public class MZXMLMultiSpectraParser extends MultiSpectraParser
| Modifier and Type | Class and Description |
|---|---|
protected static class |
MZXMLMultiSpectraParser.ATTR |
class |
MZXMLMultiSpectraParser.MZXMLIndexBuilder |
protected static class |
MZXMLMultiSpectraParser.TAG |
protected class |
MZXMLMultiSpectraParser.VarsHolder |
| Modifier and Type | Field and Description |
|---|---|
protected MZXMLIndex |
index |
protected ArrayList<IScan> |
parsedScans |
protected org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> |
readerPool |
protected LCMSRunInfo |
runInfo |
protected MZXMLFile |
source |
protected MZXMLMultiSpectraParser.VarsHolder |
vars |
DATA_FACTORY, is, numScansToProcess, subset| Constructor and Description |
|---|
MZXMLMultiSpectraParser(InputStream is,
LCMSDataSubset subset,
MZXMLFile source) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
addCurScanAndFlushVars() |
IndexBuilder.Result<MZXMLIndexElement> |
buildIndex(IndexBuilder.Info info)
For use with Executors, consider using instead of calling this method directly.
|
List<IScan> |
call() |
protected boolean |
doesNeedSpectrumParsing(IScan scan) |
protected javolution.text.CharArray |
fetchAttribute(javolution.xml.sax.Attributes attrs,
MZXMLMultiSpectraParser.ATTR attr) |
int |
findThisStreamFirstScanLen()
Intended use: find the length of the last scan entry in the file.
|
MZXMLMultiSpectraParser.MZXMLIndexBuilder |
getIndexBuilder(IndexBuilder.Info info) |
MZXMLFile |
getSource() |
protected int |
mapRawNumToInternalScanNum(int rawScanNum)
Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
|
void |
setReaderPool(org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool)
Set the pool of readers.
|
protected int |
tagPeaksStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader,
int eventType) |
protected int |
tagPrecursorStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader) |
protected void |
tagScanStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader) |
getNumScansToProcess, setNumScansToProcessprotected final MZXMLFile source
protected LCMSRunInfo runInfo
protected MZXMLIndex index
protected MZXMLMultiSpectraParser.VarsHolder vars
protected org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool
public MZXMLMultiSpectraParser(InputStream is, LCMSDataSubset subset, MZXMLFile source) throws FileParsingException
is - subset - the subset will only be used to determine if the spectrum
should be parsed or not.source - FileParsingExceptionpublic void setReaderPool(org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool)
readerPool - public MZXMLFile getSource()
getSource in class MultiSpectraParserpublic IndexBuilder.Result<MZXMLIndexElement> buildIndex(IndexBuilder.Info info) throws Exception
info - info about offsets in the file and in the currently read bufferFileParsingExceptionExceptionprotected int tagPeaksStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader,
int eventType)
throws javolution.xml.stream.XMLStreamException,
FileParsingException,
DataFormatException,
IOException
javolution.xml.stream.XMLStreamExceptionFileParsingExceptionDataFormatExceptionIOExceptionprotected int tagPrecursorStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader)
throws FileParsingException,
javolution.xml.stream.XMLStreamException
FileParsingExceptionjavolution.xml.stream.XMLStreamExceptionprotected void tagScanStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader)
throws FileParsingException
FileParsingExceptionprotected void addCurScanAndFlushVars()
protected javolution.text.CharArray fetchAttribute(javolution.xml.sax.Attributes attrs,
MZXMLMultiSpectraParser.ATTR attr)
throws FileParsingException
FileParsingExceptionprotected boolean doesNeedSpectrumParsing(IScan scan)
public int findThisStreamFirstScanLen()
throws FileParsingException
FileParsingExceptionpublic MZXMLMultiSpectraParser.MZXMLIndexBuilder getIndexBuilder(IndexBuilder.Info info)
protected int mapRawNumToInternalScanNum(int rawScanNum)
throws FileParsingException
rawScanNum - the number as is in the scan tagFileParsingExceptionCopyright © 2017. All rights reserved.