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

[jalview.git] / src / jalview / datamodel / features / FeatureStore.java

diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index 02ce1c5..951b7a5 100644 (file)
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -1047,13 +1047,15 @@ public class FeatureStore
   }
 
   /**
-   * Adds the shift value to the start and end of all positional features.
-   * Returns true if at least one feature was updated, else false.
+   * Adds the shift amount to the start and end of all positional features whose
+   * start position is at or after fromPosition. Returns true if at least one
+   * feature was shifted, else false.
    * 
-   * @param shift
+   * @param fromPosition
+   * @param shiftBy
    * @return
    */
-  public synchronized boolean shiftFeatures(int shift)
+  public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
   {
     /*
      * Because begin and end are final fields (to ensure the data store's
@@ -1063,21 +1065,24 @@ public class FeatureStore
     boolean modified = false;
     for (SequenceFeature sf : getPositionalFeatures())
     {
-      modified = true;
-      int newBegin = sf.getBegin() + shift;
-      int newEnd = sf.getEnd() + shift;
-
-      /*
-       * sanity check: don't shift left of the first residue
-       */
-      if (newEnd > 0)
+      if (sf.getBegin() >= fromPosition)
       {
-        newBegin = Math.max(1, newBegin);
-        SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
-                sf.getFeatureGroup(), sf.getScore());
-        addFeature(sf2);
+        modified = true;
+        int newBegin = sf.getBegin() + shiftBy;
+        int newEnd = sf.getEnd() + shiftBy;
+
+        /*
+         * sanity check: don't shift left of the first residue
+         */
+        if (newEnd > 0)
+        {
+          newBegin = Math.max(1, newBegin);
+          SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
+                  sf.getFeatureGroup(), sf.getScore());
+          addFeature(sf2);
+        }
+        delete(sf);
       }
-      delete(sf);
     }
     return modified;
   }