public String resolveURL(String urlTemplate, GenomeRange locus) {
String url = urlTemplate;
if (url == null) return url;
if (locus != null) {
if (locus.getName() != null) {
if (url.contains("%q")) url = url.replaceAll("%q", locus.getName());
if (url.contains("%qname")) url = url.replaceAll("%qname", locus.getName());
}
if (url.contains("%qstart"))
url = url.replaceAll("%qstart", Integer.toString(locus.getStart()));
if (url.contains("%qend")) url = url.replaceAll("%qend", Integer.toString(locus.getEnd()));
if (url.contains("%qlen")) url = url.replaceAll("%qlen", Integer.toString(locus.length()));
}
// replace track group properties
return resolvePropertyValues(url);
}
public static boolean isReadCoverage(GenomeRange data) {
DataChecker dataChecker = new DataChecker();
data.accept(dataChecker);
return dataChecker.flag;
}