Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 86d52b5..3e940af 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -14,11 +14,27 @@ import jalview.util.Comparison;
 public class PIDModel implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
+  private static final String NAME = "PID";
+
+  private String description;
+
+  /**
+   * Constructor
+   */
+  public PIDModel()
+  {
+  }
 
   @Override
   public String getName()
   {
-    return "% Identity (PID)";
+    return NAME;
+  }
+
+  @Override
+  public String getDescription()
+  {
+    return description;
   }
 
   @Override
@@ -65,7 +81,7 @@ public class PIDModel implements SimilarityScoreModelI,
   public MatrixI findSimilarities(AlignmentView seqData,
           SimilarityParamsI options)
   {
-    String[] seqs = seqData.getSequenceStrings(' ');
+    String[] seqs = seqData.getSequenceStrings(Comparison.GAP_DASH);
     return findSimilarities(seqs, options);
   }
 
@@ -103,7 +119,7 @@ public class PIDModel implements SimilarityScoreModelI,
    * @param options
    * @return
    */
-  protected static double computePID(String seq1, String seq2,
+  public static double computePID(String seq1, String seq2,
           SimilarityParamsI options)
   {
     int len1 = seq1.length();