import jalview.datamodel.PDBEntry.Type;
import jalview.gui.JvOptionPane;
import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
import java.io.File;
import java.util.ArrayList;
assertTrue(sq.isProtein());
}
+ @Test(groups = ("Functional"))
+ public void testIsProteinWithXorNAmbiguityCodes()
+ {
+ // test Protein with N - poly asparagine
+ assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
+ assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
+ // test Protein with X
+ assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
+ // test DNA with X
+ assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+ // test DNA with N
+ assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
+ // test RNA with X
+ assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
+ assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
+ }
+
@Test(groups = { "Functional" })
public void testGetAnnotation()
{
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));
+ }
+
/**
* Tests for the method that returns a dataset sequence position (start..) for
* an aligned column position (base 0).
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");
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();
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();
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();
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();
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));
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());
/*
*/
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());
/*
*/
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());
/*
*/
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());
}
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
*/
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" })
assertNotNull(newDs);
assertNotSame(ds, newDs);
assertNotNull(sq.getDBRefs());
- assertEquals(1, sq.getDBRefs().length);
- assertNotSame(dbr1, sq.getDBRefs()[0]);
- assertEquals(dbr1, sq.getDBRefs()[0]);
+ assertEquals(1, sq.getDBRefs().size());
+ assertNotSame(dbr1, sq.getDBRefs().get(0));
+ assertEquals(dbr1, sq.getDBRefs().get(0));
/*
* internal delete with sequence features
assertEquals(4, sq.getEnd());
assertSame(ds, PA.getValue(sq, "datasetSequence"));
assertNotNull(sq.getDBRefs());
- assertEquals(1, sq.getDBRefs().length);
- assertSame(dbr1, sq.getDBRefs()[0]);
+ assertEquals(1, sq.getDBRefs().size());
+ assertSame(dbr1, sq.getDBRefs().get(0));
}
@Test(groups = { "Functional" })
new AlignmentAnnotation("Test annot", "Test annot description",
annots));
Assert.assertEquals(sq.getDescription(), "Test sequence description..");
- Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
+ Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
// sequence
Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
Assert.assertNotNull(sq.getAnnotation());
Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
- Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
+ Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same
// as
// sq.getDBRefs()
Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
Assert.assertEquals(derived.getDescription(),
"Test sequence description..");
- Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
+ Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset
Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
Assert.assertNotNull(derived.getAnnotation());
Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
- Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
+ Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
.size(), 4);
Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
// but that doesn't distinguish it from an aligned sequence
// which has not yet generated a dataset sequence
// NB getDBRef looks inside dataset sequence if not null
- DBRefEntry[] dbrefs = copy.getDBRefs();
- assertEquals(1, dbrefs.length);
- assertFalse(dbrefs[0] == seq1.getDBRefs()[0]);
- assertTrue(dbrefs[0].equals(seq1.getDBRefs()[0]));
+ List<DBRefEntry> dbrefs = copy.getDBRefs();
+ assertEquals(1, dbrefs.size());
+ assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0));
+ assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0)));
}
@Test(groups = { "Functional" })
// getDBRef looks inside dataset sequence and this is shared,
// so holds the same dbref objects
- DBRefEntry[] dbrefs = copy.getDBRefs();
- assertEquals(1, dbrefs.length);
- assertSame(dbrefs[0], seq1.getDBRefs()[0]);
+ List<DBRefEntry> dbrefs = copy.getDBRefs();
+ assertEquals(1, dbrefs.size());
+ assertSame(dbrefs.get(0), seq1.getDBRefs().get(0));
}
/**
assertNull(sq.getDBRefs());
DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
sq.addDBRef(dbref);
- assertEquals(1, sq.getDBRefs().length);
- assertSame(dbref, sq.getDBRefs()[0]);
+ assertEquals(1, sq.getDBRefs().size());
+ assertSame(dbref, sq.getDBRefs().get(0));
/*
* change of version - new entry
*/
DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
sq.addDBRef(dbref2);
- assertEquals(2, sq.getDBRefs().length);
- assertSame(dbref, sq.getDBRefs()[0]);
- assertSame(dbref2, sq.getDBRefs()[1]);
+ assertEquals(2, sq.getDBRefs().size());
+ assertSame(dbref, sq.getDBRefs().get(0));
+ assertSame(dbref2, sq.getDBRefs().get(1));
/*
* matches existing entry - not added
*/
sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
- assertEquals(2, sq.getDBRefs().length);
+ assertEquals(2, sq.getDBRefs().size());
/*
* different source = new entry
*/
DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
sq.addDBRef(dbref3);
- assertEquals(3, sq.getDBRefs().length);
- assertSame(dbref3, sq.getDBRefs()[2]);
+ assertEquals(3, sq.getDBRefs().size());
+ assertSame(dbref3, sq.getDBRefs().get(2));
/*
* different ref = new entry
*/
DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
sq.addDBRef(dbref4);
- assertEquals(4, sq.getDBRefs().length);
- assertSame(dbref4, sq.getDBRefs()[3]);
+ assertEquals(4, sq.getDBRefs().size());
+ assertSame(dbref4, sq.getDBRefs().get(3));
/*
* matching ref with a mapping - map updated
1, 1 }, 3, 1));
dbref5.setMap(map);
sq.addDBRef(dbref5);
- assertEquals(4, sq.getDBRefs().length);
- assertSame(dbref4, sq.getDBRefs()[3]);
+ assertEquals(4, sq.getDBRefs().size());
+ assertSame(dbref4, sq.getDBRefs().get(3));
assertSame(map, dbref4.getMap());
/*
DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
dbref2.getAccessionId());
sq.addDBRef(dbref6);
- assertEquals(4, sq.getDBRefs().length);
- assertSame(dbref2, sq.getDBRefs()[1]);
+ assertEquals(4, sq.getDBRefs().size());
+ assertSame(dbref2, sq.getDBRefs().get(1));
assertEquals("3", dbref2.getVersion());
/*
DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
dbref3.getAccessionId());
sq.addDBRef(dbref7);
- assertEquals(4, sq.getDBRefs().length);
- assertSame(dbref3, sq.getDBRefs()[2]);
+ assertEquals(4, sq.getDBRefs().size());
+ assertSame(dbref3, sq.getDBRefs().get(2));
assertEquals("3", dbref2.getVersion());
}
assertTrue(primaryDBRefs.isEmpty());
// empty dbrefs
- sq.setDBRefs(new DBRefEntry[] {});
+ sq.setDBRefs(null);
primaryDBRefs = sq.getPrimaryDBRefs();
assertTrue(primaryDBRefs.isEmpty());
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, check cursor is now at the found position
- assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0)));
+ 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 (no cursor update is done for this case)
- assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
+ assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, tok)));
SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
assertSame(cursor2, cursor);
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());
/*
* 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());
/*
*/
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());
}
// 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
// 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" })
{
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"));
- }
-
- @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));
+ assertEquals(3, PA.getValue(sq, "changeCount"));
}
@Test(groups = { "Functional" })
assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
}
+ @Test(groups= {"Functional"})
+ public void testTransferAnnotation() {
+ Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
+ Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
+ origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
+ toSeq.transferAnnotation(origSeq, null);
+ assertTrue(toSeq.getDBRefs().size()==1);
+
+ assertTrue(toSeq.getDBRefs().get(0).isCanonical());
+
+ // check for promotion of non-canonical
+ // to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
+ toSeq.setDBRefs(null);
+ toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
+ toSeq.transferAnnotation(origSeq, null);
+ assertTrue(toSeq.getDBRefs().size()==1);
+
+ assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());
+
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff