*/
package jalview.datamodel;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.PDBEntry.Type;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-
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 jalview.analysis.AlignmentGenerator;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
+import junit.extensions.PA;
+
public class SequenceTest
{
-
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
6, gapfield.cardinality());
- assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
+ assertEquals("getInsertionsAsBits not correct.", expectedgaps,
+ gapfield);
}
@Test(groups = ("Functional"))
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()
{
assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
}
+ @Test(groups = { "Functional" })
+ public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
+ {
+ addAnnotation("label1", "desc1", "calcId1", 1f);
+ AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
+ 1f);
+ addAnnotation("label2", "desc3", "calcId3", 1f);
+ AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
+ 1f);
+ addAnnotation("label5", "desc3", null, 1f);
+ addAnnotation(null, "desc3", "calcId3", 1f);
+
+ List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
+ "label2", "desc3");
+ assertEquals(1, anns.size());
+ assertSame(ann4, anns.get(0));
+ /**
+ * null matching should fail
+ */
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label2", null)
+ .isEmpty());
+
+ assertTrue(seq.getAlignmentAnnotations("calcId2", "label3", null)
+ .isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label5", null)
+ .isEmpty());
+ assertTrue(
+ seq.getAlignmentAnnotations("calcId2", null, null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, "label3", null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, null, null).isEmpty());
+ }
+
/**
* Tests for addAlignmentAnnotation. Note this method has the side-effect of
* setting the sequenceRef on the annotation. Adding the same annotation twice
public void testAddAlignmentAnnotation()
{
assertNull(seq.getAnnotation());
- final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
- "b", 2d);
+ final AlignmentAnnotation annotation = new AlignmentAnnotation("a", "b",
+ 2d);
assertNull(annotation.sequenceRef);
seq.addAlignmentAnnotation(annotation);
assertSame(seq, annotation.sequenceRef);
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));
// 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));
+
+ /*
+ * 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));
+
+ /**
+ * now try on a sequence with no gaps
+ */
+ sq.createDatasetSequence();
+ assertEquals(new Range(8, 13),
+ sq.getDatasetSequence().findPositions(1, 99));
+ assertEquals(new Range(8, 13),
+ sq.getDatasetSequence().findPositions(0, 99));
+
}
/**
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" })
/*
* SequenceFeature on sequence
*/
- SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
+ SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+ null);
sq.addSequenceFeature(sf);
List<SequenceFeature> sfs = sq.getSequenceFeatures();
assertEquals(1, sfs.size());
try
{
sq.getDatasetSequence().setDatasetSequence(sq); // loop!
- Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
+ Assert.fail(
+ "Expected Error to be raised when calling setDatasetSequence with self reference");
} catch (IllegalArgumentException e)
{
// TODO Jalview error/exception class for raising implementation errors
- assertTrue(e.getMessage().toLowerCase()
+ assertTrue(e.getMessage().toLowerCase(Locale.ROOT)
.contains("implementation error"));
}
assertTrue(sq.getSequenceFeatures().isEmpty());
public void testCreateDatasetSequence()
{
SequenceI sq = new Sequence("my", "ASDASD");
- sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
- "group"));
+ sq.addSequenceFeature(
+ new SequenceFeature("type", "desc", 1, 10, 1f, "group"));
sq.addDBRef(new DBRefEntry("source", "version", "accession"));
assertNull(sq.getDatasetSequence());
assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
- List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
- pdb2pdb });
+ List<DBRefEntry> primRefs = Arrays
+ .asList(new DBRefEntry[]
+ { pdb1pdb, pdb2pdb });
sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
- sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
- sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
+ sq.getDatasetSequence()
+ .addDBRef(new DBRefEntry("PDB", "version3", "3PDB")); // should do
+ // nothing
+ sq.getDatasetSequence()
+ .addDBRef(new DBRefEntry("PDB", "version4", "4PDB")); // should do
+ // nothing
PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
/*
* test we added pdb entries to the dataset sequence
*/
- Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
- .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
+ Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(),
+ Arrays.asList(new PDBEntry[]
+ { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
"PDB Entries were not found on dataset sequence.");
/*
* we should recover a pdb entry that is on the dataset sequence via PDBEntry
