-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.schemes;\r
-\r
-public class ScoreMatrix\r
-{\r
- String name;\r
-\r
- /**\r
- * reference to integer score matrix\r
- */\r
- int[][] matrix;\r
-\r
- /**\r
- * 0 for Protein Score matrix. 1 for dna score matrix\r
- */\r
- int type;\r
-\r
- ScoreMatrix(String name, int[][] matrix, int type)\r
- {\r
- this.matrix = matrix;\r
- this.type = type;\r
- }\r
-\r
- public boolean isDNA()\r
- {\r
- return type == 1;\r
- }\r
-\r
- public boolean isProtein()\r
- {\r
- return type == 0;\r
- }\r
-\r
- public int[][] getMatrix()\r
- {\r
- return matrix;\r
- }\r
-\r
- /**\r
- * \r
- * @param A1\r
- * @param A2\r
- * @return score for substituting first char in A1 with first char in A2\r
- */\r
- public int getPairwiseScore(String A1, String A2)\r
- {\r
- return getPairwiseScore(A1.charAt(0), A2.charAt(0));\r
- }\r
-\r
- public int getPairwiseScore(char c, char d)\r
- {\r
- int pog = 0;\r
-\r
- try\r
- {\r
- int a = (type == 0) ? ResidueProperties.aaIndex[c]\r
- : ResidueProperties.nucleotideIndex[c];\r
- int b = (type == 0) ? ResidueProperties.aaIndex[d]\r
- : ResidueProperties.nucleotideIndex[d];\r
-\r
- pog = matrix[a][b];\r
- } catch (Exception e)\r
- {\r
- // System.out.println("Unknown residue in " + A1 + " " + A2);\r
- }\r
-\r
- return pog;\r
- }\r
-\r
- /**\r
- * pretty print the matrix\r
- */\r
- public String toString()\r
- {\r
- return outputMatrix(false);\r
- }\r
- public String outputMatrix(boolean html)\r
- {\r
- StringBuffer sb=new StringBuffer();\r
- int[] symbols=(type==0) ? ResidueProperties.aaIndex : ResidueProperties.nucleotideIndex;\r
- int symMax = (type==0) ? ResidueProperties.maxProteinIndex :ResidueProperties.maxNucleotideIndex;\r
- boolean header=true;\r
- if (html)\r
- {\r
- sb.append("<table>");\r
- }\r
- for (char sym='A';sym<='Z';sym++)\r
- {\r
- if (symbols[sym]>=0 && symbols[sym]<symMax)\r
- {\r
- if (header) {\r
- sb.append(html ? "<tr><td></td>" : "");\r
- for (char sym2='A';sym2<='Z';sym2++)\r
- {\r
- if (symbols[sym2]>=0 && symbols[sym2]<symMax)\r
- {\r
- sb.append((html ? "<td> " : "\t")+sym2 +(html ? " </td>": ""));\r
- }\r
- }\r
- header=false;\r
- sb.append(html ? "</tr>\n" : "\n");\r
- } \r
- if (html)\r
- {\r
- sb.append("<tr>");\r
- }\r
- sb.append((html ? "<td>" : "")+sym+(html ? "</td>" : ""));\r
- for (char sym2='A';sym2<='Z';sym2++)\r
- {\r
- if (symbols[sym2]>=0 && symbols[sym2]<symMax)\r
- {\r
- sb.append((html ? "<td>" : "\t")+matrix[symbols[sym]][symbols[sym2]]+(html ? "</td>" : ""));\r
- }\r
- }\r
- sb.append(html ? "</tr>\n" : "\n");\r
- }\r
- }\r
- if (html)\r
- {\r
- sb.append("</table>");\r
- }\r
- return sb.toString();\r
- }\r
-}\r
+/*
+ * 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