private void parseGenePositionText() {
String genomeID = hic.getDataset().getGenomeId();
// Currently only human and mouse, not worrying about small differences in location between
// genomes
if (genomeID.equals("b37")) genomeID = "hg19";
if (geneLocationHashMap == null || !genomeID.equals(this.genomeID)) {
initializeGeneHashMap(genomeID);
} else {
extractGeneLocation();
}
}
private void unsafeInitializeGeneHashMap(String genomeID) {
// Custom format parsed from ref Gene file.
// Name1 Name2 chromosome position (where position is midpoint of transcription start and end)
String path = "http://hicfiles.s3.amazonaws.com/internal/" + genomeID + "_refGene.txt";
BufferedReader reader;
try {
SeekableHTTPStream stream = new SeekableHTTPStream(new URL(path));
reader = new BufferedReader(new InputStreamReader(stream), HiCGlobals.bufferSize);
MessageUtils.showMessage(
"Loading gene database for " + genomeID + ".\nIt might take a minute or so. ");
} catch (Exception error) {
MessageUtils.showErrorMessage("Failed to read gene database", error);
positionChrTop.setBackground(Color.yellow);
geneLocationHashMap = null;
return;
}
geneLocationHashMap = new HashMap<String, GeneLocation>();
String nextLine;
try {
while ((nextLine = reader.readLine()) != null) {
String[] values = nextLine.split(" ");
GeneLocation location =
new GeneLocation(values[2].trim(), Integer.valueOf(values[3].trim()));
geneLocationHashMap.put(values[0].trim().toLowerCase(), location);
geneLocationHashMap.put(values[1].trim().toLowerCase(), location);
}
} catch (Exception error) {
MessageUtils.showErrorMessage("Failed to parse gene database", error);
positionChrTop.setBackground(Color.yellow);
geneLocationHashMap = null;
}
if (geneLocationHashMap != null) this.genomeID = genomeID;
extractGeneLocation();
}
