public static void main(String[] args) {
if (args.length != 2) {
System.err.println(
"Usage: MemoryBasedLeft2Right <in score file> <out aggregated scores redis file>");
System.exit(0);
}
String infile = args[0];
String redisSimilarityFile = args[1];
try {
BufferedReader reader = new BufferedReader(new FileReader(new File(infile)));
String line;
TIntObjectMap<TIntDoubleMap> scoresMap = new TIntObjectHashMap<TIntDoubleMap>();
while ((line = reader.readLine()) != null) {
String[] toks = line.split("\t");
int id1 = Integer.parseInt(toks[0]);
int id2 = Integer.parseInt(toks[1]);
double score = Double.parseDouble(toks[2]);
TIntDoubleMap scores = scoresMap.get(id1);
if (scores == null) {
scores = new TIntDoubleHashMap();
scoresMap.put(id1, scores);
}
scores.put(id2, score);
}
reader.close();
RedisBasedIDKeyPersistentBasicMap<LinkedHashMap<Integer, Double>> redis =
new RedisBasedIDKeyPersistentBasicMap<LinkedHashMap<Integer, Double>>(
redisSimilarityFile, false);
redis.clear();
TIntObjectIterator<TIntDoubleMap> it = scoresMap.iterator();
while (it.hasNext()) {
it.advance();
int id1 = it.key();
TIntDoubleMap scores = it.value();
redis.put(id1, SortUtil.sortMapByValue(scores, true));
}
} catch (Exception e) {
e.printStackTrace();
}
}
private void initial() {
NormalDistribution nd = new NormalDistribution();
String[] seqList = this.sequence.split(";");
for (String seq : seqList) {
BaseIsotopomer bIso = new BaseIsotopomer(seq, this.isotopomerWidth);
TIntDoubleMap chargeScaleMap = new TIntDoubleHashMap();
int centralCharge = bIso.getCentralChargeState();
int totalChargeState = (bIso.getMaxChargeState() - centralCharge) * 2;
double step = 6.0 / totalChargeState;
// calculate right side of the central charge state (inclusive) to 10+ charge
double x = 0.0;
for (int i = centralCharge; i > 8; i--) {
double factor = nd.density(x);
x += step;
chargeScaleMap.put(i, factor);
}
// calculate left side of the central charge state (exclusive) to max charge
x = step;
for (int i = centralCharge + 1; i <= bIso.getMaxChargeState(); i++) {
double factor = nd.density(x);
x += step;
chargeScaleMap.put(i, factor);
}
// build list of Isotopomer
for (int charge : chargeScaleMap.keys()) {
ChargedIsotopomer cIso = new ChargedIsotopomer(bIso, charge);
isotopomerList.add(cIso);
TDoubleDoubleMap tempPeakMap = cIso.getScaledPeakMap(chargeScaleMap.get(charge));
for (double mz : tempPeakMap.keys()) {
double intensity = peakMap.get(mz);
if (intensity == peakMap.getNoEntryValue()) {
peakMap.put(mz, tempPeakMap.get(mz));
} else {
peakMap.put(mz, intensity + tempPeakMap.get(mz));
}
}
}
}
}
@Override
public int getSerializedSizeUnlocked() {
return (Integer.SIZE + params.size() * (Integer.SIZE + Double.SIZE)) / Byte.SIZE;
}