本文整理汇总了Java中uk.ac.babraham.FastQC.Sequence.SequenceFormatException类的典型用法代码示例。如果您正苦于以下问题：Java SequenceFormatException类的具体用法？Java SequenceFormatException怎么用？Java SequenceFormatException使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
SequenceFormatException类属于uk.ac.babraham.FastQC.Sequence包，在下文中一共展示了SequenceFormatException类的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: next
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());
}
示例2: next
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());
}
示例3: processFile
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();
}
示例4: processSequences
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);
}
}
}