JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / datamodel / MappingTest.java

diff --git a/test/jalview/datamodel/MappingTest.java b/test/jalview/datamodel/MappingTest.java
index 378d708..b326d90 100644 (file)
--- a/test/jalview/datamodel/MappingTest.java
+++ b/test/jalview/datamodel/MappingTest.java
@@ -1,6 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
 
 import jalview.util.MapList;
 
@@ -17,21 +38,18 @@ public class MappingTest
    * trite test of the intersectVisContigs method for a simple DNA -> Protein
    * exon map and a range of visContigs
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testIntersectVisContigs()
   {
-    MapList fk = new MapList(new int[]
-    { 1, 6, 8, 13, 15, 23 }, new int[]
-    { 1, 7 }, 3, 1);
+    MapList fk = new MapList(new int[] { 1, 6, 8, 13, 15, 23 }, new int[] {
+        1, 7 }, 3, 1);
     Mapping m = new Mapping(fk);
-    Mapping m_1 = m.intersectVisContigs(new int[]
-    { fk.getFromLowest(), fk.getFromHighest() });
-    Mapping m_2 = m.intersectVisContigs(new int[]
-    { 1, 7, 11, 20 });
+    Mapping m_1 = m.intersectVisContigs(new int[] { fk.getFromLowest(),
+        fk.getFromHighest() });
+    Mapping m_2 = m.intersectVisContigs(new int[] { 1, 7, 11, 20 });
 
     // assertions from output values 'as is', not checked for correctness
-    String result = Arrays.deepToString(m_1.map.getFromRanges()
-            .toArray());
+    String result = Arrays.deepToString(m_1.map.getFromRanges().toArray());
     System.out.println(result);
     assertEquals("[[1, 6], [8, 13], [15, 23]]", result);
 
@@ -40,4 +58,36 @@ public class MappingTest
     assertEquals("[[1, 6], [11, 13], [15, 20]]", result);
   }
 
+  @Test(groups = { "Functional" })
+  public void testToString()
+  {
+    /*
+     * with no sequence
+     */
+    MapList fk = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 },
+            3, 1);
+    Mapping m = new Mapping(fk);
+    assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] ", m.toString());
+
+    /*
+     * with a sequence
+     */
+    SequenceI seq = new Sequence("Seq1", "");
+    m = new Mapping(seq, fk);
+    assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] Seq1", m.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCopyConstructor()
+  {
+    MapList ml = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 },
+            3, 1);
+    SequenceI seq = new Sequence("seq1", "agtacg");
+    Mapping m = new Mapping(seq, ml);
+    m.setMappedFromId("abc");
+    Mapping copy = new Mapping(m);
+    assertEquals("abc", copy.getMappedFromId());
+    assertEquals(ml, copy.getMap());
+    assertSame(seq, copy.getTo());
+  }
 }