/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
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[][] matrix;
/**
* 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
*/
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
*/
public int getPairwiseScore(String A1, String A2)
{
return getPairwiseScore(A1.charAt(0), A2.charAt(0));
}
@Override
public int getPairwiseScore(char c, char d)
{
int score = 0;
try
{
int a = (type == 0) ? ResidueProperties.aaIndex[c]
: ResidueProperties.nucleotideIndex[c];
int b = (type == 0) ? ResidueProperties.aaIndex[d]
: ResidueProperties.nucleotideIndex[d];
score = matrix[a][b];
} catch (Exception e)
{
// System.out.println("Unknown residue in " + A1 + " " + A2);
}
return score;
}
/**
* pretty print the matrix
*/
@Override
public String toString()
{
return outputMatrix(false);
}
public String outputMatrix(boolean html)
{
StringBuffer sb = new StringBuffer();
int[] symbols = (type == 0) ? ResidueProperties.aaIndex
: ResidueProperties.nucleotideIndex;
int symMax = (type == 0) ? ResidueProperties.maxProteinIndex
: ResidueProperties.maxNucleotideIndex;
boolean header = true;
if (html)
{
sb.append("
");
}
for (char sym = 'A'; sym <= 'Z'; sym++)
{
if (symbols[sym] >= 0 && symbols[sym] < symMax)
{
if (header)
{
sb.append(html ? " | " : "");
for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
{
if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
{
sb.append((html ? " " : "\t") + sym2
+ (html ? " | " : ""));
}
}
header = false;
sb.append(html ? "
\n" : "\n");
}
if (html)
{
sb.append("");
}
sb.append((html ? "" : "") + sym + (html ? " | " : ""));
for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
{
if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
{
sb.append((html ? "" : "\t")
+ matrix[symbols[sym]][symbols[sym2]]
+ (html ? " | " : ""));
}
}
sb.append(html ? "
\n" : "\n");
}
}
if (html)
{
sb.append("
");
}
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);
}
}