import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.io.File;
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;
public class SequenceTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Sequence seq;
@BeforeMethod(alwaysRun = true)
public void testIsProtein()
{
// test Protein
- assertTrue(new Sequence("prot","ASDFASDFASDF").isProtein());
+ assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
// test DNA
- assertFalse(new Sequence("prot","ACGTACGTACGT").isProtein());
+ assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
// test RNA
- SequenceI sq = new Sequence("prot","ACGUACGUACGU");
+ SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
assertFalse(sq.isProtein());
// change sequence, should trigger an update of cached result
sq.setSequence("ASDFASDFADSF");
/*
* SequenceFeature on sequence
*/
- SequenceFeature sf = new SequenceFeature();
+ SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
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
* is there a usecase for this ? setDatasetSequence should throw an error if
* this actually occurs.
*/
- sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+ try
+ {
+ sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+ 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()
+ .contains("implementation error"));
+ }
assertNull(sq.getSequenceFeatures());
}
@Test(groups = { "Functional" })
public void testCreateDatasetSequence()
{
- SequenceI sq = new Sequence("my","ASDASD");
+ SequenceI sq = new Sequence("my", "ASDASD");
+ sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
+ "group"));
+ sq.addDBRef(new DBRefEntry("source", "version", "accession"));
assertNull(sq.getDatasetSequence());
+ assertNotNull(PA.getValue(sq, "sequenceFeatures")); // to be removed!
+ assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
+ assertNotNull(PA.getValue(sq, "dbrefs"));
+
SequenceI rds = sq.createDatasetSequence();
assertNotNull(rds);
assertNull(rds.getDatasetSequence());
- assertEquals(sq.getDatasetSequence(), rds);
+ assertSame(sq.getDatasetSequence(), rds);
+
+ // sequence features and dbrefs transferred to dataset sequence
+ assertNull(PA.getValue(sq, "sequenceFeatures"));
+ assertNull(PA.getValue(sq, "sequenceFeatureStore"));
+ assertNull(PA.getValue(sq, "dbrefs"));
+ assertNotNull(PA.getValue(rds, "sequenceFeatures"));
+ assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
+ assertNotNull(PA.getValue(rds, "dbrefs"));
}
/**
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"));
-
+
+ // these are the same as ones already added
DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
- DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
+ DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
-
List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
pdb2pdb });
- sq.getDatasetSequence().addDBRef(pdb1pdb);
- sq.getDatasetSequence().addDBRef(pdb2pdb);
+ sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
+ sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version3", "3PDB"));
+ new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version4", "4PDB"));
-
- PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
+ 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");
- 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);
+ 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);
new AlignmentAnnotation("Test annot", "Test annot description",
annots));
Assert.assertEquals(sq.getDescription(), "Test sequence description..");
- Assert.assertEquals(sq.getDBRefs().length, 5);
+ Assert.assertEquals(sq.getDBRefs().length, 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, 4);
+ Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
+ // as
+ // sq.getDBRefs()
Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
4);
Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
Assert.assertEquals(derived.getDescription(),
"Test sequence description..");
- Assert.assertEquals(derived.getDBRefs().length, 4); // come from dataset
+ Assert.assertEquals(derived.getDBRefs().length, 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, 4);
+ Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
.size(), 4);
Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
assertNotNull(sq.getSequenceFeatures());
assertArrayEquals(sq.getSequenceFeatures(),
derived.getSequenceFeatures());
-
+
/*
* verify we have primary db refs *just* for PDB IDs with associated
* PDBEntry objects
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());
// copy has a copy of the sequence feature:
SequenceFeature[] sfs = copy.getSequenceFeatures();
assertEquals(1, sfs.length);
- if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
+ if (seq1.getDatasetSequence() != null
+ && copy.getDatasetSequence() == seq1.getDatasetSequence())
+ {
assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
- } else {
+ }
+ else
+ {
assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
}
assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
assertEquals(' ', sq.getCharAt(-1));
}
+ @Test(groups = { "Functional" })
+ public void testAddSequenceFeatures()
+ {
+ 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)));
+ // can't add a duplicate feature
+ 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
+ assertEquals(8, sq.getFeatures().getAllFeatures().size());
+ }
+
/**
* Tests for adding (or updating) dbrefs
*
public void testGetPrimaryDBRefs_nucleotide()
{
SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
-
+
// primary - Ensembl
DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
sq.addDBRef(dbr1);
-
+
// 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 },
// not primary - to protein
DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
sq.addDBRef(dbr5);
-
+
List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
assertEquals(2, primaryDBRefs.size());
assertTrue(primaryDBRefs.contains(dbr1));
seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
// 7 is not a valid chain code:
seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
-
+
seq.updatePDBIds();
List<PDBEntry> pdbIds = seq.getAllPDBEntries();
assertEquals(4, pdbIds.size());
assertEquals(4, seq.getAllPDBEntries().size());
assertSame(pdbe5, seq.getAllPDBEntries().get(3));
}
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testSetDatasetSequence_toSelf()
+ {
+ seq.setDatasetSequence(seq);
+ }
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testSetDatasetSequence_cascading()
+ {
+ SequenceI seq2 = new Sequence("Seq2", "xyz");
+ seq2.createDatasetSequence();
+ seq.setDatasetSequence(seq2);
+ }
}
git://source.jalview.org / jalview.git / blobdiff