public class MZMLFile extends AbstractXMLBasedDataSource<MZMLIndexElement,MZMLIndex>
readerPoolexcludeEmptyScans, parsingTimeout, runInfo, tasksPerCpuPerBatchBUF_SIZE, path| Modifier and Type | Method and Description |
|---|---|
MZMLIndex |
fetchIndex()
Returns the index, or parses it from the original file and caches for future reuse.
|
MZMLRunInfo |
fetchRunInfo()
Gets the run info, parsing it if it yet hasn't been, and caches for reuse.
|
MZMLIndex |
getIndex()
Gets the index without an attempt to parse it.
|
IndexBuilder<MZMLIndexElement> |
getIndexBuilder(IndexBuilder.Info info) |
org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> |
getReaderPool() |
MZMLMultiSpectraParser |
getSpectraParser(InputStream inputStream,
LCMSDataSubset subset,
org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool,
Integer numSpectra)
File type specific parser.
|
MZMLIndex |
parseIndex() |
MZMLRunInfo |
parseRunInfo() |
protected void |
releaseResources()
This method will be called by
AbstractXMLBasedDataSource.releaseMemory() in addition to cleaning up resources,
used by this abstract implementation. |
buildIndex, distributeParseLoad, fixIndex, getName, parse, parse, parseScan, parseSpectrum, readContinuousBatchOfSpectra, releaseMemory, submitParseTasksgetNumThreadsForParsing, getParsingTimeout, getRunInfo, getTasksPerCpuPerBatch, isExcludeEmptyScans, setExcludeEmptyScans, setNumThreadsForParsing, setParsingTimeout, setTasksPerCpuPerBatchclose, getBufferedInputStream, getPath, getRandomAccessFilepublic MZMLFile(String path)
public org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> getReaderPool()
public MZMLIndex getIndex()
LCMSDataSourceLCMSDataSource.fetchIndex() was called before.public MZMLIndex fetchIndex() throws FileParsingException
LCMSDataSourceLCMSDataSource.parseIndex() instead.FileParsingExceptionpublic MZMLIndex parseIndex() throws FileParsingException
FileParsingExceptionpublic MZMLRunInfo fetchRunInfo() throws FileParsingException
LCMSDataSourcefetchRunInfo in interface LCMSDataSource<MZMLIndex>fetchRunInfo in class AbstractLCMSDataSource<MZMLIndex>FileParsingExceptionpublic MZMLRunInfo parseRunInfo() throws FileParsingException
FileParsingExceptionprotected void releaseResources()
AbstractXMLBasedDataSourceAbstractXMLBasedDataSource.releaseMemory() in addition to cleaning up resources,
used by this abstract implementation.
Clean up here anything additional, that your subclass has created, such as a file-type-specific index.releaseResources in class AbstractXMLBasedDataSource<MZMLIndexElement,MZMLIndex>public MZMLMultiSpectraParser getSpectraParser(InputStream inputStream, LCMSDataSubset subset, org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool, Integer numSpectra)
AbstractXMLBasedDataSourcegetSpectraParser in class AbstractXMLBasedDataSource<MZMLIndexElement,MZMLIndex>inputStream - a stream, from which the parser will parse the actual scan. If this stream is some sort of a
FileStream, make sure you use buffering, because reading from the stream in the parser is
normally unbuffered.subset - the only purpose of this subset object is to identify scans, for which spectra should be parsedreaderPool - can be null, then a new reader will be created every time. It is highly recommended to provide
a valid poolnumSpectra - can be null. If you know how many spectra can be parsed from the inputStream, then
pass it here. If set, and this number of spectra was not reached when parsing, an exception will
be thrown.public IndexBuilder<MZMLIndexElement> getIndexBuilder(IndexBuilder.Info info)
getIndexBuilder in class AbstractXMLBasedDataSource<MZMLIndexElement,MZMLIndex>Copyright © 2017. All rights reserved.