JAL-3725 helper methods for computing mapped feature range overlap

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 4e07a08..33decb4 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -29,6 +29,7 @@ import java.util.Map;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -78,7 +79,7 @@ public final class MappingUtils
       action = action.getUndoAction();
     }
     // TODO write this
-    System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+    Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
   }
 
   /**
@@ -835,7 +836,7 @@ public final class MappingUtils
     {
       if (range.length % 2 != 0)
       {
-        System.err.println(
+        Cache.log.error(
                 "Error unbalance start/end ranges: " + ranges.toString());
         return 0;
       }
@@ -991,7 +992,7 @@ public final class MappingUtils
         /*
          * not coded for [start1, end1, start2, end2, ...]
          */
-        System.err.println(
+        Cache.log.error(
                 "MappingUtils.removeEndPositions doesn't handle multiple  ranges");
         return;
       }
@@ -1002,7 +1003,7 @@ public final class MappingUtils
         /*
          * not coded for a reverse strand range (end < start)
          */
-        System.err.println(
+        Cache.log.error(
                 "MappingUtils.removeEndPositions doesn't handle reverse strand");
         return;
       }
@@ -1039,4 +1040,66 @@ public final class MappingUtils
     }
     return result;
   }
+
+  /*
+   * Returns the maximal start-end positions in the given (ordered) list of
+   * ranges which is overlapped by the given begin-end range, or null if there
+   * is no overlap.
+   * 
+   * <pre>
+   * Examples:
+   *   if ranges is {[4, 8], [10, 12], [16, 19]}
+   * then
+   *   findOverlap(ranges, 1, 20) == [4, 19]
+   *   findOverlap(ranges, 6, 11) == [6, 11]
+   *   findOverlap(ranges, 9, 15) == [10, 12]
+   *   findOverlap(ranges, 13, 15) == null
+   * </pre>
+   * 
+   * @param ranges
+   * @param begin
+   * @param end
+   * @return
+   */
+  protected static int[] findOverlap(List<int[]> ranges, final int begin,
+          final int end)
+  {
+    boolean foundStart = false;
+    int from = 0;
+    int to = 0;
+
+    /*
+     * traverse the ranges to find the first position (if any) >= begin,
+     * and the last position (if any) <= end
+     */
+    for (int[] range : ranges)
+    {
+      if (!foundStart)
+      {
+        if (range[0] >= begin)
+        {
+          /*
+           * first range that starts with, or follows, begin
+           */
+          foundStart = true;
+          from = Math.max(range[0], begin);
+        }
+        else if (range[1] >= begin)
+        {
+          /*
+           * first range that contains begin
+           */
+          foundStart = true;
+          from = begin;
+        }
+      }
+
+      if (range[0] <= end)
+      {
+        to = Math.min(end, range[1]);
+      }
+    }
+
+    return foundStart && to >= from ? new int[] { from, to } : null;
+  }
 }