org.expasy.mzjava.core.io.ms.spectrum

Class MzxmlReader

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<PeakAnnotation,MsnSpectrum>

org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader

All Implemented Interfaces:

IterativeReader<MsnSpectrum>

public class MzxmlReader
extends AbstractMsReader<PeakAnnotation,MsnSpectrum>

Author:

fnikitin Date: 6/24/13, Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MzxmlReader.ConsistencyCheck
static class	MzxmlReader.ConsistencyCheckException
static class	MzxmlReader.XMLEventUtils

Nested classes/interfaces inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

AbstractMsReader.ParseContext

Field Summary

Fields inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, precision

Fields inherited from interface org.expasy.mzjava.core.io.IterativeReader

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
MzxmlReader(File file, PeakList.Precision precision)
MzxmlReader(File file, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)

Method Summary

Methods

Modifier and Type	Method and Description
void	addConsistencyChecks(Set<MzxmlReader.ConsistencyCheck> ccs)
void	close() Closes the reader and releases any system resources associated with it.
protected void	consistencyChecks(MsnSpectrum spectrum) Check for all spectrum consistencies
static void	convert64bitsAndPopulate(byte[] bytes, double[] mzs, double[] intensities, int expectedScanNumber)
int	getExpectedScanCount()
protected void	init(AbstractMsReader.ParseContext context)
protected MsnSpectrum	newSpectrum(StartElement scanElement, AbstractMsReader.ParseContext context) Create a spectrum
static MzxmlReader	newStrictReader(File file, PeakList.Precision precision) Create an instance of MzxmlReader that strictly checks that the decoded spectrum is consistent with xml attributes (see also addConsistencyChecks()/removeConsistencyChecks() method)
static MzxmlReader	newStrictReader(File file, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain) Create an instance of MzxmlReader that strictly checks that the decoded spectrum is consistent with xml attributes (see also addConsistencyChecks()/removeConsistencyChecks() method)
static MzxmlReader	newTolerantReader(File file, PeakList.Precision precision) Create an instance of MzxmlReader that does not check for inconsistencies
MsnSpectrum	next() Returns the next element in the reader.
protected String	parseHeader(AbstractMsReader.ParseContext context) This is called on reader initialization.
protected MsnSpectrum	parseNextEntry(AbstractMsReader.ParseContext context)
void	removeConsistencyChecks(Set<MzxmlReader.ConsistencyCheck> ccs)
void	setDelta(float delta)

Methods inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, addPeaksToSpectrum, addPeakToSpectrum, getContext, getHeader, hasNext

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MzxmlReader

public MzxmlReader(File file,
           PeakList.Precision precision)
            throws IOException

Throws:

IOException

MzxmlReader

public MzxmlReader(File file,
           PeakList.Precision precision,
           PeakProcessorChain<PeakAnnotation> processorChain)
            throws IOException

Throws:

IOException

Method Detail

newStrictReader

public static MzxmlReader newStrictReader(File file,
                          PeakList.Precision precision)
                                   throws IOException

Create an instance of MzxmlReader that strictly checks that the decoded spectrum is consistent with xml attributes (see also addConsistencyChecks()/removeConsistencyChecks() method)

Parameters:

file - the mzxml file to read

precision - the peak precision

Returns:

MzxmlReader object

Throws:

IOException

newStrictReader

public static MzxmlReader newStrictReader(File file,
                          PeakList.Precision precision,
                          PeakProcessorChain<PeakAnnotation> processorChain)
                                   throws IOException

Create an instance of MzxmlReader that strictly checks that the decoded spectrum is consistent with xml attributes (see also addConsistencyChecks()/removeConsistencyChecks() method)

Parameters:

file - the mzxml file to read

precision - the peak precision

processorChain - PeakProcessorChain to process the peaks while reading

Returns:

MzxmlReader object

Throws:

IOException

newTolerantReader

public static MzxmlReader newTolerantReader(File file,
                            PeakList.Precision precision)
                                     throws IOException

Create an instance of MzxmlReader that does not check for inconsistencies

Parameters:

file - the mzxml file to read

precision - the peak precision

Returns:

MzxmlReader object

Throws:

IOException

removeConsistencyChecks

public void removeConsistencyChecks(Set<MzxmlReader.ConsistencyCheck> ccs)

addConsistencyChecks

public void addConsistencyChecks(Set<MzxmlReader.ConsistencyCheck> ccs)

init

protected void init(AbstractMsReader.ParseContext context)
             throws IOException

Overrides:

init in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Throws:

IOException

setDelta

public void setDelta(float delta)

close

public void close()
           throws IOException

Description copied from interface: IterativeReader

Closes the reader and releases any system resources associated with it. Once the reader has been closed, further hasNext() or next() invocations will throw an IOException. Closing a previously closed reader has no effect.

Specified by:

close in interface IterativeReader<MsnSpectrum>

Overrides:

close in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Throws:

IOException - If an I/O error occurs

parseHeader

protected String parseHeader(AbstractMsReader.ParseContext context)
                      throws IOException

Description copied from class: AbstractMsReader

This is called on reader initialization. Subclasses should parse any information that occurs before the first spectrum. The information can returned as a string

Specified by:

parseHeader in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Parameters:

context - the parser context

Returns:

the data that is before the first spectrum

Throws:

IOException

getExpectedScanCount

public int getExpectedScanCount()

next

public MsnSpectrum next()
                 throws IOException

Description copied from interface: IterativeReader

Returns the next element in the reader.

Specified by:

next in interface IterativeReader<MsnSpectrum>

Overrides:

next in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Returns:

the next element in the iteration

Throws:

IOException - if there is an io exception

parseNextEntry

protected MsnSpectrum parseNextEntry(AbstractMsReader.ParseContext context)
                              throws IOException

Specified by:

parseNextEntry in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Returns:

the next T-object or null if no more object to read.

Throws:

IOException

consistencyChecks

protected void consistencyChecks(MsnSpectrum spectrum)

Check for all spectrum consistencies

Parameters:

spectrum - the spectrum on which checks are done

Throws:

IllegalStateException - if xml stream error

MzxmlReader.ConsistencyCheckException - if a check reveals inconsistencies

newSpectrum

protected MsnSpectrum newSpectrum(StartElement scanElement,
                      AbstractMsReader.ParseContext context)
                           throws XMLStreamException

Create a spectrum

Parameters:

scanElement - the container providing data to spectrum

Returns:

a new instance of MsnSpectrum

Throws:

XMLStreamException

convert64bitsAndPopulate

public static void convert64bitsAndPopulate(byte[] bytes,
                            double[] mzs,
                            double[] intensities,
                            int expectedScanNumber)