JAL-3725 helper methods for computing mapped feature range overlap

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

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 36fb450..c5654fb 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -24,6 +24,8 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import jalview.bin.Cache;
+
 /**
  * A simple way of bijectively mapping a non-contiguous linear range to another
  * non-contiguous linear range.
@@ -308,7 +310,7 @@ public class MapList
       if (range.length != 2)
       {
         // throw new IllegalArgumentException(range);
-        System.err.println("Invalid format for fromRange "
+        Cache.log.error("Invalid format for fromRange "
                 + Arrays.toString(range) + " may cause errors");
       }
       fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
@@ -322,7 +324,7 @@ public class MapList
       if (range.length != 2)
       {
         // throw new IllegalArgumentException(range);
-        System.err.println("Invalid format for toRange "
+        Cache.log.error("Invalid format for toRange "
                 + Arrays.toString(range) + " may cause errors");
       }
       toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
@@ -1207,4 +1209,36 @@ public class MapList
   {
     return fromShifts.size() == 1 && toShifts.size() == 1;
   }
+
+  /**
+   * Returns the [start, end...] positions in the range mapped from, that are
+   * mapped to by part or all of the given begin-end of the range mapped to.
+   * Returns null if begin-end does not overlap any position mapped to.
+   * 
+   * @param begin
+   * @param end
+   * @return
+   */
+  public int[] getOverlapsInFrom(final int begin, final int end)
+  {
+    int[] overlaps = MappingUtils.findOverlap(toShifts, begin, end);
+
+    return overlaps == null ? null : locateInFrom(overlaps[0], overlaps[1]);
+  }
+
+  /**
+   * Returns the [start, end...] positions in the range mapped to, that are
+   * mapped to by part or all of the given begin-end of the range mapped from.
+   * Returns null if begin-end does not overlap any position mapped from.
+   * 
+   * @param begin
+   * @param end
+   * @return
+   */
+  public int[] getOverlapsInTo(final int begin, final int end)
+  {
+    int[] overlaps = MappingUtils.findOverlap(fromShifts, begin, end);
+
+    return overlaps == null ? null : locateInTo(overlaps[0], overlaps[1]);
+  }
 }