/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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 <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.schemes;
-public class ScoreMatrix
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
+
+public class ScoreMatrix extends PairwiseSeqScoreModel
{
String name;
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+
/**
* reference to integer 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
+ */
ScoreMatrix(String name, int[][] matrix, int type)
{
this.matrix = matrix;
this.type = type;
+ this.name = name;
}
+ @Override
public boolean isDNA()
{
return type == 1;
}
+ @Override
public boolean isProtein()
{
return type == 0;
}
+ @Override
public int[][] getMatrix()
{
return matrix;
}
/**
+ * 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 b = (type == 0) ? ResidueProperties.aaIndex[d]
: ResidueProperties.nucleotideIndex[d];
+ /*
+ * FIXME: 2.10.1 PCA treats gap as [22] or 'X', but Tree
+ * calculation treats as [23]; which is correct?
+ */
+ /*
+ * hack to convert unassigned / unknown (including gap)
+ * to index of unknown (X for amino acids, N for nucleotide)
+ * TODO: statically assign gap characters to this index?
+ */
+// if (type == 0)
+// {
+// if (a == ResidueProperties.maxProteinIndex)
+// {
+// a = ResidueProperties.aaIndex['X'];
+// }
+// if (b == ResidueProperties.maxProteinIndex)
+// {
+// b = ResidueProperties.aaIndex['X'];
+// }
+// }
+// if (type != 0)
+// {
+// if (a == ResidueProperties.maxNucleotideIndex)
+// {
+// a = ResidueProperties.nucleotideIndex['N'];
+// }
+// if (b == ResidueProperties.maxNucleotideIndex)
+// {
+// b = ResidueProperties.nucleotideIndex['N'];
+// }
+// }
pog = matrix[a][b];
} catch (Exception e)
{
/**
* pretty print the matrix
*/
+ @Override
public String toString()
{
return outputMatrix(false);
boolean header = true;
if (html)
{
- sb.append("<table>");
+ sb.append("<table border=\"1\">");
}
for (char sym = 'A'; sym <= 'Z'; sym++)
{
}
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
+ * <ul>
+ * <li>Sequences:</li>
+ * <li>FKL</li>
+ * <li>R-D</li>
+ * <li>QIA</li>
+ * <li>GWC</li>
+ * <li>Score matrix is BLOSUM62</li>
+ * <li>Gaps treated same as X (unknown)</li>
+ * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
+ * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
+ * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
+ * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
+ * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+ * <li>and so on</li>
+ * </ul>
+ */
+ 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);
+ }
}