X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStore.java;h=1b6277c59deafeb76512f88bc28237cd3aa95bb5;hb=807f5945ffa954c38f07cbf9d2a4ebc22cfe5eb9;hp=c6a49dbbc56b3a39d26cf26f3ea2080d23953d64;hpb=c8863c027ddace3961405ed0051f104f1ec99581;p=jalview.git

diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index c6a49db..1b6277c 100644
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -1,5 +1,6 @@
 package jalview.datamodel.features;
 
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 
 import java.util.ArrayList;
@@ -1017,4 +1018,40 @@ public class FeatureStore
     }
     return result;
   }
+
+  /**
+   * Adds the shift value to the start and end of all positional features.
+   * Returns true if at least one feature was updated, else false.
+   * 
+   * @param shift
+   * @return
+   */
+  public synchronized boolean shiftFeatures(int shift)
+  {
+    /*
+     * Because begin and end are final fields (to ensure the data store's
+     * integrity), we have to delete each feature and re-add it as amended.
+     * (Although a simple shift of all values would preserve data integrity!)
+     */
+    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)
+      {
+        newBegin = Math.max(1, newBegin);
+        SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
+                sf.getFeatureGroup(), sf.getScore());
+        addFeature(sf2);
+      }
+      delete(sf);
+    }
+    return modified;
+  }
 }