JAL-2674 Tidies

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

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 142762b..192a822 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -32,7 +32,6 @@ import jalview.util.Comparison;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Iterator;
-import java.util.List;
 import java.util.Random;
 
 import org.testng.annotations.BeforeClass;
@@ -184,12 +183,14 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = { "Functional" })
-  public void testGetVisibleContigs()
+  public void testVisibleContigsIterator()
   {
     HiddenColumns cs = new HiddenColumns();
 
-    List<int[]> visible = cs.getVisibleContigs(3, 10);
-    assertEquals("[3, 9]", Arrays.toString(visible.get(0)));
+    Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
+    int[] region = visible.next();
+    assertEquals("[3, 9]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     cs.hideColumns(3, 6);
     cs.hideColumns(8, 9);
@@ -198,30 +199,44 @@ public class HiddenColumnsTest
     // Test both ends visible region
 
     // start position is inclusive, end position exclusive
-    visible = cs.getVisibleContigs(1, 13);
-    assertEquals("[1, 2]", Arrays.toString(visible.get(0)));
-    assertEquals("[7, 7]", Arrays.toString(visible.get(1)));
-    assertEquals("[10, 11]", Arrays.toString(visible.get(2)));
+    visible = cs.getVisContigsIterator(1, 13);
+    region = visible.next();
+    assertEquals("[1, 2]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[10, 11]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     // Test start hidden, end visible
-    visible = cs.getVisibleContigs(4, 14);
-    assertEquals("[7, 7]", Arrays.toString(visible.get(0)));
-    assertEquals("[10, 11]", Arrays.toString(visible.get(1)));
-    assertEquals("[13, 13]", Arrays.toString(visible.get(2)));
+    visible = cs.getVisContigsIterator(4, 14);
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[10, 11]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[13, 13]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     // Test start hidden, end hidden
-    visible = cs.getVisibleContigs(3, 10);
-    assertEquals("[7, 7]", Arrays.toString(visible.get(0)));
+    visible = cs.getVisContigsIterator(3, 10);
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     // Test start visible, end hidden
-    visible = cs.getVisibleContigs(0, 13);
-    assertEquals("[0, 2]", Arrays.toString(visible.get(0)));
-    assertEquals("[7, 7]", Arrays.toString(visible.get(1)));
-    assertEquals("[10, 11]", Arrays.toString(visible.get(2)));
+    visible = cs.getVisContigsIterator(0, 13);
+    region = visible.next();
+    assertEquals("[0, 2]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[10, 11]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     // Test empty result
-    visible = cs.getVisibleContigs(4, 6);
-    assertEquals(0, visible.size());
+    visible = cs.getVisContigsIterator(4, 6);
+    assertFalse(visible.hasNext());
   }
 
   @Test(groups = { "Functional" })
@@ -827,49 +842,6 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = { "Functional" })
-  public void testFindHiddenRegionPositions()
-  {
-    HiddenColumns hc = new HiddenColumns();
-
-    List<Integer> positions = hc.findHiddenRegionPositions(0, 20);
-    assertTrue(positions.isEmpty());
-
-    hc.hideColumns(3, 7);
-    hc.hideColumns(10, 10);
-    hc.hideColumns(14, 15);
-
-    positions = hc.findHiddenRegionPositions(0, 20);
-    assertEquals(3, positions.size());
-    assertEquals(3, positions.get(0).intValue());
-    assertEquals(5, positions.get(1).intValue());
-    assertEquals(8, positions.get(2).intValue());
-
-    positions = hc.findHiddenRegionPositions(7, 20);
-    assertEquals(2, positions.size());
-    assertEquals(5, positions.get(0).intValue());
-    assertEquals(8, positions.get(1).intValue());
-
-    positions = hc.findHiddenRegionPositions(11, 13);
-    assertEquals(0, positions.size());
-
-    positions = hc.findHiddenRegionPositions(7, 20);
-    assertEquals(2, positions.size());
-    assertEquals(5, positions.get(0).intValue());
-    assertEquals(8, positions.get(1).intValue());
-
-    positions = hc.findHiddenRegionPositions(0, 1);
-    assertEquals(0, positions.size());
-
-    positions = hc.findHiddenRegionPositions(17, 20);
-    assertEquals(0, positions.size());
-
-    positions = hc.findHiddenRegionPositions(10, 15);
-    assertEquals(2, positions.size());
-    assertEquals(5, positions.get(0).intValue());
-    assertEquals(8, positions.get(1).intValue());
-  }
-
-  @Test(groups = { "Functional" })
   public void testRegionsToString()
   {
     HiddenColumns hc = new HiddenColumns();
@@ -976,18 +948,22 @@ public class HiddenColumnsTest
             false);
 
     // confirm that original contigs are as expected
-    List<int[]> visible = hidden.getVisibleContigs(0, 25);
-    assertEquals("[0, 14]", Arrays.toString(visible.get(0)));
-    assertEquals("[18, 24]", Arrays.toString(visible.get(1)));
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
+    int[] region = visible.next();
+    assertEquals("[0, 14]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[18, 24]", Arrays.toString(region));
 
     // propagate insertions
     HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
             view);
 
     // confirm that the contigs have changed to account for the gaps
-    visible = result.getVisibleContigs(0, 25);
-    assertEquals("[0, 10]", Arrays.toString(visible.get(0)));
-    assertEquals("[14, 24]", Arrays.toString(visible.get(1)));
+    visible = result.getVisContigsIterator(0, 25);
+    region = visible.next();
+    assertEquals("[0, 10]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[14, 24]", Arrays.toString(region));
 
     // confirm the alignment has been changed so that the other sequences have
     // gaps inserted where the columns are hidden
@@ -1030,18 +1006,24 @@ public class HiddenColumnsTest
             false);
 
     // confirm that original contigs are as expected
-    List<int[]> visible = hidden.getVisibleContigs(0, 20);
-    assertEquals("[0, 6]", Arrays.toString(visible.get(0)));
-    assertEquals("[11, 19]", Arrays.toString(visible.get(1)));
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
+    int[] region = visible.next();
+    assertEquals("[0, 6]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[11, 19]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     // propagate insertions
     HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
             view);
 
     // confirm that the contigs have changed to account for the gaps
-    visible = result.getVisibleContigs(0, 20);
-    assertEquals("[0, 4]", Arrays.toString(visible.get(0)));
-    assertEquals("[7, 19]", Arrays.toString(visible.get(1)));
+    visible = result.getVisContigsIterator(0, 20);
+    region = visible.next();
+    assertEquals("[0, 4]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 19]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
     // confirm the alignment has been changed so that the other sequences have
     // gaps inserted where the columns are hidden