/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.PDBEntry.Type;
import java.util.Arrays;
import java.util.List;
import java.util.Vector;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class SequenceTest
{
SequenceI seq;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
seq = new Sequence("FER1", "AKPNGVL");
}
@Test(groups = { "Functional" })
public void testInsertGapsAndGapmaps()
{
SequenceI aseq = seq.deriveSequence();
aseq.insertCharAt(2, 3, '-');
aseq.insertCharAt(6, 3, '-');
assertEquals("Gap insertions not correct", "AK---P---NGVL",
aseq.getSequenceAsString());
List gapInt = aseq.getInsertions();
assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
}
@Test(groups = { "Functional" })
public void testGetAnnotation()
{
// initial state returns null not an empty array
assertNull(seq.getAnnotation());
AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
1f);
AlignmentAnnotation[] anns = seq.getAnnotation();
assertEquals(1, anns.length);
assertSame(ann, anns[0]);
// removing all annotations reverts array to null
seq.removeAlignmentAnnotation(ann);
assertNull(seq.getAnnotation());
}
@Test(groups = { "Functional" })
public void testGetAnnotation_forLabel()
{
AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
1f);
AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
1f);
AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
1f);
AlignmentAnnotation[] anns = seq.getAnnotation("label1");
assertEquals(2, anns.length);
assertSame(ann1, anns[0]);
assertSame(ann3, anns[1]);
}
private AlignmentAnnotation addAnnotation(String label,
String description, String calcId, float value)
{
final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
description, value);
annotation.setCalcId(calcId);
seq.addAlignmentAnnotation(annotation);
return annotation;
}
@Test(groups = { "Functional" })
public void testGetAlignmentAnnotations_forCalcIdAndLabel()
{
AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
1f);
AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
1f);
AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
1f);
AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
1f);
AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
List anns = seq.getAlignmentAnnotations("calcId2",
"label2");
assertEquals(2, anns.size());
assertSame(ann2, anns.get(0));
assertSame(ann4, anns.get(1));
assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
assertTrue(seq.getAlignmentAnnotations(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
* should be ignored.
*/
@Test(groups = { "Functional" })
public void testAddAlignmentAnnotation()
{
assertNull(seq.getAnnotation());
final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
"b", 2d);
assertNull(annotation.sequenceRef);
seq.addAlignmentAnnotation(annotation);
assertSame(seq, annotation.sequenceRef);
AlignmentAnnotation[] anns = seq.getAnnotation();
assertEquals(1, anns.length);
assertSame(annotation, anns[0]);
// re-adding does nothing
seq.addAlignmentAnnotation(annotation);
anns = seq.getAnnotation();
assertEquals(1, anns.length);
assertSame(annotation, anns[0]);
// an identical but different annotation can be added
final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
"b", 2d);
seq.addAlignmentAnnotation(annotation2);
anns = seq.getAnnotation();
assertEquals(2, anns.length);
assertSame(annotation, anns[0]);
assertSame(annotation2, anns[1]);
}
@Test(groups = { "Functional" })
public void testGetStartGetEnd()
{
SequenceI sq = new Sequence("test", "ABCDEF");
assertEquals(1, sq.getStart());
assertEquals(6, sq.getEnd());
sq = new Sequence("test", "--AB-C-DEF--");
assertEquals(1, sq.getStart());
assertEquals(6, sq.getEnd());
sq = new Sequence("test", "----");
assertEquals(1, sq.getStart());
assertEquals(0, sq.getEnd()); // ??
}
/**
* Tests for the method that returns an alignment column position (base 1) for
* a given sequence position (base 1).
*/
@Test(groups = { "Functional" })
public void testFindIndex()
{
SequenceI sq = new Sequence("test", "ABCDEF");
assertEquals(0, sq.findIndex(0));
assertEquals(1, sq.findIndex(1));
assertEquals(5, sq.findIndex(5));
assertEquals(6, sq.findIndex(6));
assertEquals(6, sq.findIndex(9));
sq = new Sequence("test", "-A--B-C-D-E-F--");
assertEquals(2, sq.findIndex(1));
assertEquals(5, sq.findIndex(2));
assertEquals(7, sq.findIndex(3));
// before start returns 0
assertEquals(0, sq.findIndex(0));
assertEquals(0, sq.findIndex(-1));
// beyond end returns last residue column
assertEquals(13, sq.findIndex(99));
}
/**
* Tests for the method that returns a dataset sequence position (base 1) for
* an aligned column position (base 0).
