JAL-2361 make a modified saved scheme the backout checkpoint for Cancel

[jalview.git] / src / jalview / schemes / ScoreMatrix.java

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 8ef7930..d82f54c 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,30 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.api.analysis.ScoreModelI;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
 
-public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
+public class ScoreMatrix extends PairwiseSeqScoreModel
 {
   String name;
-  
+
   @Override
   public String getName()
   {
@@ -40,11 +43,15 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
    * 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
+   * @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)
   {
@@ -58,6 +65,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
   {
     return type == 1;
   }
+
   @Override
   public boolean isProtein()
   {
@@ -71,19 +79,21 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
   }
 
   /**
+   * Answers the score for substituting first char in A1 with first char in A2
    * 
    * @param A1
    * @param A2
-   * @return score for substituting first char in A1 with first char in 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 pog = 0;
+    int score = 0;
 
     try
     {
@@ -91,19 +101,19 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
               : ResidueProperties.nucleotideIndex[c];
       int b = (type == 0) ? ResidueProperties.aaIndex[d]
               : ResidueProperties.nucleotideIndex[d];
-
-      pog = matrix[a][b];
+      score = matrix[a][b];
     } catch (Exception e)
     {
       // System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
-    return pog;
+    return score;
   }
 
   /**
    * pretty print the matrix
    */
+  @Override
   public String toString()
   {
     return outputMatrix(false);
@@ -119,7 +129,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
     boolean header = true;
     if (html)
     {
-      sb.append("<table>");
+      sb.append("<table border=\"1\">");
     }
     for (char sym = 'A'; sym <= 'Z'; sym++)
     {
@@ -162,4 +172,47 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
     }
     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);
+  }
 }