JAL-2544 check feature overlaps selection region

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 6c46a3e..693e794 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -811,17 +811,23 @@ public class AlignmentSorter
       for (int f = 0; f < sf.length; f++)
       {
         // filter for selection criteria
-        if (
-        // ignore features outwith alignment start-stop positions.
-        (sf[f].end < sstart || sf[f].begin > sstop) ||
-        // or ignore based on selection criteria
-                (featureLabels != null && !AlignmentSorter
-                        .containsIgnoreCase(sf[f].type, featureLabels))
-                || (groupLabels != null
-                // problem here: we cannot eliminate null feature group features
-                && (sf[f].getFeatureGroup() != null && !AlignmentSorter
-                        .containsIgnoreCase(sf[f].getFeatureGroup(),
-                                groupLabels))))
+        SequenceFeature feature = sf[f];
+
+        /*
+         * double-check feature overlaps columns (JAL-2544)
+         * (could avoid this with a findPositions(fromCol, toCol) method)
+         * findIndex returns base 1 column values, startCol/endCol are base 0
+         */
+        boolean noOverlap = seqs[i].findIndex(feature.getBegin()) > stop + 1
+                || seqs[i].findIndex(feature.getEnd()) < start + 1;
+        boolean skipFeatureType = featureLabels != null
+                && !AlignmentSorter.containsIgnoreCase(feature.type,
+                        featureLabels);
+        boolean skipFeatureGroup = groupLabels != null
+                && (feature.getFeatureGroup() != null && !AlignmentSorter
+                        .containsIgnoreCase(feature.getFeatureGroup(),
+                                groupLabels));
+        if (noOverlap || skipFeatureType || skipFeatureGroup)
         {
           // forget about this feature
           sf[f] = null;
@@ -830,7 +836,7 @@ public class AlignmentSorter
         else
         {
           // or, also take a look at the scores if necessary.
-          if (!ignoreScore && !Float.isNaN(sf[f].getScore()))
+          if (!ignoreScore && !Float.isNaN(feature.getScore()))
           {
             if (seqScores[i] == 0)
             {
@@ -838,7 +844,7 @@ public class AlignmentSorter
             }
             seqScores[i]++;
             hasScore[i] = true;
-            scores[i] += sf[f].getScore(); // take the first instance of this
+            scores[i] += feature.getScore(); // take the first instance of this
             // score.
           }
         }