*/
- Assert.assertEquals(pdbe1a,
- sq.getDatasetSequence().getPDBEntry("1PDB"),
+ Assert.assertEquals(pdbe1a, sq.getDatasetSequence().getPDBEntry("1PDB"),
"PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
- ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+ ArrayList<Annotation> 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));
Annotation[] annots = annotsList.toArray(new Annotation[0]);
sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
"Test annot description", annots));
- sq.getDatasetSequence().addAlignmentAnnotation(
- new AlignmentAnnotation("Test annot", "Test annot description",
- annots));
+ sq.getDatasetSequence().addAlignmentAnnotation(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().getAllPDBEntries()
- .size(), 4);
+ Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
+ Assert.assertEquals(
+ derived.getDatasetSequence().getAllPDBEntries().size(), 4);
Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
assertEquals("CD", derived.getSequenceAsString());
assertEquals(6, sq.getEnd());
SequenceI derived = sq.deriveSequence();
assertEquals("ABCDEF", derived.getSequenceAsString());
- assertEquals("ABCDEF", derived.getDatasetSequence()
- .getSequenceAsString());
+ assertEquals("ABCDEF",
+ derived.getDatasetSequence().getSequenceAsString());
}
/**
assertNull(sq.getDatasetSequence());
SequenceI derived = sq.deriveSequence();
assertEquals("AB-C.D EF", derived.getSequenceAsString());
- assertEquals("ABCDEF", derived.getDatasetSequence()
- .getSequenceAsString());
+ assertEquals("ABCDEF",
+ derived.getDatasetSequence().getSequenceAsString());
}
@Test(groups = { "Functional" })
{
SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
seq1.setDescription("description");
- seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
- 1.3d));
- seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
- 12.4f, "group"));
+ seq1.addAlignmentAnnotation(
+ new AlignmentAnnotation("label", "desc", 1.3d));
+ seq1.addSequenceFeature(
+ new SequenceFeature("type", "desc", 22, 33, 12.4f, "group"));
seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
// 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" })
SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
seq1.createDatasetSequence();
seq1.setDescription("description");
- seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
- 1.3d));
+ seq1.addAlignmentAnnotation(
+ new AlignmentAnnotation("label", "desc", 1.3d));
// JAL-2046 - what is the contract for using a derived sequence's
// addSequenceFeature ?
- seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
- 12.4f, "group"));
+ seq1.addSequenceFeature(
+ new SequenceFeature("type", "desc", 22, 33, 12.4f, "group"));
seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
// here we add DBRef to the dataset sequence:
- seq1.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBL", "1.2", "AZ12345"));
+ seq1.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
SequenceI copy = new Sequence(seq1);
// 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));
}
/**
{
SequenceI sq = new Sequence("", "abcde");
// type may not be null
- assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
- 8, 0f, null)));
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, 0f, null)));
+ assertFalse(sq.addSequenceFeature(
+ new SequenceFeature(null, "desc", 4, 8, 0f, null)));
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 0f, null)));
// can't add a duplicate feature
- assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
- 4, 8, 0f, null)));
+ assertFalse(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 0f, null)));
// can add a different feature
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
- 8, 0f, null))); // different type
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
- "description", 4, 8, 0f, null)));// different description
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
- 8, 0f, null))); // different start position
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 9, 0f, null))); // different end position
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, 1f, null))); // different score
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, Float.NaN, null))); // score NaN
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, 0f, "Metal"))); // different group
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Scop", "desc", 4, 8, 0f, null))); // different
+ // type
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "description", 4, 8, 0f, null)));// different
+ // description
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 3, 8, 0f, null))); // different
+ // start
+ // position
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 9, 0f, null))); // different
+ // end
+ // position
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 1f, null))); // different
+ // score
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, Float.NaN, null))); // score
+ // NaN
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 0f, "Metal"))); // different
