From 0e6751ef949bc0bad9a44220262b7e0d6e46c563 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 1 Apr 2016 11:44:04 +0100
Subject: [PATCH] JAL-1705 generalised getLength() to handle [start1, end1,
 start2, end2..]

---
 src/jalview/util/MappingUtils.java      |   15 ++++++++++++---
 test/jalview/util/MappingUtilsTest.java |   13 +++++++++++++
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index c2cad1f..ae4e55d 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -770,7 +770,8 @@ public final class MappingUtils
   }
 
   /**
-   * 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
@@ -784,7 +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;
   }
@@ -848,7 +858,6 @@ public final class MappingUtils
     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)
       {
diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index b53d513..3c417c3 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -861,6 +861,10 @@ public class MappingUtilsTest
   public void testGetLength()
   {
     assertEquals(0, MappingUtils.getLength(null));
+
+    /*
+     * [start, end] ranges
+     */
     List<int[]> ranges = new ArrayList<int[]>();
     assertEquals(0, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 1, 1 });
@@ -869,6 +873,15 @@ public class MappingUtilsTest
     assertEquals(10, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 20, 10 });
     assertEquals(21, MappingUtils.getLength(ranges));
+
+    /*
+     * [start, end, start, end...] ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 5, 8, 4 });
+    ranges.add(new int[] { 8, 2 });
+    ranges.add(new int[] { 12, 12 });
+    assertEquals(18, MappingUtils.getLength(ranges));
   }
 
   @Test(groups = { "Functional" })
-- 
1.7.10.2