/**
* Loads a gene database from a stream.
*
* @param reader Input stream
* @throws IOException
* @throws FileFormatException
*/
public boolean read(Reader reader, IProgressNotifier notifier)
throws IOException, FileFormatException {
if (notifier != null) notifier.setText("loading genes ...");
clear();
LineNumberReader in = new LineNumberReader(reader);
boolean header = true;
long geneCount = 0;
Band band = new Band();
while (in.ready()) {
if (notifier != null && notifier.isCancelled()) {
clear();
return false;
}
String line = in.readLine();
if (header) {
header = false;
continue;
}
line.trim();
String[] L = line.split("\t");
if (L.length < 13)
throw new FileFormatException("Not enough columns in line " + in.getLineNumber());
if (L[11].compareToIgnoreCase("GENE") == 0 && L[12].compareToIgnoreCase("reference") == 0) {
long gene_id;
String gene_name;
Interval interval;
// parse line
String[] lst = L[1].split("[|]");
if (lst.length != 1) continue;
try {
band.setChromosome(lst[0]);
} catch (IllegalArgumentException e) {
continue;
}
interval = new Interval();
interval.from = Long.parseLong(L[2]);
interval.to = Long.parseLong(L[3]);
if (!L[10].startsWith("GeneID:"))
throw new FileFormatException("Error in line " + in.getLineNumber() + " illegal gene id");
gene_id = Long.parseLong(L[10].split(":")[1]);
gene_name = L[9];
// insert new gene
if (band.chromosome < 1 || band.chromosome > genes.length)
throw new FileFormatException(
"Error in line " + in.getLineNumber() + " illegal chromosome");
Marker m = new Marker();
m.interval = interval;
m.info = new GeneInfo(gene_id, gene_name);
genes[band.chromosome - 1].add(m);
++geneCount;
if ((notifier != null) && (geneCount % 100 == 0))
notifier.setText(
"loading genes ... (" + (geneCount / 1000) + "." + ((geneCount % 1000) / 100) + "k)");
}
}
return true;
}