+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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 static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.util.MapList;
+
+import java.io.File;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Vector;
+import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class SequenceTest
{
- SequenceI seq;
+ Sequence seq;
@BeforeMethod(alwaysRun = true)
public void setUp()
assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
}
+ @Test(groups = ("Functional"))
+ public void testIsProtein()
+ {
+ // test Protein
+ assertTrue(new Sequence("prot","ASDFASDFASDF").isProtein());
+ // test DNA
+ assertFalse(new Sequence("prot","ACGTACGTACGT").isProtein());
+ // test RNA
+ SequenceI sq = new Sequence("prot","ACGUACGUACGU");
+ assertFalse(sq.isProtein());
+ // change sequence, should trigger an update of cached result
+ sq.setSequence("ASDFASDFADSF");
+ assertTrue(sq.isProtein());
+ /*
+ * in situ change of sequence doesn't change hashcode :-O
+ * (sequence should not expose internal implementation)
+ */
+ for (int i = 0; i < sq.getSequence().length; i++)
+ {
+ sq.getSequence()[i] = "acgtu".charAt(i % 5);
+ }
+ assertTrue(sq.isProtein()); // but it isn't
+ }
+
@Test(groups = { "Functional" })
public void testGetAnnotation()
{
{
AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
1f);
- AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
- 1f);
+ addAnnotation("label2", "desc2", "calcId2", 1f);
AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
1f);
AlignmentAnnotation[] anns = seq.getAnnotation("label1");
@Test(groups = { "Functional" })
public void testGetAlignmentAnnotations_forCalcIdAndLabel()
{
- AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
- 1f);
+ addAnnotation("label1", "desc1", "calcId1", 1f);
AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
1f);
- AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
- 1f);
+ 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);
+ addAnnotation("label5", "desc3", null, 1f);
+ addAnnotation(null, "desc3", "calcId3", 1f);
+
List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
"label2");
assertEquals(2, anns.size());
assertEquals(2, anns.length);
assertSame(annotation, anns[0]);
assertSame(annotation2, anns[1]);
-
}
@Test(groups = { "Functional" })
public void testGetStartGetEnd()
{
- SequenceI seq = new Sequence("test", "ABCDEF");
- assertEquals(1, seq.getStart());
- assertEquals(6, seq.getEnd());
+ SequenceI sq = new Sequence("test", "ABCDEF");
+ assertEquals(1, sq.getStart());
+ assertEquals(6, sq.getEnd());
- seq = new Sequence("test", "--AB-C-DEF--");
- assertEquals(1, seq.getStart());
- assertEquals(6, seq.getEnd());
+ sq = new Sequence("test", "--AB-C-DEF--");
+ assertEquals(1, sq.getStart());
+ assertEquals(6, sq.getEnd());
- seq = new Sequence("test", "----");
- assertEquals(1, seq.getStart());
- assertEquals(0, seq.getEnd()); // ??
+ sq = new Sequence("test", "----");
+ assertEquals(1, sq.getStart());
+ assertEquals(0, sq.getEnd()); // ??
