/** * 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 }