From 13a51d07c7bdc6d567eff0eea3bb7ee36edee34a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 1 Oct 2020 12:42:32 +0100
Subject: [PATCH] JAL-3761 failing tests for locateInFrom/To with overlapping
 ranges

---
 test/jalview/util/MapListTest.java |   53 ++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 71fbdfd..4017055 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -957,4 +957,57 @@ public class MapListTest
             1);
     assertTrue(ml.isToForwardStrand());
   }
+
+  /**
+   * Test for mapping with overlapping ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateInFrom_withOverlap()
+  {
+    int[] codons = new int[] { 1, 12, 12, 17 };
+    int[] protein = new int[] { 1, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
+    assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
+    assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
+    assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
+    assertEquals("[12, 14]", Arrays.toString(ml.locateInFrom(5, 5)));
+    assertEquals("[15, 17]", Arrays.toString(ml.locateInFrom(6, 6)));
+    assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
+    assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
+    assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
+    assertEquals("[1, 12, 12, 14]", Arrays.toString(ml.locateInFrom(1, 5)));
+    assertEquals("[1, 12, 12, 17]", Arrays.toString(ml.locateInFrom(1, 6)));
+    assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
+    assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6)));
+  
+    assertNull(ml.locateInFrom(0, 0));
+    assertNull(ml.locateInFrom(1, 7));
+    assertNull(ml.locateInFrom(-1, 1));
+  }
+
+  /**
+   * Test for mapping with overlapping ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateInTo_withOverlap()
+  {
+    int[] codons = new int[] { 1, 12, 12, 17 };
+    int[] protein = new int[] { 1, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
+    assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(3, 8)));
+    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(2, 11)));
+    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
+    
+    // we want 'greedy' mapping of base 12 to both peptides it codes for
+    assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(12, 12)));
+    assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(11, 12)));
+    assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15)));
+    assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17)));
+  
+    assertNull(ml.locateInTo(0, 0));
+    assertNull(ml.locateInTo(1, 18));
+    assertNull(ml.locateInTo(-1, 1));
+  }
 }
-- 
1.7.10.2