X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=6cdfacbe56695b322b074d05cf90fef8565b37ea;hb=af65be61ff37a024b694150efed2c6c9b81382ef;hp=84e91aebc3c555aba5efc0dad30cb6533b4c9b27;hpb=2a9d6da50bb346c1f8cd38f104c958b7e8e6eff0;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 84e91ae..6cdfacb 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -20,9 +20,10 @@
  */
 package jalview.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
@@ -32,16 +33,20 @@ import java.util.Arrays;
 
 /**
  * A class that models a substitution score matrix for any given alphabet of
- * symbols
+ * symbols. Instances of this class are immutable and thread-safe, so the same
+ * object is returned from calls to getInstance().
  */
-public class ScoreMatrix implements SimilarityScoreModelI,
-        PairwiseScoreModelI
+public class ScoreMatrix extends SimilarityScoreModel
+        implements PairwiseScoreModelI
 {
+  private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+
   /*
-   * this fields records which gap character (if any) is used in the alphabet;
-   * space, dash or dot are recognised as gap symbols
+   * an arbitrary score to assign for identity of an unknown symbol
+   * (this is the value on the diagonal in the * column of the NCBI matrix)
+   * (though a case could be made for using the minimum diagonal value)
    */
-  private char gapCharacter = '0';
+  private static final int UNKNOWN_IDENTITY_SCORE = 1;
 
   /*
    * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
@@ -108,6 +113,26 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    */
   public ScoreMatrix(String theName, char[] alphabet, float[][] values)
   {
+    this(theName, null, alphabet, values);
+  }
+
+  /**
+   * Constructor given a name, description, symbol alphabet, and matrix of
+   * scores for pairs of symbols. The matrix should be square and of the same
+   * size as the alphabet, for example 20x20 for a 20 symbol alphabet.
+   * 
+   * @param theName
+   *          Unique, human readable name for the matrix
+   * @param theDescription
+   *          descriptive display name suitable for use in menus
+   * @param alphabet
+   *          the symbols to which scores apply
+   * @param values
+   *          Pairwise scores indexed according to the symbol alphabet
+   */
+  public ScoreMatrix(String theName, String theDescription, char[] alphabet,
+          float[][] values)
+  {
     if (alphabet.length != values.length)
     {
       throw new IllegalArgumentException(
@@ -124,6 +149,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
     this.matrix = values;
     this.name = theName;
+    this.description = theDescription;
     this.symbols = alphabet;
 
     symbolIndex = buildSymbolIndex(alphabet);
@@ -185,11 +211,6 @@ public class ScoreMatrix implements SimilarityScoreModelI,
     short pos = 0;
     for (char c : alphabet)
     {
-      if (Comparison.isGap(c))
-      {
-        gapCharacter = c;
-      }
-
       if (c <= MAX_ASCII)
       {
         index[c] = pos;
@@ -276,21 +297,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   /**
-   * Answers the matrix index for the gap character, or -1 if unmapped in the
-   * matrix. Use this method only if using <code>getMatrix</code> in order to
-   * compute scores directly (without symbol lookup) for efficiency.
-   * 
-   * @return
-   * @see #getMatrix()
-   */
-  public int getGapIndex()
-  {
-    return getMatrixIndex(gapCharacter);
-  }
-
-  /**
-   * Returns the pairwise score for substituting c with d, or zero if c or d is
-   * an unscored or unexpected character
+   * Returns the pairwise score for substituting c with d. If either c or d is
+   * an unexpected character, returns 1 for identity (c == d), else the minimum
+   * score value in the matrix.
    */
   @Override
   public float getPairwiseScore(char c, char d)
@@ -315,10 +324,11 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
     /*
      * one or both symbols not found in the matrix
-     * note: a possible strategy here would be to return the minimum
-     * matrix value if c != d
+     * currently scoring as 1 (for identity) or the minimum
+     * matrix score value (otherwise)
+     * (a case could be made for using minimum row/column value instead)
      */
-    return 0;
+    return c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
   }
 
   /**
@@ -424,13 +434,14 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
    * <li>and so on</li>
    * </ul>
+   * This method is thread-safe.
    */
   @Override
   public MatrixI findSimilarities(AlignmentView seqstrings,
           SimilarityParamsI options)
   {
     char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
-            : gapCharacter;
+            : GAP_CHARACTER;
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
     return findSimilarities(seqs, options);
   }
@@ -443,7 +454,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * @param params
    * @return
    */
-  protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
+  protected MatrixI findSimilarities(String[] seqs,
+          SimilarityParamsI params)
   {
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)
@@ -489,8 +501,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
         }
       }
 
-      char c1 = i >= len1 ? gapCharacter : seq1.charAt(i);
-      char c2 = i >= len2 ? gapCharacter : seq2.charAt(i);
+      char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
+      char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
       boolean gap1 = Comparison.isGap(c1);
       boolean gap2 = Comparison.isGap(c2);
 
@@ -565,11 +577,6 @@ public class ScoreMatrix implements SimilarityScoreModelI,
     return new String(symbols);
   }
 
-  public void setDescription(String desc)
-  {
-    description = desc;
-  }
-
   public float getMinimumScore()
   {
     return minValue;
@@ -579,4 +586,10 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   {
     return maxValue;
   }
+
+  @Override
+  public ScoreModelI getInstance(AlignmentViewPanel avp)
+  {
+    return this;
+  }
 }