From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 2 Dec 2020 20:37:16 +0000 (+0000)
Subject: JAL-3751 second occurrence of bug squashed
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=refs%2Fheads%2Fbug%2FJAL-3751_revisited

JAL-3751 second occurrence of bug squashed
---

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 745f367..6b65713 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -960,15 +960,6 @@ public class MapList
     boolean newForward = range[1] >= range[0];
 
     /*
-     * contiguous range in the same direction - just update endpoint
-     */
-    if (lastForward == newForward && last[1] == range[0])
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
      * next range starts at +1 in forward sense - update endpoint
      */
     if (lastForward && newForward && range[0] == last[1] + 1)
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index cf10aba..ff3488f 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -661,7 +661,15 @@ public class MapListTest
     MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, 1,
             3);
     ml.addMapList(ml2);
-    assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
+    assertEquals("[ [11, 15] [15, 16] ] 1:3 to [ [72, 58] [58, 53] ]", ml.toString());
+
+    MapList ml3 = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
+            3);
+
+    MapList ml4 = new MapList(new int[] { 15, 16 }, new int[] { 1, 6 }, 1,
+            3);
+    ml3.addMapList(ml4);
+    assertEquals("[ [11, 15] [15, 16] ] 1:3 to [ [72, 58] [1, 6] ]", ml3.toString());
   }
 
   @Test(groups = "Functional")
@@ -675,47 +683,51 @@ public class MapListTest
     assertEquals(1, ranges.size());
     assertSame(range, ranges.get(0));
 
-    // extend contiguous (same position):
+    // extend overlapping (same position):
     MapList.addRange(new int[] { 5, 10 }, ranges);
-    assertEquals(1, ranges.size());
+    assertEquals(2, ranges.size());
     assertEquals(1, ranges.get(0)[0]);
-    assertEquals(10, ranges.get(0)[1]);
+    assertEquals(5, ranges.get(0)[1]);
+    assertEquals(5, ranges.get(1)[0]);
+    assertEquals(10, ranges.get(1)[1]);
 
     // extend contiguous (next position):
     MapList.addRange(new int[] { 11, 15 }, ranges);
-    assertEquals(1, ranges.size());
+    assertEquals(2, ranges.size());
     assertEquals(1, ranges.get(0)[0]);
-    assertEquals(15, ranges.get(0)[1]);
+    assertEquals(5, ranges.get(0)[1]);
+    assertEquals(5, ranges.get(1)[0]);
+    assertEquals(15, ranges.get(1)[1]);
 
     // change direction: range is not merged:
     MapList.addRange(new int[] { 16, 10 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(10, ranges.get(1)[1]);
+    assertEquals(3, ranges.size());
+    assertEquals(16, ranges.get(2)[0]);
+    assertEquals(10, ranges.get(2)[1]);
 
-    // extend reverse contiguous (same position):
+    // extend reverse overlapping (same position):
     MapList.addRange(new int[] { 10, 8 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(8, ranges.get(1)[1]);
+    assertEquals(4, ranges.size());
+    assertEquals(10, ranges.get(3)[0]);
+    assertEquals(8, ranges.get(3)[1]);
 
     // extend reverse contiguous (next position):
     MapList.addRange(new int[] { 7, 6 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(6, ranges.get(1)[1]);
+    assertEquals(4, ranges.size());
+    assertEquals(10, ranges.get(3)[0]);
+    assertEquals(6, ranges.get(3)[1]);
 
     // change direction: range is not merged:
     MapList.addRange(new int[] { 6, 9 }, ranges);
-    assertEquals(3, ranges.size());
-    assertEquals(6, ranges.get(2)[0]);
-    assertEquals(9, ranges.get(2)[1]);
+    assertEquals(5, ranges.size());
+    assertEquals(6, ranges.get(4)[0]);
+    assertEquals(9, ranges.get(4)[1]);
 
     // not contiguous: not merged
     MapList.addRange(new int[] { 11, 12 }, ranges);
-    assertEquals(4, ranges.size());
-    assertEquals(11, ranges.get(3)[0]);
-    assertEquals(12, ranges.get(3)[1]);
+    assertEquals(6, ranges.size());
+    assertEquals(11, ranges.get(5)[0]);
+    assertEquals(12, ranges.get(5)[1]);
   }
 
   /**