X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=b552c21413d761a427ed227c8876ffad801e5b7e;hb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;hp=9c5c1092cab8e744b0d195d6e5f769e7bed7e070;hpb=5fba3a87f8eaa121a8139f37e6822c15283e1a2c;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 9c5c109..b552c21 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -542,9 +542,11 @@ public final class MappingUtils
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : hiddencols.getHiddenColumnsCopy())
+    Iterator<int[]> regions = hiddencols.iterator();
+    while (regions.hasNext())
     {
-      mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
+      mapHiddenColumns(regions.next(), codonFrames, newHidden,
+              fromSequences,
               toSequences, fromGapChar);
     }
     return; // mappedColumns;
@@ -941,6 +943,34 @@ public final class MappingUtils
   }
 
   /**
+   * Answers true if range's start-end positions include those of queryRange,
+   * where either range might be in reverse direction, else false
+   * 
+   * @param range
+   *          a start-end range
+   * @param queryRange
+   *          a candidate subrange of range (start2-end2)
+   * @return
+   */
+  public static boolean rangeContains(int[] range, int[] queryRange)
+  {
+    if (range == null || queryRange == null || range.length != 2
+            || queryRange.length != 2)
+    {
+      /*
+       * invalid arguments
+       */
+      return false;
+    }
+
+    int min = Math.min(range[0], range[1]);
+    int max = Math.max(range[0], range[1]);
+  
+    return (min <= queryRange[0] && max >= queryRange[0]
+            && min <= queryRange[1] && max >= queryRange[1]);
+  }
+
+  /**
    * 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.