JAL-2416 score matrix gap symbol (if any) dynamically determined

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1a6826d..d04e897 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -352,7 +352,7 @@ public class AlignSeq
     scoreModel = ScoreModels.getInstance().getDefaultModel(
             PEP.equals(type));
     lookup = scoreModel.getMatrix();
-    gapIndex = scoreModel.getMatrixIndex(' ');
+    gapIndex = scoreModel.getGapIndex();
   }
 
   /**

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d1a3c37..55881d7 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -172,7 +172,7 @@ public class Conservation
    */
   private void calcSeqNum(int i, ScoreMatrix sm)
   {
-    int gapIndex = sm.getMatrixIndex(' ');
+    int gapIndex = sm.getGapIndex();
     int sSize = sequences.length;
 
     if ((i > -1) && (i < sSize))
@@ -554,7 +554,7 @@ public class Conservation
       calcSeqNum(i, sm);
     }
 
-    int gapIndex = sm.getMatrixIndex(' ');
+    int gapIndex = sm.getGapIndex();
 
     if ((cons2 == null) || seqNumsChanged)
     {
@@ -597,7 +597,6 @@ public class Conservation
     double max = -Double.MAX_VALUE;
     ScoreMatrix blosum62 = ScoreModels.getInstance().getBlosum62();
     float[][] blosumScores = blosum62.getMatrix();
-    int gapIndex = blosum62.getMatrixIndex(' ');
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();
@@ -618,6 +617,7 @@ public class Conservation
     // todo ? remove '*' (unused?) from score matrix and
     // use getSize() here instead of getSize() - 1 ??
     final int symbolCount = blosum62.getSize() - 1; // 24;
+    int gapIndex = blosum62.getGapIndex();
 
     for (j = startRes; j <= endRes; j++)
     {

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index b73f826..b904432 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -30,10 +30,18 @@ import jalview.util.Comparison;
 
 import java.util.Arrays;
 
+/**
+ * A class that models a substitution score matrix for any given alphabet of
+ * symbols
+ */
 public class ScoreMatrix implements SimilarityScoreModelI,
         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
+   */
+  private char gapCharacter = '0';
 
   /*
    * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
@@ -132,17 +140,25 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * Mappings are added automatically for lower case symbols (for non case
    * sensitive scoring), unless they are explicitly present in the alphabet (are
    * scored separately in the score matrix).
+   * <p>
+   * the gap character (space, dash or dot) included in the alphabet (if any) is
+   * recorded in a field
    * 
    * @param alphabet
    * @return
    */
-  static short[] buildSymbolIndex(char[] alphabet)
+  short[] buildSymbolIndex(char[] alphabet)
   {
     short[] index = new short[MAX_ASCII + 1];
     Arrays.fill(index, UNMAPPED);
     short pos = 0;
     for (char c : alphabet)
     {
+      if (Comparison.isGap(c))
+      {
+        gapCharacter = c;
+      }
+
       if (c <= MAX_ASCII)
       {
         index[c] = pos;
@@ -229,6 +245,19 @@ 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
    */
@@ -424,8 +453,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
         }
       }
 
-      char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
-      char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
+      char c1 = i >= len1 ? gapCharacter : seq1.charAt(i);
+      char c2 = i >= len2 ? gapCharacter : seq2.charAt(i);
       boolean gap1 = Comparison.isGap(c1);
       boolean gap2 = Comparison.isGap(c2);
 

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 5c699d1..24db894 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -38,6 +38,8 @@ public class ScoreMatrixTest
     assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
     assertEquals(sm.getMatrixIndex('c'), 2);
     assertEquals(sm.getMatrixIndex(' '), -1);
+
+    assertEquals(sm.getGapIndex(), -1); // no gap symbol
   }
 
   @Test(
@@ -76,7 +78,12 @@ public class ScoreMatrixTest
   @Test(groups = "Functional")
   public void testBuildSymbolIndex()
   {
-    short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f, 4f };
+    ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' },
+            scores);
+    short[] index = sm.buildSymbolIndex("AX-yxYp".toCharArray());
 
     assertEquals(index.length, 128); // ASCII character set size
 
@@ -84,12 +91,10 @@ public class ScoreMatrixTest
     assertEquals(index['a'], 0); // lower-case mapping added
     assertEquals(index['X'], 1);
     assertEquals(index['-'], 2);
-    assertEquals(index['.'], 3);
-    assertEquals(index[' '], 4);
-    assertEquals(index['y'], 5); // lower-case override
-    assertEquals(index['x'], 6); // lower-case override
-    assertEquals(index['Y'], 7);
-    assertEquals(index['p'], 8);
+    assertEquals(index['y'], 3); // lower-case override
+    assertEquals(index['x'], 4); // lower-case override
+    assertEquals(index['Y'], 5);
+    assertEquals(index['p'], 6);
     assertEquals(index['P'], -1); // lower-case doesn't map upper-case
 
     /*
@@ -110,8 +115,13 @@ public class ScoreMatrixTest
   @Test(groups = "Functional")
   public void testBuildSymbolIndex_nonAscii()
   {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 3f, 4f };
+    ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' },
+            scores);
     char[] weird = new char[] { 128, 245, 'P' };
-    short[] index = ScoreMatrix.buildSymbolIndex(weird);
+    short[] index = sm.buildSymbolIndex(weird);
     assertEquals(index.length, 128);
     assertEquals(index['P'], 2);
     assertEquals(index['p'], 2);
@@ -157,6 +167,13 @@ public class ScoreMatrixTest
   }
 
   @Test(groups = "Functional")
+  public void testGetGapIndex()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    assertEquals(sm.getGapIndex(), 23);
+  }
+
+  @Test(groups = "Functional")
   public void testGetSize()
   {
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
@@ -477,4 +494,27 @@ public class ScoreMatrixTest
               String.format("%s->%s", res, c2));
     }
   }
+
+  @Test(groups = "Functional")
+  public void testConstructor_gapDash()
+  {
+    float[][] scores = new float[2][];
+    scores[0] = new float[] { 1f, 2f };
+    scores[1] = new float[] { 4f, 5f };
+    ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '-' },
+            scores);
+    assertEquals(sm.getSize(), 2);
+    assertArrayEquals(scores, sm.getMatrix());
+    assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+    assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
+    assertEquals(sm.getPairwiseScore('a', '-'), 2f);
+    assertEquals(sm.getPairwiseScore('-', 'A'), 4f);
+    assertEquals(sm.getMatrixIndex('a'), 0);
+    assertEquals(sm.getMatrixIndex('A'), 0);
+    assertEquals(sm.getMatrixIndex('-'), 1);
+    assertEquals(sm.getMatrixIndex(' '), -1);
+    assertEquals(sm.getMatrixIndex('.'), -1);
+  
+    assertEquals(sm.getGapIndex(), 1);
+  }
 }