*/
package jalview.datamodel;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
assertTrue(sq.isProtein());
}
+ @Test(groups = ("Functional"))
+ public void testIsProteinWithXorNAmbiguityCodes()
+ {
+ // test Protein with N - poly asparagine
+ assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
+ assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
+ // test Protein with X
+ assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
+ // test DNA with X
+ assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+ // test DNA with N
+ assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
+ // test RNA with X
+ assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
+ assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
+ }
+
@Test(groups = { "Functional" })
public void testGetAnnotation()
{
assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
+ {
+ addAnnotation("label1", "desc1", "calcId1", 1f);
+ AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
+ 1f);
+ addAnnotation("label2", "desc3", "calcId3", 1f);
+ AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
+ 1f);
+ addAnnotation("label5", "desc3", null, 1f);
+ addAnnotation(null, "desc3", "calcId3", 1f);
+
+ List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
+ "label2", "desc3");
+ assertEquals(1, anns.size());
+ assertSame(ann4, anns.get(0));
+ /**
+ * null matching should fail
+ */
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
+
+ assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, 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
} catch (IllegalArgumentException e)
{
// TODO Jalview error/exception class for raising implementation errors
- assertTrue(e.getMessage().toLowerCase()
+ assertTrue(e.getMessage().toLowerCase(Locale.ROOT)
.contains("implementation error"));
}
assertTrue(sq.getSequenceFeatures().isEmpty());
seq.addPDBId(pdbe5);
assertEquals(4, seq.getAllPDBEntries().size());
assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+
+ // add with a fake pdbid
+ // (models don't have an embedded ID)
+ String realId = "RealIDQ";
+ PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
+ PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
+ pdbe7.setFakedPDBId(true);
+ seq.addPDBId(pdbe6);
+ assertEquals(5,seq.getAllPDBEntries().size());
+ seq.addPDBId(pdbe7);
+ assertEquals(5,seq.getAllPDBEntries().size());
+ assertFalse(pdbe6.fakedPDBId());
+ assertSame(pdbe6,seq.getAllPDBEntries().get(4));
+ assertEquals("C",pdbe6.getChainCode());
+ assertEquals(realId, pdbe6.getId());
}
@Test(