+ /**
+ * Variant of test with autocalculated annotations sorted to front
+ */
+ @Test(groups = { "Functional" })
+ public void testSortByTypeAndSequence_autocalcFirst()
+ {
+ // @formatter:off
+ anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
+ anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
+ anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
+ anns[3].autoCalculated = true; anns[3].label = "Quality";
+ anns[4].autoCalculated = true; anns[4].label = "Consensus";
+ anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
+ anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
+ // @formatter:on
+
+ AnnotationSorter testee = new AnnotationSorter(al, true);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ assertEquals("Quality", anns[0].label); // autocalc annotations
+ assertEquals("Consensus", anns[1].label); // retain ordering
+ assertEquals("IRON", anns[2].label); // IRON / sequence 0
+ assertEquals("iron", anns[3].label); // iron / sequence 3
+ assertEquals("label0", anns[4].label); // label0 / sequence 1
+ assertEquals("Structure", anns[5].label); // Structure / sequence 2
+ assertEquals("structure", anns[6].label); // structure / sequence 3
+ }
+
+ /**
+ * Variant of test with autocalculated annotations sorted to front but
+ * otherwise no change.
+ */
+ @Test(groups = { "Functional" })
+ public void testNoSort_autocalcFirst()
+ {
+ // @formatter:off
+ anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
+ anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
+ anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
+ anns[3].autoCalculated = true; anns[3].label = "Quality";
+ anns[4].autoCalculated = true; anns[4].label = "Consensus";
+ anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
+ anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
+ // @formatter:on
+
+ AnnotationSorter testee = new AnnotationSorter(al, true);
+ testee.sort(anns, SequenceAnnotationOrder.NONE);
+ assertEquals("Quality", anns[0].label); // autocalc annotations
+ assertEquals("Consensus", anns[1].label); // retain ordering
+ assertEquals("label0", anns[2].label);
+ assertEquals("structure", anns[3].label);
+ assertEquals("iron", anns[4].label);
+ assertEquals("IRON", anns[5].label);
+ assertEquals("Structure", anns[6].label);
+ }
+
+ @Test(groups = { "Functional" })