X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=cd8821def75f988e10ea52a41f6bba3c575a29b7;hb=ed581b841fe9361bfe80bb006df190a29df264fb;hp=d21eac39a3ed6183b93c376d422f210cf42394c7;hpb=5baf7de79f1a31bb199ba619e221a1cdac99ce7d;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index d21eac3..cd8821d 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;
@@ -967,4 +969,110 @@ public final class MappingUtils
     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();
+      }
+    }
+  }
+
+  /**
+   * 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);
+  }
 }