import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
/**
 * Gets the set (no duplicates) of chromosomes from a bed file.
 *
 * @param bedFilePath Path to the bed file.
 *
 * @return The set of chromosomes (no duplicates)
 *
 * @throws FileNotFoundException, IOException
 */
public static Set<String> getChromosomes(String bedFilePath) throws FileNotFoundException, IOException {
    Set<String> chrs = new LinkedHashSet<>();
    File bedFile = FileUtils.getFile(bedFilePath);
    try (InputStream is = new FileInputStream(bedFile);
            AsciiLineReader alr = new AsciiLineReader(is);
            LineIteratorImpl lineIterator = new LineIteratorImpl(alr);) {
        BEDCodec bc = new BEDCodec();
        while (!bc.isDone(lineIterator)) {
            BEDFeature bf = bc.decode(lineIterator);
            if (bf != null) {
                //see https://github.com/samtools/htsjdk/issues/197
                chrs.add(bf.getContig());
            }
        }
    }
    return chrs;
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
/** returns the number of lines in the file that contain a regular expression (decorated with "MV=" and
 * expected to be in an INFO field in a vcf)
 *
 * @param file File to examine
 * @param regex String containing a regular expression to look for in the file
 * @return the number of lines that contain regex
 */
private int grep(final File file, final String regex) {

    int results = 0;
    final Pattern pattern = Pattern.compile(".*"+regex+".*");
    try (final LineIteratorImpl li = new LineIteratorImpl(new AsciiLineReader(IOUtil.openFileForReading(file)))) {

        while (li.hasNext()) {
            final String line = li.next();
            if (pattern.matcher(line).matches()) {
                results++;
            }
        }
    } catch (final IOException e) {
        e.printStackTrace();
    }
    return results;
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test
public void testDecodeHeader2(){
    TableCodec tc = new TableCodec();
    final String str2= "1:1  1   2   3";
    LineReader reader= makeReader(asList("HEADER a b c", str2));
    LineIterator li= new LineIteratorImpl(reader);
    List<String> hd = tc.readActualHeader(li);
    Assert.assertEquals(hd, asList("HEADER", "a", "b", "c"));

    final TableFeature decode = tc.decode(str2);
    Assert.assertEquals(decode.get("a"), "1");
    Assert.assertEquals(decode.get("b"), "2");
    Assert.assertEquals(decode.get("c"), "3");
    Assert.assertEquals(decode.getLocation().getContig(), "1");
    Assert.assertEquals(decode.getContig(), "1");
    Assert.assertEquals(decode.getLocation().getStart(), 1);
    Assert.assertEquals(decode.getLocation().getEnd(), 1);
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
public MUTCodec(String path, Genome genome) {
    super(Mutation.class);
    this.path = path;
    this.genome = genome;
    try {
        LineIterator reader = new LineIteratorImpl(new AsciiLineReader(ParsingUtils.openInputStream(path)));
        readActualHeader(reader);
    } catch (IOException e) {
        log.error(e.getMessage(), e);
    }
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
public Iterator<D> decodeAll(InputStream is, boolean strictParsing) throws IOException {

        List<D> featuresList = new ArrayList<D>();
        String line;
        D feat;

        LineIterator lrw = new LineIteratorImpl(new AsciiLineReader(is));
        lineFeatureDecoder.readActualHeader(lrw);

        while (lrw.hasNext()) {
            line = lrw.next();
            try {
                feat = decode(line);
                if (feat != null) {
                    featuresList.add(feat);
                }
            } catch (Exception e) {
                log.error(e.getMessage(), e);
                if (strictParsing) {
                    throw new RuntimeException(e);
                }
            }
        }

