JAL-2579 Moved locateVisibleStartOfSequence to Sequence (refactored)

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

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 316b003..6730626 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -259,175 +259,6 @@ public class HiddenColumnsTest
     assertFalse(cs2.hasHiddenColumns());
   }
 
-  /**
-   * Test the code used to locate the reference sequence ruler origin
-   */
-  @Test(groups = { "Functional" })
-  public void testLocateVisibleStartofSequence()
-  {
-    // create random alignment
-    AlignmentGenerator gen = new AlignmentGenerator(false);
-    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
-
-    HiddenColumns cs = al.getHiddenColumns();
-    ColumnSelection colsel = new ColumnSelection();
-
-    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
-    assertEquals(2, seq.findIndex(seq.getStart()));
-
-    // no hidden columns
-    assertEquals(seq.findIndex(seq.getStart()) - 1, cs.locateVisibleStartOfSequence(seq));
-
-    // hidden column on gap after end of sequence - should not affect bounds
-    colsel.hideSelectedColumns(13, al.getHiddenColumns());
-    assertEquals(seq.findIndex(seq.getStart()) - 1,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    // hidden column on gap before beginning of sequence - should vis bounds by
-    // one
-    colsel.hideSelectedColumns(0, al.getHiddenColumns());
-    assertEquals(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    // hide columns around most of sequence - leave one residue remaining
-    cs.hideColumns(1, 3);
-    cs.hideColumns(6, 11);
-
-    Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
-
-    assertEquals("-D", seq.getSequenceStringFromIterator(it));
-    // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
-    // { seq })[0]);
-
-    assertEquals(1, cs.locateVisibleStartOfSequence(seq));
-    cs.revealAllHiddenColumns(colsel);
-
-    // hide whole sequence - should just get location of hidden region
-    // containing sequence
-    cs.hideColumns(1, 11);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 15);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(7, 17);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(3, 17);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(3, 19);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 0);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 1);
-    assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 2);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(1, 1);
-    assertEquals(2,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(1, 2);
-    assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(1, 3);
-    assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 2);
-    cs.hideColumns(5, 6);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 2);
-    cs.hideColumns(5, 6);
-    cs.hideColumns(9, 10);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 2);
-    cs.hideColumns(7, 11);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(2, 4);
-    cs.hideColumns(7, 11);
-    assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(2, 4);
-    cs.hideColumns(7, 12);
-    assertEquals(1,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(1, 11);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 12);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 4);
-    cs.hideColumns(6, 12);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 1);
-    cs.hideColumns(3, 12);
-    assertEquals(0,cs.locateVisibleStartOfSequence(seq));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(3, 14);
-    cs.hideColumns(17, 19);
-    assertEquals(3,cs.locateVisibleStartOfSequence(seq2));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(3, 7);
-    cs.hideColumns(9, 14);
-    cs.hideColumns(17, 19);
-    assertEquals(9,cs.locateVisibleStartOfSequence(seq2));
-
-    cs.revealAllHiddenColumns(colsel);
-    cs.hideColumns(0, 1);
-    cs.hideColumns(3, 4);
-    cs.hideColumns(6, 8);
-    cs.hideColumns(10, 12);
-    assertEquals(6, cs.locateVisibleStartOfSequence(seq));
-
-  }
-
-  @Test(groups = { "Functional" })
-  public void testLocateVisibleStartPathologicals()
-  {
-    // test some pathological cases we missed
-    AlignmentI al = new Alignment(
-            new SequenceI[]
-    { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
-    HiddenColumns cs = new HiddenColumns();
-    cs.hideList(al.getSequenceAt(0).getInsertions());
-    assertEquals("G", ""
-            + al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
-
-    // KM: no idea what this is meant to be testing... seems to be an unfinished
-    // test
-  }
 
   @Test(groups = { "Functional" })
   public void testHideColumns()