import uk.ac.babraham.FastQC.Sequence.SequenceFormatException; //导入依赖的package包/类
@Override
public Sequence next() throws SequenceFormatException {

  final ReadSequence read = this.reader.next();
  this.count++;

  return new Sequence(this, read.getSequence(), read.getQuality(),
      read.getName());
}
 

import uk.ac.babraham.FastQC.Sequence.SequenceFormatException; //导入依赖的package包/类
@Override
public Sequence next() throws SequenceFormatException {

  final SAMRecord record = this.iterator.next();
  this.count++;

  return new Sequence(this, record.getReadString(),
      record.getBaseQualityString(), record.getReadName());
}
 

import uk.ac.babraham.FastQC.Sequence.SequenceFormatException; //导入依赖的package包/类
/**
 * Process an input file by FastQC.
 * @param inputFile the input file
 * @param fastqFormat true if the format of the input file is FASTQ
 * @param outputFile the report output file
 * @param tmpDir the temporary directory
 * @param status the task status
 * @throws SequenceFormatException if an error occurs while processing
 *           sequences
 * @throws IOException if an error occurs while processing sequences
 * @throws XMLStreamException if an error occurs while creating report
 */
private void processFile(DataFile inputFile, final boolean fastqFormat,
    final DataFile outputFile, final File tmpDir, final TaskStatus status)
    throws SequenceFormatException, IOException, XMLStreamException {

  // Set the description of the context
  status.setDescription("Process sequence of " + inputFile + " for FastQC");

  // Get the SequenceFile object
  final CounterSequenceFile seqFile;
  if (fastqFormat) {

    seqFile = new FastqSequenceFile(inputFile);
  } else {

    seqFile = new SAMSequenceFile(inputFile);
  }

  // Define modules list
  final OverRepresentedSeqs os = new OverRepresentedSeqs();

  final List<AbstractQCModule> modules = Lists.newArrayList(new BasicStats(),
      new PerBaseQualityScores(), new PerTileQualityScores(),
      new PerSequenceQualityScores(), new PerBaseSequenceContent(),
      new PerSequenceGCContent(), new NContent(),
      new SequenceLengthDistribution(), os.duplicationLevelModule(), os,
      new AdapterContent(), new KmerContent());

  // Process sequences
  processSequences(modules, seqFile);

  // If no entries in the input file use a dedicated module
  final List<AbstractQCModule> reportModules = seqFile.getCount() > 0
      ? modules
      : singletonList((AbstractQCModule) new EmptyFileQC(inputFile));

  // Set the description of the context
  status.setDescription(
      "Create FastQC report on " + inputFile + " in " + outputFile.getName());

  // Create the report
  createReport(reportModules, seqFile, outputFile, tmpDir);

  // Keep module data is now unnecessary
  modules.clear();
}
 

import uk.ac.babraham.FastQC.Sequence.SequenceFormatException; //导入依赖的package包/类
/**
 * Process sequences.
 * @param modules the modules
 * @param seqFile the sequence file
 * @throws SequenceFormatException the sequence format exception
 */
private void processSequences(final List<AbstractQCModule> modules,
    final SequenceFile seqFile) throws SequenceFormatException {

  while (seqFile.hasNext()) {

    final Sequence seq = seqFile.next();

    for (final QCModule module : modules) {

      module.processSequence(seq);
    }
  }

}