/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ * 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/>.
+ * 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 java.util.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.api.analysis.ScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
* DOCUMENT ME!
*/
public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
- String pwtype, int start, int end)
+ String pwtype, ScoreModelI sm, int start, int end)
{
this.sequence = sequence;
this.node = new Vector();
type = "AV";
}
- if (!(pwtype.equals("PID")))
+ if (sm == null && !(pwtype.equals("PID")))
{
if (ResidueProperties.getScoreMatrix(pwtype) == null)
{
noseqs = i++;
- distance = findDistances(this.seqData
- .getSequenceStrings(Comparison.GapChars.charAt(0)));
+ distance = findDistances(sm);
// System.err.println("Made distances");// dbg
makeLeaves();
// System.err.println("Made leaves");// dbg
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) list.get(j);
+ seqs[j] = list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
}
/**
- * DOCUMENT ME!
+ * Calculate a distance matrix given the sequence input data and score model
*
- * @return DOCUMENT ME!
+ * @return similarity matrix used to compute tree
*/
- public float[][] findDistances(String[] sequenceString)
+ public float[][] findDistances(ScoreModelI _pwmatrix)
{
- float[][] distance = new float[noseqs][noseqs];
- if (pwtype.equals("PID"))
+ float[][] distance = new float[noseqs][noseqs];
+ if (_pwmatrix == null)
{
- for (int i = 0; i < (noseqs - 1); i++)
+ // Resolve substitution model
+ _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+ if (_pwmatrix == null)
{
- 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];
- }
- }
+ _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
}
}
- else
- {
- // Pairwise substitution score (with no gap penalties)
- ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
- if (pwmatrix == null)
- {
- pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- 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 += pwmatrix.getPairwiseScore(
- sequenceString[i].charAt(k),
- sequenceString[j].charAt(k));
- } 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];
- }
- }
-
- }
+ distance = _pwmatrix.findDistances(seqData);
return distance;
- // else
- /*
- * 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];
- * } } }/
- */
}
/**
{
System.out
.println("Leaf = " + ((SequenceI) node.element()).getName());
- System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Dist " + node.dist);
System.out.println("Boot " + node.getBootstrap());
}
else
{
- System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Dist " + node.dist);
printNode((SequenceNode) node.left());
printNode((SequenceNode) node.right());
}
if ((node.left() == null) && (node.right() == null))
{
- float dist = ((SequenceNode) node).dist;
+ float dist = node.dist;
if (dist > maxDistValue)
{
- maxdist = (SequenceNode) node;
+ maxdist = node;
maxDistValue = dist;
}
}
+ ((SequenceI) node.element()).getName());
}
- System.out.println(" dist = " + ((SequenceNode) node).dist + " "
- + ((SequenceNode) node).count + " "
- + ((SequenceNode) node).height);
+ System.out.println(" dist = " + node.dist + " "
+ + node.count + " "
+ + node.height);
}
/**
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;
+ node.count = l.count + r.count;
+ node.ycount = (l.ycount + r.ycount) / 2;
}
else
{
- ((SequenceNode) node).count = 1;
- ((SequenceNode) node).ycount = ycount++;
+ node.count = 1;
+ node.ycount = ycount++;
}
_lycount--;
}
{
for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
.transform((BinaryNode) nodes.nextElement()))
+ {
;
+ }
}
}