}
/**
@Test(groups = { "Functional" })
public void testFindIndex()
{
- SequenceI seq = new Sequence("test", "ABCDEF");
- assertEquals(0, seq.findIndex(0));
- assertEquals(1, seq.findIndex(1));
- assertEquals(5, seq.findIndex(5));
- assertEquals(6, seq.findIndex(6));
- assertEquals(6, seq.findIndex(9));
-
- seq = new Sequence("test", "-A--B-C-D-E-F--");
- assertEquals(2, seq.findIndex(1));
- assertEquals(5, seq.findIndex(2));
- assertEquals(7, seq.findIndex(3));
+ 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, seq.findIndex(0));
- assertEquals(0, seq.findIndex(-1));
+ assertEquals(0, sq.findIndex(0));
+ assertEquals(0, sq.findIndex(-1));
// beyond end returns last residue column
- assertEquals(13, seq.findIndex(99));
+ assertEquals(13, sq.findIndex(99));
}
@Test(groups = { "Functional" })
public void testFindPosition()
{
- SequenceI seq = new Sequence("test", "ABCDEF");
- assertEquals(1, seq.findPosition(0));
- assertEquals(6, seq.findPosition(5));
+ SequenceI sq = new Sequence("test", "ABCDEF");
+ assertEquals(1, sq.findPosition(0));
+ assertEquals(6, sq.findPosition(5));
// assertEquals(-1, seq.findPosition(6)); // fails
- seq = new Sequence("test", "AB-C-D--");
- assertEquals(1, seq.findPosition(0));
- assertEquals(2, seq.findPosition(1));
+ 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, seq.findPosition(2));
- assertEquals(3, seq.findPosition(3));
- assertEquals(4, seq.findPosition(4));
- assertEquals(4, seq.findPosition(5));
+ 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, seq.findPosition(6));
- assertEquals(5, seq.findPosition(7));
-
- seq = new Sequence("test", "--AB-C-DEF--");
- assertEquals(1, seq.findPosition(0));
- assertEquals(1, seq.findPosition(1));
- assertEquals(1, seq.findPosition(2));
- assertEquals(2, seq.findPosition(3));
- assertEquals(3, seq.findPosition(4));
- assertEquals(3, seq.findPosition(5));
- assertEquals(4, seq.findPosition(6));
- assertEquals(4, seq.findPosition(7));
- assertEquals(5, seq.findPosition(8));
- assertEquals(6, seq.findPosition(9));
- assertEquals(7, seq.findPosition(10));
- assertEquals(7, seq.findPosition(11));
+ 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 seq = new Sequence("test", "ABCDEF");
- assertEquals(1, seq.getStart());
- assertEquals(6, seq.getEnd());
- seq.deleteChars(2, 3);
- assertEquals("ABDEF", seq.getSequenceAsString());
- assertEquals(1, seq.getStart());
- assertEquals(5, seq.getEnd());
-
- seq = new Sequence("test", "ABCDEF");
- seq.deleteChars(0, 2);
- assertEquals("CDEF", seq.getSequenceAsString());
- assertEquals(3, seq.getStart());
- assertEquals(6, seq.getEnd());
+ 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 seq = new Sequence("test", "ABCDEF");
- seq.insertCharAt(0, 'z');
- assertEquals("zABCDEF", seq.getSequenceAsString());
- seq.insertCharAt(2, 2, 'x');
- assertEquals("zAxxBCDEF", seq.getSequenceAsString());
+ 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(groups = { "Functional" })
public void testGapMap()
{
- SequenceI seq = new Sequence("test", "-A--B-CD-E--F-");
- seq.createDatasetSequence();
- assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(seq.gapMap()));
+ SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
+ sq.createDatasetSequence();
+ assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
}
/**
@Test(groups = { "Functional" })
public void testGetSequenceFeatures()
{
- SequenceI seq = new Sequence("test", "GATCAT");
- seq.createDatasetSequence();
+ SequenceI sq = new Sequence("test", "GATCAT");
+ sq.createDatasetSequence();
- assertNull(seq.getSequenceFeatures());
+ assertNull(sq.getSequenceFeatures());
/*
* SequenceFeature on sequence
*/
SequenceFeature sf = new SequenceFeature();
- seq.addSequenceFeature(sf);
- SequenceFeature[] sfs = seq.getSequenceFeatures();
+ 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
+ *
+ * Note JAL-2046: spurious: we have no use case for this at the moment.
+ * This test also buggy - as sf2.equals(sf), no new feature is added
*/
SequenceFeature sf2 = new SequenceFeature();
- seq.getDatasetSequence().addSequenceFeature(sf2);
- sfs = seq.getSequenceFeatures();
+ sq.getDatasetSequence().addSequenceFeature(sf2);
+ sfs = sq.getSequenceFeatures();
assertEquals(1, sfs.length);
assertSame(sf, sfs[0]);
/*
* SequenceFeature on dataset sequence only
+ * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
*/
- seq.setSequenceFeatures(null);
- sfs = seq.getSequenceFeatures();
- assertEquals(1, sfs.length);
- assertSame(sf2, sfs[0]);
+ sq.setSequenceFeatures(null);
+ assertNull(sq.getDatasetSequence().getSequenceFeatures());
/*
* Corrupt case - no SequenceFeature, dataset's dataset is the original
* sequence. Test shows no infinite loop results.
