/*
* DNA seq1 maps to AA seq2
*/
- assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
- .getSequenceAt(0).getDatasetSequence(), aa));
+ assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(
+ cdna.getSequenceAt(0).getDatasetSequence(), aa));
// can also find this from the dna aligned sequence
assertEquals(aa.getSequenceAt(1),
acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
- assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
- .getSequenceAt(1).getDatasetSequence(), cdna));
+ assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(
+ aa.getSequenceAt(1).getDatasetSequence(), cdna));
}
/**
* Set up the mappings for the exons (upper-case bases)
* Note residue Q is unmapped
*/
- MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
- 3, 4 }, 3, 1);
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
+ new int[]
+ { 3, 4 }, 3, 1);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
- MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 9 },
- 3, 1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
+ new int[]
+ { 7, 9 }, 3, 1);
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
/*
* No mapping from dna1 to pep2
*/
assertNull(acf.getMappedRegion(dna1, pep2, 7));
-
+
/*
* get peptide position for codon position
*/
/*
* 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(1, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
- .size());
- assertEquals(
- "[G, T, A]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 1).get(0)));
- assertEquals(
- "[C, T, T]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 2).get(0)));
+ assertEquals(1,
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 1).size());
+ assertEquals("[G, T, A]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 1).get(0)));
+ assertEquals("[C, T, T]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 2).get(0)));
}
/**
/*
* 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);
acf.addMap(seq2.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(2, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
- .size());
- List<char[]> codonsForV = acf.getMappedCodons(
- aseq1.getDatasetSequence(), 1);
+ assertEquals(2,
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 1).size());
+ List<char[]> codonsForV = acf
+ .getMappedCodons(aseq1.getDatasetSequence(), 1);
assertEquals("[G, T, A]", Arrays.toString(codonsForV.get(0)));
assertEquals("[G, T, T]", Arrays.toString(codonsForV.get(1)));
- List<char[]> codonsForL = acf.getMappedCodons(
- aseq1.getDatasetSequence(), 2);
+ List<char[]> codonsForL = acf
+ .getMappedCodons(aseq1.getDatasetSequence(), 2);
assertEquals("[C, T, T]", Arrays.toString(codonsForL.get(0)));
assertEquals("[T, T, A]", Arrays.toString(codonsForL.get(1)));
}
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
- new int[] { 12, 13 }, 3, 1);
+ new int[]
+ { 12, 13 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(
- "[G, T, A]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 12).get(0)));
- assertEquals(
- "[C, T, T]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 13).get(0)));
+ assertEquals("[G, T, A]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 12).get(0)));
+ assertEquals("[C, T, T]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 13).get(0)));
}
@Test(groups = { "Functional" })
assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
17));
// map to region overlapping sequence is ok
- assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5,
- 10));
+ assertTrue(
+ AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5, 10));
assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 21,
26));
// map to region before sequence is not ok
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4,
- 9));
+ assertFalse(
+ AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4, 9));
// map to region after sequence is not ok
assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 22,
27));
* a real sequence can't replace a real one
*/
SequenceI seq1a = new Sequence("Seq1/10-21", "aaacccgggttt");
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
+ assertFalse(
+ AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
}
/**
* map Seq1 to all of Seq2 and part of Seq3
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
+ 1);
acf.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
map = new MapList(new int[] { 1, 12 }, new int[] { 3, 6 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), seq3.getDatasetSequence(), map);
aseq1.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
- 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(1, acf.getMappingsFromSequence(seq1).size());
Mapping before = acf.getMappingsFromSequence(seq1).get(0);
assertEquals(1, acf.getMappingsFromSequence(seq1).size());
assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
}
-
+
@Test(groups = { "Functional" })
public void testGetCoveringMapping()
{
SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
cds.setDatasetSequence(dna);
SequenceI pep = new Sequence("pep", "MAD");
-
+
/*
* with null argument or no mappings
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- assertNull(acf.getCoveringMapping(null, null));
- assertNull(acf.getCoveringMapping(dna, null));
- assertNull(acf.getCoveringMapping(null, pep));
- assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(null, null));
+ assertNull(acf.getCoveringMapping(dna, null));
+ assertNull(acf.getCoveringMapping(null, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
/*
* with a non-covering mapping e.g. overlapping exon
*/
- MapList map = new MapList(new int[] { 7, 9 }, new int[] {
- 1, 1 }, 3, 1);
+ MapList map = new MapList(new int[] { 7, 9 }, new int[] { 1, 1 }, 3, 1);
acf.addMap(dna, pep, map);
- assertNull(acf.getCoveringMapping(dna, pep));
-
+ assertNull(acf.getCoveringMapping(dna, pep));
+
acf = new AlignedCodonFrame();
- MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
- 2, 2 }, 3, 1);
