Java AsciiLineReader.close方法代码示例

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/** A VCFHeader is read from the input Path. */
public GaeaVCFRecordWriter(
		Path output, Path input, boolean writeHeader, TaskAttemptContext ctx)
	throws IOException
{
	final AsciiLineReader r = new AsciiLineReader(
		input.getFileSystem(ContextUtil.getConfiguration(ctx)).open(input));

	final Object h = codec.readHeader(new AsciiLineReaderIterator(r));
	if (!(h instanceof VCFHeader))
		throw new IOException("No VCF header found in "+ input);

	r.close();

	init(output, (VCFHeader)h, writeHeader, ctx);
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public static boolean parsableMAGE_TAB(ResourceLocator file) throws IOException {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(file);
        String nextLine = null;

        //skip first row
        reader.readLine();

        //check second row for MAGE_TAB identifiers
        if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") ||
                nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") ||
                nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") ||
                nextLine.contains("Coordinates REF"))) {
            return true;
        }
    } finally {
        if (reader != null) {
            reader.close();
        }
    }

    return false;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
 * Load attributes from an ascii file in "Sample Info" format.
 */
public void loadSampleInfo(ResourceLocator locator) {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(locator);

        loadSampleTable(reader, locator.getPath());

        loadedResources.add(locator);

        if (!Globals.isHeadless()) {
            IGV.getInstance().resetOverlayTracks();
            IGV.getInstance().doRefresh();
        }

    } catch (IOException ex) {
        log.error("Error loading attribute file", ex);
        throw new DataLoadException("Error reading attribute file", locator.getPath());
    } finally {
        if (reader != null) {
            reader.close();

        }
        firePropertyChange(this, ATTRIBUTES_LOADED_PROPERTY, null, null);
    }
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
 * Utility method.  Returns true if this looks like a wiggle locator.  The criteria is to scan
 * the first 100 lines looking for a valid "track" line.  According to UCSC documentation
 * track lines must contain a type attribute,  which must be equal to "wiggle_0".
 *
 * @param file
 * @return
 */
public static boolean isWiggle(ResourceLocator file) {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(file);
        String nextLine = null;
        int lineNo = 0;
        while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
            if (nextLine.startsWith("track") && nextLine.contains("wiggle_0")) {
                return true;
            }
            if (lineNo++ > 100) {
                break;
            }
        }
    } catch (IOException e) {
        e.printStackTrace();
        return false;
    } finally {
        if (reader != null) {
            reader.close();
        }
    }
    return false;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/** A VCFHeader is read from the input Path. */
public VCFRecordWriter(
		Path output, Path input, boolean writeHeader, TaskAttemptContext ctx)
	throws IOException
{
	final AsciiLineReader r = new AsciiLineReader(
		input.getFileSystem(ctx.getConfiguration()).open(input));

	final FeatureCodecHeader h = codec.readHeader(new AsciiLineReaderIterator(r));
	if (h == null || !(h.getHeaderValue() instanceof VCFHeader))
		throw new IOException("No VCF header found in "+ input);

	r.close();

	init(output, (VCFHeader) h.getHeaderValue(), writeHeader, ctx);
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
 * Load segmented data from a file could be remote)
 * Return a map of trackId -> segment datasource
 *
 * @return
 */
public SegmentedAsciiDataSet loadFromFile() {

    dataset = new SegmentedAsciiDataSet(genome);

    if (birdsuite) {
        dataset.setTrackType(TrackType.CNV);
    }

    AsciiLineReader reader = null;
    String nextLine = null;
    int lineNumber = 0;

    IParser<String[], Integer> parser = IParserFactory.getIndexParser(new String[0]);

    try {
        reader = ParsingUtils.openAsciiReader(locator);
        lineNumber = readHeader(reader);

        while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
            lineNumber++;
            String[] tokens = Globals.tabPattern.split(nextLine, -1);
            parseLine(parser, tokens);
        }

    } catch (IOException e) {
        if (nextLine != null && lineNumber != 0) {
            throw new ParserException(e.getMessage(), e, lineNumber, nextLine);
        } else {
            throw new RuntimeException(e);
        }
    } finally {
        if (reader != null) {
            reader.close();
        }
    }

    dataset.sortLists();
    return dataset;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
 * Load the set of known snps from a tab delimited file, format
 * chr < tab> location
 * The location is "1 base"  (first nucleotide is position 1).
 *
 * @param snpFile
 */
private static synchronized void loadKnownSnps(String snpFile) {

    // This method might get called many times concurrently, but we only want to load these once.
    if (knownSnps != null) {
        return;
    }

    knownSnps = new HashMap();
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(new ResourceLocator(snpFile));
        String nextLine = "";
        while ((nextLine = reader.readLine()) != null) {
            String[] tokens = nextLine.split("\t");
            String chr = tokens[0];
            Set<Integer> snps = knownSnps.get(chr);
            if (snps == null) {
                snps = new HashSet(10000);
                knownSnps.put(chr, snps);
            }
            snps.add(new Integer(tokens[1]));
        }
    } catch (Exception e) {
        knownSnps = null;
        log.error("", e);
        MessageUtils.showMessage("Error loading snps file: " + snpFile + " (" + e.toString() + ")");
    } finally {
        reader.close();
    }


