X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=b73f826e40a51c8f4fb745c7234fbfacb328261c;hb=dd97032c11b883017a9c8125ff30a58dfb2144bd;hp=a4b834305603fe909502bc1631198e197e54fa45;hpb=582493a5b56d3e01d901c6da9906685c31a32abb;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index a4b8343..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;
@@ -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);
 
@@ -484,4 +499,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   {
     return new String(symbols);
   }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
 }