private Location createLocation(
BioEntity object,
BioEntity subject,
String strand,
int start,
int end,
Class<?> locationClass) {
Location loc = (Location) DynamicUtil.createObject(Collections.singleton(locationClass));
loc.setLocatedOn(object);
loc.setFeature(subject);
loc.setStrand(strand);
loc.setStart(new Integer(start));
loc.setEnd(new Integer(end));
loc.setStrand(strand);
return loc;
}
/**
* Create a GAFRecord from a LocatedSequenceFeature.
*
* @param lsf the LocatedSequenceFeature
* @return the GAFRecord or null
*/
public static GAFRecord makeGAFRecord(SequenceFeature lsf) {
String chrom = null;
int chromStart = -1;
int chromEnd = -1;
String name = null;
int score = 0;
String strand = ".";
if (lsf instanceof Chromosome) {
return null;
} else {
Chromosome chr = lsf.getChromosome();
if (chr == null) {
return null;
}
if (lsf.getSymbol() == null) {
if (lsf.getPrimaryIdentifier() == null) {
name = "(Unknown)";
} else {
name = lsf.getPrimaryIdentifier();
}
} else {
name = lsf.getSymbol();
}
name = name.replaceAll(" ", "_"); // replace white space in name to under score
Location chrLocation = lsf.getChromosomeLocation();
if (chrLocation == null) {
return null;
}
chromStart = chrLocation.getStart().intValue() - 1; // Interbase Coordinate
chromEnd = chrLocation.getEnd().intValue();
if (chrLocation.getStrand() != null) {
if ("1".equals(chrLocation.getStrand())) {
strand = "+";
} else if ("-1".equals(chrLocation.getStrand())) {
strand = "-";
}
}
}
return new GAFRecord(chrom, chromStart, chromEnd, name, score, strand);
}
private void createOverlapTestData() throws Exception {
Chromosome chr = (Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr.setPrimaryIdentifier("X");
chr.setLength(new Integer(1000));
chr.setId(new Integer(101));
Set<InterMineObject> toStore = new HashSet<InterMineObject>();
toStore.add(chr);
int[][] exonInfo = {
{1000, 1, 1},
{1001, 2, 10},
{1002, 10, 15},
{1003, 16, 19},
{1004, 16, 19},
{1005, 20, 29},
{1006, 30, 100},
{1007, 30, 34},
{1008, 32, 95},
{1009, 38, 53},
{1010, 40, 50},
{1011, 44, 44},
{1012, 54, 54},
{1013, 54, 54},
{1014, 60, 70},
{1015, 120, 140},
{1016, 141, 145},
{1017, 146, 180},
{1018, 220, 240},
{1019, 240, 245},
{1020, 245, 280},
};
Exon[] exons = new Exon[exonInfo.length];
Location[] exonLocs = new Location[exonInfo.length];
for (int i = 0; i < exons.length; i++) {
exons[i] = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
int exonId = exonInfo[i][0];
int start = exonInfo[i][1];
int end = exonInfo[i][2];
exons[i].setId(new Integer(exonId));
exons[i].setLength(new Integer(end - start + 1));
exons[i].setChromosome(chr);
exonLocs[i] = createLocation(chr, exons[i], "1", start, end, Location.class);
exonLocs[i].setId(new Integer(1000 + exonId));
}
ReversePrimer rp =
(ReversePrimer) DynamicUtil.createObject(Collections.singleton(ReversePrimer.class));
rp.setId(new Integer(3000));
rp.setLength(new Integer(100));
rp.setChromosome(chr);
Location rpLoc = createLocation(chr, rp, "1", 1, 100, Location.class);
rpLoc.setId(new Integer(3001));
toStore.add(rp);
toStore.add(rpLoc);
toStore.addAll(Arrays.asList(exons));
toStore.addAll(Arrays.asList(exonLocs));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
}
public void testSetChromosomeLocationsAndLengths() throws Exception {
Chromosome chr1 =
(Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr1.setPrimaryIdentifier("1");
chr1.setId(new Integer(101));
Chromosome chr2 =
(Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr1.setPrimaryIdentifier("2");
chr1.setId(new Integer(102));
Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon1.setId(new Integer(107));
exon1.setLength(new Integer(1000));
Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon2.setId(new Integer(108));
Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon3.setId(new Integer(109));
// exon 2 has two chromosome locations, shouldn't get chromosome[Location] references
Location exon1OnChr = createLocation(chr1, exon1, "1", 51, 100, Location.class);
exon1OnChr.setId(new Integer(1010));
Location exon2OnChr = createLocation(chr2, exon2, "1", 201, 250, Location.class);
exon2OnChr.setId(new Integer(1011));
Location exon2OnChrDup = createLocation(chr1, exon2, "1", 501, 550, Location.class);
exon2OnChrDup.setId(new Integer(1012));