        is.close();
        return featuresList.iterator();
    }
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test(dataProvider = "stringFeature")
private void testDecodeLoc(final String pileupString, final SAMPileupFeature expected) throws Exception {
    final Feature feature = CODEC.decodeLoc(new LineIteratorImpl(makeReader(pileupString)));
    Assert.assertEquals(feature.getContig(), expected.getContig());
    Assert.assertEquals(feature.getStart(), expected.getStart());
    Assert.assertEquals(feature.getEnd(), expected.getEnd());
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test
public void testDecodeHeader(){
    TableCodec tc = new TableCodec();
    LineReader reader= makeReader(asList("HEADER a b c"));
    LineIterator li= new LineIteratorImpl(reader);
    List<String> hd = tc.readActualHeader(li);
    Assert.assertEquals(hd, asList("HEADER", "a", "b", "c"));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test(expectedExceptions = UserException.MalformedFile.class)
public void testDecodeFailsNoHeader(){
    TableCodec tc = new TableCodec();
    LineReader reader= makeReader(asList("1:1  1   2   3"));
    LineIterator li= new LineIteratorImpl(reader);
    tc.readActualHeader(li);
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test
public void testDecodeOnlyComments(){
    TableCodec tc = new TableCodec();
    LineReader reader= makeReader(asList("#HEADER a b c", "#HEADER d e f"));
    LineIterator li= new LineIteratorImpl(reader);
    final List<String> strings = tc.readActualHeader(li);
    Assert.assertEquals(strings, emptyList());
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test
public void testTwoHeaders(){
    TableCodec tc = new TableCodec();
    LineReader reader= makeReader(asList("HEADER a b c", "HEADER d e f"));
    LineIterator li= new LineIteratorImpl(reader);
    final List<String> strings = tc.readActualHeader(li);
    Assert.assertEquals(strings, asList("HEADER", "a", "b", "c"));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test(expectedExceptions =  UserException.MalformedFile.class)
public void testTwoHeadersFailsOnRepeat(){
    TableCodec tc = new TableCodec();
    Assert.assertEquals(tc.readActualHeader(new LineIteratorImpl(makeReader(asList("HEADER a b c")))), asList("HEADER", "a", "b", "c"));

    Assert.assertEquals(tc.readActualHeader(new LineIteratorImpl(makeReader(asList("HEADER a b c")))), asList("HEADER", "a", "b", "c"));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Test
public void testDecodeComment(){
    TableCodec tc = new TableCodec();
    LineReader reader= makeReader(asList("#HEADER a b c", "HEADER d e f"));
    LineIterator li= new LineIteratorImpl(reader);
    List<String> hd = tc.readActualHeader(li);
    Assert.assertEquals(hd, asList("HEADER", "d", "e", "f"));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
protected void loadEnsemblProtein() throws IOException
{
	
BiomartQuery q=new BiomartQuery();
q.setDataSetName("hsapiens_gene_ensembl");
q.setAttributes(
		"chromosome_name",
		"start_position",
		"end_position",
		"ensembl_peptide_id"
		);
q.setUniqRows(true);
LOG.info("sending "+q);
LOG.info("invoking biomart "+q);
LineReader r=q.execute();
LineIteratorImpl iter = new LineIteratorImpl(r);
while(iter.hasNext()) {
	String line=iter.next();
	String param[]=line.split("[\t]");
	if(param.length<4 || param[3].isEmpty()) continue;
	String ensp=param[3];
	
	if(!ensemblProtein2doid.containsKey(ensp)) continue;
	ensemblProteinMap.put(new Interval(param[0],Integer.parseInt(param[1]),Integer.parseInt(param[2])),ensp);
}

iter.close();
r.close();
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@SuppressWarnings("resource")
protected int doWork(InputStream in,PrintStream out)
		throws IOException
	{
	final int chromColumn0=chromColumn1-1;

	Pattern tab=Pattern.compile("[\t]");
	LineIterator lr=new LineIteratorImpl(new AsciiLineReader(in));
	
	
	while(lr.hasNext())
		{	
		String line=lr.next();
		if(BedLine.isBedHeader(line))
			{
			out.println(line);
			continue;
			}
		final String tokens[]=tab.split(line, (chromColumn0+2));
		if(chromColumn0 >=tokens.length) throw new IOException("Bad BED line : "+line+" extected at least "+(chromColumn0+2)+" columns");
		final String chrom=convertName(tokens[chromColumn0]);
		if(chrom==null) continue;
		for(int i=0;i< tokens.length;++i)
			{
			if(i>0) out.print("\t");
			out.print(i==chromColumn0?chrom:tokens[i]);
			}
		out.println();
		}
	out.flush();
	return 0;
	}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
/** @return a LineIterator that should be closed with CloserUtils */
public static LineIterator openFileForLineIterator(File file) throws IOException
{
return  new LineIteratorImpl(openFileForLineReader(file));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
/** @return a LineIterator that should be closed with CloserUtils */
public static LineIterator openStreamForLineIterator(final InputStream in) throws IOException
{
return  new LineIteratorImpl(openStreamForLineReader(in));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
/** @return a LineIterator that should be closed with CloserUtils */
public static LineIterator openURIForLineIterator(String uri) throws IOException
{
return  new LineIteratorImpl(openURIForLineReader(uri));
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
protected void loadEntrezGenes(SAMSequenceDictionary dict) throws IOException
{
this.ncbiGeneMap=new IntervalTreeMap<Integer>();
BiomartQuery q=new BiomartQuery();
q.setDataSetName("hsapiens_gene_ensembl");
q.setAttributes(
		"chromosome_name",
		"start_position",
		"end_position",
		"entrezgene"
		);
q.setUniqRows(true);
LOG.info("sending "+q);


