for (int flnk = -1; flnk < 25; flnk++)
{
AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
System.out.println("\nFlank size: " + flnk);
for (int flnk = -1; flnk < 25; flnk++)
{
AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
System.out.println("\nFlank size: " + flnk);
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Clustal, exp, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Clustal, exp, true));
{
String ung = sq.getSequenceAsString().replaceAll("-+", "");
final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
{
String ung = sq.getSequenceAsString().replaceAll("-+", "");
final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
- assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
- .getSequenceAsString()));
+ assertTrue(errorMsg, ung.equalsIgnoreCase(
+ sq.getDatasetSequence().getSequenceAsString()));
* Expand the subsequence to the full sequence abcDEFghi
*/
AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
* Expand the subsequence to the full sequence abcDEFghi
*/
AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
- assertEquals("abcDEFghi", expanded.getSequenceAt(0)
- .getSequenceAsString());
+ assertEquals("abcDEFghi",
+ expanded.getSequenceAt(0).getSequenceAsString());
- AlignmentI a = new FormatAdapter().readFile(data,
- DataSourceType.PASTE, format);
+ AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+ format);
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped to A33333
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped to A33333
* Exons at codon 2 (AAA) and 4 (TTT)
*/
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
* Exons at codon 2 (AAA) and 4 (TTT)
*/
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
- false, false, map, "GGG---AAACCCTTTGGG");
+ checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-", false,
+ false, map, "GGG---AAACCCTTTGGG");
- checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
- true, false, map, "GGG---A--A---ACCCT-TTGGG");
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
+ false, map, "GGG---A--A---ACCCT-TTGGG");
- checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
- true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
+ true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
- checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
- true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
+ true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
- final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
- 1, 1, 3, 3 }, 3, 1);
+ final MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[]
+ { 1, 1, 3, 3 }, 3, 1);
SequenceI alignFrom = new Sequence("Seq2", alignModel);
alignFrom.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
SequenceI alignFrom = new Sequence("Seq2", alignModel);
alignFrom.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(alignMe.getDatasetSequence(),
- alignFrom.getDatasetSequence(), map);
+ acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(),
+ map);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
preserveMappedGaps, preserveUnmappedGaps);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
preserveMappedGaps, preserveUnmappedGaps);
- MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3,
+ 1);
checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
"GG-G-AA-ACCCTTT");
checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
"GG-G-AA-ACCCTTT");
SequenceI prot2 = new Sequence("Seq2", "CHYQ");
SequenceI prot3 = new Sequence("Seq3", "CHYQ");
SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
SequenceI prot2 = new Sequence("Seq2", "CHYQ");
SequenceI prot3 = new Sequence("Seq3", "CHYQ");
SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
- AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
- prot3, prot4 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { prot1, prot2, prot3, prot4 });
- 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);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPMG".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPMG".toCharArray()));
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPK".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPK".toCharArray()));
- assertFalse(AlignmentUtils.translatesAs(
- "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaagggttt".toCharArray(),
+ 0, "FPKG".toCharArray()));
// dna + stop codon + more
assertFalse(AlignmentUtils.translatesAs(
"tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
// overlong protein
// dna + stop codon + more
assertFalse(AlignmentUtils.translatesAs(
"tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
// overlong protein
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPKGQ".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPKGQ".toCharArray()));
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped from A33333 starting position 4
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped from A33333 starting position 4
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12347 mapped to A11111 starting position 4
assertEquals(1, mapList.getToRanges().size());
// V12347 mapped to A11111 starting position 4
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// no mapping involving the 'extra' A44444
assertEquals(1, mapList.getToRanges().size());
// no mapping involving the 'extra' A44444
List<SequenceI> dnaseqs = new ArrayList<>();
dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
List<SequenceI> dnaseqs = new ArrayList<>();
dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
ann2.setSequenceRef(seq2);
AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
anns);
ann2.setSequenceRef(seq2);
AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
anns);
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
al.addAnnotation(ann1); // Structure for Seq1
al.addAnnotation(ann2); // Structure for Seq2
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
al.addAnnotation(ann1); // Structure for Seq1
al.addAnnotation(ann2); // Structure for Seq2
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
- dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
- 0f, null));
+ dna2.addSequenceFeature(
+ new SequenceFeature("variant", "hgmd", 8, 8, 0f, null));
* CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
* dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
*/
* CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
* dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
*/
- MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
- 1, 2 }, 3, 1);
+ MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[]
+ { 1, 2 }, 3, 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
mapfordna1);
dna.addCodonFrame(acf);
MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
mapfordna1);
dna.addCodonFrame(acf);
MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
mapfordna2);
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
mapfordna2);
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2 }, dna.getDataset(), null);
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2 }, dna.getDataset(), null);
assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
assertNotNull(dbref.getMap());
assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
assertNotNull(dbref.getMap());
assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
- MapList cdsMapping = new MapList(new int[] { 1, 6 },
- new int[] { 1, 2 }, 3, 1);
+ MapList cdsMapping = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 },
+ 3, 1);
DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
assertSame(cds1Dss, dbRefEntry.getMap().getTo());
MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
assertSame(cds1Dss, dbRefEntry.getMap().getTo());
MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
assertEquals(3, dna2.getDBRefs().size());
dbRefEntry = dna2.getDBRefs().get(2);
assertSame(cds2Dss, dbRefEntry.getMap().getTo());
dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
assertEquals(3, dna2.getDBRefs().size());
dbRefEntry = dna2.getDBRefs().get(2);
assertSame(cds2Dss, dbRefEntry.getMap().getTo());
dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
assertEquals(2, cds1Dss.getDBRefs().size());
dbRefEntry = cds1Dss.getDBRefs().get(1);
assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
assertEquals(2, cds1Dss.getDBRefs().size());
dbRefEntry = cds1Dss.getDBRefs().get(1);
assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
- MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
- 4, 6, 10, 12 }, 1, 1);
+ MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 },
+ new int[]
+ { 4, 6, 10, 12 }, 1, 1);
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
assertEquals(2, cds2Dss.getDBRefs().size());
dbRefEntry = cds2Dss.getDBRefs().get(1);
assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
assertEquals(2, cds2Dss.getDBRefs().size());
dbRefEntry = cds2Dss.getDBRefs().get(1);
assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
- cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
- 9, 13, 15 }, 1, 1);
+ cdsToDnaMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3, 7, 9, 13, 15 }, 1, 1);
pep1.createDatasetSequence();
pep2.createDatasetSequence();
pep3.createDatasetSequence();
pep1.createDatasetSequence();
pep2.createDatasetSequence();
pep3.createDatasetSequence();
- pep1.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "2", "A12345"));
- pep2.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "3", "A12346"));
- pep3.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "4", "A12347"));
+ pep1.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBLCDS", "2", "A12345"));
+ pep2.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBLCDS", "3", "A12346"));
+ pep3.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBLCDS", "4", "A12347"));
*/
// map ...GGG...TTT to GF
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
*/
// map ...GGG...TTT to GF
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
- AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
- new SequenceI[] { dna1 }, dna.getDataset(), null);
+ AlignmentI cdsal = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1 }, dna.getDataset(), null);
.findMappingsForSequence(pep1, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
.findMappingsForSequence(pep1, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
- assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
- .get(0).getMapping().getTo());
+ assertSame(pep1.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
.getMapping();
assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
.getMapping();
assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
- assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
- .getMap().getToPosition(1));
