JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index d21eac3..4e07a08 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -20,6 +20,13 @@
  */
 package jalview.util;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
 import jalview.commands.CommandI;
@@ -39,13 +46,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * Helper methods for manipulations involving sequence mappings.
  * 
@@ -542,10 +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,
-              toSequences, fromGapChar);
+      mapHiddenColumns(regions.next(), codonFrames, newHidden,
+              fromSequences, toSequences, fromGapChar);
     }
     return; // mappedColumns;
   }
@@ -963,8 +964,79 @@ public final class MappingUtils
 
     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 {@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;
+  }
 }