*/
- seq.getDatasetSequence().setSequenceFeatures(null);
- seq.getDatasetSequence().setDatasetSequence(seq); // loop!
- assertNull(seq.getSequenceFeatures());
+ sq.getDatasetSequence().setSequenceFeatures(null);
+ /**
+ * is there a usecase for this ? setDatasetSequence should throw an error if
+ * this actually occurs.
+ */
+ sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+ assertNull(sq.getSequenceFeatures());
}
/**
* right. Also it returns a non-existent residue position for a gap beyond
* the sequence.
*/
- Sequence seq = new Sequence("TestSeq", "AB.C-D E.");
- int[] map = seq.findPositionMap();
+ 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(groups = { "Functional" })
public void testGetSubsequence()
{
- SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
- seq.createDatasetSequence();
+ SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
+ sq.createDatasetSequence();
// positions are base 0, end position is exclusive
- SequenceI subseq = seq.getSubSequence(2, 4);
+ 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(seq.getDatasetSequence(), subseq.getDatasetSequence());
+ assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
+ }
+
+ /**
+ * test createDatasetSequence behaves to doc
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateDatasetSequence()
+ {
+ SequenceI sq = new Sequence("my","ASDASD");
+ assertNull(sq.getDatasetSequence());
+ SequenceI rds = sq.createDatasetSequence();
+ assertNotNull(rds);
+ assertNull(rds.getDatasetSequence());
+ assertEquals(sq.getDatasetSequence(), rds);
}
/**
@Test(groups = { "Functional" })
public void testDeriveSequence_existingDataset()
{
- SequenceI seq = new Sequence("Seq1", "CD");
- seq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
- seq.setStart(3);
- seq.setEnd(4);
- SequenceI derived = seq.deriveSequence();
+ Sequence 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);
+
+ sq.setDescription("Test sequence description..");
+ sq.setVamsasId("TestVamsasId");
+ sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
+
+ sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
+ sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
+ sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
+ sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
+
+ sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
+ sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+ sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+ sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+
+ DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
+ DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
+
+
+ List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
+ pdb2pdb });
+
+ sq.getDatasetSequence().addDBRef(pdb1pdb);
+ sq.getDatasetSequence().addDBRef(pdb2pdb);
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version3", "3PDB"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version4", "4PDB"));
+
+ PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
+ PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
+ PDBEntry pdbe2a=new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2");
+ PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2");
+ sq.getDatasetSequence().addPDBId(
+ pdbe1a);
+ sq.getDatasetSequence().addPDBId(
+ pdbe1b);
+ sq.getDatasetSequence().addPDBId(pdbe2a);
+ sq.getDatasetSequence().addPDBId(pdbe2b);
+
+ /*
+ * test we added pdb entries to the dataset sequence
+ */
+ 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"),
+ "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
+ ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+ 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));
+ Assert.assertEquals(sq.getDescription(), "Test sequence description..");
+ Assert.assertEquals(sq.getDBRefs().length, 5);
+ Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
+ Assert.assertNotNull(sq.getAnnotation());
+ Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
+ Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 4);
+ Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
+ 4);
+ Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
+
+ Sequence derived = (Sequence) sq.deriveSequence();
+
+ Assert.assertEquals(derived.getDescription(),
+ "Test sequence description..");
+ Assert.assertEquals(derived.getDBRefs().length, 4); // 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, 4);
+ Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
+ .size(), 4);
+ Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
+
assertEquals("CD", derived.getSequenceAsString());
- assertSame(seq.getDatasetSequence(), derived.getDatasetSequence());
+ assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
+
+ assertNull(sq.sequenceFeatures);
+ assertNull(derived.sequenceFeatures);
+ // derived sequence should access dataset sequence features