+ assertEquals("G(1) in CDS should map to G(4) in DNA", 4,
+ mapping.getMap().getToPosition(1));
mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
- assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
- .get(0).getMapping().getTo());
+ assertSame(pep2.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
.findMappingsForSequence(cds.get(1), dnaMappings);
mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
.findMappingsForSequence(cds.get(1), dnaMappings);
mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
- assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
- .getMap().getToPosition(4));
+ assertEquals("c(4) in CDS should map to c(7) in DNA", 7,
+ mapping.getMap().getToPosition(4));
mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
- assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
- .get(0).getMapping().getTo());
+ assertSame(pep3.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
.findMappingsForSequence(cds.get(2), dnaMappings);
mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
.findMappingsForSequence(cds.get(2), dnaMappings);
mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
- assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
- .getMap().getToPosition(4));
+ assertEquals("T(4) in CDS should map to T(10) in DNA", 10,
+ mapping.getMap().getToPosition(4));
AlignedCodonFrame acf = new AlignedCodonFrame();
// this is like a domain or motif match of part of a peptide sequence
AlignedCodonFrame acf = new AlignedCodonFrame();
// this is like a domain or motif match of part of a peptide sequence
- MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
- acf.addMap(alignFrom.getDatasetSequence(),
- alignMe.getDatasetSequence(), map);
+ MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1,
+ 1);
+ acf.addMap(alignFrom.getDatasetSequence(), alignMe.getDatasetSequence(),
+ map);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
true);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
true);
- dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type1", "desc1", 1, 2, 1f, null));
- dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type2", "desc2", 3, 4, 2f, null));
- dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type3", "desc3", 4, 6, 3f, null));
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
- dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
- dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type6", "desc6", 7, 9, 6f, null));
- dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
- 7f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type7", "desc7", 13, 15, 7f, null));
- dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
- 8f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
- dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
- 9f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type9", "desc9", 12, 13, 9f, null));
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
- dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
- dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
- 8f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
// desc4 and desc8 are the 'omit these' varargs
AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
// desc4 and desc8 are the 'omit these' varargs
AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
- dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
- dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
- 8f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
// "type5" is the 'select this type' argument
AlignmentUtils.transferFeatures(dna, cds, map, "type5");
// "type5" is the 'select this type' argument
AlignmentUtils.transferFeatures(dna, cds, map, "type5");
dna.setDataset(null);
MapList map = new MapList(new int[] { 4, 12, 16, 18 },
dna.setDataset(null);
MapList map = new MapList(new int[] { 4, 12, 16, 18 },
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
dna.addCodonFrame(acf);
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
dna.addCodonFrame(acf);
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2, dna3 }, dna.getDataset(), null);
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2, dna3 }, dna.getDataset(), null);
List<SequenceI> cdsSeqs = cds.getSequences();
assertEquals(2, cdsSeqs.size());
assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
List<SequenceI> cdsSeqs = cds.getSequences();
assertEquals(2, cdsSeqs.size());
assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
pep1CdsMappings);
assertEquals(1, sr.getResults().size());
SearchResultMatchI m = sr.getResults().get(0);
pep1CdsMappings);
assertEquals(1, sr.getResults().size());
SearchResultMatchI m = sr.getResults().get(0);
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
SequenceI prot2 = new Sequence("Seq2", "NG");
SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
SequenceI prot2 = new Sequence("Seq2", "NG");
SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
- AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
- prot3 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { prot1, prot2, prot3 });
protein.setDataset(null);
// map dna1 [3, 11] to prot1 [2, 4] KFG
protein.setDataset(null);
// map dna1 [3, 11] to prot1 [2, 4] KFG
- MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3,
+ 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
AlignmentUtils.alignAs(cds, dna);
assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
dna.addCodonFrame(acf);
AlignmentUtils.alignAs(cds, dna);
assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
SequenceI seq1 = new Sequence("cds", "AAATTT");
from.createDatasetSequence();
seq1.createDatasetSequence();
SequenceI seq1 = new Sequence("cds", "AAATTT");
from.createDatasetSequence();
seq1.createDatasetSequence();
- Mapping mapping = new Mapping(seq1, new MapList(
- new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
+ Mapping mapping = new Mapping(seq1,
+ new MapList(new int[]
+ { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
SequenceI seq1 = new Sequence("cds", "AAATTT");
from.createDatasetSequence();
seq1.createDatasetSequence();
SequenceI seq1 = new Sequence("cds", "AAATTT");
from.createDatasetSequence();
seq1.createDatasetSequence();
- Mapping mapping = new Mapping(seq1, new MapList(
- new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
+ Mapping mapping = new Mapping(seq1,
+ new MapList(new int[]
+ { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
dna.addCodonFrame(acf);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
dna.addCodonFrame(acf);
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2 }, dna.getDataset(),
+ emblPeptides.getSequencesArray());
assertEquals(2, cds.getSequences().size());
assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
assertEquals(2, cds.getSequences().size());
assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
*/
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
String aligned1 = "-cc-GG-GTTT-aaa";
*/
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
String aligned1 = "-cc-GG-GTTT-aaa";
SequenceI uas1 = dna1.deriveSequence();
SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
SequenceI uas3 = dna2.deriveSequence();
SequenceI uas1 = dna1.deriveSequence();
SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
SequenceI uas3 = dna2.deriveSequence();
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
// add dna to peptide mapping
seqMappings.add(acf1);
acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
// add dna to peptide mapping
seqMappings.add(acf1);
acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
// need to tidy up use of lists of mappings in AlignedCodonFrame
AlignedCodonFrame acf2 = new AlignedCodonFrame();
mappings.add(acf2);
// need to tidy up use of lists of mappings in AlignedCodonFrame
AlignedCodonFrame acf2 = new AlignedCodonFrame();
mappings.add(acf2);
- MapList cdsToPeptideMapping = new MapList(new int[]
- { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3 }, 3, 1);
acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
cdsToPeptideMapping);
assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
cdsToPeptideMapping);
assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
List<AlignedCodonFrame> mappings = new ArrayList<>();
AlignedCodonFrame acf1 = new AlignedCodonFrame();
mappings.add(acf1);
List<AlignedCodonFrame> mappings = new ArrayList<>();
AlignedCodonFrame acf1 = new AlignedCodonFrame();
mappings.add(acf1);
SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
dna1.createDatasetSequence();
SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
dna1.createDatasetSequence();
// NB we currently exclude STOP codon from CDS sequences
// the test would need to change if this changes in future
SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
cds1.createDatasetSequence();
// NB we currently exclude STOP codon from CDS sequences
// the test would need to change if this changes in future
SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
cds1.createDatasetSequence();
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
- MapList mapList = new MapList(
- new int[]
- { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ MapList mapList = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
+ 1);
// add dna to peptide mapping
seqMappings.add(acf1);
acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
mapList);
// add dna to peptide mapping
seqMappings.add(acf1);
acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
mapList);
SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
seqMappings, dnaToPeptide);
assertSame(seq, dna1.getDatasetSequence());
SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
seqMappings, dnaToPeptide);
assertSame(seq, dna1.getDatasetSequence());
/*
* second case - transcript has CDS feature - this means it is
* not returned as a match for CDS (CDS sequences don't have CDS features)
/*
* second case - transcript has CDS feature - this means it is
* not returned as a match for CDS (CDS sequences don't have CDS features)
// need to tidy up use of lists of mappings in AlignedCodonFrame
AlignedCodonFrame acf2 = new AlignedCodonFrame();
mappings.add(acf2);
// need to tidy up use of lists of mappings in AlignedCodonFrame
AlignedCodonFrame acf2 = new AlignedCodonFrame();
mappings.add(acf2);
- MapList cdsToPeptideMapping = new MapList(new int[]
- { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3 }, 3, 1);
acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
cdsToPeptideMapping);
assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
dnaToPeptide));
acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
cdsToPeptideMapping);
assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
dnaToPeptide));