != 1))
- {
- float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
-
- if (tmp < min)
- {
- mini = i;
- minj = j;
-
- min = tmp;
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findMinDistance()
- {
- float min = 100000;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i + 1; j < noseqs; j++)
- {
- if ((done[i] != 1) && (done[j] != 1))
- {
- if (distance[i][j] < min)
- {
- mini = i;
- minj = j;
-
- min = distance[i][j];
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float[][] findDistances(String[] sequenceString)
- {
- float[][] distance = new float[noseqs][noseqs];
-
- if (pwtype.equals("PID"))
- {
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- if (j == i)
- {
- distance[i][i] = 0;
- }
- else
- {
- distance[i][j] = 100 -
- Comparison.PID(sequenceString[i], sequenceString[j]);
-
- distance[j][i] = distance[i][j];
- }
- }
- }
- }
- else if (pwtype.equals("BL"))
- {
- int maxscore = 0;
- int end = sequenceString[0].length();
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- int score = 0;
-
- for (int k = 0; k < end; k++)
- {
- try
- {
- score += ResidueProperties.getBLOSUM62(
- sequenceString[i].substring(k, k + 1),
- sequenceString[j].substring(k, k + 1));
- }
- catch (Exception ex)
- {
- System.err.println("err creating BLOSUM62 tree");
- ex.printStackTrace();
- }
- }
-
- distance[i][j] = (float) score;
-
- if (score > maxscore)
- {
- maxscore = score;
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = (float) maxscore - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
- }
- /* else if (pwtype.equals("SW"))
- {
- float max = -1;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- as.printAlignment(System.out);
- distance[i][j] = (float) as.maxscore;
-
- if (max < distance[i][j])
- {
- max = distance[i][j];
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = max - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
- }/*/
-
- return distance;
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makeLeaves()
- {
- cluster = new Vector();
-
- for (int i = 0; i < noseqs; i++)
- {
- SequenceNode sn = new SequenceNode();
-
- sn.setElement(sequence[i]);
- sn.setName(sequence[i].getName());
- node.addElement(sn);
-
- int[] value = new int[1];
- value[0] = i;
-
- Cluster c = new Cluster(value);
- cluster.addElement(c);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param leaves DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector findLeaves(SequenceNode node, Vector leaves)
- {
- if (node == null)
- {
- return leaves;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- leaves.addElement(node);
-
- return leaves;
- }
- else
- {
- findLeaves((SequenceNode) node.left(), leaves);
- findLeaves((SequenceNode) node.right(), leaves);
- }
-
- return leaves;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param count DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Object findLeaf(SequenceNode node, int count)
- {
- found = _findLeaf(node, count);
-
- return found;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param count DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Object _findLeaf(SequenceNode node, int count)
- {
- if (node == null)
- {
- return null;
- }
-
- if (node.ycount == count)
- {
- found = node.element();
-
- return found;
- }
- else
- {
- _findLeaf((SequenceNode) node.left(), count);
- _findLeaf((SequenceNode) node.right(), count);
- }
-
- return found;
- }
-
- /**
- * printNode is mainly for debugging purposes.
- *
- * @param node SequenceNode
- */
- public void printNode(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
+ /**
+ * Constructor given a viewport, tree type and score model
+ *
+ * @param av
+ * the current alignment viewport
+ * @param sm
+ * a distance or similarity score model to use to compute the tree
+ * @param scoreParameters
+ */
+ public NJTree(AlignmentViewport av, ScoreModelI sm,
+ SimilarityParamsI scoreParameters)
+ {
+ super(av, sm, scoreParameters);
+ }
- if ((node.left() == null) && (node.right() == null))
- {
- System.out.println("Leaf = " +
- ((SequenceI) node.element()).getName());
- System.out.println("Dist " + ((SequenceNode) node).dist);
- System.out.println("Boot " + node.getBootstrap());
- }
- else
- {
- System.out.println("Dist " + ((SequenceNode) node).dist);
- printNode((SequenceNode) node.left());
- printNode((SequenceNode) node.right());
- }
- }
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ protected double findMinDistance()
+ {
+ double min = Double.MAX_VALUE;
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void findMaxDist(SequenceNode node)
+ for (int i = 0; i < (noseqs - 1); i++)
{
- if (node == null)
+ for (int j = i + 1; j < noseqs; j++)
+ {
+ if (!done.get(i) && !done.get(j))
{
- return;
- }
+ double tmp = distances.getValue(i, j)
+ - (findr(i, j) + findr(j, i));
- if ((node.left() == null) && (node.right() == null))
- {
- float dist = ((SequenceNode) node).dist;
+ if (tmp < min)
+ {
+ mini = i;
+ minj = j;
- if (dist > maxDistValue)
- {
- maxdist = (SequenceNode) node;
- maxDistValue = dist;
- }
- }
- else
- {
- findMaxDist((SequenceNode) node.left());
- findMaxDist((SequenceNode) node.right());
+ min = tmp;
+ }
}
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getGroups()
- {
- return groups;
- }
+ return min;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float getMaxHeight()
- {
- return maxheight;
- }
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+ double dist)
+ {
+ nodei.dist = ((dist + ri) - rj) / 2;
+ nodej.dist = (dist - nodei.dist);
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param threshold DOCUMENT ME!
