X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=4ac8c5bc1f3f387efd4ab502e69129ae0ab770de;hb=refs%2Fheads%2Fbug%2FJAL-3296changeStartInvalidateCursor;hp=23e8cf709eff21671b2ff3a55f63723bd241a34b;hpb=98558735e9208afa98bb155bd5350ad0a680ca24;p=jalview.git diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index 23e8cf7..4ac8c5b 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -28,6 +28,7 @@ import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.analysis.AlignmentGenerator; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.datamodel.PDBEntry.Type; @@ -38,19 +39,19 @@ import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.BitSet; +import java.util.Iterator; import java.util.List; import java.util.Vector; -import junit.extensions.PA; - import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import junit.extensions.PA; + public class SequenceTest { - @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { @@ -245,7 +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)); @@ -261,6 +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)); } /** @@ -277,7 +358,7 @@ public class SequenceTest SequenceI sq = new Sequence("test/8-13", "ABCDEF"); assertEquals(8, sq.findPosition(0)); // Sequence should now hold a cursor at [8, 0] - assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0", + assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1", PA.getValue(sq, "cursor").toString()); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); int token = (int) PA.getValue(sq, "changeCount"); @@ -293,24 +374,24 @@ public class SequenceTest cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(++token, (int) PA.getValue(sq, "changeCount")); assertEquals(new SequenceCursor(sq, 13, 6, token), cursor); - assertEquals("test:Pos13:Col6:startCol1:endCol6:tok1", + assertEquals("test:Pos13:Col6:startCol1:endCol6:tok2", PA.getValue(sq, "cursor").toString()); // assertEquals(-1, seq.findPosition(6)); // fails sq = new Sequence("test/8-11", "AB-C-D--"); - token = (int) PA.getValue(sq, "changeCount"); // 0 + token = (int) PA.getValue(sq, "changeCount"); // 1 for setStart assertEquals(8, sq.findPosition(0)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 8, 1, token), cursor); - assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0", + assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(9, sq.findPosition(1)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor); - assertEquals("test:Pos9:Col2:startCol1:endCol0:tok1", + assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -319,14 +400,14 @@ public class SequenceTest assertEquals(10, sq.findPosition(2)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor); - assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2", + assertEquals("test:Pos9:Col2:startCol1:endCol0:tok3", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(10, sq.findPosition(3)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor); - assertEquals("test:Pos10:Col4:startCol1:endCol0:tok3", + assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -335,7 +416,7 @@ public class SequenceTest assertEquals(11, sq.findPosition(4)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor); - assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4", + assertEquals("test:Pos10:Col4:startCol1:endCol0:tok5", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -343,7 +424,7 @@ public class SequenceTest cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor); // lastCol has been found and saved in the cursor - assertEquals("test:Pos11:Col6:startCol1:endCol6:tok5", + assertEquals("test:Pos11:Col6:startCol1:endCol6:tok6", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -359,6 +440,7 @@ public class SequenceTest sq = new Sequence("test/8-13", "--AB-C-DEF--"); assertEquals(8, sq.findPosition(0)); assertNull(PA.getValue(sq, "cursor")); + assertEquals(1, PA.getValue(sq, "changeCount")); sq.sequenceChanged(); assertEquals(8, sq.findPosition(1)); @@ -366,41 +448,41 @@ public class SequenceTest sq.sequenceChanged(); assertEquals(8, sq.findPosition(2)); - assertEquals("test:Pos8:Col3:startCol3:endCol0:tok2", + assertEquals("test:Pos8:Col3:startCol3:endCol0:tok3", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(9, sq.findPosition(3)); - assertEquals("test:Pos9:Col4:startCol3:endCol0:tok3", + assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[4] is a gap, returns next residue pos (C10) // cursor is set to last residue found [B] assertEquals(10, sq.findPosition(4)); - assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4", + assertEquals("test:Pos9:Col4:startCol3:endCol0:tok5", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(10, sq.findPosition(5)); - assertEquals("test:Pos10:Col6:startCol3:endCol0:tok5", + assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[6] is a gap, returns next residue pos (D11) // cursor is set to last residue found [C] assertEquals(11, sq.findPosition(6)); - assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6", + assertEquals("test:Pos10:Col6:startCol3:endCol0:tok7", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(11, sq.findPosition(7)); - assertEquals("test:Pos11:Col8:startCol3:endCol0:tok7", + assertEquals("test:Pos11:Col8:startCol3:endCol0:tok8", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(12, sq.findPosition(8)); - assertEquals("test:Pos12:Col9:startCol3:endCol0:tok8", + assertEquals("test:Pos12:Col9:startCol3:endCol0:tok9", PA.getValue(sq, "cursor").toString()); /* @@ -408,12 +490,12 @@ public class SequenceTest */ sq.sequenceChanged(); assertEquals(13, sq.findPosition(9)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok9", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(14, sq.findPosition(10)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11", PA.getValue(sq, "cursor").toString()); /* @@ -422,12 +504,12 @@ public class SequenceTest */ sq.sequenceChanged(); assertEquals(14, sq.findPosition(11)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(14, sq.findPosition(99)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok13", PA.getValue(sq, "cursor").toString()); /* @@ -435,20 +517,19 @@ public class SequenceTest */ sq = new Sequence("test/8-13", "--AB-C-DEF"); assertEquals(13, sq.findPosition(9)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1", 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", + assertEquals("test:Pos12:Col9:startCol3:endCol0:tok2", cursor.toString()); // findPosition with cursor accepts base 1 column values assertEquals(13, ((Sequence) sq).findPosition(10, cursor)); assertEquals(13, sq.findPosition(9)); // F13 // lastResidueColumn has now been found and saved in cursor - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok2", PA.getValue(sq, "cursor").toString()); } @@ -478,6 +559,13 @@ 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 */ @@ -487,6 +575,21 @@ 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" }) @@ -799,7 +902,7 @@ public class SequenceTest Assert.assertEquals(pdbe1a, sq.getDatasetSequence().getPDBEntry("1PDB"), "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry."); - ArrayList annotsList = new ArrayList(); + ArrayList annotsList = new ArrayList<>(); System.out.println(">>>>>> " + sq.getSequenceAsString().length()); annotsList.add(new Annotation("A", "A", 'X', 0.1f)); annotsList.add(new Annotation("A", "A", 'X', 0.1f)); @@ -1399,56 +1502,112 @@ public class SequenceTest public void testFindIndex_withCursor() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); + final int tok = (int) PA.getValue(sq, "changeCount"); + assertEquals(1, tok); - // find F given A - assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0))); + // find F given A, check cursor is now at the found position + assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, tok))); + 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))); + assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, tok))); + cursor = (SequenceCursor) PA.getValue(sq, "cursor"); + assertEquals(8, cursor.residuePosition); + assertEquals(2, cursor.columnPosition); - // find C given C - assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0))); + // find C given C (no cursor update is done for this case) + assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, tok))); + 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" }) public void testFindPosition_withCursor() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); + final int tok = (int) PA.getValue(sq, "changeCount"); + assertEquals(1, tok); // find F pos given A - lastCol gets set in cursor - assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0))); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals(13, + sq.findPosition(10, new SequenceCursor(sq, 8, 2, tok))); + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); // find A pos given F - first residue column is saved in cursor - assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0))); - assertEquals("test:Pos8:Col2:startCol2:endCol10:tok0", + assertEquals(8, + sq.findPosition(2, new SequenceCursor(sq, 13, 10, tok))); + assertEquals("test:Pos8:Col2:startCol2:endCol10:tok1", PA.getValue(sq, "cursor").toString()); // find C pos given C (neither startCol nor endCol is set) - assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0))); - assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0", + assertEquals(10, + sq.findPosition(6, new SequenceCursor(sq, 10, 6, tok))); + assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1", PA.getValue(sq, "cursor").toString()); // now the grey area - what residue position for a gapped column? JAL-2562 // find 'residue' for column 3 given cursor for D (so working left) // returns B9; cursor is updated to [B 5] - assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0))); - assertEquals("test:Pos9:Col5:startCol0:endCol0:tok0", + assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, tok))); + assertEquals("test:Pos9:Col5:startCol0:endCol0:tok1", PA.getValue(sq, "cursor").toString()); // find 'residue' for column 8 given cursor for D (so working right) // returns E12; cursor is updated to [D 7] - assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0))); - assertEquals("test:Pos11:Col7:startCol0:endCol0:tok0", + assertEquals(12, + sq.findPosition(8, new SequenceCursor(sq, 11, 7, tok))); + assertEquals("test:Pos11:Col7:startCol0:endCol0:tok1", PA.getValue(sq, "cursor").toString()); // find 'residue' for column 12 given cursor for B // returns 1 more than last residue position; cursor is updated to [F 10] // lastCol position is saved in cursor - assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0))); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals(14, + sq.findPosition(12, new SequenceCursor(sq, 9, 5, tok))); + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); /* @@ -1456,8 +1615,9 @@ public class SequenceTest * returns 1 more than the last residue position * cursor is set to last real residue position [F 10] */ - assertEquals(14, sq.findPosition(99, new SequenceCursor(sq, 8, 2, 