/**
* Compare the sequence names against sequence (chromosome) names in the genome. If no matches
* warn the user.
*
* @param filename
* @param genome
* @param seqNames
* @return true if there is at least one sequence match, false otherwise
*/
private boolean checkSequenceNames(String filename, Genome genome, List<String> seqNames) {
boolean atLeastOneMatch = false;
for (String seqName : seqNames) {
if (genome.getChromosome(seqName) != null) {
atLeastOneMatch = true;
break;
}
}
if (!atLeastOneMatch) {
StringBuffer message = new StringBuffer();
message.append(
"<html>File: "
+ filename
+ "<br>does not contain any sequence names which match the current genome.");
message.append("<br><br>File: ");
int n = 0;
for (String sn : seqNames) {
message.append(sn + ", ");
n++;
if (n > 3) {
message.append(" ...");
break;
}
}
message.append("<br>Genome: ");
n = 0;
for (String cn : genome.getAllChromosomeNames()) {
message.append(cn + ", ");
n++;
if (n > 3) {
message.append(" ...");
break;
}
}
MessageUtils.showMessage(message.toString());
}
return atLeastOneMatch;
}
