+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.scoremodels;
import jalview.analysis.AlignSeq;
@Override
public float[][] findDistances(AlignmentView seqData)
{
- SequenceI[] sequenceString = seqData
- .getVisibleAlignment(Comparison.GapChars.charAt(0)).getSequencesArray();
+ SequenceI[] sequenceString = seqData.getVisibleAlignment(
+ Comparison.GapChars.charAt(0)).getSequencesArray();
int noseqs = sequenceString.length;
float[][] distance = new float[noseqs][noseqs];
-
- float max = -1;
-
- for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- { AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j], seqData.isNa() ? "dna" : "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];
- } }
-
+
+ float max = -1;
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j],
+ seqData.isNa() ? "dna" : "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;
}
{
return "Smith Waterman Score";
}
+
@Override
public boolean isDNA()
{
return true;
}
+
@Override
public boolean isProtein()
{
return true;
}
- public String toString() {
+
+ public String toString()
+ {
return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
}
}