/**
* Builds a SgrScoreCalculator object
*
* @param data - name of file containing sgr data
* @param winSize - size of display window
* @throws IOException - if the file cannot be accessed
*/
public SgrScoreCalculator(String data, int winSize, CurationSet curation) throws IOException {
super(winSize);
BufferedReader br = new BufferedReader(new FileReader(data));
String line;
double minAbsScore = Double.POSITIVE_INFINITY;
Set<String> unmatchedIds = new HashSet<String>();
while ((line = br.readLine()) != null) {
String[] tokens = line.split("\t");
String refId = curation.getRefSequence().getName();
if (!tokens[0].equals(refId)) {
if (!unmatchedIds.contains(tokens[0])) {
logger.warn(
"Score id "
+ tokens[0]
+ " does not match main sequence id "
+ refId
+ ". Skipping score.");
unmatchedIds.add(tokens[0]);
}
continue;
}
Double score = new Double(Double.parseDouble(tokens[2]));
// chuck out scores outside of the given range
int pos = Integer.parseInt(tokens[1]);
if (pos >= curation.getLow() && pos <= curation.getHigh()) {
scoreMap.put(pos, score);
}
if (Math.abs(score) < minAbsScore) {
minAbsScore = Math.abs(score);
}
if (score.doubleValue() < minScore) {
minScore = score;
}
if (score.doubleValue() > maxScore) {
maxScore = score;
}
}
while (minAbsScore * factor < 1) {
factor *= 10;
}
}
