+ sq.setDescription("Test sequence description..");
+ sq.setVamsasId("TestVamsasId");
+ sq.setSourceDBRef(new DBRefEntry("PDB", "version0", "1TST"));
+
+ sq.addDBRef(new DBRefEntry("PDB", "version1", "1Tst"));
+ sq.addDBRef(new DBRefEntry("PDB", "version2", "2Tst"));
+ sq.addDBRef(new DBRefEntry("PDB", "version3", "3Tst"));
+ sq.addDBRef(new DBRefEntry("PDB", "version4", "4Tst"));
+
+ 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"));
+
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version1", "1Tst"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version2", "2Tst"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version3", "3Tst"));
+ sq.getDatasetSequence().addDBRef(
+ new DBRefEntry("PDB", "version4", "4Tst"));
+
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
+ sq.getDatasetSequence().addPDBId(
+ new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+
+ 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, 4);
+ 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());
+