X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=022e2d6006dfac37f39921c5fb15989f911ad274;hb=648e4d6232f149d6844a2a6b5c2613938a917f2f;hp=bd97ad822f09504dc38b2b2d5eba7a927848ec4b;hpb=1b911af46e474fd504a4d505327e02b684d9a397;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index bd97ad8..022e2d6 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -50,6 +50,7 @@ import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Iterator;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -689,7 +690,7 @@ 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 +765,7 @@ 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 +822,7 @@ 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 });
@@ -913,9 +914,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaHidden.getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 4]", Arrays.toString(regions.next()));
 
     /*
      * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
@@ -930,9 +931,9 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(1, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
@@ -944,7 +945,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(2, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    assertTrue(dnaHidden.getListOfCols().isEmpty());
+    assertEquals(0, dnaHidden.getNumberOfRegions());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
@@ -959,9 +960,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaHidden.getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
 
     /*
      * Combine hiding columns 1 and 3 to get discontiguous hidden columns
@@ -974,10 +975,10 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(3, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getListOfCols();
-    assertEquals(2, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+    regions = dnaHidden.iterator();
+    assertEquals(2, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
   }
 
   @Test(groups = { "Functional" })
@@ -988,7 +989,7 @@ 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 +1012,7 @@ 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 +1150,49 @@ 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]);
+  }
 }