Merge branch 'bug/JAL-2617mappedStopCodon' into develop

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 3682239..9c5c109 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -939,4 +939,55 @@ public final class MappingUtils
     }
     return copy;
   }
+
+  /**
+   * Removes the specified number of positions from the given ranges. Provided
+   * to allow a stop codon to be stripped from a CDS sequence so that it matches
+   * the peptide translation length.
+   * 
+   * @param positions
+   * @param ranges
+   *          a list of (single) [start, end] ranges
+   * @return
+   */
+  public static void removeEndPositions(int positions,
+          List<int[]> ranges)
+  {
+    int toRemove = positions;
+    Iterator<int[]> it = new ReverseListIterator<>(ranges);
+    while (toRemove > 0)
+    {
+      int[] endRange = it.next();
+      if (endRange.length != 2)
+      {
+        /*
+         * not coded for [start1, end1, start2, end2, ...]
+         */
+        System.err
+                .println("MappingUtils.removeEndPositions doesn't handle multiple  ranges");
+        return;
+      }
+
+      int length = endRange[1] - endRange[0] + 1;
+      if (length <= 0)
+      {
+        /*
+         * not coded for a reverse strand range (end < start)
+         */
+        System.err
+                .println("MappingUtils.removeEndPositions doesn't handle reverse strand");
+        return;
+      }
+      if (length > toRemove)
+      {
+        endRange[1] -= toRemove;
+        toRemove = 0;
+      }
+      else
+      {
+        toRemove -= length;
+        it.remove();
+      }
+    }
+  }
 }