X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=e7733e9b065ac3c9ce062cf054999ffdc9a01b87;hb=60e252f7e0084336b0a85620842ce3db8f63e5b0;hp=681d3b75ee2f3996bf4200bf884e32eb24b1d125;hpb=c689b58a9aaa704f5e5160e44da5b84e8984d6a0;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 681d3b7..e7733e9 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -771,8 +771,25 @@ public class AlignmentSorter
       {
         SequenceFeature sf = it.next();
 
+        /*
+         * 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
+         */
+        if (seqs[i].findIndex(sf.getBegin()) > endCol + 1
+                || seqs[i].findIndex(sf.getEnd()) < startCol + 1)
+        {
+          it.remove();
+          continue;
+        }
+
+        /*
+         * accept all features with null or empty group, otherwise
+         * check group is one of the currently visible groups
+         */
         String featureGroup = sf.getFeatureGroup();
         if (groups != null && featureGroup != null
+                && !"".equals(featureGroup)
                 && !groups.contains(featureGroup))
         {
           it.remove();