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
+ 1);
acf.addMap(dna, pep, map2);
- assertNull(acf.getCoveringMapping(dna, pep));
-
+ assertNull(acf.getCoveringMapping(dna, pep));
+
/*
* with a covering mapping from CDS (dataset) to protein
*/
acf = new AlignedCodonFrame();
- MapList map3 = new MapList(new int[] { 7, 15 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map3 = new MapList(new int[] { 7, 15 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(dna, pep, map3);
- assertNull(acf.getCoveringMapping(dna, pep));
- SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
assertNotNull(mapping);
-
+
/*
* with a mapping that extends to stop codon
*/
acf = new AlignedCodonFrame();
- MapList map4 = new MapList(new int[] { 7, 18 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map4 = new MapList(new int[] { 7, 18 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(dna, pep, map4);
- assertNull(acf.getCoveringMapping(dna, pep));
- assertNull(acf.getCoveringMapping(cds, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(cds, pep));
SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
cds2.setDatasetSequence(dna);
- mapping = acf.getCoveringMapping(cds2, pep);
+ mapping = acf.getCoveringMapping(cds2, pep);
assertNotNull(mapping);
}
dna1.createDatasetSequence();
final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
dna2.createDatasetSequence();
-
+
final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
pep1.createDatasetSequence();
final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
pep2.createDatasetSequence();
-
+
/*
* First with no mappings
*/
SearchResults sr = new SearchResults();
acf.markMappedRegion(dna1, 12, sr);
assertTrue(sr.isEmpty());
-
+
/*
* Set up the mappings for the exons (upper-case bases)
* Note residue Q is unmapped
*/
- MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
- 3, 4 }, 3, 1);
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
+ new int[]
+ { 3, 4 }, 3, 1);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
- MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 8 },
- 3, 1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
+ new int[]
+ { 7, 8 }, 3, 1);
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
-
+
/*
* intron bases are not mapped
*/
acf.markMappedRegion(dna1, 10, sr);
assertTrue(sr.isEmpty());
-
+
/*
* Q is not mapped
*/
*/
acf.markMappedRegion(dna1, 11, sr);
SearchResults expected = new SearchResults();
- expected.addResult(pep1.getDatasetSequence(), 3, 3);
+ expected.addResult(pep1.getDatasetSequence(), 3, 3);
assertEquals(sr, expected);
/*
sr = new SearchResults();
acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
assertEquals(sr, expected);
-
+
/*
* marking the same position a second time should not create a duplicate match
*/
acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
assertEquals(sr, expected);
-
+
/*
* mark exon positions for peptide position (of aligned sequence)
*/
sr = new SearchResults();
acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
expected = new SearchResults();
- expected.addResult(dna2.getDatasetSequence(), 20, 21);
- expected.addResult(dna2.getDatasetSequence(), 23, 23);
+ expected.addResult(dna2.getDatasetSequence(), 20, 21);
+ expected.addResult(dna2.getDatasetSequence(), 23, 23);
assertEquals(sr, expected);
-
+
/*
* add another codon to the same SearchResults
*/
- acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions 15, 17, 18
- expected.addResult(dna1.getDatasetSequence(), 15, 15);
- expected.addResult(dna1.getDatasetSequence(), 17, 18);
+ acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions
+ // 15, 17, 18
+ expected.addResult(dna1.getDatasetSequence(), 15, 15);
+ expected.addResult(dna1.getDatasetSequence(), 17, 18);
assertEquals(sr, expected);
}
SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
cds.createDatasetSequence();
SequenceI pep = new Sequence("pep/1-3", "MAD");
-
+
/*
* with null argument or no mappings
*/
assertNull(acf.getCoveringCodonMapping(null));
assertNull(acf.getCoveringCodonMapping(dna));
assertNull(acf.getCoveringCodonMapping(pep));
-
+
/*
* with a non-covering mapping e.g. overlapping exon
*/
- MapList map = new MapList(new int[] { 16, 18 }, new int[] {
- 1, 1 }, 3, 1);
+ MapList map = new MapList(new int[] { 16, 18 }, new int[] { 1, 1 }, 3,
+ 1);
acf.addMap(dna, pep, map);
assertNull(acf.getCoveringCodonMapping(dna));
assertNull(acf.getCoveringCodonMapping(pep));
-
+
acf = new AlignedCodonFrame();
- MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
- 2, 2 }, 3, 1);
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
+ 1);
acf.addMap(dna, pep, map2);
assertNull(acf.getCoveringCodonMapping(dna));
assertNull(acf.getCoveringCodonMapping(pep));
-
+
/*
* with a covering mapping from CDS (dataset) to protein
*/
acf = new AlignedCodonFrame();
- MapList map3 = new MapList(new int[] { 1, 9 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map3 = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(cds.getDatasetSequence(), pep, map3);
assertNull(acf.getCoveringCodonMapping(dna));
SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
assertNotNull(mapping);
- SequenceToSequenceMapping mapping2 = acf.getCoveringCodonMapping(cds.getDatasetSequence());
+ SequenceToSequenceMapping mapping2 = acf
+ .getCoveringCodonMapping(cds.getDatasetSequence());
assertSame(mapping, mapping2);
-
+
/*
* with a mapping that extends to stop codon
* (EMBL CDS location often includes the stop codon)
SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
cds2.createDatasetSequence();
acf = new AlignedCodonFrame();
- MapList map4 = new MapList(new int[] { 1, 12 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map4 = new MapList(new int[] { 1, 12 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(cds2, pep, map4);
mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
assertNotNull(mapping);
git://source.jalview.org / jalview.git / blobdiff