List of readHeader() Examples

Examples of readHeader()

com.mobixess.jodb.core.io.ObjectDataContainer.readHeader()
@param ioTicket @return true if object deleted @throws IOException
de.netseeker.ejoe.io.DataChannel.readHeader()
Receives a EJOE specific header containing the size of the next ByteBuffer. @param timeout read timeout @return the length of the following data package @throws IOException
htsjdk.variant.bcf2.BCF2Codec.readHeader()
htsjdk.variant.vcf.VCFCodec.readHeader()
info.unipax.bina.analysis.data.csv.CsvReader.readHeader()
org.apache.maven.index.updater.IndexDataReader.readHeader()
org.jboss.marshalling.StreamHeader.readHeader()
Read the stream header from the stream. @param input the stream header @throws IOException if the header is invalid or an error occurs
org.jpos.iso.channel.ASCIIChannel.readHeader()
org.jpos.iso.channel.NACChannel.readHeader()

Examples of htsjdk.variant.vcf.VCFCodec.readHeader()


        // confirm that the FisherStrand values are identical for the two pipelines
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);


        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);

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Examples of htsjdk.variant.vcf.VCFCodec.readHeader()

        codec.readHeader(lineIterator);


        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);


        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

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Examples of htsjdk.variant.vcf.VCFCodec.readHeader()

        // QD values won't be identical because some filtered reads are missing during re-annotation


        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);


        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);

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Examples of htsjdk.variant.vcf.VCFCodec.readHeader()

        codec.readHeader(lineIterator);


        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);


        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

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Examples of info.unipax.bina.analysis.data.csv.CsvReader.readHeader()

      if (controller != null)
      {        
        CsvReader reader = (CsvReader) new CsvReaderFactory().getReader(session, file);
        try 
        {
          reader.readHeader(task);
          SeriesFilterSettingsEditor settingsEditor = reader.getSettingsEditor();
      
          if (settingsEditor != null)
          {
            String title = "Select settings for gene expresion data";

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Examples of org.apache.maven.index.updater.IndexDataReader.readHeader()

        FileInputStream fis = new FileInputStream( new File( packTargetDir, "nexus-maven-repository-index.gz" ) );
        IndexDataReader reader = new IndexDataReader( fis );
        try
        {
            // read header and neglect it
            reader.readHeader();


            // read docs
            int totalDocs = 0;
            int specialDocs = 0;
            int artifactDocs = 0;

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Examples of org.jboss.marshalling.StreamHeader.readHeader()


    public Marshaller create(final MarshallingConfiguration config, final ByteOutput target) throws IOException {
        final StreamHeader header = config.getStreamHeader();
        config.setStreamHeader(new StreamHeader() {
            public void readHeader(final ByteInput input) throws IOException {
                if (header != null) header.readHeader(input);
            }


            public void writeHeader(final ByteOutput output) throws IOException {
                if (header != null) header.writeHeader(output);
                output.write(0);

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Examples of org.jpos.iso.channel.ASCIIChannel.readHeader()


    @Test
    public void testReadHeaderThrowsNullPointerException() throws Throwable {
        BaseChannel aSCIIChannel = new ASCIIChannel();
        try {
            aSCIIChannel.readHeader(100);
            fail("Expected NullPointerException to be thrown");
        } catch (NullPointerException ex) {
            assertNull("ex.getMessage()", ex.getMessage());
            assertNull("(ASCIIChannel) aSCIIChannel.serverIn", ((ASCIIChannel) aSCIIChannel).serverIn);
        }

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Examples of org.jpos.iso.channel.NACChannel.readHeader()


    @Test
    public void testReadHeaderThrowsNegativeArraySizeException() throws Throwable {
        BaseChannel nACChannel = new NACChannel();
        try {
            nACChannel.readHeader(-1);
            fail("Expected NegativeArraySizeException to be thrown");
        } catch (NegativeArraySizeException ex) {
            assertNull("ex.getMessage()", ex.getMessage());
            assertNull("(NACChannel) nACChannel.serverIn", ((NACChannel) nACChannel).serverIn);
        }

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