public void wirteChainsIntoAGffFile(
ArrayList<Double> PDScores, String blockId, String pathToChainsDir, double scoreThreshold)
throws IOException {
String blockSpecfications[] = blockId.split("_");
String Chr = blockSpecfications[0];
String gffoutputFileName = pathToChainsDir + "/" + blockId + ".gff";
PrintWriter pw = new PrintWriter(new FileWriter(gffoutputFileName));
final GFFWriter gffw = new GFFWriter(pw);
int numberOfPDScores = PDScores.size();
int oneStart = 0;
int oneEnd = 0;
int dummyPos = 0;
for (int i = 0; i < numberOfPDScores - 1; i++) {
double thisScore = PDScores.get(i);
double nextScore = PDScores.get(i + 1);
if (PDScores.get(0) >= scoreThreshold) {
thisScore = thisScore - 0.001;
}
if (thisScore < scoreThreshold && nextScore >= scoreThreshold) {
oneStart = i + 1;
dummyPos = i + 1;
double sum = 0;
while (PDScores.get(dummyPos) >= scoreThreshold && dummyPos < numberOfPDScores - 1) {
sum = sum + PDScores.get(dummyPos + 1);
dummyPos++;
} /*while*/
// System.out.println(" start = " + oneStart + " end = " + dummyPos);
oneEnd = dummyPos;
int oneChainLength = oneEnd - oneStart;
SimpleGFFRecord oneRecord = new SimpleGFFRecord();
oneRecord.setStart(oneStart + 1);
oneRecord.setEnd(oneEnd);
oneRecord.setSeqName(Chr);
oneRecord.setScore(sum / oneChainLength); // oneRecord.setScore(sum/oneChainLength+1);
oneRecord.setSource("composure");
oneRecord.setFeature("chainFromPD");
int minChainLength = getMinPeakLengths();
if (oneChainLength > 5) {
// System.out.println(Chr + "\t" + oneStart + "\t" + oneEnd + "\t" + oneChainLength);
gffw.recordLine(oneRecord);
}
i = oneEnd - 1;
} /*if*/
} /*for*/
pw.flush();
} /*wirteChainsIntoAGffFile*/
