JAL-1705 include stop codons in derived CDS; support ensemblgenomes

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 16db13a..0780b2a 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -770,57 +770,6 @@ public final class MappingUtils
   }
 
   /**
-   * Remove the last 3 mapped positions from the given ranges
-   * 
-   * @param ranges
-   * @param mappedLength
-   */
-  public static void unmapStopCodon(List<int[]> ranges,
-          int mappedLength)
-  {
-    if (mappedLength < 3)
-    {
-      return;
-    }
-    boolean done = false;
-    int targetLength = mappedLength - 3;
-    int mapped = 0;
-    Iterator<int[]> it = ranges.iterator();
-    while (!done && it.hasNext())
-    {
-      int[] range = it.next();
-      int length = Math.abs(range[1] - range[0]) + 1;
-      if (mapped + length == targetLength)
-      {
-        done = true;
-      }
-      else if (mapped + length < targetLength)
-      {
-        mapped += length;
-        continue;
-      }
-      else
-      {
-        /*
-         * need just a bit of this range
-         */
-        int needed = targetLength - mapped;
-        int sense = range[1] >= range[0] ? 1 : -1;
-        range[1] = range[0] + (sense * (needed - 1));
-        done = true;
-      }
-    }
-    /*
-     * remove any trailing ranges
-     */
-    while (it.hasNext())
-    {
-      it.next();
-      it.remove();
-    }
-  }
-
-  /**
    * Returns the total length of the supplied ranges
    * 
    * @param ranges