JAL-653 AlignedCodonFrame internal refactor, merge ranges with

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

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 8ff640b..e0cad6e 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -190,7 +190,8 @@ public class MapList
 
   /**
    * Constructor given from and to ranges as [start1, end1, start2, end2,...].
-   * If any end is equal to the next start, the ranges will be merged.
+   * If any end is equal to the next start, the ranges will be merged. There is
+   * no validation check that the ranges do not overlap each other.
    * 
    * @param from
    *          contiguous regions as [start1, end1, start2, end2, ...]
@@ -206,14 +207,18 @@ public class MapList
     this();
     this.fromRatio = fromRatio;
     this.toRatio = toRatio;
-    fromLowest = from[0];
-    fromHighest = from[1];
+    fromLowest = Integer.MAX_VALUE;
+    fromHighest = Integer.MIN_VALUE;
     int added = 0;
 
     for (int i = 0; i < from.length; i += 2)
     {
-      fromLowest = Math.min(fromLowest, from[i]);
-      fromHighest = Math.max(fromHighest, from[i + 1]);
+      /*
+       * note lowest and highest values - bearing in mind the
+       * direction may be revesed
+       */
+      fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1]));
+      fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1]));
       if (added > 0 && from[i] == fromShifts.get(added - 1)[1])
       {
         /*
@@ -228,13 +233,13 @@ public class MapList
       }
     }
 
-    toLowest = to[0];
-    toHighest = to[1];
+    toLowest = Integer.MAX_VALUE;
+    toHighest = Integer.MIN_VALUE;
     added = 0;
     for (int i = 0; i < to.length; i += 2)
     {
-      toLowest = Math.min(toLowest, to[i]);
-      toHighest = Math.max(toHighest, to[i + 1]);
+      toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1]));
+      toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1]));
       if (added > 0 && to[i] == toShifts.get(added - 1)[1])
       {
         toShifts.get(added - 1)[1] = to[i + 1];
@@ -280,7 +285,8 @@ public class MapList
   }
 
   /**
-   * Constructor given ranges as lists of [start, end] positions
+   * Constructor given ranges as lists of [start, end] positions. There is no
+   * validation check that the ranges do not overlap each other.
    * 
    * @param fromRange
    * @param toRange
@@ -297,19 +303,19 @@ public class MapList
     this.toRatio = toRatio;
 
     fromLowest = Integer.MAX_VALUE;
-    fromHighest = 0;
+    fromHighest = Integer.MIN_VALUE;
     for (int[] range : fromRange)
     {
-      fromLowest = Math.min(fromLowest, range[0]);
-      fromHighest = Math.max(fromHighest, range[1]);
+      fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
+      fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
     }
 
     toLowest = Integer.MAX_VALUE;
-    toHighest = 0;
+    toHighest = Integer.MIN_VALUE;
     for (int[] range : toRange)
     {
-      toLowest = Math.min(toLowest, range[0]);
-      toHighest = Math.max(toHighest, range[1]);
+      toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
+      toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
     }
   }
 
@@ -897,4 +903,76 @@ public class MapList
     sb.append(" ]");
     return sb.toString();
   }
+
+  /**
+   * Extend this map list by adding the given map's ranges. There is no
+   * validation check that the ranges do not overlap existing ranges (or each
+   * other), but contiguous ranges are merged.
+   * 
+   * @param map
+   */
+  public void addMapList(MapList map)
+  {
+    this.fromLowest = Math.min(fromLowest, map.fromLowest);
+    this.toLowest = Math.min(toLowest, map.toLowest);
+    this.fromHighest = Math.max(fromHighest, map.fromHighest);
+    this.toHighest = Math.max(toHighest, map.toHighest);
+
+    for (int[] range : map.getFromRanges())
+    {
+      addRange(range, fromShifts);
+    }
+    for (int[] range : map.getToRanges())
+    {
+      addRange(range, toShifts);
+    }
+  }
+
+  public static void addRange(int[] range, List<int[]> addTo)
+  {
+    /*
+     * list is empty - add to it!
+     */
+    if (addTo.size() == 0)
+    {
+      addTo.add(range);
+      return;
+    }
+
+    int[] last = addTo.get(addTo.size() - 1);
+    boolean lastForward = last[1] >= last[0];
+    boolean newForward = range[1] >= range[0];
+
+    /*
+     * contiguous range in the same direction - just update endpoint
+     */
+    if (lastForward == newForward && last[1] == range[0])
+    {
+      last[1] = range[1];
+      return;
+    }
+
+    /*
+     * next range starts at +1 in forward sense - update endpoint
+     */
+    if (lastForward && newForward && range[0] == last[1] + 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+
+    /*
+     * next range starts at -1 in reverse sense - update endpoint
+     */
+    if (!lastForward && !newForward && range[0] == last[1] - 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+
+    /*
+     * just add the new range
+     */
+    addTo.add(range);
+  }
 }