X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=e2aa232fba0f2e2733b69d651f5e5ce328f6a054;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=93415096e204476e1ed20a56903f6c4e5a30c9a6;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 9341509..e2aa232 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,147 +1,173 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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();
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.api.analysis.ScoreModelI;
+
+public class ScoreMatrix extends PairwiseSeqScoreModel implements
+ ScoreModelI
+{
+ 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;
+ }
+
+ /**
+ *
+ * @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();
+ }
+}