org.expasy.mzjava.external.io.ms.spectrum.mzml

Class EbiMzmlReader<S extends MsnSpectrum>

java.lang.Object

org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader<S>

All Implemented Interfaces:

IterativeReader<S>, ConsistencyCheckHandler<MzmlConsistencyCheck>

public class EbiMzmlReader<S extends MsnSpectrum>
extends Object
implements IterativeReader<S>, ConsistencyCheckHandler<MzmlConsistencyCheck>

EbiMzmlReader is a wrapper over jmzml reader provided by EBI (https://code.google.com/p/jmzml/) that fully support mzML 1.1.0 specifications (http://www.psidev.info/mzml_1_0_0%20). Scan number are extracted from spectrum id with SpectrumIdParser (default set with ScanNumberIncrementer).

Field Summary

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

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
EbiMzmlReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision)
EbiMzmlReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	checkConsistencies(S spectrum, uk.ac.ebi.jmzml.model.mzml.Spectrum mzmlSpectrum)
void	close() Closes the reader and releases any system resources associated with it.
protected void	handleIsolationWindow(double targetMz, double lowerOffset, double upperOffset, S spectrum) Handle isolation window parameters.
protected void	handleMsLevelAtLeast(uk.ac.ebi.jmzml.model.mzml.Spectrum src, S dest) Extract information from mzml spectrum to msn spectrum.
boolean	hasNext() Returns true if the reader has more elements.
protected S	newSpectrum(PeakList.Precision precision) Override this method to make an instance of S (MsnSpectrum by default)
static EbiMzmlReader	newStrictReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision)
static <S extends MsnSpectrum> EbiMzmlReader	newStrictReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)
static <A extends PeakAnnotation> EbiMzmlReader	newTolerantReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision)
static <S extends MsnSpectrum> EbiMzmlReader	newTolerantReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)
S	next() Returns the next element in the reader.
void	setDelta(float delta) Set delta value
void	setSpectrumIdParser(SpectrumIdParser spectrumIdParser) Set parser that extract scan number from spectrum id attribute.
int	size()
void	turnStrict(Set<MzmlConsistencyCheck> ccs) Make these checks strict (throw a ConsistencyCheckException if a check fails)
void	turnTolerant(Set<MzmlConsistencyCheck> ccs) Make these checks tolerant (log a message if a check fails)

Methods inherited from class java.lang.Object

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

Constructor Detail

EbiMzmlReader

public EbiMzmlReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller,
             PeakList.Precision precision)

EbiMzmlReader

public EbiMzmlReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller,
             PeakList.Precision precision,
             PeakProcessorChain<PeakAnnotation> processorChain)

Method Detail

newStrictReader

public static EbiMzmlReader newStrictReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller,
                            PeakList.Precision precision)

newStrictReader

public static <S extends MsnSpectrum> EbiMzmlReader newStrictReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller,
                                                    PeakList.Precision precision,
                                                    PeakProcessorChain<PeakAnnotation> processorChain)

newTolerantReader

public static <A extends PeakAnnotation> EbiMzmlReader newTolerantReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller,
                                                         PeakList.Precision precision)

newTolerantReader

public static <S extends MsnSpectrum> EbiMzmlReader newTolerantReader(uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller unmarshaller,
                                                      PeakList.Precision precision,
                                                      PeakProcessorChain<PeakAnnotation> processorChain)

setDelta

public void setDelta(float delta)

Description copied from interface: ConsistencyCheckHandler

Set delta value

Specified by:

setDelta in interface ConsistencyCheckHandler<MzmlConsistencyCheck>

Parameters:

delta - the maximum delta between expected and actual for which both numbers are still considered equal.

turnTolerant

public void turnTolerant(Set<MzmlConsistencyCheck> ccs)

Description copied from interface: ConsistencyCheckHandler

Make these checks tolerant (log a message if a check fails)

Specified by:

turnTolerant in interface ConsistencyCheckHandler<MzmlConsistencyCheck>

Parameters:

ccs - consistency checks

turnStrict

public void turnStrict(Set<MzmlConsistencyCheck> ccs)

Description copied from interface: ConsistencyCheckHandler

Make these checks strict (throw a ConsistencyCheckException if a check fails)

Specified by:

turnStrict in interface ConsistencyCheckHandler<MzmlConsistencyCheck>

Parameters:

ccs - consistency checks

setSpectrumIdParser

public void setSpectrumIdParser(SpectrumIdParser spectrumIdParser)

Set parser that extract scan number from spectrum id attribute.

Parameters:

spectrumIdParser - the parser

size

public int size()

Returns:

the number of spectra to read

hasNext

public boolean hasNext()

Description copied from interface: IterativeReader

Returns true if the reader has more elements. (In other words, returns true if IterativeReader.next() would return an element rather than throwing an exception.)

Specified by:

hasNext in interface IterativeReader<S extends MsnSpectrum>

Returns:

true if the reader has more elements

newSpectrum

protected S newSpectrum(PeakList.Precision precision)

Override this method to make an instance of S (MsnSpectrum by default)

Parameters:

precision - peaks precision

Returns:

an S instance

next

public S next()
                           throws IOException

Description copied from interface: IterativeReader

Returns the next element in the reader.

Specified by:

next in interface IterativeReader<S extends MsnSpectrum>

Returns:

the next element in the iteration

Throws:

IOException - if there is an io exception

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<S extends MsnSpectrum>

Throws:

IOException - If an I/O error occurs

checkConsistencies

protected void checkConsistencies(S spectrum,
                      uk.ac.ebi.jmzml.model.mzml.Spectrum mzmlSpectrum)

handleMsLevelAtLeast

protected void handleMsLevelAtLeast(uk.ac.ebi.jmzml.model.mzml.Spectrum src,
                        S dest)

Extract information from mzml spectrum to msn spectrum. This default implementation only extract ms level. [This method is meant to be overriden if more data have to be extracted from the source spectrum]

Parameters:

src - the mzxml spectrum source

dest - the msn spectrum destination

handleIsolationWindow

protected void handleIsolationWindow(double targetMz,
                         double lowerOffset,
                         double upperOffset,
                         S spectrum)

Handle isolation window parameters.

Parameters:

targetMz - center of window m/z

lowerOffset - lower bound offset

upperOffset - upper bound offset

spectrum - the destination spectrum