JAL-838 move two callers off Comparison.PID and deprecate it

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index ceca6d6..1a6826d 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,8 +20,10 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
@@ -1059,6 +1061,8 @@ public class AlignSeq
 
     // long start = System.currentTimeMillis();
 
+    SimilarityParams pidParams = new SimilarityParams(true, true, true,
+            true);
     float pid;
     String seqi, seqj;
     for (int i = 0; i < height; i++)
@@ -1099,7 +1103,7 @@ public class AlignSeq
             seqj = ug;
           }
         }
-        pid = Comparison.PID(seqi, seqj);
+        pid = (float) PIDModel.computePID(seqi, seqj, pidParams);
 
         // use real sequence length rather than string length
         if (lngth[j] < lngth[i])