/** @return */
private void readHits() {
pbar.setProgressMode(ProgressBar.PROGRESSABLE_MODE, true);
pbar.setMessage("Extracting hits");
pbar.setMaxVal(maxHits);
BufferedReader reader = null;
int val = 0;
RADSProtein p = null;
proteins = new TreeSet<RADSProtein>();
try {
reader = read(results.getXdomUrl());
String line = null;
while ((line = reader.readLine()) != null) {
if (line.substring(0, 1).equals(">")) {
if ((maxHits != -1) && (val >= maxHits)) break;
String[] fields = line.split("\\t");
String pid = fields[0].replace(">", "");
if (p != null) proteins.add(p);
p = new RADSProtein(pid, Integer.valueOf(fields[1]));
p.setRADSScore(radsScores.get(pid));
if (query.isRampageRun()) p.setRAMPAGEScore(rampageScores.get(pid));
val++;
pbar.setCurrentVal(val);
} else {
String[] fields = line.split("\\t");
RADSDomain d =
new RADSDomain(fields[2], Integer.valueOf(fields[0]), Integer.valueOf(fields[1]));
if (fields.length == 4) d.addEvalue(Double.valueOf(fields[3]));
p.addDomain(d);
}
}
proteins.add(p);
val++;
pbar.setCurrentVal(val);
pbar.finish(true);
} catch (MalformedURLException mue) {
mue.printStackTrace();
} catch (IOException ioe) {
ioe.printStackTrace();
}
}
private void readScoreTable() {
BufferedReader reader = null;
String subject = null;
String line = null;
int radsScore = 0, rampageScore = 0;
radsScores = new HashMap<String, Integer>();
rampageScores = new HashMap<String, Integer>();
pbar.setMessage("Reading score table");
try {
reader = read(results.getCrampageOut());
while ((line = reader.readLine()) != null) {
if (line.contains("QUERY")) {
if (subject != null) {
radsScores.put(subject, radsScore);
rampageScores.put(subject, rampageScore);
}
} else if (line.contains("SUBJECT")) {
String[] fields = line.split("\\s+");
subject = fields[1];
} else if (line.contains("RADS SCORE")) {
String[] fields = line.split("\\s+");
radsScore = Integer.valueOf(fields[2]);
} else if (line.contains("RAMPAGE SCORE")) {
String[] fields = line.split("\\s+");
rampageScore = Integer.valueOf(fields[2]);
}
}
if (subject != null) {
radsScores.put(subject, radsScore);
rampageScores.put(subject, rampageScore);
}
} catch (IOException ioe) {
}
}
/** @param results */
public RADSParser(RADSResults results) {
this.results = results;
this.query = results.getQuery();
this.pbar = query.getProgressBar();
this.maxHits = results.getHitsNumber();
}