0))); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals(14, + sq.findPosition(99, new SequenceCursor(sq, 8, 2, tok))); + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); /* @@ -1465,14 +1625,14 @@ public class SequenceTest */ sq = new Sequence("test/8-13", "-A--BCD-EF"); // first find C from A - assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, 0))); + assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, tok))); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); - assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0", + assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1", cursor.toString()); // now 'find' 99 from C // cursor is set to [F 10] and saved lastCol assertEquals(14, sq.findPosition(99, cursor)); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); } @@ -1540,6 +1700,10 @@ 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 @@ -1575,6 +1739,17 @@ public class SequenceTest // cursor should now be at [F 10] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor); + + /* + * changing sequence start should invalidate cursor + */ + sq = new Sequence("test/8-13", "-A--BCD-EF--"); + assertEquals(8, sq.getStart()); + assertEquals(9, sq.findPosition(4)); // B(9) + sq.setStart(7); + assertEquals(8, sq.findPosition(4)); // is now B(8) + sq.setStart(10); + assertEquals(11, sq.findPosition(4)); // is now B(11) } @Test(groups = { "Functional" }) @@ -1599,81 +1774,41 @@ public class SequenceTest { String seqstring = "-A--BCD-EF--"; SequenceI sq = new Sequence("test/8-13", seqstring); - assertEquals(0, PA.getValue(sq, "changeCount")); + // changeCount is incremented for setStart + assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(0, sq.replace('A', 'A')); // same char assertEquals(seqstring, sq.getSequenceAsString()); - assertEquals(0, PA.getValue(sq, "changeCount")); + assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(0, sq.replace('X', 'Y')); // not there assertEquals(seqstring, sq.getSequenceAsString()); - assertEquals(0, PA.getValue(sq, "changeCount")); + assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(1, sq.replace('A', 'K')); assertEquals("-K--BCD-EF--", sq.getSequenceAsString()); - assertEquals(1, PA.getValue(sq, "changeCount")); + assertEquals(2, PA.getValue(sq, "changeCount")); assertEquals(6, sq.replace('-', '.')); assertEquals(".K..BCD.EF..", sq.getSequenceAsString()); - assertEquals(2, PA.getValue(sq, "changeCount")); + assertEquals(3, PA.getValue(sq, "changeCount")); } @Test(groups = { "Functional" }) - public void testFindPositions() + public void testGapBitset() { SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--"); + BitSet bs = sq.gapBitset(); + BitSet expected = new BitSet(); + expected.set(0); + expected.set(4, 7); + expected.set(9); + expected.set(11, 13); - /* - * 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)); + assertTrue(bs.equals(expected)); - /* - * 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 testFindFeatures_largeEndPos() { /* @@ -1704,4 +1839,339 @@ public class SequenceTest found = sq.findFeatures(10, 11); assertEquals(0, found.size()); } + + @Test(groups = { "Functional" }) + public void testSetName() + { + SequenceI sq = new Sequence("test", "-ABC---DE-F--"); + assertEquals("test", sq.getName()); + assertEquals(1, sq.getStart()); + assertEquals(6, sq.getEnd()); + + sq.setName("testing"); + assertEquals("testing", sq.getName()); + + sq.setName("test/8-10"); + assertEquals("test", sq.getName()); + assertEquals(8, sq.getStart()); + assertEquals(13, sq.getEnd()); // note end is recomputed + + sq.setName("testing/7-99"); + assertEquals("testing", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); // end may be beyond physical end + + sq.setName("/2-3"); + assertEquals("", sq.getName()); + assertEquals(2, sq.getStart()); + assertEquals(7, sq.getEnd()); + + sq.setName("test/"); // invalid + assertEquals("test/", sq.getName()); + assertEquals(2, sq.getStart()); + assertEquals(7, sq.getEnd()); + + sq.setName("test/6-13/7-99"); + assertEquals("test/6-13", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/0-5"); // 0 is invalid - ignored + assertEquals("test/0-5", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/a-5"); // a is invalid - ignored + assertEquals("test/a-5", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/6-5"); // start > end is invalid - ignored + assertEquals("test/6-5", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/5"); // invalid - ignored + assertEquals("test/5", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/-5"); // invalid - ignored + assertEquals("test/-5", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/5-"); // invalid - ignored + assertEquals("test/5-", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName("test/5-6-7"); // invalid - ignored + assertEquals("test/5-6-7", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + + sq.setName(null); // invalid, gets converted to space + assertEquals("", sq.getName()); + assertEquals(7, sq.getStart()); + assertEquals(99, sq.getEnd()); + } + + @Test(groups = { "Functional" }) + public void testCheckValidRange() + { + Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--"); + assertEquals(7, sq.getStart()); + assertEquals(12, sq.getEnd()); + + /* + * checkValidRange ensures end is at least the last residue position + */ + PA.setValue(sq, "end", 2); + sq.checkValidRange(); + assertEquals(12, sq.getEnd()); + + /* + * end may be beyond the last residue position + */ + PA.setValue(sq, "end", 22); + sq.checkValidRange(); + assertEquals(22, sq.getEnd()); + } + + @Test(groups = { "Functional" }) + public void testDeleteChars_withGaps() + { + /* + * delete gaps only + */ + SequenceI sq = new Sequence("test/8-10", "A-B-C"); + sq.createDatasetSequence(); + assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); + sq.deleteChars(1, 2); // delete first gap + assertEquals("AB-C", sq.getSequenceAsString()); + assertEquals(8, sq.getStart()); + assertEquals(10, sq.getEnd()); + assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); + + /* + * delete gaps and residues at start (no new dataset sequence) + */ + sq = new Sequence("test/8-10", "A-B-C"); + sq.createDatasetSequence(); + sq.deleteChars(0, 3); // delete A-B + assertEquals("-C", sq.getSequenceAsString()); + assertEquals(10, sq.getStart()); + assertEquals(10, sq.getEnd()); + assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); + + /* + * delete gaps and residues at end (no new dataset sequence) + */ + sq = new Sequence("test/8-10", "A-B-C"); + sq.createDatasetSequence(); + sq.deleteChars(2, 5); // delete B-C + assertEquals("A-", sq.getSequenceAsString()); + assertEquals(8, sq.getStart()); + assertEquals(8, sq.getEnd()); + assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString()); + + /* + * delete gaps and residues internally (new dataset sequence) + * first delete from gap to residue + */ + sq = new Sequence("test/8-10", "A-B-C"); + sq.createDatasetSequence(); + sq.deleteChars(1, 3); // delete -B + assertEquals("A-C", sq.getSequenceAsString()); + assertEquals(8, sq.getStart()); + assertEquals(9, sq.getEnd()); + assertEquals("AC", sq.getDatasetSequence().getSequenceAsString()); + assertEquals(8, sq.getDatasetSequence().getStart()); + assertEquals(9, sq.getDatasetSequence().getEnd()); + + /* + * internal delete from gap to gap + */ + sq = new Sequence("test/8-10", "A-B-C"); + sq.createDatasetSequence(); + sq.deleteChars(1, 4); // delete -B- + assertEquals("AC", sq.getSequenceAsString()); + assertEquals(8, sq.getStart()); + assertEquals(9, sq.getEnd()); + assertEquals("AC", sq.getDatasetSequence().getSequenceAsString()); + assertEquals(8, sq.getDatasetSequence().getStart()); + assertEquals(9, sq.getDatasetSequence().getEnd()); + + /* + * internal delete from residue to residue + */ + sq = new Sequence("test/8-10", "A-B-C"); + sq.createDatasetSequence(); + sq.deleteChars(2, 3); // delete B + assertEquals("A--C", sq.getSequenceAsString()); + assertEquals(8, sq.getStart()); + assertEquals(9, sq.getEnd()); + assertEquals("AC", sq.getDatasetSequence().getSequenceAsString()); + assertEquals(8, sq.getDatasetSequence().getStart()); + assertEquals(9, sq.getDatasetSequence().getEnd()); + } + + /** + * 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, + seq.firstResidueOutsideIterator(cs.iterator())); + + // hidden column on gap after end of sequence - should not affect bounds + colsel.hideSelectedColumns(13, al.getHiddenColumns()); + assertEquals(seq.findIndex(seq.getStart()) - 1, + seq.firstResidueOutsideIterator(cs.iterator())); + + 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.absoluteToVisibleColumn( + seq.firstResidueOutsideIterator(cs.iterator()))); + + cs.revealAllHiddenColumns(colsel); + // hide columns around most of sequence - leave one residue remaining + cs.hideColumns(1, 3); + cs.hideColumns(6, 11); + + Iterator it = cs.getVisContigsIterator(0, 6, false); + + assertEquals("-D", seq.getSequenceStringFromIterator(it)); + // cs.getVisibleSequenceStrings(0, 5, new SequenceI[] + // { seq })[0]); + + assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator())); + cs.revealAllHiddenColumns(colsel); + + // hide whole sequence - should just get location of hidden region + // containing sequence + cs.hideColumns(1, 11); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 15); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---"); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(7, 17); + assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 17); + assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 19); + assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 0); + assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 1); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 1); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 2); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 3); + assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + cs.hideColumns(5, 6); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + cs.hideColumns(5, 6); + cs.hideColumns(9, 10); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 2); + cs.hideColumns(7, 11); + assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(2, 4); + cs.hideColumns(7, 11); + assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(2, 4); + cs.hideColumns(7, 12); + assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(1, 11); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 12); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 4); + cs.hideColumns(6, 12); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 1); + cs.hideColumns(3, 12); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 14); + cs.hideColumns(17, 19); + assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(3, 7); + cs.hideColumns(9, 14); + cs.hideColumns(17, 19); + assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator())); + + cs.revealAllHiddenColumns(colsel); + cs.hideColumns(0, 1); + cs.hideColumns(3, 4); + cs.hideColumns(6, 8); + cs.hideColumns(10, 12); + assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator())); + + } }