JAL-2110 add 'products' parameter to filter results in madeCdsAlignment

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 16db13a..ae4e55d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -770,58 +770,8 @@ 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
+   * Returns the total length of the supplied ranges, which may be as single
+   * [start, end] or multiple [start, end, start, end ...]
    * 
    * @param ranges
    * @return
@@ -835,7 +785,16 @@ public final class MappingUtils
     int length = 0;
     for (int[] range : ranges)
     {
-      length += Math.abs(range[1] - range[0]) + 1;
+      if (range.length % 2 != 0)
+      {
+        System.err.println("Error unbalance start/end ranges: "
+                + ranges.toString());
+        return 0;
+      }
+      for (int i = 0; i < range.length - 1; i += 2)
+      {
+        length += Math.abs(range[i + 1] - range[i]) + 1;
+      }
     }
     return length;
   }
@@ -872,4 +831,65 @@ 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)
+    {
+      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;
+  }
 }