Properly integrated endGaps option for AlignSeq.traceAlignment()

[jalview.git] / src / jalview / datamodel / ColumnSelection.java

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 3c2d166..4a38ec0 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -278,6 +278,27 @@ public class ColumnSelection
   }
 
   /**
+   * add a series of start,end (inclusive) ranges to the column selection
+   * 
+   * @param rng
+   *          [start_0, end_0, start_1, end_1, ... ]
+   * @param baseOne
+   *          - when true, ranges are base 1 and will be mapped to base 0
+   */
+  public void addRangeOfElements(int[] rng, boolean baseOne)
+  {
+    int base = baseOne ? -1 : 0;
+    for (int c = 0; c < rng.length; c += 2)
+    {
+      for (int p = rng[c]; p <= rng[c + 1]; p++)
+      {
+        selection.add(base + p);
+      }
+    }
+
+  }
+
+  /**
    * clears column selection
    */
   public void clear()