X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=915293e1da6f6963dc0650447930e79cee5654c6;hb=7428d315297907b3bb52ddb099a348acffb87636;hp=3682239c2d4a516154d26aee7ef09ec6fd70a801;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 3682239..915293e 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;
@@ -939,4 +941,102 @@ public final class MappingUtils
     }
     return copy;
   }
+
+  /**
+   * 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.
+   * 
+   * @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();
+      }
+    }
+  }
+
+  /**
+   * Converts a list of [start, end] ranges to a single array of [start, end,
+   * start, end ...]
+   * 
+   * @param ranges
+   * @return
+   */
+  public static int[] listToArray(List<int[]> ranges)
+  {
+    int[] result = new int[ranges.size() * 2];
+    int i = 0;
+    for (int[] range : ranges)
+    {
+      result[i++] = range[0];
+      result[i++] = range[1];
+    }
+    return result;
+  }
 }