/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* 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 .
*/
package jalview.schemes;
public class ScoreMatrix
{
String name;
/**
* reference to integer score matrix
*/
int[][] matrix;
/**
* 0 for Protein Score matrix. 1 for dna score matrix
*/
int type;
ScoreMatrix(String name, int[][] matrix, int type)
{
this.matrix = matrix;
this.type = type;
}
public boolean isDNA()
{
return type == 1;
}
public boolean isProtein()
{
return type == 0;
}
public int[][] getMatrix()
{
return matrix;
}
/**
*
* @param A1
* @param A2
* @return score for substituting first char in A1 with first char in A2
*/
public int getPairwiseScore(String A1, String A2)
{
return getPairwiseScore(A1.charAt(0), A2.charAt(0));
}
public int getPairwiseScore(char c, char d)
{
int pog = 0;
try
{
int a = (type == 0) ? ResidueProperties.aaIndex[c]
: ResidueProperties.nucleotideIndex[c];
int b = (type == 0) ? ResidueProperties.aaIndex[d]
: ResidueProperties.nucleotideIndex[d];
pog = matrix[a][b];
} catch (Exception e)
{
// System.out.println("Unknown residue in " + A1 + " " + A2);
}
return pog;
}
/**
* pretty print the matrix
*/
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();
}
}