JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 0780b2a..c2cad1f 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -821,4 +821,66 @@ public final class MappingUtils
     }
     return false;
   }
+
+  /**
+   * Removes a specified number of positions from the start of a ranges list.
+   * For example, could be used to adjust cds ranges to allow for an incomplete
+   * start codon. Subranges are removed completely, or their start positions
+   * adjusted, until the required number of positions has been removed from the
+   * range. Reverse strand ranges are supported. The input array is not
+   * modified.
+   * 
+   * @param removeCount
+   * @param ranges
+   *          an array of [start, end, start, end...] positions
+   * @return a new array with the first removeCount positions removed
+   */
+  public static int[] removeStartPositions(int removeCount,
+          final int[] ranges)
+  {
+    if (removeCount <= 0)
+    {
+      return ranges;
+    }
+  
+    int[] copy = Arrays.copyOf(ranges, ranges.length);
+    int sxpos = -1;
+    int cdspos = 0;
+    for (int x = 0; x < copy.length && sxpos == -1; x += 2)
+    {
+      // fixme handle reverse strand
+      cdspos += Math.abs(copy[x + 1] - copy[x]) + 1;
+      if (removeCount < cdspos)
+      {
+        /*
+         * we have removed enough, time to finish
+         */
+        sxpos = x;
+
+        /*
+         * increment start of first exon, or decrement if reverse strand
+         */
+        if (copy[x] <= copy[x + 1])
+        {
+          copy[x] = copy[x + 1] - cdspos + removeCount + 1;
+        }
+        else
+        {
+          copy[x] = copy[x + 1] + cdspos - removeCount - 1;
+        }
+        break;
+      }
+    }
+  
+    if (sxpos > 0)
+    {
+      /*
+       * we dropped at least one entire sub-range - compact the array
+       */
+      int[] nxon = new int[copy.length - sxpos];
+      System.arraycopy(copy, sxpos, nxon, 0, copy.length - sxpos);
+      return nxon;
+    }
+    return copy;
+  }
 }