Merge branch 'releases/Release_2_10_4_Branch' into develop

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

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index ae530f9..7f1abc4 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1103,8 +1103,33 @@ public class MapList
    */
   public boolean isFromForwardStrand()
   {
+    return isForwardStrand(getFromRanges());
+  }
+
+  /**
+   * Returns true if mapping is to forward strand, false if to reverse strand.
+   * Result is just based on the first 'to' range that is not a single position.
+   * Default is true unless proven to be false. Behaviour is not well defined if
+   * the mapping has a mixture of forward and reverse ranges.
+   * 
+   * @return
+   */
+  public boolean isToForwardStrand()
+  {
+    return isForwardStrand(getToRanges());
+  }
+
+  /**
+   * A helper method that returns true unless at least one range has start > end.
+   * Behaviour is undefined for a mixture of forward and reverse ranges.
+   * 
+   * @param ranges
+   * @return
+   */
+  private boolean isForwardStrand(List<int[]> ranges)
+  {
     boolean forwardStrand = true;
-    for (int[] range : getFromRanges())
+    for (int[] range : ranges)
     {
       if (range[1] > range[0])
       {
@@ -1129,4 +1154,63 @@ public class MapList
             || (fromRatio == 3 && toRatio == 1);
   }
 
+  /**
+   * Returns a map which is the composite of this one and the input map. That
+   * is, the output map has the fromRanges of this map, and its toRanges are the
+   * toRanges of this map as transformed by the input map.
+   * <p>
+   * Returns null if the mappings cannot be traversed (not all toRanges of this
+   * map correspond to fromRanges of the input), or if this.toRatio does not
+   * match map.fromRatio.
+   * 
+   * <pre>
+   * Example 1:
+   *    this:   from [1-100] to [501-600]
+   *    input:  from [10-40] to [60-90]
+   *    output: from [10-40] to [560-590]
+   * Example 2 ('reverse strand exons'):
+   *    this:   from [1-100] to [2000-1951], [1000-951] // transcript to loci
+   *    input:  from [1-50]  to [41-90] // CDS to transcript
+   *    output: from [10-40] to [1960-1951], [1000-971] // CDS to gene loci
+   * </pre>
+   * 
+   * @param map
+   * @return
+   */
+  public MapList traverse(MapList map)
+  {
+    if (map == null)
+    {
+      return null;
+    }
+
+    /*
+     * compound the ratios by this rule:
+     * A:B with M:N gives A*M:B*N
+     * reduced by greatest common divisor
+     * so 1:3 with 3:3 is 3:9 or 1:3
+     * 1:3 with 3:1 is 3:3 or 1:1
+     * 1:3 with 1:3 is 1:9
+     * 2:5 with 3:7 is 6:35
+     */
+    int outFromRatio = getFromRatio() * map.getFromRatio();
+    int outToRatio = getToRatio() * map.getToRatio();
+    int gcd = MathUtils.gcd(outFromRatio, outToRatio);
+    outFromRatio /= gcd;
+    outToRatio /= gcd;
+
+    List<int[]> toRanges = new ArrayList<>();
+    for (int[] range : getToRanges())
+    {
+      int[] transferred = map.locateInTo(range[0], range[1]);
+      if (transferred == null)
+      {
+        return null;
+      }
+      toRanges.add(transferred);
+    }
+
+    return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
+  }
+
 }