*/
@Test(groups = { "Functional" })
public void testFindPosition()
{
SequenceI sq = new Sequence("test", "ABCDEF");
assertEquals(1, sq.findPosition(0));
assertEquals(6, sq.findPosition(5));
// assertEquals(-1, seq.findPosition(6)); // fails
sq = new Sequence("test", "AB-C-D--");
assertEquals(1, sq.findPosition(0));
assertEquals(2, sq.findPosition(1));
// gap position 'finds' residue to the right (not the left as per javadoc)
assertEquals(3, sq.findPosition(2));
assertEquals(3, sq.findPosition(3));
assertEquals(4, sq.findPosition(4));
assertEquals(4, sq.findPosition(5));
// returns 1 more than sequence length if off the end ?!?
assertEquals(5, sq.findPosition(6));
assertEquals(5, sq.findPosition(7));
sq = new Sequence("test", "--AB-C-DEF--");
assertEquals(1, sq.findPosition(0));
assertEquals(1, sq.findPosition(1));
assertEquals(1, sq.findPosition(2));
assertEquals(2, sq.findPosition(3));
assertEquals(3, sq.findPosition(4));
assertEquals(3, sq.findPosition(5));
assertEquals(4, sq.findPosition(6));
assertEquals(4, sq.findPosition(7));
assertEquals(5, sq.findPosition(8));
assertEquals(6, sq.findPosition(9));
assertEquals(7, sq.findPosition(10));
assertEquals(7, sq.findPosition(11));
}
@Test(groups = { "Functional" })
public void testDeleteChars()
{
SequenceI sq = new Sequence("test", "ABCDEF");
assertEquals(1, sq.getStart());
assertEquals(6, sq.getEnd());
sq.deleteChars(2, 3);
assertEquals("ABDEF", sq.getSequenceAsString());
assertEquals(1, sq.getStart());
assertEquals(5, sq.getEnd());
sq = new Sequence("test", "ABCDEF");
sq.deleteChars(0, 2);
assertEquals("CDEF", sq.getSequenceAsString());
assertEquals(3, sq.getStart());
assertEquals(6, sq.getEnd());
}
@Test(groups = { "Functional" })
public void testInsertCharAt()
{
// non-static methods:
SequenceI sq = new Sequence("test", "ABCDEF");
sq.insertCharAt(0, 'z');
assertEquals("zABCDEF", sq.getSequenceAsString());
sq.insertCharAt(2, 2, 'x');
assertEquals("zAxxBCDEF", sq.getSequenceAsString());
// for static method see StringUtilsTest
}
/**
* Test the method that returns an array of aligned sequence positions where
* the array index is the data sequence position (both base 0).
*/
@Test(groups = { "Functional" })
public void testGapMap()
{
SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
sq.createDatasetSequence();
assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
}
/**
* Test the method that gets sequence features, either from the sequence or
* its dataset.
*/
@Test(groups = { "Functional" })
public void testGetSequenceFeatures()
{
SequenceI sq = new Sequence("test", "GATCAT");
sq.createDatasetSequence();
assertNull(sq.getSequenceFeatures());
/*
* SequenceFeature on sequence
*/
SequenceFeature sf = new SequenceFeature();
sq.addSequenceFeature(sf);
SequenceFeature[] sfs = sq.getSequenceFeatures();
assertEquals(1, sfs.length);
assertSame(sf, sfs[0]);
/*
* SequenceFeature on sequence and dataset sequence; returns that on
* sequence
*/
SequenceFeature sf2 = new SequenceFeature();
sq.getDatasetSequence().addSequenceFeature(sf2);
sfs = sq.getSequenceFeatures();
assertEquals(1, sfs.length);
assertSame(sf, sfs[0]);
/*
* SequenceFeature on dataset sequence only
*/
sq.setSequenceFeatures(null);
sfs = sq.getSequenceFeatures();
assertEquals(1, sfs.length);
assertSame(sf2, sfs[0]);
/*
* Corrupt case - no SequenceFeature, dataset's dataset is the original
* sequence. Test shows no infinite loop results.
*/
sq.getDatasetSequence().setSequenceFeatures(null);
sq.getDatasetSequence().setDatasetSequence(sq); // loop!
assertNull(sq.getSequenceFeatures());
}
/**
* Test the method that returns an array, indexed by sequence position, whose
* entries are the residue positions at the sequence position (or to the right
* if a gap)
*/
@Test(groups = { "Functional" })
public void testFindPositionMap()
{
/*
* Note: Javadoc for findPosition says it returns the residue position to
* the left of a gapped position; in fact it returns the position to the
* right. Also it returns a non-existent residue position for a gap beyond
* the sequence.
