JAL-1705 align CDS and peptide products to transcripts

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 267e871..16db13a 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -819,4 +819,57 @@ public final class MappingUtils
       it.remove();
     }
   }
+
+  /**
+   * Returns the total length of the supplied ranges
+   * 
+   * @param ranges
+   * @return
+   */
+  public static int getLength(List<int[]> ranges)
+  {
+    if (ranges == null)
+    {
+      return 0;
+    }
+    int length = 0;
+    for (int[] range : ranges)
+    {
+      length += Math.abs(range[1] - range[0]) + 1;
+    }
+    return length;
+  }
+
+  /**
+   * Answers true if any range includes the given value
+   * 
+   * @param ranges
+   * @param value
+   * @return
+   */
+  public static boolean contains(List<int[]> ranges, int value)
+  {
+    if (ranges == null)
+    {
+      return false;
+    }
+    for (int[] range : ranges)
+    {
+      if (range[1] >= range[0] && value >= range[0] && value <= range[1])
+      {
+        /*
+         * value within ascending range
+         */
+        return true;
+      }
+      if (range[1] < range[0] && value <= range[0] && value >= range[1])
+      {
+        /*
+         * value within descending range
+         */
+        return true;
+      }
+    }
+    return false;
+  }
 }