Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index 5bf4b11..0aa77fa 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -22,9 +22,8 @@ package jalview.analysis.scoremodels;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.analysis.DistanceScoreModelI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceFeature;
@@ -38,8 +37,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-public class FeatureDistanceModel implements DistanceScoreModelI,
-        ViewBasedAnalysisI
+public class FeatureDistanceModel extends DistanceScoreModel
 {
   private static final String NAME = "Sequence Feature Similarity";
 
@@ -55,7 +53,26 @@ public class FeatureDistanceModel implements DistanceScoreModelI,
   }
 
   @Override
-  public boolean configureFromAlignmentView(AlignmentViewPanel view)
+  public ScoreModelI getInstance(AlignmentViewPanel view)
+  {
+    FeatureDistanceModel instance;
+    try
+    {
+      instance = this.getClass().getDeclaredConstructor().newInstance();
+      instance.configureFromAlignmentView(view);
+      return instance;
+    } catch (InstantiationException | IllegalAccessException e)
+    {
+      System.err.println("Error in " + getClass().getName()
+              + ".getInstance(): " + e.getMessage());
+      return null;
+    } catch (ReflectiveOperationException roe)
+    {
+      return null;
+    }
+  }
+
+  boolean configureFromAlignmentView(AlignmentViewPanel view)
 
   {
     fr = view.cloneFeatureRenderer();
@@ -110,8 +127,8 @@ public class FeatureDistanceModel implements DistanceScoreModelI,
         /*
          * first record feature types in this column for each sequence
          */
-        Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(
-                seqs, cpos);
+        Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(seqs,
+                cpos);
 
         /*
          * count feature types on either i'th or j'th sequence but not both
@@ -163,24 +180,29 @@ public class FeatureDistanceModel implements DistanceScoreModelI,
   /**
    * Builds and returns a map containing a (possibly empty) list (one per
    * SeqCigar) of visible feature types at the given column position. The map
-   * has no entry for sequences which are gapped at the column position.
+   * does not include entries for features which straddle a gapped column
+   * positions.
    * 
    * @param seqs
    * @param columnPosition
+   *          (0..)
    * @return
    */
   protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
           SeqCigar[] seqs, int columnPosition)
   {
-    Map<SeqCigar, Set<String>> sfap = new HashMap<SeqCigar, Set<String>>();
+    Map<SeqCigar, Set<String>> sfap = new HashMap<>();
     for (SeqCigar seq : seqs)
     {
       int spos = seq.findPosition(columnPosition);
       if (spos != -1)
       {
-        Set<String> types = new HashSet<String>();
-        List<SequenceFeature> sfs = fr.findFeaturesAtRes(seq.getRefSeq(),
-                spos);
+        /*
+         * position is not a gap
+         */
+        Set<String> types = new HashSet<>();
+        List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
+                seq.getRefSeq(), spos, spos);
         for (SequenceFeature sf : sfs)
         {
           types.add(sf.getType());