JAL-3076 fetch Ensembl sequence as JSON instead of Fasta

[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 b082b56..02ce1c5 100644 (file)
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.features;
 
 import jalview.datamodel.ContiguousI;
@@ -54,7 +74,7 @@ public class FeatureStore
 
     /**
      * serves a search condition for finding the first feature whose end
-     * position follows a given target location
+     * position is at or follows a given target location
      * 
      * @param target
      * @return
@@ -596,28 +616,15 @@ public class FeatureStore
   protected void findNonNestedFeatures(long from, long to,
           List<SequenceFeature> result)
   {
+    /*
+     * find the first feature whose end position is
+     * after the target range start
+     */
     int startIndex = binarySearch(nonNestedFeatures,
             SearchCriterion.byEnd(from));
 
-    findNonNestedFeatures(startIndex, from, to, result);
-  }
-
-  /**
-   * Scans the list of non-nested features, starting from startIndex, to find
-   * those that overlap the from-to range, and adds them to the result list.
-   * Returns the index of the first feature whose start position is after the
-   * target range (or the length of the whole list if no such feature exists).
-   * 
-   * @param startIndex
-   * @param from
-   * @param to
-   * @param result
-   * @return
-   */
-  protected int findNonNestedFeatures(final int startIndex, long from,
-          long to, List<SequenceFeature> result)
-  {
-    int i = startIndex;
+    final int startIndex1 = startIndex;
+    int i = startIndex1;
     while (i < nonNestedFeatures.size())
     {
       SequenceFeature sf = nonNestedFeatures.get(i);
@@ -631,7 +638,6 @@ public class FeatureStore
       }
       i++;
     }
-    return i;
   }
 
   /**