+++ /dev/null
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * 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("<table border=\"1\">");
- }
- for (char sym = 'A'; sym <= 'Z'; sym++)
- {
- if (symbols[sym] >= 0 && symbols[sym] < symMax)
- {
- if (header)
- {
- sb.append(html ? "<tr><td></td>" : "");
- for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
- {
- if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
- {
- sb.append((html ? "<td> " : "\t") + sym2
- + (html ? " </td>" : ""));
- }
- }
- header = false;
- sb.append(html ? "</tr>\n" : "\n");
- }
- if (html)
- {
- sb.append("<tr>");
- }
- sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));
- for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
- {
- if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
- {
- sb.append((html ? "<td>" : "\t")
- + matrix[symbols[sym]][symbols[sym2]]
- + (html ? "</td>" : ""));
- }
- }
- sb.append(html ? "</tr>\n" : "\n");
- }
- }
- if (html)
- {
- sb.append("</table>");
- }
- 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);
- }
-}
git://source.jalview.org / jalview.git / blobdiff