JAL-653 AlignedCodonFrame internal refactor, merge ranges with

[jalview.git] / test / jalview / util / MapListTest.java

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index e0a2d30..54e8311 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -23,6 +23,7 @@ package jalview.util;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import java.util.ArrayList;
@@ -450,6 +451,17 @@ public class MapListTest
     assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
             prettyPrint(ml2.getFromRanges()));
     assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
+
+    /*
+     * reverse direction
+     */
+    codons = new int[] { 9, 6 };
+    protein = new int[] { 100, 91, 80, 79 };
+    ml = new MapList(codons, protein, 3, 1);
+    assertEquals(6, ml.getFromLowest());
+    assertEquals(9, ml.getFromHighest());
+    assertEquals(79, ml.getToLowest());
+    assertEquals(100, ml.getToHighest());
   }
 
   /**
@@ -525,4 +537,113 @@ public class MapListTest
     assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
             s);
   }
+
+  @Test(groups = { "Functional" })
+  public void testAddMapList()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[] { 72, 22 }, 1, 3);
+    assertEquals(11, ml.getFromLowest());
+    assertEquals(35, ml.getFromHighest());
+    assertEquals(22, ml.getToLowest());
+    assertEquals(72, ml.getToHighest());
+
+    MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 }, new int[] { 12,
+        17, 78, 83, 88, 96 }, 1, 3);
+    ml.addMapList(ml2);
+    assertEquals(2, ml.getFromLowest());
+    assertEquals(40, ml.getFromHighest());
+    assertEquals(12, ml.getToLowest());
+    assertEquals(96, ml.getToHighest());
+
+    String s = ml.toString();
+    assertEquals(
+            "From (1:3) [ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] To [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
+            s);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testAddMapList_contiguous()
+  {
+    MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
+            3);
+
+    MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
+            1, 3);
+    ml.addMapList(ml2);
+    assertEquals("From (1:3) [ [11, 16] ] To [ [72, 53] ]", ml.toString());
+  }
+
+  @Test(groups = "Functional")
+  public void testAddRange()
+  {
+    int[] range = { 1, 5 };
+    List<int[]> ranges = new ArrayList<int[]>();
+
+    // add to empty list:
+    MapList.addRange(range, ranges);
+    assertEquals(1, ranges.size());
+    assertSame(range, ranges.get(0));
+
+    // extend contiguous (same position):
+    MapList.addRange(new int[] { 5, 10 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(10, ranges.get(0)[1]);
+
+    // extend contiguous (next position):
+    MapList.addRange(new int[] { 11, 15 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(15, ranges.get(0)[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]);
+
+    // extend reverse contiguous (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]);
+
+    // 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]);
+
+    // 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]);
+
+    // 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]);
+  }
+
+  /**
+   * Check state after construction
+   */
+  @Test(groups = { "Functional" })
+  public void testConstructor_withLists()
+  {
+    /*
+     * reverse direction
+     */
+    int[][] codons = new int[][] { { 9, 6 } };
+    int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } };
+    MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein),
+            3, 1);
+    assertEquals(6, ml.getFromLowest());
+    assertEquals(9, ml.getFromHighest());
+    assertEquals(79, ml.getToLowest());
+    assertEquals(100, ml.getToHighest());
+  }
 }