Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_...

[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 1347213..7651016 100644 (file)
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel.features;
 
-import jalview.datamodel.SequenceFeature;
-
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -30,7 +28,9 @@ import java.util.Set;
 
 import intervalstore.api.IntervalStoreI;
 import intervalstore.impl.BinarySearcher;
+import intervalstore.impl.BinarySearcher.Compare;
 import intervalstore.impl.IntervalStore;
+import jalview.datamodel.SequenceFeature;
 
 /**
  * A data store for a set of sequence features that supports efficient lookup of
@@ -277,7 +277,7 @@ public class FeatureStore
      * binary search the sorted list to find the insertion point
      */
     int insertPosition = BinarySearcher.findFirst(contactFeatureStarts,
-            f -> f.getBegin() >= feature.getBegin());
+            true, Compare.GE, feature.getBegin());
     contactFeatureStarts.add(insertPosition, feature);
 
 
@@ -286,7 +286,7 @@ public class FeatureStore
      * binary search the sorted list to find the insertion point
      */
     insertPosition = BinarySearcher.findFirst(contactFeatureEnds,
-            f -> f.getEnd() >= feature.getEnd());
+            false, Compare.GE, feature.getEnd());
     contactFeatureEnds.add(insertPosition, feature);
 
     return true;
@@ -314,8 +314,8 @@ public class FeatureStore
      */
     // int pos = binarySearch(features,
     // SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
-    int pos = BinarySearcher.findFirst(features,
-            val -> val.getBegin() >= feature.getBegin());
+    int pos = BinarySearcher.findFirst(features, true, Compare.GE,
+            feature.getBegin());
     int len = features.size();
     while (pos < len)
     {
@@ -396,7 +396,7 @@ public class FeatureStore
      * whose end point is not before the target range
      */
     int index = BinarySearcher.findFirst(contactFeatureEnds,
-            f -> f.getEnd() >= from);
+            false, Compare.GE, (int) from);
 
     while (index < contactFeatureEnds.size())
     {
@@ -449,7 +449,7 @@ public class FeatureStore
           List<SequenceFeature> result)
   {
     int index = BinarySearcher.findFirst(contactFeatureStarts,
-            f -> f.getBegin() >= from);
+            true, Compare.GE, (int) from);
 
     while (index < contactFeatureStarts.size())
     {
@@ -812,13 +812,15 @@ 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
@@ -828,21 +830,24 @@ 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;
   }