Java LittleEndianOutputStream.writeInt方法代码示例

import htsjdk.tribble.util.LittleEndianOutputStream; //导入方法依赖的package包/类
public void addFeature(int tid, Node feature, long filepointer, LittleEndianOutputStream los) throws IOException {
		if(tid > BinIndexWriter.SHORT_MAX) throw new IllegalArgumentException("Currently we don't support to index file which has chr numbers larger than 32767.");
		los.writeShort(tid);
		
		//edit for case: start == end
		if(feature.beg > feature.end) {
			 throw new IllegalArgumentException(String.format("Feature start position %d > feature end position %d", feature.beg, feature.end));
		}
		los.writeInt(feature.beg);
		if((feature.end - feature.beg) > BinIndexWriter.SHORT_MAX) {
//			System.out.println("range:" + (feature.end - feature.beg));
			los.writeShort(BinIndexWriter.INT_START);
			los.writeInt(feature.end - feature.beg); 
		} else {
			los.writeShort(feature.end - feature.beg); 
		}
   
		los.writeLong(filepointer);
	}
 

import htsjdk.tribble.util.LittleEndianOutputStream; //导入方法依赖的package包/类
public void makeIndex() {
	try {
		final String outputPath = path + IntervalIndex.PLUS_EXTENSION;
		final File outputFile = new File(outputPath + IntervalIndex.TEMP);
			
		BlockCompressedInputStream reader = checkStream(new File(path));
		LittleEndianOutputStream los = new LittleEndianOutputStream(new BlockCompressedOutputStream(outputFile));
		readBGZInputstream(reader, los);
			
		los.writeInt(IntervalIndex.PLUS_FILE_END);
		writeOthers(los);
		los.close();
		
		boolean success = outputFile.renameTo(new File(outputPath));
		if (!success) {
		   System.err.println("Make index has completed. But rename from '" + outputFile.getAbsolutePath() + "' to '" + outputPath + "' with error. ");
		} else {
			throw new IllegalArgumentException("We currently support bgz file format. please use bgzip to compress your file!");
		} 
	} catch (IOException e) {
		e.printStackTrace();
	} 
}
 

import htsjdk.tribble.util.LittleEndianOutputStream; //导入方法依赖的package包/类
public void addFeature(int tid, Node feature, long filepointer, LittleEndianOutputStream los) throws IOException {
		los.writeInt(tid);
		if(feature.beg >= feature.end) {
			 throw new IllegalArgumentException(String.format("Feature start position %d >= feature end position %d", feature.beg, feature.end));
		}
		los.writeInt(feature.beg);
//		System.out.println(feature.beg + "," + feature.end);
		los.writeInt(feature.end-feature.beg);
		los.writeLong(filepointer);
	}
 

import htsjdk.tribble.util.LittleEndianOutputStream; //导入方法依赖的package包/类
private static void writeChromosomeData(LittleEndianOutputStream peakWriter,
                                        LinkedHashMap<String, Long> chrIndex,
                                        String currentChr,
                                        List<PeakRecord> records) throws IOException {

    chrIndex.put(currentChr, peakWriter.getWrittenCount());

    // Compress data for chromosome, then write it out.
    BufferedByteWriter buffer = new BufferedByteWriter(100000);

    buffer.putNullTerminatedString(currentChr);
    buffer.putInt(records.size());
    for (PeakRecord record : records) {
        buffer.putInt(record.start);
        buffer.putInt(record.end);
        buffer.putFloat(record.score);
        for (int i = 0; i < record.timeScores.length; i++) {
            buffer.putFloat(record.timeScores[i]);
        }
    }

    byte[] bytes = buffer.getBytes();
    bytes = compressionUtils.compress(bytes);
    peakWriter.writeInt(bytes.length);
    peakWriter.write(bytes);

    records.clear();
}
 

import htsjdk.tribble.util.LittleEndianOutputStream; //导入方法依赖的package包/类
/**
 * @param inputPath
 * @param outputFile
 * @param chromosomeHandler
 */
public static void convert(String inputPath, String outputFile, ChromosomeHandler chromosomeHandler) throws IOException {

    Map<String, Integer> chromosomeOrdinals = new HashMap<>();
    for (Chromosome c : chromosomeHandler.getChromosomeArray()) {
        chromosomeOrdinals.put(c.getName(), c.getIndex());
    }

    AsciiPairIterator iter = null;
    BufferedOutputStream bos = null;
    try {
        bos = new BufferedOutputStream(new FileOutputStream(outputFile));
        LittleEndianOutputStream les = new LittleEndianOutputStream(bos);
        iter = new AsciiPairIterator(inputPath, chromosomeOrdinals
        );

        while (iter.hasNext()) {
            AlignmentPair pair = iter.next();
            les.writeBoolean(pair.getStrand1());
            les.writeInt(pair.getChr1());
            les.writeInt(pair.getPos1());
            les.writeInt(pair.getFrag1());
            les.writeBoolean(pair.getStrand2());
            les.writeInt(pair.getChr2());
            les.writeInt(pair.getPos2());
            les.writeInt(pair.getFrag2());
        }
        les.flush();
        bos.flush();
    } finally {
        if (iter != null) iter.close();
        if (bos != null) bos.close();

    }
}
 

import htsjdk.tribble.util.LittleEndianOutputStream; //导入方法依赖的package包/类
private void writeHeader(LittleEndianOutputStream les, int dim, float lower, float upper) throws IOException {

        // Magic number - 4 bytes
        les.writeByte('h');
        les.writeByte('i');
        les.writeByte('c');
        les.writeByte(0);

        // Version number
        les.writeInt(1);

        // Genome --
        les.writeString(dataset.getGenomeId());

        // Chromosomes
        les.writeString(chromosome1.getName());
        les.writeString(chromosome1.getName());

        // Resolution (bin size)
        les.writeInt(binSize);

        // Statistics, other attributes
        les.writeFloat(lower);  // this is supposed to be lower quartile
        les.writeFloat(upper);  // this is supposed to be upper quartile
        les.writeInt(dim);  // # rows
        les.writeInt(dim);  // # cols
        les.writeInt(BLOCK_TILE);
    }