X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=d82f54c68dad59cfac976a86ec2c9f6ed2e1eb1b;hb=33984e02c5687dc011d13da4b17cb0815970e0f5;hp=8ef7930a95e24da355446bcb1e73aa7e60fc535c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 8ef7930..d82f54c 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,30 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
-import jalview.api.analysis.ScoreModelI;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
-public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
+public class ScoreMatrix extends PairwiseSeqScoreModel
{
String name;
-
+
@Override
public String getName()
{
@@ -40,11 +43,15 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
* 0 for Protein Score matrix. 1 for dna score matrix
*/
int type;
+
/**
*
- * @param name Unique, human readable name for the matrix
- * @param matrix Pairwise scores indexed according to appropriate symbol alphabet
- * @param type 0 for Protein, 1 for NA
+ * @param name
+ * Unique, human readable name for the matrix
+ * @param matrix
+ * Pairwise scores indexed according to appropriate symbol alphabet
+ * @param type
+ * 0 for Protein, 1 for NA
*/
ScoreMatrix(String name, int[][] matrix, int type)
{
@@ -58,6 +65,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
{
return type == 1;
}
+
@Override
public boolean isProtein()
{
@@ -71,19 +79,21 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
}
/**
+ * Answers the score for substituting first char in A1 with first char in A2
*
* @param A1
* @param A2
- * @return score for substituting first char in A1 with first char in A2
+ * @return
*/
public int getPairwiseScore(String A1, String A2)
{
return getPairwiseScore(A1.charAt(0), A2.charAt(0));
}
+ @Override
public int getPairwiseScore(char c, char d)
{
- int pog = 0;
+ int score = 0;
try
{
@@ -91,19 +101,19 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
: ResidueProperties.nucleotideIndex[c];
int b = (type == 0) ? ResidueProperties.aaIndex[d]
: ResidueProperties.nucleotideIndex[d];
-
- pog = matrix[a][b];
+ score = matrix[a][b];
} catch (Exception e)
{
// System.out.println("Unknown residue in " + A1 + " " + A2);
}
- return pog;
+ return score;
}
/**
* pretty print the matrix
*/
+ @Override
public String toString()
{
return outputMatrix(false);
@@ -119,7 +129,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
boolean header = true;
if (html)
{
- sb.append("
");
+ sb.append("");
}
for (char sym = 'A'; sym <= 'Z'; sym++)
{
@@ -162,4 +172,47 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
}
return sb.toString();
}
+
+ /**
+ * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
+ * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
+ * computed using the current score matrix. For example
+ *
+ * - Sequences:
+ * - FKL
+ * - R-D
+ * - QIA
+ * - GWC
+ * - Score matrix is BLOSUM62
+ * - Gaps treated same as X (unknown)
+ * - product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15
+ * - product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10
+ * - product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13
+ * - product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26
+ * - product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+ *
- and so on
+ *
+ */
+ public MatrixI computePairwiseScores(String[] seqs)
+ {
+ double[][] values = new double[seqs.length][];
+ for (int row = 0; row < seqs.length; row++)
+ {
+ values[row] = new double[seqs.length];
+ for (int col = 0; col < seqs.length; col++)
+ {
+ int total = 0;
+ int width = Math.min(seqs[row].length(), seqs[col].length());
+ for (int i = 0; i < width; i++)
+ {
+ char c1 = seqs[row].charAt(i);
+ char c2 = seqs[col].charAt(i);
+ int score = getPairwiseScore(c1, c2);
+ total += score;
+ }
+ values[row][col] = total;
+ }
+ }
+ return new Matrix(values);
+ }
}