+ assertNotNull(sq.getSequenceFeatures());
+ assertArrayEquals(sq.getSequenceFeatures(),
+ derived.getSequenceFeatures());
+
+ /*
+ * verify we have primary db refs *just* for PDB IDs with associated
+ * PDBEntry objects
+ */
+
+ assertEquals(primRefs, sq.getPrimaryDBRefs());
+ assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
+
+ assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
+
}
/**
@Test(groups = { "Functional" })
public void testDeriveSequence_noDatasetUngapped()
{
- SequenceI seq = new Sequence("Seq1", "ABCDEF");
- assertEquals(1, seq.getStart());
- assertEquals(6, seq.getEnd());
- SequenceI derived = seq.deriveSequence();
+ 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(groups = { "Functional" })
public void testDeriveSequence_noDatasetGapped()
{
- SequenceI seq = new Sequence("Seq1", "AB-C.D EF");
- assertEquals(1, seq.getStart());
- assertEquals(6, seq.getEnd());
- assertNull(seq.getDatasetSequence());
- SequenceI derived = seq.deriveSequence();
+ 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));
+ // 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.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);
+ if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
+ assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
+ } else {
+ assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
+ }
+ assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
+
+ // copy has a copy of the PDB entry
+ Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
+ assertEquals(1, pdbs.size());
+ assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
+ assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetCharAt()
+ {
+ SequenceI sq = new Sequence("", "abcde");
+ assertEquals('a', sq.getCharAt(0));
+ assertEquals('e', sq.getCharAt(4));
+ assertEquals(' ', sq.getCharAt(5));
+ assertEquals(' ', sq.getCharAt(-1));
+ }
+
+ /**
+ * Tests for adding (or updating) dbrefs
+ *
+ * @see DBRefEntry#updateFrom(DBRefEntry)
+ */
+ @Test(groups = { "Functional" })
+ public void testAddDBRef()
+ {
+ SequenceI sq = new Sequence("", "abcde");
+ assertNull(sq.getDBRefs());
+ DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
+ sq.addDBRef(dbref);
+ assertEquals(1, sq.getDBRefs().length);
+ assertSame(dbref, sq.getDBRefs()[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]);
+
+ /*
+ * matches existing entry - not added
+ */
+ sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
+ assertEquals(2, sq.getDBRefs().length);
+
+ /*
+ * different source = new entry
+ */
+ DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
+ sq.addDBRef(dbref3);
+ assertEquals(3, sq.getDBRefs().length);
+ assertSame(dbref3, sq.getDBRefs()[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]);
+
+ /*
+ * 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));
+ dbref5.setMap(map);
+ sq.addDBRef(dbref5);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref4, sq.getDBRefs()[3]);
+ assertSame(map, dbref4.getMap());
+
+ /*
+ * 'real' version replaces "0" version
+ */
+ dbref2.setVersion("0");
+ DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
+ dbref2.getAccessionId());
+ sq.addDBRef(dbref6);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref2, sq.getDBRefs()[1]);
+ assertEquals("3", dbref2.getVersion());
+
+ /*
+ * 'real' version replaces "source:0" version
+ */
+ dbref3.setVersion("Uniprot:0");
+ DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
+ dbref3.getAccessionId());
+ sq.addDBRef(dbref7);
+ assertEquals(4, sq.getDBRefs().length);
+ assertSame(dbref3, sq.getDBRefs()[2]);
+ assertEquals("3", dbref2.getVersion());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetPrimaryDBRefs()
+ {
+ /*
+ * test PDB relationships for for getPrimaryDBRefs
+ */
+ SequenceI seq = new Sequence("aseq", "ASDF");
+ DBRefEntry upentry = new DBRefEntry("UNIPROT", "0", "1qip");
+ // primary - uniprot
+ seq.addDBRef(upentry);
+ // primary - type is PDB
+ DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
+ seq.addDBRef(pdbentry);
+ // not primary - PDBEntry has no file
+ seq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
+ // not primary - no PDBEntry
+ seq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
+ // add corroborating PDB entry for primary DBref - needs to have a file as
+ // well as matching ID
+ seq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
+ .toString()));
+ // not valid DBRef - no file..
+ seq.addPDBId(new PDBEntry("1AAA", null, null, null));
+ assertTrue("Couldn't find simple primary reference (UNIPROT)", seq
+ .getPrimaryDBRefs().contains(upentry));
+ assertTrue("Couldn't find expected PDB primary reference", seq
+ .getPrimaryDBRefs().contains(pdbentry));
+ assertEquals(2, seq.getPrimaryDBRefs().size());
+ }
}
git://source.jalview.org / jalview.git / blobdiff