public String encode(LocusScore score) {
String[] tokens = new String[4];
tokens[0] = score.getChr();
tokens[1] = "" + score.getStart();
tokens[2] = "" + score.getEnd();
tokens[3] = "" + score.getScore();
String out = StringUtils.join(tokens, delimiter);
return out;
}
@Override
protected DataTile getRawData(String chr, int startLocation, int endLocation) {
int queryLength = endLocation - startLocation;
int longestFeature = getLongestFeature(chr);
int adjustedStart = startLocation;
int adjustedEnd = endLocation;
if (queryLength < longestFeature) {
int halfDiff = (longestFeature - queryLength) / 2;
adjustedStart = startLocation - halfDiff - 1;
adjustedEnd = endLocation + halfDiff;
}
try {
Iterator<LocusScore> iter =
pluginFeatureSource.getFeatures(chr, adjustedStart, adjustedEnd, -1);
List<LocusScore> list = new ArrayList<LocusScore>(1000);
LocusScore score;
dataMin = Double.MAX_VALUE;
dataMax = -Double.MAX_VALUE;
while (iter.hasNext()) {
score = iter.next();
dataMin = Math.min(dataMin, score.getScore());
dataMax = Math.max(dataMax, score.getScore());
list.add(score);
longestFeature = Math.max(longestFeature, score.getEnd() - score.getStart());
}
longestFeatureMap.put(chr, longestFeature);
int length = list.size();
int[] startLocations = new int[length];
int[] endLocations = new int[length];
float[] scores = new float[length];
String[] names = new String[length];
int idx = 0;
for (LocusScore locusScore : list) {
startLocations[idx] = locusScore.getStart();
endLocations[idx] = locusScore.getEnd();
scores[idx] = locusScore.getScore();
names[idx] =
Locus.getFormattedLocusString(
locusScore.getChr(), locusScore.getStart(), locusScore.getEnd());
idx++;
}
return new DataTile(startLocations, endLocations, scores, names);
} catch (IOException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e);
}
}