import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
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.gui.JvOptionPane;
import jalview.util.MapList;
import java.io.File;
import java.util.List;
import java.util.Vector;
+import junit.extensions.PA;
+
+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");
@Test(groups = { "Functional" })
public void testDeleteChars()
{
+ /*
+ * internal delete
+ */
SequenceI sq = new Sequence("test", "ABCDEF");
+ assertNull(PA.getValue(sq, "datasetSequence"));
assertEquals(1, sq.getStart());
assertEquals(6, sq.getEnd());
sq.deleteChars(2, 3);
assertEquals("ABDEF", sq.getSequenceAsString());
assertEquals(1, sq.getStart());
assertEquals(5, sq.getEnd());
+ assertNull(PA.getValue(sq, "datasetSequence"));
+
+ /*
+ * delete at start
+ */
+ sq = new Sequence("test", "ABCDEF");
+ sq.deleteChars(0, 2);
+ assertEquals("CDEF", sq.getSequenceAsString());
+ assertEquals(3, sq.getStart());
+ assertEquals(6, sq.getEnd());
+ assertNull(PA.getValue(sq, "datasetSequence"));
+
+ /*
+ * delete at end
+ */
+ sq = new Sequence("test", "ABCDEF");
+ sq.deleteChars(4, 6);
+ assertEquals("ABCD", sq.getSequenceAsString());
+ assertEquals(1, sq.getStart());
+ assertEquals(4, sq.getEnd());
+ assertNull(PA.getValue(sq, "datasetSequence"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testDeleteChars_withDbRefsAndFeatures()
+ {
+ /*
+ * internal delete - new dataset sequence created
+ * gets a copy of any dbrefs
+ */
+ SequenceI sq = new Sequence("test", "ABCDEF");
+ sq.createDatasetSequence();
+ DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
+ sq.addDBRef(dbr1);
+ Object ds = PA.getValue(sq, "datasetSequence");
+ assertNotNull(ds);
+ assertEquals(1, sq.getStart());
+ assertEquals(6, sq.getEnd());
+ sq.deleteChars(2, 3);
+ assertEquals("ABDEF", sq.getSequenceAsString());
+ assertEquals(1, sq.getStart());
+ assertEquals(5, sq.getEnd());
+ Object newDs = PA.getValue(sq, "datasetSequence");
+ assertNotNull(newDs);
+ assertNotSame(ds, newDs);
+ assertNotNull(sq.getDBRefs());
+ assertEquals(1, sq.getDBRefs().length);
+ assertNotSame(dbr1, sq.getDBRefs()[0]);
+ assertEquals(dbr1, sq.getDBRefs()[0]);
+
+ /*
+ * internal delete with sequence features
+ * (failure case for JAL-2541)
+ */
+ sq = new Sequence("test", "ABCDEF");
+ sq.createDatasetSequence();
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+ "CathGroup");
+ sq.addSequenceFeature(sf1);
+ ds = PA.getValue(sq, "datasetSequence");
+ assertNotNull(ds);
+ assertEquals(1, sq.getStart());
+ assertEquals(6, sq.getEnd());
+ sq.deleteChars(2, 4);
+ assertEquals("ABEF", sq.getSequenceAsString());
+ assertEquals(1, sq.getStart());
+ assertEquals(4, sq.getEnd());
+ newDs = PA.getValue(sq, "datasetSequence");
+ assertNotNull(newDs);
+ assertNotSame(ds, newDs);
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ assertNotNull(sfs);
+ assertEquals(1, sfs.length);
+ assertNotSame(sf1, sfs[0]);
+ assertEquals(sf1, sfs[0]);
+ /*
+ * delete at start - no new dataset sequence created
+ * any sequence features remain as before
+ */
sq = new Sequence("test", "ABCDEF");
+ sq.createDatasetSequence();
+ ds = PA.getValue(sq, "datasetSequence");
+ sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
+ sq.addSequenceFeature(sf1);
sq.deleteChars(0, 2);
assertEquals("CDEF", sq.getSequenceAsString());
assertEquals(3, sq.getStart());
assertEquals(6, sq.getEnd());
+ assertSame(ds, PA.getValue(sq, "datasetSequence"));
+ sfs = sq.getSequenceFeatures();
+ assertNotNull(sfs);
+ assertEquals(1, sfs.length);
+ assertSame(sf1, sfs[0]);
+
+ /*
+ * delete at end - no new dataset sequence created
+ * any dbrefs remain as before
+ */
+ sq = new Sequence("test", "ABCDEF");
+ sq.createDatasetSequence();
+ ds = PA.getValue(sq, "datasetSequence");
+ dbr1 = new DBRefEntry("Uniprot", "0", "a123");
+ sq.addDBRef(dbr1);
+ sq.deleteChars(4, 6);
+ assertEquals("ABCD", sq.getSequenceAsString());
+ assertEquals(1, sq.getStart());
+ assertEquals(4, sq.getEnd());
+ assertSame(ds, PA.getValue(sq, "datasetSequence"));
+ assertNotNull(sq.getDBRefs());
+ assertEquals(1, sq.getDBRefs().length);
+ assertSame(dbr1, sq.getDBRefs()[0]);
}
@Test(groups = { "Functional" })
/*
* 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
@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", "version2", "2PDB");
-
List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
pdb2pdb });
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 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);
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());
git://source.jalview.org / jalview.git / blobdiff