+ // group
assertEquals(8, sq.getFeatures().getAllFeatures().size());
}
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
*/
DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
- Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
- 1, 1 }, 3, 1));
+ Mapping map = new Mapping(
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 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());
// primary - uniprot with congruent map
DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
- upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
- new int[] { 10, 22 }, 1, 1)));
+ upentry2.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 10, 22 }, new int[] { 10, 22 }, 1, 1)));
sq.addDBRef(upentry2);
// primary - uniprot with map of enclosing sequence
DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
- upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
- new int[] { 8, 24 }, 1, 1)));
+ upentry3.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 8, 24 }, new int[] { 8, 24 }, 1, 1)));
sq.addDBRef(upentry3);
// not primary - uniprot with map of sub-sequence (5')
DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
- upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
- new int[] { 10, 18 }, 1, 1)));
+ upentry4.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 10, 18 }, new int[] { 10, 18 }, 1, 1)));
sq.addDBRef(upentry4);
// not primary - uniprot with map that overlaps 3'
DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
- upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
- new int[] { 12, 22 }, 1, 1)));
+ upentry5.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 12, 22 }, new int[] { 12, 22 }, 1, 1)));
sq.addDBRef(upentry5);
// not primary - uniprot with map to different coordinates frame
DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
- upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
- new int[] { 112, 118 }, 1, 1)));
+ upentry6.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 12, 18 }, new int[] { 112, 118 }, 1, 1)));
sq.addDBRef(upentry6);
// not primary - dbref to 'non-core' database
// add corroborating PDB entry for primary DBref -
// needs to have a file as well as matching ID
// note PDB ID is not treated as case sensitive
- sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
- .toString()));
+ sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB,
+ new File("/blah").toString()));
// not valid DBRef - no file..
sq.addPDBId(new PDBEntry("1AAA", null, null, null));
@Test(groups = { "Functional" })
public void testGetPrimaryDBRefs_nucleotide()
{
- SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
+ SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10,
+ 34);
// primary - Ensembl
DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
// not primary - Ensembl 'transcript' mapping of sub-sequence
DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
- dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
- new int[] { 1, 11 }, 1, 1)));
+ dbr2.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 15, 25 }, new int[] { 1, 11 }, 1, 1)));
sq.addDBRef(dbr2);
// primary - EMBL with congruent map
DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
- dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
- new int[] { 10, 34 }, 1, 1)));
+ dbr3.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 10, 34 }, new int[] { 10, 34 }, 1, 1)));
sq.addDBRef(dbr3);
// not primary - to non-core database
seq.addPDBId(pdbe5);
assertEquals(4, seq.getAllPDBEntries().size());
assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+
+ // add with a fake pdbid
+ // (models don't have an embedded ID)
+ String realId = "RealIDQ";
+ PDBEntry pdbe6 = new PDBEntry(realId, null, Type.PDB, "real/localpath");
+ PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath", "C", Type.MMCIF,
+ "real/localpath");
+ pdbe7.setFakedPDBId(true);
+ seq.addPDBId(pdbe6);
+ assertEquals(5, seq.getAllPDBEntries().size());
+ seq.addPDBId(pdbe7);
+ assertEquals(5, seq.getAllPDBEntries().size());
+ assertFalse(pdbe6.fakedPDBId());
+ assertSame(pdbe6, seq.getAllPDBEntries().get(4));
+ assertEquals("C", pdbe6.getChainCode());
+ assertEquals(realId, pdbe6.getId());
}
@Test(
- groups = { "Functional" },
- expectedExceptions = { IllegalArgumentException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDatasetSequence_toSelf()
{
seq.setDatasetSequence(seq);
}
@Test(
- groups = { "Functional" },
- expectedExceptions = { IllegalArgumentException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDatasetSequence_cascading()
{
SequenceI seq2 = new Sequence("Seq2", "xyz");
SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
"desc", 13, 14, 2f, null);
sq.addSequenceFeature(sfContactFG);
+ // add single position feature at [I]
+ SequenceFeature sfI = new SequenceFeature("Disulfide Bond", "desc", 16,
+ 16, null);
+ sq.addSequenceFeature(sfI);
// no features in columns 1-2 (-A)
List<SequenceFeature> found = sq.findFeatures(1, 2);
// columns 10-11 (--) should find nothing
