JAL-2759 Moved propagateInsertions out of HiddenColumns

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

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 151e31d..07a4810 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -26,7 +26,6 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
-import jalview.util.Comparison;
 
 import java.util.Arrays;
 import java.util.BitSet;
@@ -859,123 +858,6 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = "Functional")
-  public void testPropagateInsertions()
-  {
-    // create an alignment with no gaps - this will be the profile seq and other
-    // JPRED seqs
-    AlignmentGenerator gen = new AlignmentGenerator(false);
-    AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
-
-    // get the profileseq
-    SequenceI profileseq = al.getSequenceAt(0);
-    SequenceI gappedseq = new Sequence(profileseq);
-    gappedseq.insertCharAt(5, al.getGapCharacter());
-    gappedseq.insertCharAt(6, al.getGapCharacter());
-    gappedseq.insertCharAt(7, al.getGapCharacter());
-    gappedseq.insertCharAt(8, al.getGapCharacter());
-
-    // force different kinds of padding
-    al.getSequenceAt(3).deleteChars(2, 23);
-    al.getSequenceAt(4).deleteChars(2, 27);
-    al.getSequenceAt(5).deleteChars(10, 27);
-
-    // create an alignment view with the gapped sequence
-    SequenceI[] seqs = new SequenceI[1];
-    seqs[0] = gappedseq;
-    AlignmentI newal = new Alignment(seqs);
-    HiddenColumns hidden = new HiddenColumns();
-    hidden.hideColumns(15, 17);
-
-    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
-            false);
-
-    // confirm that original contigs are as expected
-    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
-    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.getVisContigsIterator(0, 25, false);
-    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
-    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
-    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
-    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
-    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
-    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
-
-  }
-
-  @Test(groups = "Functional")
-  public void testPropagateInsertionsOverlap()
-  {
-    // test propagateInsertions where gaps and hiddenColumns overlap
-
-    // create an alignment with no gaps - this will be the profile seq and other
-    // JPRED seqs
-    AlignmentGenerator gen = new AlignmentGenerator(false);
-    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
-
-    // get the profileseq
-    SequenceI profileseq = al.getSequenceAt(0);
-    SequenceI gappedseq = new Sequence(profileseq);
-    gappedseq.insertCharAt(5, al.getGapCharacter());
-    gappedseq.insertCharAt(6, al.getGapCharacter());
-    gappedseq.insertCharAt(7, al.getGapCharacter());
-    gappedseq.insertCharAt(8, al.getGapCharacter());
-
-    // create an alignment view with the gapped sequence
-    SequenceI[] seqs = new SequenceI[1];
-    seqs[0] = gappedseq;
-    AlignmentI newal = new Alignment(seqs);
-
-    // hide columns so that some overlap with the gaps
-    HiddenColumns hidden = new HiddenColumns();
-    hidden.hideColumns(7, 10);
-
-    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
-            false);
-
-    // confirm that original contigs are as expected
-    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
-    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.getVisContigsIterator(0, 20, false);
-    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
-    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
-    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
-    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
-    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
-  }
-
-  @Test(groups = "Functional")
   public void testHasHiddenColumns()
   {
     HiddenColumns h = new HiddenColumns();