*/
Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
int[] map = sq.findPositionMap();
assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
Arrays.toString(map));
}
/**
* Test for getSubsequence
*/
@Test(groups = { "Functional" })
public void testGetSubsequence()
{
SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
sq.createDatasetSequence();
// positions are base 0, end position is exclusive
SequenceI subseq = sq.getSubSequence(2, 4);
assertEquals("CD", subseq.getSequenceAsString());
// start/end are base 1 positions
assertEquals(3, subseq.getStart());
assertEquals(4, subseq.getEnd());
// subsequence shares the full dataset sequence
assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
}
/**
* Test for deriveSequence applied to a sequence with a dataset
*/
@Test(groups = { "Functional" })
public void testDeriveSequence_existingDataset()
{
SequenceI sq = new Sequence("Seq1", "CD");
sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
sq.getDatasetSequence().addSequenceFeature(
new SequenceFeature("", "", 1, 2, 0f, null));
sq.setStart(3);
sq.setEnd(4);
SequenceI derived = sq.deriveSequence();
assertEquals("CD", derived.getSequenceAsString());
assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
assertNull(((Sequence) seq).sequenceFeatures);
assertNull(((Sequence) derived).sequenceFeatures);
assertNotNull(seq.getSequenceFeatures());
assertSame(seq.getSequenceFeatures(), derived.getSequenceFeatures());
}
/**
* Test for deriveSequence applied to an ungapped sequence with no dataset
*/
@Test(groups = { "Functional" })
public void testDeriveSequence_noDatasetUngapped()
{
SequenceI sq = new Sequence("Seq1", "ABCDEF");
assertEquals(1, sq.getStart());
assertEquals(6, sq.getEnd());
SequenceI derived = sq.deriveSequence();
assertEquals("ABCDEF", derived.getSequenceAsString());
assertEquals("ABCDEF", derived.getDatasetSequence()
.getSequenceAsString());
}
/**
* Test for deriveSequence applied to a gapped sequence with no dataset
*/
@Test(groups = { "Functional" })
public void testDeriveSequence_noDatasetGapped()
{
SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
assertEquals(1, sq.getStart());
assertEquals(6, sq.getEnd());
assertNull(sq.getDatasetSequence());
SequenceI derived = sq.deriveSequence();
assertEquals("AB-C.D EF", derived.getSequenceAsString());
assertEquals("ABCDEF", derived.getDatasetSequence()
.getSequenceAsString());
}
@Test(groups = { "Functional" })
public void testCopyConstructor_noDataset()
{
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.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
SequenceI copy = new Sequence(seq1);
assertNull(copy.getDatasetSequence());
verifyCopiedSequence(seq1, copy);
// copy has a copy of the DBRefEntry
// this is murky - DBrefs are only copied for dataset sequences
// where the test for 'dataset sequence' is 'dataset is null'
// 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]));
}
@Test(groups = { "Functional" })
public void testCopyConstructor_withDataset()
{
SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
seq1.createDatasetSequence();
seq1.setDescription("description");
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"));
// here we add DBRef to the dataset sequence:
seq1.getDatasetSequence().addDBRef(
new DBRefEntry("EMBL", "1.2", "AZ12345"));
SequenceI copy = new Sequence(seq1);
assertNotNull(copy.getDatasetSequence());
assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
verifyCopiedSequence(seq1, copy);
// 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]);
}
/**
* Helper to make assertions about a copied sequence
*
* @param seq1
* @param copy
*/
protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
{
// verify basic properties:
assertEquals(copy.getName(), seq1.getName());
assertEquals(copy.getDescription(), seq1.getDescription());
assertEquals(copy.getStart(), seq1.getStart());
assertEquals(copy.getEnd(), seq1.getEnd());
assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
// copy has a copy of the annotation:
AlignmentAnnotation[] anns = copy.getAnnotation();
assertEquals(1, anns.length);
assertFalse(anns[0] == seq1.getAnnotation()[0]);
assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
// copy has a copy of the sequence feature:
SequenceFeature[] sfs = copy.getSequenceFeatures();
assertEquals(1, sfs.length);
assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
// copy has a copy of the PDB entry
Vector pdbs = copy.getAllPDBEntries();
assertEquals(1, pdbs.size());
assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
}
}