X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=fe95f4b3f367727bc7031cf3c864554e3074f80c;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=f5dd88366976c3a028865e8458f44f513b887eda;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f5dd883..fe95f4b 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;
@@ -1018,4 +1020,79 @@ public final class MappingUtils
       }
     }
   }
+  /**
+   * Adds the given range to a list of ranges. If the new range just extends
+   * existing ranges, the current endpoint is updated instead.
+   * 
+   * @param range
+   * @param addTo
+   */
+  public static void addRange(int[] range, List<int[]> addTo)
+  {
+    /*
+     * list is empty - add to it!
+     */
+    if (addTo.size() == 0)
+    {
+      addTo.add(range);
+      return;
+    }
+  
+    int[] last = addTo.get(addTo.size() - 1);
+    boolean lastForward = last[1] >= last[0];
+    boolean newForward = range[1] >= range[0];
+  
+    /*
+     * contiguous range in the same direction - just update endpoint
+     */
+    if (lastForward == newForward && last[1] == range[0])
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at +1 in forward sense - update endpoint
+     */
+    if (lastForward && newForward && range[0] == last[1] + 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at -1 in reverse sense - update endpoint
+     */
+    if (!lastForward && !newForward && range[0] == last[1] - 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * just add the new range
+     */
+    addTo.add(range);
+  }
+
+  /**
+   * Converts a list of {@code start-end} ranges to a single array of
+   * {@code start1, end1, start2, ... } ranges
+   * 
+   * @param ranges
+   * @return
+   */
+  public static int[] rangeListToArray(List<int[]> ranges)
+  {
+    int rangeCount = ranges.size();
+    int[] result = new int[rangeCount * 2];
+    int j = 0;
+    for (int i = 0; i < rangeCount; i++)
+    {
+      int[] range = ranges.get(i);
+      result[j++] = range[0];
+      result[j++] = range[1];
+    }
+    return result;
+  }
 }