Java Code Examples for org.apache.commons.math3.stat.descriptive.moment.StandardDeviation#increment()

private void setMeanAndStd(){
	Mean mu = new Mean();
	StandardDeviation dev = new StandardDeviation();
	for (String chr : bedgraph.keySet()){
		
		ArrayList<TagNode> inTemp = bedgraph.get(chr);
		Collections.sort(inTemp,  TagNode.basepairComparator);
		for (int i = 0; i < inTemp.size();i++){
			int length = inTemp.get(i).getLength();
			double value = inTemp.get(i).getScore2();
			for (int a = 0; a < length;a++){
				mu.increment(value);
				dev.increment(value);
			}
		}
	}
	mean = mu.getResult();
	std = dev.getResult();
}
 

/**
 * Set the data across a specific region
 * @param node a TagNode representing a specific region for calculation
 * @throws IOException
 */
private void SetMeanAndStd2(TagNode node) throws IOException{
	BBFileReader wigReader = new BBFileReader(wigFile);
	String chrom = node.getChrom();
	int begin = node.getStart();
	int end = node.getStop();
	BigWigIterator iter = wigReader.getBigWigIterator(chrom, begin, chrom, end, false);
	Mean mu = new Mean();
	StandardDeviation dev = new StandardDeviation();
	while(iter.hasNext()){
		WigItem item = iter.next();
		int start = item.getStartBase();
		int stop = item.getEndBase();
		double value = item.getWigValue();
		for (int i = start; i < stop;i++){
			mu.increment(value);
			dev.increment(value);
		}
		
	}
	mean = mu.getResult();
	std = dev.getResult();
	wigReader=null;
}
 

/**
 * Set the data across the entire genome
 * @throws IOException
 */
private void SetMeanAndStd() throws IOException{
	BBFileReader wigReader = new BBFileReader(wigFile);
	BigWigIterator iter = wigReader.getBigWigIterator();
	Mean mu = new Mean();
	StandardDeviation dev = new StandardDeviation();
	while(iter.hasNext()){
		WigItem item = iter.next();
		int start = item.getStartBase();
		int stop = item.getEndBase();
		double value = item.getWigValue();
		for (int i = start; i < stop;i++){
			mu.increment(value);
			dev.increment(value);
		}
		
	}
	mean = mu.getResult();
	std = dev.getResult();
}
 

public Double evaluate(Collection<?> values, boolean biasCorrected){
	StandardDeviation statistic = new StandardDeviation();
	statistic.setBiasCorrected(biasCorrected);

	for(Object value : values){
		Number number = (Number)TypeUtil.parseOrCast(DataType.DOUBLE, value);

		statistic.increment(number.doubleValue());
	}

	return statistic.getResult();
}
 

private void Generate(){
	SAMFileReader reader = new SAMFileReader(bam,index);
	Mean mu = new Mean();
	StandardDeviation std = new StandardDeviation();
	for (int i = 0; i < genome.size();i++){
		String chr = genome.get(i).getChrom();
		int start = genome.get(i).getStart();
		int stop = genome.get(i).getStop();
		ArrayList<PileupNode2> temp = new ArrayList<PileupNode2>();
		for (int a = start;a < stop;a++){
			//new
			int begin;
			int end;
			if (a >= 1000){
				begin = a -1000;
			}else{
				begin = 0;
			}
			if (a <= stop - 1000){
				end = a + 1000;
			}else{
				end = stop;
			}
			//above is new
			CloseableIterator<SAMRecord> iter = reader.query(chr, begin, end, false);
			double value = 0;
			while(iter.hasNext()){
				SAMRecord record = iter.next();
				if(!record.getReadUnmappedFlag() && !record.getMateUnmappedFlag() && record.getFirstOfPairFlag()) {
					int tagstart = -1;
					int tagstop = -1;
				
					if(record.getInferredInsertSize() > 0) {
						tagstart = record.getAlignmentStart();
						
						tagstop = record.getAlignmentStart() + record.getInferredInsertSize() - 1;
					}else if (record.getInferredInsertSize() < 0 ) {
						tagstart = record.getAlignmentEnd() + record.getInferredInsertSize() + 1;
						tagstop = record.getAlignmentEnd();
					}
					if (tagstart == a || tagstop == a || (tagstart < a && tagstop > a)){
						value+=1;
					}
				}
				
			}
			iter.close();
			PileupNode2 node = new PileupNode2(a,value,chr);
			temp.add(node);
			mu.increment(value);
			std.increment(value);
		}
		PileupToBedGraph convert = new PileupToBedGraph(temp,1);
		bedgraph.addAll(convert.getBedGraph());
		
	}
	reader.close();
	mean = mu.getResult();
	stddev = std.getResult();
}