/**
* Test the method that locates the first aligned sequence that has a mapping.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testFindAlignedSequence()
{
- AlignmentI cdna = new Alignment(new SequenceI[]
- {});
+ AlignmentI cdna = new Alignment(new SequenceI[] {});
final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
seq1.createDatasetSequence();
cdna.addSequence(seq1);
seq2.createDatasetSequence();
cdna.addSequence(seq2);
- AlignmentI aa = new Alignment(new SequenceI[]
- {});
+ AlignmentI aa = new Alignment(new SequenceI[] {});
final Sequence aseq1 = new Sequence("Seq1", "-P-R");
aseq1.createDatasetSequence();
aa.addSequence(aseq1);
assertNull(acf.findAlignedSequence(seq1, aa));
- MapList map = new MapList(new int[]
- { 1, 6 }, new int[]
- { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
/*
* DNA seq1 maps to AA seq2
*/
- assertEquals(aa.getSequenceAt(1),
- acf.findAlignedSequence(cdna
+ assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
.getSequenceAt(0).getDatasetSequence(), aa));
- assertEquals(cdna.getSequenceAt(0),
- acf.findAlignedSequence(aa
+ assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
.getSequenceAt(1).getDatasetSequence(), cdna));
}
/**
* Test the method that locates the mapped codon for a protein position.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetMappedRegion()
{
// introns lower case, exons upper case
/*
* Set up the mappings for the exons (upper-case bases)
*/
- MapList map = new MapList(new int[]
- { 2, 4, 6, 6, 8, 9 }, new int[]
- { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+ 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- map = new MapList(new int[]
- { 1, 2, 4, 5, 7, 8 }, new int[]
- { 1, 2 }, 3, 1);
+ map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
+ 3, 1);
acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
assertEquals("[2, 4]",
assertNull(acf.getMappedRegion(seq1, aseq2, 1));
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetMappedCodon()
{
final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
/*
* Set up the mappings for the exons (upper-case bases)
*/
- MapList map = new MapList(new int[]
- { 2, 4, 6, 6, 8, 9 }, new int[]
- { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+ 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-
+
assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
aseq1.getDatasetSequence(), 1)));
assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(