Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 74ac146..266b90a 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -34,6 +34,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
 import jalview.util.MapList;
 
 import java.io.IOException;
@@ -1350,4 +1351,135 @@ public class AlignmentTest
     assertEquals(seq, ala.sequenceRef);
     assertEquals("", ala.calcId);
   }
+
+  @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 = al.propagateInsertions(profileseq, 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 = al.propagateInsertions(profileseq, 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 testPadGaps()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setGapCharacter('.'); // this replaces existing gaps
+    assertEquals("ABCDEF..", seq1.getSequenceAsString());
+    a.padGaps();
+    // trailing gaps are pruned, short sequences padded with gap character
+    assertEquals("ABCDEF.", seq1.getSequenceAsString());
+    assertEquals(".JKLMNO", seq2.getSequenceAsString());
+    assertEquals(".PQR...", seq3.getSequenceAsString());
+  }
 }