X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=b73f826e40a51c8f4fb745c7234fbfacb328261c;hb=dd97032c11b883017a9c8125ff30a58dfb2144bd;hp=41d73838b98e6b83c690c7d0d009816d40d1d5b9;hpb=baad2f0ba2b171dd3d52c17afa46ef800334ea5e;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 41d7383..b73f826 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -33,6 +33,8 @@ import java.util.Arrays;
 public class ScoreMatrix implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
+  private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+
   /*
    * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
    * for pairwise scoring; 2.10.2 uses gap score (last column) in
@@ -49,10 +51,16 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
   /*
    * the name of the model as shown in menus
+   * each score model in use should have a unique name
    */
   private String name;
 
   /*
+   * a description for the model as shown in tooltips
+   */
+  private String description;
+
+  /*
    * the characters that the model provides scores for
    */
   private char[] symbols;
@@ -79,21 +87,21 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * of symbols. The matrix should be square and of the same size as the
    * alphabet, for example 20x20 for a 20 symbol alphabet.
    * 
-   * @param name
+   * @param theName
    *          Unique, human readable name for the matrix
    * @param alphabet
    *          the symbols to which scores apply
-   * @param matrix
+   * @param values
    *          Pairwise scores indexed according to the symbol alphabet
    */
-  public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
+  public ScoreMatrix(String theName, char[] alphabet, float[][] values)
   {
-    if (alphabet.length != matrix.length)
+    if (alphabet.length != values.length)
     {
       throw new IllegalArgumentException(
               "score matrix size must match alphabet size");
     }
-    for (float[] row : matrix)
+    for (float[] row : values)
     {
       if (row.length != alphabet.length)
       {
@@ -102,8 +110,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
       }
     }
 
-    this.matrix = matrix;
-    this.name = name;
+    this.matrix = values;
+    this.name = theName;
     this.symbols = alphabet;
 
     symbolIndex = buildSymbolIndex(alphabet);
@@ -163,6 +171,12 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   @Override
+  public String getDescription()
+  {
+    return description;
+  }
+
+  @Override
   public boolean isDNA()
   {
     return !peptide;
@@ -350,7 +364,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   public MatrixI findSimilarities(AlignmentView seqstrings,
           SimilarityParamsI options)
   {
-    char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
+    char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+            : Comparison.GAP_DASH;
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
     return findSimilarities(seqs, options);
   }
@@ -408,9 +423,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
           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);
+
+      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);
 
@@ -429,7 +444,7 @@ public class ScoreMatrix implements SimilarityScoreModelI,
         /*
          * gap-residue: score if options say so
          */
-        if (!params.includesGaps())
+        if (!params.includeGaps())
         {
           continue;
         }
@@ -484,4 +499,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   {
     return new String(symbols);
   }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
 }