public Transcript getTranscript() {
if (marker != null) {
if (marker instanceof Transcript) return (Transcript) marker;
return (Transcript) marker.findParent(Transcript.class);
}
return null;
}
/** Get intron (if any) */
public Intron getIntron() {
if (marker != null) {
if (marker instanceof Intron) return (Intron) marker;
return (Intron) marker.findParent(Intron.class);
}
return null;
}
public Gene getGene() {
if (marker != null) {
if (marker instanceof Gene) return (Gene) marker;
return (Gene) marker.findParent(Gene.class);
}
return null;
}
/** Get exon (if any) */
public Exon getExon() {
if (marker != null) {
if (marker instanceof Exon) return (Exon) marker;
return (Exon) marker.findParent(Exon.class);
}
return null;
}
/**
* Add into to a hash
*
* @param hits
* @param marker
* @param hit2add
* @param showGeneDetails
* @param compareTemplate
*/
void regionsAddHit(
HashSet<String> hits,
Marker hit2add,
Marker marker,
boolean showGeneDetails,
boolean compareTemplate) {
String hitStr = hit2add.getClass().getSimpleName();
if (compareTemplate) {
Gene gene = (Gene) hit2add.findParent(Gene.class);
if (gene != null)
hitStr +=
(hit2add.isStrandPlus() == marker.isStrandPlus())
? "_TEMPLATE_STRAND"
: "_NON_TEMPLATE_STRAND";
}
if (showGeneDetails && (hit2add instanceof Gene)) {
Gene gene = (Gene) hit2add;
hitStr +=
"["
+ gene.getBioType()
+ ", "
+ gene.getGeneName()
+ ", "
+ (gene.isProteinCoding() ? "protein" : "not-protein")
+ "]";
}
hits.add(hitStr); // Add marker name to the list
}
/**
* Name of the regions hit by a marker
*
* @param marker
* @param showGeneDetails
* @param compareTemplate
* @param id : Only use genes or transcripts matching this ID
* @return
*/
public Set<String> regions(
Marker marker, boolean showGeneDetails, boolean compareTemplate, String id) {
if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(marker))
throw new RuntimeEOFException("Chromosome missing for marker: " + marker);
boolean hitChromo = false;
HashSet<String> hits = new HashSet<String>();
Markers intersects = query(marker);
if (intersects.size() > 0) {
for (Marker markerInt : intersects) {
if (markerInt instanceof Chromosome) {
hitChromo = true; // OK (we have to hit a chromosome, otherwise it's an error
hits.add(markerInt.getClass().getSimpleName()); // Add marker name to the list
} else if (markerInt instanceof Gene) {
// Analyze Genes
Gene gene = (Gene) markerInt;
regionsAddHit(hits, gene, marker, showGeneDetails, compareTemplate);
// For all transcripts...
for (Transcript tr : gene) {
if ((id == null)
|| gene.getId().equals(id)
|| tr.getId().equals(id)) { // Mathes ID? (...or no ID to match)
// Does it intersect this transcript?
if (tr.intersects(marker)) {
regionsAddHit(hits, tr, marker, showGeneDetails, compareTemplate);
// Does it intersect a UTR?
for (Utr utr : tr.getUtrs())
if (utr.intersects(marker))
regionsAddHit(hits, utr, marker, showGeneDetails, compareTemplate);
// Does it intersect an exon?
for (Exon ex : tr)
if (ex.intersects(marker))
regionsAddHit(hits, ex, marker, showGeneDetails, compareTemplate);
// Does it intersect an intron?
for (Intron intron : tr.introns())
if (intron.intersects(marker))
regionsAddHit(hits, intron, marker, showGeneDetails, compareTemplate);
}
}
}
} else {
// No ID to match?
if (id == null) regionsAddHit(hits, markerInt, marker, showGeneDetails, compareTemplate);
else {
// Is ID from transcript?
Transcript tr = (Transcript) markerInt.findParent(Transcript.class);
if ((tr != null) && (tr.getId().equals(id))) {
regionsAddHit(
hits,
markerInt,
marker,
showGeneDetails,
compareTemplate); // Transcript ID matches => count
} else {
// Is ID from gene?
Gene gene = (Gene) markerInt.findParent(Gene.class);
if ((gene != null) && (gene.getId().equals(id)))
regionsAddHit(
hits,
markerInt,
marker,
showGeneDetails,
compareTemplate); // Gene ID matches => count
}
}
}
}
}
if (!hitChromo) throw new RuntimeException("ERROR: Out of chromosome range. " + marker);
return hits;
}
