From 67538ac6c16cf7a413023a1faf0593a20b1634e3 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 19 May 2016 17:14:09 +0100
Subject: [PATCH] JAL-2114 added single-locus case and more error tests

---
 src/jalview/util/DnaUtils.java      |   16 ++++++++++++++--
 test/jalview/util/DnaUtilsTest.java |   14 +++++++++++++-
 2 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/src/jalview/util/DnaUtils.java b/src/jalview/util/DnaUtils.java
index 639eb8e..9ab4fda 100644
--- a/src/jalview/util/DnaUtils.java
+++ b/src/jalview/util/DnaUtils.java
@@ -32,13 +32,17 @@ public class DnaUtils
       System.err.println(errorMessage);
       return null;
     }
+
+    /*
+     * try to parse m..n (or simply m)
+     */
     String[] range = location.split("\\.\\.");
-    if (range.length == 2)
+    if (range.length == 1 || range.length == 2)
     {
       try
       {
         int start = Integer.valueOf(range[0]);
-        int end = Integer.valueOf(range[1]);
+        int end = range.length == 1 ? start : Integer.valueOf(range[1]);
         return Collections.singletonList(new int[] { start, end });
       } catch (NumberFormatException e)
       {
@@ -70,6 +74,10 @@ public class DnaUtils
     /*
      * take what is inside complement()
      */
+    if (!location.endsWith(")"))
+    {
+      return null;
+    }
     String toComplement = location.substring("complement(".length(),
             location.length() - 1);
     List<int[]> ranges = parseLocation(toComplement);
@@ -107,6 +115,10 @@ public class DnaUtils
     /*
      * take what is inside join()
      */
+    if (!location.endsWith(")"))
+    {
+      return null;
+    }
     String joinedLocs = location.substring("join(".length(),
             location.length() - 1);
     String[] locations = joinedLocs.split(",");
diff --git a/test/jalview/util/DnaUtilsTest.java b/test/jalview/util/DnaUtilsTest.java
index af76885..9e978fe 100644
--- a/test/jalview/util/DnaUtilsTest.java
+++ b/test/jalview/util/DnaUtilsTest.java
@@ -19,9 +19,17 @@ public class DnaUtilsTest
   public void testParseLocation()
   {
     /*
+     * single locus
+     */
+    List<int[]> ranges = DnaUtils.parseLocation("467");
+    assertEquals(1, ranges.size());
+    assertEquals(467, ranges.get(0)[0]);
+    assertEquals(467, ranges.get(0)[1]);
+
+    /*
      * simple range
      */
-    List<int[]> ranges = DnaUtils.parseLocation("12..78");
+    ranges = DnaUtils.parseLocation("12..78");
     assertEquals(1, ranges.size());
     assertEquals(12, ranges.get(0)[0]);
     assertEquals(78, ranges.get(0)[1]);
@@ -87,6 +95,7 @@ public class DnaUtilsTest
     assertNull(DnaUtils.parseLocation("34..>126"));
     assertNull(DnaUtils.parseLocation("34.126"));
     assertNull(DnaUtils.parseLocation("34^126"));
+    assertNull(DnaUtils.parseLocation("order(34..126,130..180)"));
 
     /*
      * invalid things
@@ -94,6 +103,9 @@ public class DnaUtilsTest
     assertNull(DnaUtils.parseLocation(""));
     assertNull(DnaUtils.parseLocation("JOIN(1..2)"));
     assertNull(DnaUtils.parseLocation("join(1..2"));
+    assertNull(DnaUtils.parseLocation("join(1..2("));
+    assertNull(DnaUtils.parseLocation("complement(1..2"));
+    assertNull(DnaUtils.parseLocation("complement(1..2("));
     try
     {
       assertNull(DnaUtils.parseLocation(null));
-- 
1.7.10.2