/**
* 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
}
