/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.api.analysis.ScoreModelI;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.*;
noseqs = i++;
- distance = findDistances(this.seqData
- .getSequenceStrings(Comparison.GapChars.charAt(0)));
+ distance = findDistances();
// System.err.println("Made distances");// dbg
makeLeaves();
// System.err.println("Made leaves");// dbg
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
- return fout.print(isHasBootstrap(),
- isHasDistances(), isHasRootDistance()); // output all data available for tree
+ return fout.print(isHasBootstrap(), isHasDistances(),
+ isHasRootDistance()); // output all data available for tree
}
/**
*
* used when the alignment associated to a tree has changed.
*
- * @param alignment
- * Vector
+ * @param list
+ * Sequence set to be associated with tree nodes
*/
- public void UpdatePlaceHolders(Vector alignment)
+ public void UpdatePlaceHolders(List<SequenceI> list)
{
Vector leaves = new Vector();
findLeaves(top, leaves);
{
SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
- if (alignment.contains(leaf.element()))
+ if (list.contains(leaf.element()))
{
leaf.setPlaceholder(false);
}
if (seqmatcher == null)
{
// Only create this the first time we need it
- SequenceI[] seqs = new SequenceI[alignment.size()];
+ SequenceI[] seqs = new SequenceI[list.size()];
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) alignment.elementAt(j);
+ seqs[j] = (SequenceI) list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
}
}
}
+
/**
- * rename any nodes according to their associated sequence.
- * This will modify the tree's metadata! (ie the original NewickFile or newly generated BinaryTree's label data)
+ * rename any nodes according to their associated sequence. This will modify
+ * the tree's metadata! (ie the original NewickFile or newly generated
+ * BinaryTree's label data)
*/
- public void renameAssociatedNodes() {
- applyToNodes(new NodeTransformI() {
+ public void renameAssociatedNodes()
+ {
+ applyToNodes(new NodeTransformI()
+ {
@Override
public void transform(BinaryNode node)
{
Object el = node.element();
- if (el!=null && el instanceof SequenceI)
+ if (el != null && el instanceof SequenceI)
{
- node.setName(((SequenceI)el).getName());
+ node.setName(((SequenceI) el).getName());
}
}
});
}
+
/**
* DOCUMENT ME!
*/
}
/**
- * 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()
{
- 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]);
+ float[][] distance = new float[noseqs][noseqs];
- distance[j][i] = distance[i][j];
- }
- }
- }
- }
- else
+ // Pairwise substitution score (with no gap penalties)
+ ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+ if (_pwmatrix == null)
{
- // 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];
- }
- }
-
+ _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
}
+ 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];
- * } } }/
- */
}
/**
git://source.jalview.org / jalview.git / blobdiff