public class MZMLMultiSpectraParser extends MultiSpectraParser
| Modifier and Type | Class and Description |
|---|---|
protected static class |
MZMLMultiSpectraParser.ATTR |
class |
MZMLMultiSpectraParser.MZMLIndexBuilder |
protected static class |
MZMLMultiSpectraParser.TAG |
| Modifier and Type | Field and Description |
|---|---|
protected MZMLIndex |
index |
protected ArrayList<IScan> |
parsedScans |
protected org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> |
readerPool |
protected LCMSRunInfo |
runInfo |
protected MZMLFile |
source |
protected umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.VarsHolder |
vars |
DATA_FACTORY, is, numScansToProcess, subset| Constructor and Description |
|---|
MZMLMultiSpectraParser(InputStream is,
LCMSDataSubset subset,
MZMLFile source) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
addCurScanAndFlushVars() |
IndexBuilder.Result<MZMLIndexElement> |
buildIndex(IndexBuilder.Info info)
For use with Executors, consider using instead of calling this method directly.
|
List<IScan> |
call() |
protected boolean |
doesNeedSpectrumParsing(IScan scan) |
int |
findThisStreamFirstScanLen()
Intended use: find the length of the last scan entry in the file.
|
protected boolean |
flushVarsIfNoCurScan()
If the current
vars variable doesn't contain a scan, that we've started processing, then flushes all
the fields in vars and returns true, otherwise does nothing and returns false. |
MZMLMultiSpectraParser.MZMLIndexBuilder |
getIndexBuilder(IndexBuilder.Info info) |
org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> |
getReaderPool() |
MZMLFile |
getSource() |
protected int |
mapIdRefToInternalScanNum(javolution.text.CharArray id)
Given a scan ID goes to the index and tries to find a mapping.
|
protected int |
mapRawNumToInternalScanNum(int spectrumIndex)
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) |
getNumScansToProcess, setNumScansToProcessprotected final MZMLFile source
protected LCMSRunInfo runInfo
protected MZMLIndex index
protected umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.VarsHolder vars
protected org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool
public MZMLMultiSpectraParser(InputStream is, LCMSDataSubset subset, MZMLFile source) throws FileParsingException
FileParsingExceptionpublic MZMLFile getSource()
getSource in class MultiSpectraParserpublic org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> getReaderPool()
public void setReaderPool(org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool)
public int findThisStreamFirstScanLen()
throws FileParsingException
FileParsingExceptionpublic IndexBuilder.Result<MZMLIndexElement> buildIndex(IndexBuilder.Info info) throws Exception
info - info about offsets in file and in currently read bufferFileParsingExceptionExceptionprotected void addCurScanAndFlushVars()
protected boolean flushVarsIfNoCurScan()
vars variable doesn't contain a scan, that we've started processing, then flushes all
the fields in vars and returns true, otherwise does nothing and returns false.protected int mapIdRefToInternalScanNum(javolution.text.CharArray id)
throws FileParsingException
id - FileParsingException - in case the mapping can't be doneprotected int mapRawNumToInternalScanNum(int spectrumIndex)
throws FileParsingException
spectrumIndex - FileParsingExceptionprotected boolean doesNeedSpectrumParsing(IScan scan)
public MZMLMultiSpectraParser.MZMLIndexBuilder getIndexBuilder(IndexBuilder.Info info)
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