LOG.info("invoking biomart "+q);
LineReader r=q.execute();
@SuppressWarnings("resource")
LineIterator lr=new LineIteratorImpl(r);
Pattern pattern=Pattern.compile("[\t]");
while(lr.hasNext())
	{
	String line=lr.next();
	String param[]=pattern.split(line);
	if(param.length<4 || param[3].isEmpty()) continue;
	SAMSequenceRecord rec=null;
	if((rec=dict.getSequence(param[0]))==null) continue;
	try
		{
		int start=Integer.parseInt(param[0]);
		int end=Integer.parseInt(param[1]);
		int ncbiGene=Integer.parseInt(param[3]);
		if(!gene2doid.containsKey(ncbiGene)) continue;
		ncbiGeneMap.put(new Interval(rec.getSequenceName(),start,end),ncbiGene);
		}
	catch (Exception e)
		{
		LOG.warning(e);
		continue;
		}
	
	
	}
r.close();
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
private void scan(Graphics2D g,InputStream input) throws IOException
{
Set<String> unknownC=new HashSet<String>();
Pattern tab=Pattern.compile("[\t]");
LineIterator in=new LineIteratorImpl(new SynchronousLineReader(input));
while(in.hasNext())
	{	
	String line=in.next();
	String tokens[]=tab.split(line,5);
	if(tokens.length<4)
		{
		LOG.warning("Ignoring "+line);
		continue;
		}
	SAMSequenceRecord rec=this.context.getDictionary().getSequence(tokens[0]);
	if(rec==null)
		{
		LOG.warning("unknown chromosome "+tokens[0]);
		continue;
		}
	String country=tokens[3].toLowerCase().replaceAll("[ ]", "");
	Shape shape=this.country2shape.get(country);
	if(shape==null)
		{
		if(!unknownC.contains(country))
			{
			unknownC.add(country);
			LOG.warning("unknown country "+country);
			}
		continue;
		}
	seen.incr(country);
	int midpos=(Integer.parseInt(tokens[1])+Integer.parseInt(tokens[2]))/2;
	//country center
	Point2D.Double pt1 =new Point2D.Double(shape.getBounds2D().getCenterX(),shape.getBounds2D().getCenterY());
	//circle point
	Point2D pt3= this.context.convertPositionToPoint(tokens[0],midpos,getRadiusInt());
	double angle= this.context.convertPositionToRadian(rec, midpos);
	double angle2=angle-=Math.PI/10.0;
	
	double distance13= context.getCenter().distance(new Point2D.Double(
			(pt1.getX()+pt3.getX())/2.0,
			(pt1.getY()+pt3.getY())/2.0
			));
	//mid point
	Point2D pt2 =new Point2D.Double(
			context.getCenterX()+distance13*Math.cos(angle2),
			context.getCenterX()+distance13*Math.sin(angle2)
			);
	
	Composite old=g.getComposite();
	Stroke olds=g.getStroke();
	g.setStroke(new BasicStroke(0.8f));
	g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.02f));
	g.setColor(Color.DARK_GRAY);
	GeneralPath p=new GeneralPath();
	p.moveTo(pt1.getX(), pt1.getY());
	p.quadTo(pt2.getX(), pt2.getY(),pt3.getX(), pt3.getY());
	p.closePath();
	g.draw(p);
	g.setComposite(old);
	g.setStroke(olds);
	}
CloserUtil.close(in);
}
 

import htsjdk.tribble.readers.LineIteratorImpl; //导入依赖的package包/类
@Override
public int doWork(List<String> args) {
	if(jasparUri==null)
		{
		LOG.error("Undefined jaspar-uri");
		return -1;
		}
	PrintWriter out=null;
	try
		{
		out = super.openFileOrStdoutAsPrintWriter(OUT);
		LOG.info("Reading "+jasparUri);
		LineReader lr= IOUtils.openURIForLineReader(jasparUri);
		LineIterator liter=new LineIteratorImpl(lr);
		Iterator<Matrix> miter=Matrix.iterator(liter);
		while(miter.hasNext())
			{
			Matrix matrix = miter.next();
			this.jasparDb.add(matrix.convertToPWM());
			}
		lr.close();
		LOG.info("JASPAR size: "+this.jasparDb.size());
		
		
		if(args.isEmpty())
			{
			LOG.info("Reading from stdin");
			run(out,new InputStreamReader(stdin()));
			}
		else
			{
			for(final String fname:args)
				{
				LOG.info("Opening "+fname);
				Reader in=IOUtils.openURIForBufferedReading(fname);
				run(out,in);
				in.close();
				}
				
			}
		out.flush();
		out.close();
		out=null;
		return 0;
		}
	catch(Throwable err)
		{
		LOG.error(err);
		return -1;
		}
	finally
		{
		CloserUtil.close(out);
		}
	}