JAL-2416 revert to '*' not '-' in score matrix, handle gaps explicitly

[jalview.git] / src / jalview / analysis / scoremodels / ScoreMatrix.java

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index e2c14e9..8bc2c04 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -37,6 +37,8 @@ import java.util.Arrays;
 public class ScoreMatrix implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
+  private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+
   /*
    * 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)
@@ -45,12 +47,6 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   private static final int UNKNOWN_IDENTITY_SCORE = 1;
 
   /*
-   * 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)
    * for pairwise scoring; 2.10.2 uses gap score (last column) in
    * score matrix (JAL-2397)
@@ -192,11 +188,6 @@ 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;
@@ -283,19 +274,6 @@ 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. If either c or d is
    * an unexpected character, returns 1 for identity (c == d), else the minimum
    * score value in the matrix.
@@ -439,7 +417,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
           SimilarityParamsI options)
   {
     char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
-            : gapCharacter;
+            : GAP_CHARACTER;
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
     return findSimilarities(seqs, options);
   }
@@ -498,8 +476,8 @@ 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);