fixed getIntervals bug to ensure it returns range from start of token at fromPosition...

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 826ead7..2464264 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -446,15 +446,13 @@ public class MapList
    * @param fromStart
    * @param fromEnd
    * @param fromRatio2
-   * @return
+   * @return series of from,to intervals from from first position of starting region to final position of ending region inclusive
    */
   private int[] getIntervals(Vector fromShifts2, int[] fromStart, int[] fromEnd, int fromRatio2)
   {
-    // TODO: correct for word boundary w.r.t. fromStart->fromEnd direction for startpos and endpos.
-    // test is (1,8,12,17) to (1,5) and features on to : 2,2; 3,3; 4,3; 3,4; 4,4; 5,3; 3,5; 2,4; 4,2;
-    // correct for word direction for start and end :
-    int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1); // Math.min(fromStart[0], .. );
-    int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1); // Math.max(fromEnd[0],);
+    int startpos,endpos;
+    startpos = fromStart[0]; // first position in fromStart 
+    endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1); // last position in fromEnd
     int intv=0,intvSize= fromShifts2.size();
     int iv[],i=0,fs=-1,fe=-1; // containing intervals
     while (intv<intvSize && (fs==-1 || fe==-1)) {