found = sq.findFeatures(10, 11);
assertEquals(0, found.size());
+
+ // columns 14-14 (I) should find variant feature
+ found = sq.findFeatures(14, 14);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sfI));
}
+ @Test(groups = { "Functional"} )
+ public void testGetRootDatasetSequence_datasetIsNull_returnNull()
+ {
+ Sequence dseq = new Sequence("test", "ABCDEF");
+ assertNull(dseq.getRootDatasetSequence());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetRootDatasetSequence_datasetImplicit_returnDataset()
+ {
+ Sequence seq = new Sequence("test", "--AB-CDEF");
+ SequenceI dseq = seq.createDatasetSequence();
+ assertEquals(seq.getRootDatasetSequence(), dseq);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetRootDatasetSequence_datasetExplicit_returnDataset()
+ {
+ Sequence seq = new Sequence("test", "--AB-CDEF");
+ Sequence dseq = new Sequence("test", "ABCDEF");
+ seq.setDatasetSequence(dseq);
+ assertEquals(seq.getRootDatasetSequence(), dseq);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetRootDatasetSequence_nestedDatasets_returnLastDataset()
+ {
+ Sequence seq = new Sequence("test", "--AB-CDEFE");
+ Sequence dseq = new Sequence("test", "ABCDEF");
+ seq.setDatasetSequence(dseq);
+ Sequence ddseq = new Sequence("test", "ABCDEF");
+ dseq.setDatasetSequence(ddseq);
+ assertEquals(seq.getDatasetSequence(), dseq);
+ assertEquals(seq.getRootDatasetSequence(), ddseq);
+ }
+
+
@Test(groups = { "Functional" })
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 (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);
- // find C given C
- assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
+ /*
+ * 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());
/*
* 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());
}
public void testFindPosition_withCursorAndEdits()
{
Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
-
+
// find F pos given A
assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
int token = (int) PA.getValue(sq, "changeCount"); // 0
// 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"));
+ 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);
+
+ assertTrue(bs.equals(expected));
+
+ }
+ public void testFindFeatures_largeEndPos()
+ {
/*
- * invalid inputs
+ * imitate a PDB sequence where end is larger than end position
*/
- assertNull(sq.findPositions(6, 5));
- assertNull(sq.findPositions(0, 5));
- assertNull(sq.findPositions(-1, 5));
+ SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
+ sq.createDatasetSequence();
+
+ assertTrue(sq.findFeatures(1, 9).isEmpty());
+ // should be no array bounds exception - JAL-2772
+ assertTrue(sq.findFeatures(1, 15).isEmpty());
+
+ // add feature on BCD
+ SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+ null);
+ sq.addSequenceFeature(sfBCD);
+
+ // no features in columns 1-2 (-A)
+ List<SequenceFeature> found = sq.findFeatures(1, 2);
+ assertTrue(found.isEmpty());
+
+ // columns 1-6 (-ABC--) includes BCD
+ found = sq.findFeatures(1, 6);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sfBCD));
+
+ // columns 10-11 (--) should find nothing
+ 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());
/*
- * all gapped ranges
+ * checkValidRange ensures end is at least the last residue position
*/
- assertNull(sq.findPositions(1, 1)); // 1-based columns
- assertNull(sq.findPositions(5, 5));
- assertNull(sq.findPositions(5, 6));
- assertNull(sq.findPositions(5, 7));
+ PA.setValue(sq, "end", 2);
+ sq.checkValidRange();
+ assertEquals(12, sq.getEnd());
/*
- * all ungapped ranges
+ * end may be beyond the last residue position
*/
- 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
+ PA.setValue(sq, "end", 22);
+ sq.checkValidRange();
+ assertEquals(22, sq.getEnd());
+ }
+ @Test(groups = { "Functional" })
+ public void testDeleteChars_withGaps()
+ {
/*
- * gap to ungapped range
+ * delete gaps only
*/
- assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
- assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
+ 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());
/*
- * ungapped to gapped range
+ * delete gaps and residues at start (no new dataset sequence)
*/
- assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
- assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
+ 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());
/*
- * ungapped to ungapped enclosing gaps
+ * delete gaps and residues at end (no new dataset sequence)
*/
- assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
- assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
+ 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());
/*
- * gapped to gapped enclosing ungapped
+ * delete gaps and residues internally (new dataset sequence)
+ * first delete from gap to residue
*/
- 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));
+ 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<int[]> 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()));
+
+ }
+
+ @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());
+
}
}