JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

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

diff --git a/src/jalview/analysis/scoremodels/PIDScoreModel.java b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
similarity index 92%
rename from src/jalview/analysis/scoremodels/PIDScoreModel.java
rename to src/jalview/analysis/scoremodels/PIDDistanceModel.java
index e0e8634..f72b0fc 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDScoreModel.java
+++ b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
@@ -20,18 +20,18 @@
  */
 package jalview.analysis.scoremodels;
 
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.util.Comparison;
 
-public class PIDScoreModel implements ScoreModelI
+public class PIDDistanceModel implements DistanceModelI
 {
 
   @Override
   public float[][] findDistances(AlignmentView seqData)
   {
     String[] sequenceString = seqData
-            .getSequenceStrings(Comparison.GapChars.charAt(0));
+            .getSequenceStrings(Comparison.GAP_SPACE);
     int noseqs = sequenceString.length;
     float[][] distance = new float[noseqs][noseqs];
     for (int i = 0; i < (noseqs - 1); i++)