}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public static boolean parsableMAGE_TAB(ResourceLocator file) throws IOException {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(file);
        String nextLine = null;

        //skip first row
        reader.readLine();

        //check second row for MAGE_TAB identifiers
        if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") || nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") || nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") || nextLine.contains("Coordinates REF"))) {
            int count = 0;
            // check if this mage_tab data matrix can be parsed by this class
            while ((nextLine = reader.readLine()) != null && count < 5) {
                nextLine = nextLine.trim();
                if (nextLine.startsWith("SNP_A") || nextLine.startsWith("CN_")) {
                    return true;
                }

                count++;
            }
            return false;
        }
    } finally {
        if (reader != null) {
            reader.close();
        }
    }

    return false;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public static MultiFileWrapper parse(ResourceLocator rl) {

        AsciiLineReader reader = null;

        try {
            reader = ParsingUtils.openAsciiReader(rl);

            String name = reader.readLine();
            String serverURL = reader.readLine();

            Map<String, ResourceLocator> locators = new LinkedHashMap();

            String nextLine = null;
            while ((nextLine = reader.readLine()) != null) {
                String[] tokens = nextLine.split("\t");
                String chr = tokens[0];
                String file = tokens[1];
                ResourceLocator loc = new ResourceLocator(file);
                locators.put(chr, loc);
            }

            return new MultiFileWrapper(name, locators);

        }
        catch (IOException e) {
            e.printStackTrace();
            return null;
        }
        finally {
            if (reader != null) {
                reader.close();

            }
        }

    }
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
private void parseHeader() {
    AsciiLineReader reader = null;

    // The DataConsumer interface takes an array of data per position, however wig
    // files contain a single data point.  Create an "array" once that can
    // be resused

    try {

        reader = ParsingUtils.openAsciiReader(resourceLocator);

        while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {

            // Skip comment lines
            if (nextLine.startsWith("#") || nextLine.startsWith("data") || nextLine.startsWith(
                    "browser") || nextLine.trim().length() == 0) {
                continue;
            }

            if (nextLine.startsWith("track")) {
                trackLine = nextLine;

            } else {
                return;
            }
        }
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        if (reader != null) {
            reader.close();
        }
    }
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
 * Return a map of runId -> list of mutation objects.   The "runId" field
 * is the track identifier (name) for mutation files.
 *
 * @return
 */
private Map<String, List<htsjdk.tribble.Feature>> loadMutations() {
    AsciiLineReader reader = null;
    String nextLine = null;

    try {

        MUTCodec codec = new MUTCodec(locator.getPath(), genome);

        Map<String, List<htsjdk.tribble.Feature>> mutationMap = new LinkedHashMap();

        reader = ParsingUtils.openAsciiReader(locator);

        // Skip header - handled in codec
        while ((nextLine = reader.readLine()) != null) {
            if (nextLine.startsWith("#")) continue;
            else break;

        }

        while ((nextLine = reader.readLine()) != null) {

            Mutation mut = codec.decode(nextLine);

            if (mut != null) {
                String sampleId = mut.getSampleId();
                List<htsjdk.tribble.Feature> features = mutationMap.get(sampleId);
                if (features == null) {
                    features = new ArrayList<Feature>();
                    mutationMap.put(sampleId, features);
                }


                features.add(mut);
            }
        }


        return mutationMap;
    } catch (IOException e) {
        log.error("Error loading mutation file", e);
        throw new DataLoadException("IO Exception: " + e.toString(), locator.getPath());
    } finally {
        reader.close();
    }
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public GWASData parse() throws IOException {

        AsciiLineReader reader = null;
        String nextLine = null;
        int rowCounter = 0;

        Set<String> chromos = new HashSet<String>();
        GWASEntry lastEntry = null;

        try {
            reader = ParsingUtils.openAsciiReader(locator);

            String headerLine = reader.readLine();
            if (!this.columns.parseHeader(headerLine))
                throw new ParserException("Error while parsing columns line.", 0, nextLine);

            GWASData gData = new GWASData();

            int indexCounter = 0;

            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {

                nextLine = nextLine.trim();
                rowCounter++;

                GWASEntry entry = parseLine(nextLine, rowCounter);
                if (entry == null) continue;

                gData.addLocation(entry.chr, entry.start);
                gData.addValue(entry.chr, entry.p);

                //Check that file is sorted
                if(lastEntry != null){
                    if(entry.chr.equals(lastEntry.chr)){
                        if(entry.start < lastEntry.start){
                            throw new ParserException("File is not sorted, found start position lower than previous", rowCounter);
                        }
                    }else{
                        if(chromos.contains(entry.chr)){
                            throw new ParserException("File is not sorted; chromosome repeated", rowCounter);
                        }
                        chromos.add(entry.chr);
                    }
                }

                indexCounter++;

                int indexSize = 10000;
                if (indexCounter == indexSize) {
                    gData.getFileIndex().add((int) reader.getPosition());
                    indexCounter = 0;
                }

                lastEntry = entry;
            }
            return gData;

        } catch (Exception e) {
            if (nextLine != null && rowCounter != 0) {
                throw new ParserException(e.getMessage(), e, rowCounter, nextLine);
            } else {
                throw new RuntimeException(e);
            }
        } finally {
            if(reader != null) reader.close();
        }
    }