X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=41d73838b98e6b83c690c7d0d009816d40d1d5b9;hb=baad2f0ba2b171dd3d52c17afa46ef800334ea5e;hp=22c81f19f908e634fc06b436edb50c56b16b527c;hpb=f46c404585087d8937c48504bfcff716440d5186;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 22c81f1..41d7383 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -20,13 +20,27 @@
  */
 package jalview.analysis.scoremodels;
 
+import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.api.analysis.SimilarityScoreModelI;
+import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
+import jalview.util.Comparison;
 
 import java.util.Arrays;
 
-public class ScoreMatrix implements PairwiseScoreModelI
+public class ScoreMatrix implements SimilarityScoreModelI,
+        PairwiseScoreModelI
 {
+  /*
+   * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
+   * for pairwise scoring; 2.10.2 uses gap score (last column) in
+   * score matrix (JAL-2397)
+   * Set this flag to true (via Groovy) for 2.10.1 behaviour
+   */
+  private static boolean scoreGapAsAny = false;
+
   public static final short UNMAPPED = (short) -1;
 
   private static final String BAD_ASCII_ERROR = "Unexpected character %s in getPairwiseScore";
@@ -161,16 +175,22 @@ public class ScoreMatrix implements PairwiseScoreModelI
   }
 
   /**
-   * Returns the score matrix as used in getPairwiseScore. If using this matrix
-   * directly, callers <em>must</em> also call <code>getMatrixIndex</code> in
-   * order to get the matrix index for each character (symbol).
+   * Returns a copy of the score matrix as used in getPairwiseScore. If using
+   * this matrix directly, callers <em>must</em> also call
+   * <code>getMatrixIndex</code> in order to get the matrix index for each
+   * character (symbol).
    * 
    * @return
    * @see #getMatrixIndex(char)
    */
   public float[][] getMatrix()
   {
-    return matrix;
+    float[][] v = new float[matrix.length][matrix.length];
+    for (int i = 0; i < matrix.length; i++)
+    {
+      v[i] = Arrays.copyOf(matrix[i], matrix[i].length);
+    }
+    return v;
   }
 
   /**
@@ -231,7 +251,12 @@ public class ScoreMatrix implements PairwiseScoreModelI
   }
 
   /**
-   * Print the score matrix, optionally formatted as html, with the alphabet symbols as column headings and at the start of each row
+   * Print the score matrix, optionally formatted as html, with the alphabet
+   * symbols as column headings and at the start of each row.
+   * <p>
+   * The non-html format should give an output which can be parsed as a score
+   * matrix file
+   * 
    * @param html
    * @return
    */
@@ -247,6 +272,11 @@ public class ScoreMatrix implements PairwiseScoreModelI
       sb.append("<table border=\"1\">");
       sb.append(html ? "<tr><th></th>" : "");
     }
+    else
+    {
+      sb.append("ScoreMatrix ").append(getName()).append("\n");
+      sb.append(symbols).append("\n");
+    }
     for (char sym : symbols)
     {
       if (html)
@@ -316,7 +346,24 @@ public class ScoreMatrix implements PairwiseScoreModelI
    * <li>and so on</li>
    * </ul>
    */
-  public MatrixI computePairwiseScores(String[] seqs)
+  @Override
+  public MatrixI findSimilarities(AlignmentView seqstrings,
+          SimilarityParamsI options)
+  {
+    char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
+    String[] seqs = seqstrings.getSequenceStrings(gapChar);
+    return findSimilarities(seqs, options);
+  }
+
+  /**
+   * Computes pairwise similarities of a set of sequences using the given
+   * parameters
+   * 
+   * @param seqs
+   * @param params
+   * @return
+   */
+  protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
   {
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)
@@ -324,18 +371,117 @@ public class ScoreMatrix implements PairwiseScoreModelI
       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);
-          float score = getPairwiseScore(c1, c2);
-          total += score;
-        }
+        double total = computeSimilarity(seqs[row], seqs[col], params);
         values[row][col] = total;
       }
     }
     return new Matrix(values);
   }
+
+  /**
+   * Calculates the pairwise similarity of two strings using the given
+   * calculation parameters
+   * 
+   * @param seq1
+   * @param seq2
+   * @param params
+   * @return
+   */
+  protected double computeSimilarity(String seq1, String seq2,
+          SimilarityParamsI params)
+  {
+    int len1 = seq1.length();
+    int len2 = seq2.length();
+    double total = 0;
+
+    int width = Math.max(len1, len2);
+    for (int i = 0; i < width; i++)
+    {
+      if (i >= len1 || i >= len2)
+      {
+        /*
+         * off the end of one sequence; stop if we are only matching
+         * on the shorter sequence length, else treat as trailing gap
+         */
+        if (params.denominateByShortestLength())
+        {
+          break;
+        }
+      }
+      // Change GAP_SPACE to GAP_DASH if we adopt - for gap in matrices
+      char c1 = i >= len1 ? Comparison.GAP_SPACE : seq1.charAt(i);
+      char c2 = i >= len2 ? Comparison.GAP_SPACE : seq2.charAt(i);
+      boolean gap1 = Comparison.isGap(c1);
+      boolean gap2 = Comparison.isGap(c2);
+
+      if (gap1 && gap2)
+      {
+        /*
+         * gap-gap: include if options say so, else ignore
+         */
+        if (!params.includeGappedColumns())
+        {
+          continue;
+        }
+      }
+      else if (gap1 || gap2)
+      {
+        /*
+         * gap-residue: score if options say so
+         */
+        if (!params.includesGaps())
+        {
+          continue;
+        }
+      }
+      float score = getPairwiseScore(c1, c2);
+      total += score;
+    }
+    return total;
+  }
+
+  /**
+   * Answers a hashcode computed from the symbol alphabet and the matrix score
+   * values
+   */
+  @Override
+  public int hashCode()
+  {
+    int hs = Arrays.hashCode(symbols);
+    for (float[] row : matrix)
+    {
+      hs = hs * 31 + Arrays.hashCode(row);
+    }
+    return hs;
+  }
+
+  /**
+   * Answers true if the argument is a ScoreMatrix with the same symbol alphabet
+   * and score values, else false
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof ScoreMatrix))
+    {
+      return false;
+    }
+    ScoreMatrix sm = (ScoreMatrix) obj;
+    if (Arrays.equals(symbols, sm.symbols)
+            && Arrays.deepEquals(matrix, sm.matrix))
+    {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Returns the alphabet the matrix scores for, as a string of characters
+   * 
+   * @return
+   */
+  public String getSymbols()
+  {
+    return new String(symbols);
+  }
 }