X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=c344645cd5e5d6a29558ca39148a17705aea449f;hb=a4143dac9ce4bbf4e3c60496c5818d30fc75e759;hp=5a145146cf43334a1f62e3fdc855474a3692e992;hpb=acf6d0deb9caf0148791f2993be0a2cd7987f569;p=jalview.git diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index 5a14514..c344645 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -52,7 +52,6 @@ import junit.extensions.PA; public class SequenceTest { - @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { @@ -247,7 +246,9 @@ public class SequenceTest sq.sequenceChanged(); assertEquals(6, sq.findIndex(9)); - sq = new Sequence("test/8-13", "-A--B-C-D-E-F--"); + final String aligned = "-A--B-C-D-E-F--"; + assertEquals(15, aligned.length()); + sq = new Sequence("test/8-13", aligned); assertEquals(2, sq.findIndex(8)); sq.sequenceChanged(); assertEquals(5, sq.findIndex(9)); @@ -263,6 +264,84 @@ public class SequenceTest // beyond end returns last residue column sq.sequenceChanged(); assertEquals(13, sq.findIndex(99)); + + /* + * residue before sequence 'end' but beyond end of sequence returns + * length of sequence (last column) (rightly or wrongly!) + */ + sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case + assertEquals(6, sq.getLength()); + sq.sequenceChanged(); + assertEquals(sq.getLength(), sq.findIndex(14)); + sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case + sq.sequenceChanged(); + assertEquals(sq.getLength(), sq.findIndex(65)); + + /* + * residue after sequence 'start' but before first residue returns + * zero (before first column) (rightly or wrongly!) + */ + sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case + sq.sequenceChanged(); + assertEquals(0, sq.findIndex(3)); + sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case + sq.sequenceChanged(); + assertEquals(0, sq.findIndex(2)); + } + + @Test(groups = { "Functional" }) + public void testFindPositions() + { + SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--"); + + /* + * invalid inputs + */ + assertNull(sq.findPositions(6, 5)); + assertNull(sq.findPositions(0, 5)); + assertNull(sq.findPositions(-1, 5)); + + /* + * all gapped ranges + */ + assertNull(sq.findPositions(1, 1)); // 1-based columns + assertNull(sq.findPositions(5, 5)); + assertNull(sq.findPositions(5, 6)); + assertNull(sq.findPositions(5, 7)); + + /* + * all ungapped ranges + */ + assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A + assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB + assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC + assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC + + /* + * gap to ungapped range + */ + assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC + assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE + + /* + * ungapped to gapped range + */ + assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C + assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF + + /* + * ungapped to ungapped enclosing gaps + */ + assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD + assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF + + /* + * gapped to gapped enclosing ungapped + */ + assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC + assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE + assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot + assertEquals(new Range(8, 13), sq.findPositions(1, 99)); } /** @@ -440,8 +519,7 @@ public class SequenceTest assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); - assertEquals(12, sq.findPosition(8)); - cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(12, sq.findPosition(8)); // E12 // sequenceChanged() invalidates cursor.lastResidueColumn cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1", @@ -480,6 +558,13 @@ public class SequenceTest assertEquals(6, sq.getEnd()); assertNull(PA.getValue(sq, "datasetSequence")); + sq = new Sequence("test", "ABCDE"); + sq.deleteChars(0, 3); + assertEquals("DE", sq.getSequenceAsString()); + assertEquals(4, sq.getStart()); + assertEquals(5, sq.getEnd()); + assertNull(PA.getValue(sq, "datasetSequence")); + /* * delete at end */ @@ -489,6 +574,21 @@ public class SequenceTest assertEquals(1, sq.getStart()); assertEquals(4, sq.getEnd()); assertNull(PA.getValue(sq, "datasetSequence")); + + /* + * delete more positions than there are + */ + sq = new Sequence("test/8-11", "ABCD"); + sq.deleteChars(0, 99); + assertEquals("", sq.getSequenceAsString()); + assertEquals(12, sq.getStart()); // = findPosition(99) ?!? + assertEquals(11, sq.getEnd()); + + sq = new Sequence("test/8-11", "----"); + sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2 + assertEquals("", sq.getSequenceAsString()); + assertEquals(8, sq.getStart()); + assertEquals(11, sq.getEnd()); } @Test(groups = { "Functional" }) @@ -1402,14 +1502,61 @@ public class SequenceTest { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); - // find F given A + // find F given A, check cursor is now at the found position assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0))); + SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(13, cursor.residuePosition); + assertEquals(10, cursor.columnPosition); // find A given F assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0))); + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(8, cursor.residuePosition); + assertEquals(2, cursor.columnPosition); - // find C given C + // find C given C (no cursor update is done for this case) assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0))); + SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); + assertSame(cursor2, cursor); + + /* + * sequence 'end' beyond end of sequence returns length of sequence + * (for compatibility with pre-cursor code) + * - also verify the cursor is left in a valid state + */ + sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case + assertEquals(7, sq.findIndex(10)); // establishes a cursor + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(10, cursor.residuePosition); + assertEquals(7, cursor.columnPosition); + assertEquals(sq.getLength(), sq.findIndex(65)); + cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); + assertSame(cursor, cursor2); // not updated for this case! + + sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case + sq.findIndex(10); // establishes a cursor + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(sq.getLength(), sq.findIndex(65)); + cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); + assertSame(cursor, cursor2); // not updated for this case! + + /* + * residue after sequence 'start' but before first residue should return + * zero (for compatibility with pre-cursor code) + */ + sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case + sq.findIndex(10); // establishes a cursor + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(0, sq.findIndex(3)); + cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); + assertSame(cursor, cursor2); // not updated for this case! + + sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case + sq.findIndex(10); // establishes a cursor + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(0, sq.findIndex(2)); + cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); + assertSame(cursor, cursor2); // not updated for this case! } @Test(groups = { "Functional" }) @@ -1542,6 +1689,10 @@ public class SequenceTest // cursor should now be at [D 6] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor); + assertEquals(0, cursor.lastColumnPosition); // not yet found + assertEquals(13, sq.findPosition(8)); // E13 + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(9, cursor.lastColumnPosition); // found /* * deleteChars should invalidate the cached cursor @@ -1621,61 +1772,6 @@ public class SequenceTest } @Test(groups = { "Functional" }) - public void testFindPositions() - { - SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--"); - - /* - * invalid inputs - */ - assertNull(sq.findPositions(6, 5)); - assertNull(sq.findPositions(0, 5)); - assertNull(sq.findPositions(-1, 5)); - - /* - * all gapped ranges - */ - assertNull(sq.findPositions(1, 1)); // 1-based columns - assertNull(sq.findPositions(5, 5)); - assertNull(sq.findPositions(5, 6)); - assertNull(sq.findPositions(5, 7)); - - /* - * all ungapped ranges - */ - assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A - assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB - assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC - assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC - - /* - * gap to ungapped range - */ - assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC - assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE - - /* - * ungapped to gapped range - */ - assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C - assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF - - /* - * ungapped to ungapped enclosing gaps - */ - assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD - assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF - - /* - * gapped to gapped enclosing ungapped - */ - assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC - assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE - assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot - assertEquals(new Range(8, 13), sq.findPositions(1, 99)); - } - - @Test(groups = { "Functional" }) public void testGapBitset() { SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");