public class MZXMLMultiSpectraParser extends MultiSpectraParser
| Modifier and Type | Class and Description |
|---|---|
protected static class |
MZXMLMultiSpectraParser.ATTR |
protected static class |
MZXMLMultiSpectraParser.TAG |
| 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 umich.ms.fileio.filetypes.mzxml.MzxmlVars |
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() |
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.
|
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 |
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 umich.ms.fileio.filetypes.mzxml.MzxmlVars 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 MultiSpectraParserprotected 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
FileParsingExceptionprotected int mapRawNumToInternalScanNum(int rawScanNum)
throws FileParsingException
rawScanNum - the number as is in the scan tagFileParsingExceptionCopyright © 2017. All rights reserved.