Location exon3OnChr = createLocation(chr2, exon3, "1", 601, 650, Location.class);
exon3OnChr.setId(new Integer(1013));
Set<InterMineObject> toStore =
new HashSet<InterMineObject>(
Arrays.asList(
new InterMineObject[] {
chr1, chr2, exon1, exon2, exon3, exon1OnChr, exon2OnChr, exon2OnChrDup, exon3OnChr
}));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
CalculateLocations cl = new CalculateLocations(osw);
cl.setChromosomeLocationsAndLengths();
ObjectStore os = osw.getObjectStore();
Exon resExon1 = (Exon) os.getObjectById(new Integer(107));
Exon resExon2 = (Exon) os.getObjectById(new Integer(108));
Exon resExon3 = (Exon) os.getObjectById(new Integer(109));
assertEquals(chr1.getId(), resExon1.getChromosome().getId());
assertEquals(exon1OnChr.getId(), resExon1.getChromosomeLocation().getId());
assertNull(resExon2.getChromosome());
assertNull(resExon2.getChromosomeLocation());
assertEquals(chr2.getId(), resExon3.getChromosome().getId());
assertEquals(exon3OnChr.getId(), resExon3.getChromosomeLocation().getId());
// exon1 has length set so should stay as 1000, exon3 should get length 50 set from location
assertEquals(new Integer(1000), resExon1.getLength());
assertEquals(new Integer(50), resExon3.getLength());
// nothing done to exon2
assertNull(resExon2.getLength());
}
public void testCreateSpanningLocations() throws Exception {
Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon1.setId(new Integer(107));
Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon2.setId(new Integer(108));
Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon3.setId(new Integer(109));
Location exon1OnChr = createLocation(getChromosome(), exon1, "1", 51, 100, Location.class);
exon1OnChr.setId(new Integer(1010));
Location exon2OnChr = createLocation(getChromosome(), exon2, "1", 201, 250, Location.class);
exon2OnChr.setId(new Integer(1011));
Location exon3OnChr = createLocation(getChromosome(), exon3, "1", 201, 400, Location.class);
exon3OnChr.setId(new Integer(1012));
Transcript trans1 =
(Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
trans1.setId(new Integer(201));
Transcript trans2 =
(Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
trans2.setId(new Integer(202));
Location trans2OnChr = createLocation(getChromosome(), trans2, "1", 61, 300, Location.class);
Gene gene = (Gene) DynamicUtil.createObject(Collections.singleton(Gene.class));
gene.setId(new Integer(301));
exon1.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));
exon2.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));
// the location of exon3 should be ignored by createSpanningLocations() because trans2
// already has a location
exon3.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans2})));
trans1.setGene(gene);
trans2.setGene(gene);
Set<InterMineObject> toStore =
new HashSet<InterMineObject>(
Arrays.asList(
new InterMineObject[] {
getChromosome(),
gene,
trans1,
trans2,
exon1,
exon2,
exon3,
exon1OnChr,
exon2OnChr,
trans2OnChr
}));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
CalculateLocations cl = new CalculateLocations(osw);
cl.createSpanningLocations("Transcript", "Exon", "exons");
cl.createSpanningLocations("Gene", "Transcript", "transcripts");
ObjectStore os = osw.getObjectStore();
Transcript resTrans1 = (Transcript) os.getObjectById(new Integer(201));
Assert.assertEquals(1, resTrans1.getLocations().size());
Location resTrans1Location = (Location) resTrans1.getLocations().iterator().next();
Assert.assertEquals(51, resTrans1Location.getStart().intValue());
Assert.assertEquals(250, resTrans1Location.getEnd().intValue());
Transcript resTrans2 = (Transcript) os.getObjectById(new Integer(202));
Assert.assertEquals(1, resTrans2.getLocations().size());
Location resTrans2Location = (Location) resTrans2.getLocations().iterator().next();
Assert.assertEquals(61, resTrans2Location.getStart().intValue());
Assert.assertEquals(300, resTrans2Location.getEnd().intValue());
Gene resGene = (Gene) os.getObjectById(new Integer(301));
Assert.assertEquals(1, resGene.getLocations().size());
Location resGeneLocation = (Location) resGene.getLocations().iterator().next();
Assert.assertEquals(51, resGeneLocation.getStart().intValue());
Assert.assertEquals(300, resGeneLocation.getEnd().intValue());
}