/*
* Set up 6 sequences and 7 annotations.
*/
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
al = buildAlignment(NUM_SEQS);
* sequence ref</li>
* </ul>
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortBySequenceAndType_autocalcLast()
{
// @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].sequenceRef = null; anns[3].label = "Quality";
- anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ 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 = "label5";
anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
// @formatter:on
assertEquals("iron", anns[2].label); // sequence 3 /iron
assertEquals("IRP", anns[3].label); // sequence 3/IRP
assertEquals("structure", anns[4].label); // sequence 3/structure
- assertEquals("Quality", anns[5].label); // non-sequence annotations
+ assertEquals("Quality", anns[5].label); // autocalc annotations
assertEquals("Consensus", anns[6].label); // retain ordering
}
/**
* Variant with autocalculated annotations sorting to front
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortBySequenceAndType_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].sequenceRef = null; anns[3].label = "Quality";
- anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ 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 = "label5";
anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
// @formatter:on
AnnotationSorter testee = new AnnotationSorter(al, true);
testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
- assertEquals("Quality", anns[0].label); // non-sequence annotations
+ assertEquals("Quality", anns[0].label); // autocalc annotations
assertEquals("Consensus", anns[1].label); // retain ordering
assertEquals("label5", anns[2].label); // for sequence 0
assertEquals("label0", anns[3].label); // for sequence 1
* sequence ref</li>
* </ul>
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortByTypeAndSequence_autocalcLast()
{
// @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].sequenceRef = null; anns[3].label = "Quality";
- anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ 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
assertEquals("label0", anns[2].label); // label0 / sequence 1
assertEquals("Structure", anns[3].label); // Structure / sequence 2
assertEquals("structure", anns[4].label); // structure / sequence 3
- assertEquals("Quality", anns[5].label); // non-sequence annotations
+ assertEquals("Quality", anns[5].label); // autocalc annotations
assertEquals("Consensus", anns[6].label); // retain ordering
}
/**
* Variant of test with autocalculated annotations sorted to front
*/
- @Test
+ @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].sequenceRef = null; anns[3].label = "Quality";
- anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ 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); // non-sequence annotations
+ 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
* Variant of test with autocalculated annotations sorted to front but
* otherwise no change.
*/
- @Test
+ @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].sequenceRef = null; anns[3].label = "Quality";
- anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ 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); // non-sequence annotations
+ 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("Structure", anns[6].label);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testSort_timingPresorted()
{
testTiming_presorted(50, 100);
/**
* Timing tests for sorting randomly sorted annotations for various sizes.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSort_timingUnsorted()
{
testTiming_unsorted(50, 100);
/**
* Timing test for sorting annotations with a limited range of types (labels).
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSort_timingSemisorted()
{
testTiming_semiSorted(50, 100);