JAL-3761 failing test, formatting, method renamed

[jalview.git] / src / jalview / util / MapList.java

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 36fb450..e095106 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -336,7 +336,8 @@ public class MapList
    * <p>
    * The main use case for this method is when mapping cDNA sequence to its
    * protein product, based on CDS feature ranges which derive from spliced
-   * exons, but are contiguous on the cDNA sequence. For example 
+   * exons, but are contiguous on the cDNA sequence. For example
+   * 
    * <pre>
    *   CDS 1-20  // from exon1
    *   CDS 21-35 // from exon2
@@ -568,7 +569,7 @@ public class MapList
     }
     int fromRemainder = (fromCount[0] - 1) % fromRatio;
     int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
-    int[] toPos = countToPos(shiftFrom, toCount);
+    int[] toPos = traverseToPosition(shiftFrom, toCount);
     if (toPos == null)
     {
       return null; // throw new Error("Bad Mapping!");
@@ -617,44 +618,61 @@ public class MapList
   }
 
   /**
-   * count out pos positions into a series of intervals and return the position
+   * Reads through the given intervals until {@code count} positions have been
+   * traversed, and returns an array consisting of two values:
+   * <ul>
+   * <li>the value at the {@code count'th} position</li>
+   * <li>+1 if the last interval read is forwards, -1 if reverse direction</li>
+   * </ul>
+   * Returns null if the ranges include less than {@code count} positions, or if
+   * {@code count < 1}.
    * 
-   * @param shiftFrom
-   * @param pos
-   * @return position pos in interval set
+   * @param intervals
+   *          a list of [start, end] ranges
+   * @param count
+   *          the number of positions to traverse
+   * @return
    */
-  protected static int[] countToPos(List<int[]> shiftFrom, int pos)
+  protected static int[] traverseToPosition(List<int[]> intervals,
+          final int count)
   {
-    int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
-    int[] intv = { 0, 0 };
+    int traversed = 0;
+    int ivSize = intervals.size();
+    int iv = 0;
+
+    if (count < 1)
+    {
+      return null;
+    }
+
     while (iv < ivSize)
     {
-      intv = shiftFrom.get(iv++);
-      diff = intv[1] - intv[0];
+      int[] intv = intervals.get(iv++);
+      int diff = intv[1] - intv[0];
       if (diff >= 0)
       {
-        if (pos <= count + 1 + diff)
+        if (count <= traversed + 1 + diff)
         {
-          return new int[] { pos - count - 1 + intv[0], +1 };
+          return new int[] { intv[0] + (count - traversed - 1), +1 };
         }
         else
         {
-          count += 1 + diff;
+          traversed += 1 + diff;
         }
       }
       else
       {
-        if (pos <= count + 1 - diff)
+        if (count <= traversed + 1 - diff)
         {
-          return new int[] { intv[0] - (pos - count - 1), -1 };
+          return new int[] { intv[0] - (count - traversed - 1), -1 };
         }
         else
         {
-          count += 1 - diff;
+          traversed += 1 - diff;
         }
       }
     }
-    return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
+    return null;
   }
 
   /**