Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 33de452..f555855 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -43,10 +43,7 @@ import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * 
- * Implements the SequenceI interface for a char[] based sequence object.
- * 
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
  */
 public class Sequence extends ASequence implements SequenceI
 {
@@ -797,6 +794,7 @@ public class Sequence extends ASequence implements SequenceI
      * preserve end residue column provided cursor was valid
      */
     int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+
     if (residuePos == this.end)
     {
       endColumn = column;
@@ -833,8 +831,7 @@ public class Sequence extends ASequence implements SequenceI
     /*
      * move left or right to find pos from hint.position
      */
-    int col = curs.columnPosition - 1; // convert from base 1 to 0-based array
-                                       // index
+    int col = curs.columnPosition - 1; // convert from base 1 to base 0
     int newPos = curs.residuePosition;
     int delta = newPos > pos ? -1 : 1;
 
@@ -1263,12 +1260,13 @@ public class Sequence extends ASequence implements SequenceI
     boolean createNewDs = false;
     // TODO: take a (second look) at the dataset creation validation method for
     // the very large sequence case
+
     int startIndex = findIndex(start) - 1;
     int endIndex = findIndex(end) - 1;
     int startDeleteColumn = -1; // for dataset sequence deletions
     int deleteCount = 0;
 
-    for (int s = i; s < j; s++)
+    for (int s = i; s < j && s < sequence.length; s++)
     {
       if (Comparison.isGap(sequence[s]))
       {
@@ -1913,6 +1911,15 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
+    if (datasetSequence != null)
+    {
+      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+              types);
+    }
+    else
+    {
+      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
+    }
 
     /*
      * if end column is gapped, endPos may be to the right,