From fc90b2a19f4827d0389c578c56105dc7e69e59ea Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 2 Dec 2020 19:59:33 +0000
Subject: [PATCH] JAL-3761 helper method reinstated to avoid code duplication

---
 src/jalview/util/MapList.java |   55 ++++++++++++++++++++++-------------------
 1 file changed, 30 insertions(+), 25 deletions(-)

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 198066d..745f367 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1155,27 +1155,8 @@ public class MapList
    */
   public int[] locateInFrom(int start, int end)
   {
-    if (end < start)
-    {
-      int tmp = end;
-      end = start;
-      start = tmp;
-    }
-
-    /*
-     * traverse toShifts and mark offsets in fromShifts 
-     * of any positions that lie in [start, end]
-     */
-    BitSet offsets = getMappedOffsetsForPositions(start, end, toShifts,
+    return mapPositions(start, end, toShifts, fromShifts,
             toRatio, fromRatio);
-
-    /*
-     * traverse fromShifts and collect positions at the marked offsets
-     */
-    List<int[]> mapped = getPositionsForOffsets(fromShifts, offsets);
-
-    // TODO: or just return the List and adjust calling code to match
-    return mapped.isEmpty() ? null : MappingUtils.rangeListToArray(mapped);
   }
 
   /**
@@ -1190,6 +1171,29 @@ public class MapList
    */
   public int[] locateInTo(int start, int end)
   {
+    return mapPositions(start, end, fromShifts, toShifts,
+            fromRatio, toRatio);
+  }
+
+  /**
+   * Helper method that returns the [start1, end1, start2, end2, ...] positions
+   * in {@code targetRange} that map to positions between {@code start} and
+   * {@code end} in {@code sourceRange}. Note that for a reverse strand mapping
+   * this will return ranges with end < start. Returns null if no mapped
+   * positions are found in start-end.
+   * 
+   * @param start
+   * @param end
+   * @param sourceRange
+   * @param targetRange
+   * @param sourceWordLength
+   * @param targetWordLength
+   * @return
+   */
+  final static int[] mapPositions(int start, int end,
+          List<int[]> sourceRange, List<int[]> targetRange,
+          int sourceWordLength, int targetWordLength)
+  {
     if (end < start)
     {
       int tmp = end;
@@ -1198,17 +1202,18 @@ public class MapList
     }
 
     /*
-     * traverse fromShifts and mark offsets in toShifts 
+     * traverse sourceRange and mark offsets in targetRange 
      * of any positions that lie in [start, end]
      */
-    BitSet offsets = getMappedOffsetsForPositions(start, end, fromShifts,
-            fromRatio, toRatio);
+    BitSet offsets = getMappedOffsetsForPositions(start, end, sourceRange,
+            sourceWordLength, targetWordLength);
 
     /*
-     * traverse toShifts and collect positions at the marked offsets
+     * traverse targetRange and collect positions at the marked offsets
      */
-    List<int[]> mapped = getPositionsForOffsets(toShifts, offsets);
+    List<int[]> mapped = getPositionsForOffsets(targetRange, offsets);
 
+    // TODO: or just return the List and adjust calling code to match
     return mapped.isEmpty() ? null : MappingUtils.rangeListToArray(mapped);
   }
 
-- 
1.7.10.2