X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=3ce0bb3047b15540264f4130fbe60d9b7957338e;hb=924cfa64826c1c4d7f14672d6f773567acf46282;hp=58abdc3926c1bf1badddf8e83e4b0724c06b30da;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 58abdc3..3ce0bb3 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -103,10 +103,9 @@ public class MapList
     {
       return false;
     }
-    return Arrays
-            .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
-            && Arrays
-                    .deepEquals(toShifts.toArray(), obj.toShifts.toArray());
+    return Arrays.deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
+            && Arrays.deepEquals(toShifts.toArray(),
+                    obj.toShifts.toArray());
   }
 
   /**
@@ -373,10 +372,12 @@ public class MapList
        * drop this range if it lies within the last range
        */
       if ((lastDirection == 1 && range[0] >= lastRange[0]
-              && range[0] <= lastRange[1] && range[1] >= lastRange[0] && range[1] <= lastRange[1])
+              && range[0] <= lastRange[1] && range[1] >= lastRange[0]
+              && range[1] <= lastRange[1])
               || (lastDirection == -1 && range[0] <= lastRange[0]
                       && range[0] >= lastRange[1]
-                      && range[1] <= lastRange[0] && range[1] >= lastRange[1]))
+                      && range[1] <= lastRange[0]
+                      && range[1] >= lastRange[1]))
       {
         changed = true;
         continue;
@@ -391,8 +392,10 @@ public class MapList
       boolean sameDirection = range[1] == range[0]
               || direction == lastDirection;
       boolean extending = range[0] == lastRange[1] + lastDirection;
-      boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0] && range[0] <= lastRange[1])
-              || (lastDirection == -1 && range[0] <= lastRange[0] && range[0] >= lastRange[1]);
+      boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0]
+              && range[0] <= lastRange[1])
+              || (lastDirection == -1 && range[0] <= lastRange[0]
+                      && range[0] >= lastRange[1]);
       if (sameDirection && (overlapping || extending))
       {
         lastRange[1] = range[1];
@@ -961,15 +964,17 @@ public class MapList
     // TODO not used - remove?
     if (local)
     {
-      return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
-              .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map
-              .getFromHighest()));
+      return ((getFromLowest() >= map.getFromLowest()
+              && getFromHighest() <= map.getFromHighest())
+              || (getFromLowest() <= map.getFromLowest()
+                      && getFromHighest() >= map.getFromHighest()));
     }
     else
     {
-      return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
-              .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map
-              .getToHighest()));
+      return ((getToLowest() >= map.getToLowest()
+              && getToHighest() <= map.getToHighest())
+              || (getToLowest() <= map.getToLowest()
+                      && getToHighest() >= map.getToHighest()));
     }
   }
 
@@ -1115,4 +1120,63 @@ 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);
+  }
+
 }