* - the alignmentI object to verify (either alignment or dataset)
* @param raiseAssert
* - when set, testng assertions are raised.
- * @param message
- * - null or a string message to prepend to the assert failed messages.
+ * @param message
+ * - null or a string message to prepend to the assert failed
+ * messages.
* @return true if alignment references were in order, otherwise false.
*/
public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
boolean raiseAssert, String message)
{
- if (message==null) { message = ""; }
+ if (message == null)
+ {
+ message = "";
+ }
if (alignment == null)
{
if (raiseAssert)
{
- Assert.fail(message+"Alignment for verification was null.");
+ Assert.fail(message + "Alignment for verification was null.");
}
return false;
}
{
if (raiseAssert)
{
- Assert.fail(message+" Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+ Assert.fail(message
+ + " Alignment contained a sequence who's dataset sequence has a second dataset reference.");
}
return false;
}
{
if (raiseAssert)
{
- Assert.fail(message+" Alignment contained a sequence who's dataset sequence was not in the dataset.");
+ Assert.fail(message
+ + " Alignment contained a sequence who's dataset sequence was not in the dataset.");
}
return false;
}
}
- return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, message);
+ return verifyAlignmentDatasetRefs(alignment.getDataset(),
+ raiseAssert, message);
}
else
{
{
if (raiseAssert)
{
- Assert.fail(message+" Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+ Assert.fail(message
+ + " Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
}
return false;
}
{
if (raiseAssert)
{
- Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+ Assert.fail(message
+ + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
}
return false;
{
if (raiseAssert)
{
- Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset");
+ Assert.fail(message
+ + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
}
return false;
}
{
if (raiseAssert)
{
- Assert.fail(message+" CodonFrame-SSM-FromSeq is not a dataset sequence");
+ Assert.fail(message
+ + " CodonFrame-SSM-FromSeq is not a dataset sequence");
}
return false;
}
if (raiseAssert)
{
- Assert.fail(message+" CodonFrame-SSM-FromSeq is not contained in dataset");
+ Assert.fail(message
+ + " CodonFrame-SSM-FromSeq is not contained in dataset");
}
return false;
}
{
if (raiseAssert)
{
- Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+ Assert.fail(message
+ + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
}
return false;
}
if (raiseAssert)
{
- Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+ Assert.fail(message
+ + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
}
return false;
}
+ msg);
}
}
+
@Test(groups = { "Functional" })
public void testVerifyAlignmentDatasetRefs()
{
"TTTTTT");
// construct simple valid alignment dataset
- Alignment al = new Alignment(new SequenceI[] {
- sq1, sq2 });
+ Alignment al = new Alignment(new SequenceI[] { sq1, sq2 });
// expect this to pass
assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
// check test for sequence->datasetSequence validity
sq1.setDatasetSequence(sq2);
- assertVerifyAlignment(
- al,
- false,
+ assertVerifyAlignment(al, false,
"didn't detect dataset sequence with a dataset sequence reference.");
sq1.setDatasetSequence(null);
*/
public static void assertDatasetIsNormalised(AlignmentI al, String message)
{
- if (al.getDataset()!=null)
+ if (al.getDataset() != null)
{
assertDatasetIsNormalised(al.getDataset(), message);
return;
* look for pairs of sequences with same ID, start, end, and sequence
*/
List<SequenceI> seqSet = al.getSequences();
- for (int p=0;p<seqSet.size(); p++)
+ for (int p = 0; p < seqSet.size(); p++)
{
SequenceI pSeq = seqSet.get(p);
- for (int q=p+1; q<seqSet.size(); q++)
+ for (int q = p + 1; q < seqSet.size(); q++)
{
SequenceI qSeq = seqSet.get(q);
- if (pSeq.getStart()!=qSeq.getStart())
+ if (pSeq.getStart() != qSeq.getStart())
{
continue;
}
- if (pSeq.getEnd()!=qSeq.getEnd())
+ if (pSeq.getEnd() != qSeq.getEnd())
{
continue;
}
}
}
}
-
+
@Test(groups = { "Functional", "Asserts" })
public void testAssertDatasetIsNormalised()
{
Assert.fail("Expected identical sequence to raise exception.");
}
}
+
/*
* Read in Stockholm format test data including secondary structure
* annotations.
assertAlignmentDatasetRefs(align,
"addSequence broke dataset reference integrity");
}
+
@Test(groups = "Functional")
public void getVisibleStartAndEndIndexTest()
{
SequenceI pep = new Sequence("pep", "ASD");
SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
SequenceI cds = new Sequence("cds", "GCCTCGGAT");
-
+
// add dbref from dna to peptide
DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] {
pep.addDBRef(dbr4);
AlignmentI protein = new Alignment(new SequenceI[] { pep });
-
+
/*
* create the alignment dataset
*/
((Alignment) protein).createDatasetAlignment();
-
+
AlignmentI ds = protein.getDataset();
-
+
// should be 3 sequences in dataset
assertEquals(3, ds.getHeight());
assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));