- */
- public void groupNodes(SequenceNode node, float threshold)
+ if (nodei.dist < 0)
{
- if (node == null)
- {
- return;
- }
-
- if ((node.height / maxheight) > threshold)
- {
- groups.addElement(node);
- }
- else
- {
- groupNodes((SequenceNode) node.left(), threshold);
- groupNodes((SequenceNode) node.right(), threshold);
- }
+ nodei.dist = 0;
}
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findHeight(SequenceNode node)
+ if (nodej.dist < 0)
{
- if (node == null)
- {
- return maxheight;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- node.height = ((SequenceNode) node.parent()).height + node.dist;
-
- if (node.height > maxheight)
- {
- return node.height;
- }
- else
- {
- return maxheight;
- }
- }
- else
- {
- if (node.parent() != null)
- {
- node.height = ((SequenceNode) node.parent()).height +
- node.dist;
- }
- else
- {
- maxheight = 0;
- node.height = (float) 0.0;
- }
-
- maxheight = findHeight((SequenceNode) (node.left()));
- maxheight = findHeight((SequenceNode) (node.right()));
- }
-
- return maxheight;
+ nodej.dist = 0;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode reRoot()
- {
- if (maxdist != null)
- {
- ycount = 0;
-
- float tmpdist = maxdist.dist;
-
- // New top
- SequenceNode sn = new SequenceNode();
- sn.setParent(null);
-
- // New right hand of top
- SequenceNode snr = (SequenceNode) maxdist.parent();
- changeDirection(snr, maxdist);
- System.out.println("Printing reversed tree");
- printN(snr);
- snr.dist = tmpdist / 2;
- maxdist.dist = tmpdist / 2;
-
- snr.setParent(sn);
- maxdist.setParent(sn);
-
- sn.setRight(snr);
- sn.setLeft(maxdist);
-
- top = sn;
-
- ycount = 0;
- reCount(top);
- findHeight(top);
- }
+ /**
+ * Calculates and saves the distance between the combination of cluster(i) and
+ * cluster(j) and all other clusters. The new distance to cluster k is
+ * calculated as the average of the distances from i to k and from j to k,
+ * less half the distance from i to j.
+ *
+ * @param i
+ * @param j
+ */
+ @Override
+ protected void findClusterDistance(int i, int j)
+ {
+ // New distances from cluster i to others
+ double[] newdist = new double[noseqs];
- return top;
- }
- /**
- *
- * @return true if original sequence data can be recovered
- */
- public boolean hasOriginalSequenceData() {
- return seqData!=null;
- }
- /**
- * Returns original alignment data used for calculation - or null where
- * not available.
- *
- * @return null or cut'n'pasteable alignment
- */
- public String printOriginalSequenceData(char gapChar)
+ double ijDistance = distances.getValue(i, j);
+ for (int l = 0; l < noseqs; l++)
{
- if (seqData==null)
- return null;
-
- StringBuffer sb = new StringBuffer();
- String[] seqdatas = seqData.getSequenceStrings(gapChar);
- for(int i=0; i<seqdatas.length; i++)
+ if ((l != i) && (l != j))
{
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(
- sequence[i].getName()));
- sb.append(" "+seqdatas[i]+"\n");
+ newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l)
+ - ijDistance) / 2;
+ }
+ else
+ {
+ newdist[l] = 0;
}
- return sb.toString();
- }
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void printN(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() != null) && (node.right() != null))
- {
- printN((SequenceNode) node.left());
- printN((SequenceNode) node.right());
- }
- else
- {
- System.out.println(" name = " +
- ((SequenceI) node.element()).getName());
- }
-
- System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
- ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void reCount(SequenceNode node)
- {
- ycount = 0;
- _reCount(node);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void _reCount(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() != null) && (node.right() != null))
- {
- _reCount((SequenceNode) node.left());
- _reCount((SequenceNode) node.right());
-
- SequenceNode l = (SequenceNode) node.left();
- SequenceNode r = (SequenceNode) node.right();
-
- ((SequenceNode) node).count = l.count + r.count;
- ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
- }
- else
- {
- ((SequenceNode) node).count = 1;
- ((SequenceNode) node).ycount = ycount++;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void swapNodes(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- SequenceNode tmp = (SequenceNode) node.left();
-
- node.setLeft(node.right());
- node.setRight(tmp);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param dir DOCUMENT ME!
- */
- public void changeDirection(SequenceNode node, SequenceNode dir)
- {
- if (node == null)
- {
- return;
- }
-
- if (node.parent() != top)
- {
- changeDirection((SequenceNode) node.parent(), node);
-
- SequenceNode tmp = (SequenceNode) node.parent();
-
- if (dir == node.left())
- {
- node.setParent(dir);
- node.setLeft(tmp);
- }
- else if (dir == node.right())
- {
- node.setParent(dir);
- node.setRight(tmp);
- }
- }
- else
- {
- if (dir == node.left())
- {
- node.setParent(node.left());
-
- if (top.left() == node)
- {
- node.setRight(top.right());
- }
- else
- {
- node.setRight(top.left());
- }
- }
- else
- {
- node.setParent(node.right());
-
- if (top.left() == node)
- {
- node.setLeft(top.right());
- }
- else
- {
- node.setLeft(top.left());
- }
- }
- }
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getMaxDist()
- {
- return maxdist;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getTopNode()
+ for (int ii = 0; ii < noseqs; ii++)
{
- return top;
+ distances.setValue(i, ii, newdist[ii]);
+ distances.setValue(ii, i, newdist[ii]);
}
- /**
- *
- * @return true if tree has real distances
- */
- public boolean isHasDistances() {
- return hasDistances;
- }
-
- /**
- *
- * @return true if tree has real bootstrap values
- */
- public boolean isHasBootstrap() {
- return hasBootstrap;
- }
-
- public boolean isHasRootDistance()
- {
- return hasRootDistance;
}
-
}
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-class Cluster
-{
- int[] value;
-
- /**
- * Creates a new Cluster object.
- *
- * @param value DOCUMENT ME!
- */
- public Cluster(int[] value)
- {
- this.value = value;
- }
-}
-
git://source.jalview.org / jalview.git / blobdiff