+
+ /**
+ * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
+ */
+ @Test(groups = { "Functional" })
+ public void testGetStrand()
+ {
+ SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
+ assertEquals(0, sf.getStrand());
+ sf.setValue("STRAND", "+");
+ assertEquals(1, sf.getStrand());
+ sf.setValue("STRAND", "-");
+ assertEquals(-1, sf.getStrand());
+ sf.setValue("STRAND", ".");
+ assertEquals(0, sf.getStrand());
+ }
+
+ /**
+ * Tests for equality, and that equal objects have the same hashCode
+ */
+ @Test(groups = { "Functional" })
+ public void testEqualsAndHashCode()
+ {
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
+ 12.5f, "group");
+ sf1.setValue("ID", "id");
+ sf1.setValue("Name", "name");
+ sf1.setValue("Parent", "parent");
+ sf1.setStrand("+");
+ sf1.setPhase("1");
+ SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
+ 12.5f, "group");
+ sf2.setValue("ID", "id");
+ sf2.setValue("Name", "name");
+ sf2.setValue("Parent", "parent");
+ sf2.setStrand("+");
+ sf2.setPhase("1");
+
+ assertFalse(sf1.equals(null));
+ assertTrue(sf1.equals(sf2));
+ assertTrue(sf2.equals(sf1));
+ assertEquals(sf1.hashCode(), sf2.hashCode());
+
+ // changing type breaks equals:
+ SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
+ 12.5f, "group");
+ SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
+ 12.5f, "group");
+ assertFalse(sf3.equals(sf4));
+
+ // changing description breaks equals:
+ String restores = sf2.getDescription();
+ sf2.setDescription("Desc");
+ assertFalse(sf1.equals(sf2));
+ sf2.setDescription(restores);
+
+ // changing score breaks equals:
+ float restoref = sf2.getScore();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), 10f);
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), restoref);
+
+ // NaN doesn't match a number
+ restoref = sf2.getScore();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), Float.NaN);
+ assertFalse(sf1.equals(sf2));
+
+ // NaN matches NaN
+ sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
+ sf1.getFeatureGroup(), Float.NaN);
+ assertTrue(sf1.equals(sf2));
+ sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
+ sf1.getFeatureGroup(), restoref);
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), restoref);
+
+ // changing start position breaks equals:
+ int restorei = sf2.getBegin();
+ sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore());
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
+ sf2.getFeatureGroup(), sf2.getScore());
+
+ // changing end position breaks equals:
+ restorei = sf2.getEnd();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
+ sf2.getFeatureGroup(), sf2.getScore());
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
+ sf2.getFeatureGroup(), sf2.getScore());
+
+ // changing feature group breaks equals:
+ restores = sf2.getFeatureGroup();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
+
+ // changing ID breaks equals:
+ restores = (String) sf2.getValue("ID");
+ sf2.setValue("ID", "id2");
+ assertFalse(sf1.equals(sf2));
+ sf2.setValue("ID", restores);
+
+ // changing Name breaks equals:
+ restores = (String) sf2.getValue("Name");
+ sf2.setValue("Name", "Name");
+ assertFalse(sf1.equals(sf2));
+ sf2.setValue("Name", restores);
+
+ // changing Parent breaks equals:
+ restores = (String) sf1.getValue("Parent");
+ sf1.setValue("Parent", "Parent");
+ assertFalse(sf1.equals(sf2));
+ sf1.setValue("Parent", restores);
+
+ // changing strand breaks equals:
+ restorei = sf2.getStrand();
+ sf2.setStrand("-");
+ assertFalse(sf1.equals(sf2));
+ sf2.setStrand(restorei == 1 ? "+" : "-");
+
+ // changing phase breaks equals:
+ restores = sf1.getPhase();
+ sf1.setPhase("2");
+ assertFalse(sf1.equals(sf2));
+ sf1.setPhase(restores);
+
+ // restore equality as sanity check:
+ assertTrue(sf1.equals(sf2));
+ assertTrue(sf2.equals(sf1));
+ assertEquals(sf1.hashCode(), sf2.hashCode());
+
+ // changing status doesn't change equals:
+ sf1.setStatus("new");
+ assertTrue(sf1.equals(sf2));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsContactFeature()
+ {
+ SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
+ assertFalse(sf.isContactFeature());
+ sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
+ assertFalse(sf.isContactFeature());
+ sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
+ assertFalse(sf.isContactFeature());
+ sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ }