JAL-2617 omit stop codon from synthesized CDS sequence

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

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index bd97ad8..5226819 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -689,7 +689,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
     acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
@@ -764,7 +764,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf4 = new AlignedCodonFrame();
     acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
@@ -821,7 +821,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
     acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf);
 
     AlignmentI prot = new Alignment(new SequenceI[] { protein });
@@ -913,7 +913,7 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaHidden.getListOfCols();
+    List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
 
@@ -930,7 +930,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(1, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getListOfCols();
+    hidden = dnaHidden.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
 
@@ -944,7 +944,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(2, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    assertTrue(dnaHidden.getListOfCols().isEmpty());
+    assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
@@ -959,7 +959,7 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaHidden.getListOfCols();
+    hidden = dnaHidden.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
 
@@ -974,7 +974,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(3, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getListOfCols();
+    hidden = dnaHidden.getHiddenColumnsCopy();
     assertEquals(2, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
     assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
@@ -988,7 +988,7 @@ public class MappingUtilsTest
     /*
      * [start, end] ranges
      */
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertEquals(0, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 1, 1 });
     assertEquals(1, MappingUtils.getLength(ranges));
@@ -1011,7 +1011,7 @@ public class MappingUtilsTest
   public void testContains()
   {
     assertFalse(MappingUtils.contains(null, 1));
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertFalse(MappingUtils.contains(ranges, 1));
 
     ranges.add(new int[] { 1, 4 });
@@ -1149,4 +1149,49 @@ public class MappingUtilsTest
     assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
   }
 
+  @Test(groups = "Functional")
+  public void testRemoveEndPositions()
+  {
+    List<int[]> ranges = new ArrayList<>();
+
+    /*
+     * case 1: truncate last range
+     */
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 30 });
+    MappingUtils.removeEndPositions(5, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(25, ranges.get(1)[1]);
+
+    /*
+     * case 2: remove last range
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 22 });
+    MappingUtils.removeEndPositions(3, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(10, ranges.get(0)[1]);
+
+    /*
+     * case 3: truncate penultimate range
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 21 });
+    MappingUtils.removeEndPositions(3, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(9, ranges.get(0)[1]);
+
+    /*
+     * case 4: remove last two ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 20 });
+    ranges.add(new int[] { 30, 30 });
+    MappingUtils.removeEndPositions(3, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(9, ranges.get(0)[1]);
+  }
 }