org.proteios.io
Class MzMLFileReader

java.lang.Object
  org.proteios.io.MzMLFileReader

All Implemented Interfaces:

FileValidationInterface, PeakListFileInterface, SpectrumFileContactReaderInterface, SpectrumFileInstrumentReaderInterface, SpectrumIdReaderInterface

public class MzMLFileReader
extends Object
implements PeakListFileInterface, SpectrumIdReaderInterface, FileValidationInterface, SpectrumFileContactReaderInterface, SpectrumFileInstrumentReaderInterface

This class contains methods to access spectra from an mzML file.

Author:

olle

Constructor Summary

MzMLFileReader()
Default constructor.

MzMLFileReader(InputStream xmlInputStream)
Constructor that takes an mzML XML input stream as parameter.

Method Summary

Iterator<SpectrumInterface>	getSpectrum(List<String> spectrumIds) Get an iterator for spectra with specified spectrum id values.
SpectrumInterface	getSpectrum(String spectrumId) Get the spectrum data for specified spectrum id.
SpectrumFileContact	getSpectrumContact() Get the spectrum contact data.
List<SpectrumFileInstrumentInterface>	getSpectrumFileInstrumentList() Get the spectrum file instrument list.
List<String>	getSpectrumIdList() Get spectrum id list.
InputStream	getXMLInputStream() Get mzML XML input stream.
String	getXsdFilePath() Get XSD schema file to validate against.
boolean	importable() Validates first element of input stream.
boolean	isSpectrumIdObtainedFromSpectrumOrderNumber() Specifies if the spectrum id values were obtained from the spectrum order numbers.
void	setXMLInputStream(InputStream xmlInputStream) Set mzML XML input stream.
void	setXsdFilePath(String xsdFilePath) Set XSD schema file to validate against.
boolean	valid() Validates mzML XML input stream against current mzML XSD file.

Methods inherited from class java.lang.Object

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

Constructor Detail

MzMLFileReader

public MzMLFileReader()

Default constructor.

MzMLFileReader

public MzMLFileReader(InputStream xmlInputStream)

Constructor that takes an mzML XML input stream as parameter.

Parameters:

xmlInputStream - InputStream mzML XML input stream.

Method Detail

getXMLInputStream

public InputStream getXMLInputStream()

Get mzML XML input stream.

Returns:

xmlFilePath InputStream mzML XML input stream.

setXMLInputStream

public void setXMLInputStream(InputStream xmlInputStream)

Set mzML XML input stream.

Parameters:

xmlInputStream - InputStream mzML XML input stream.

getXsdFilePath

public String getXsdFilePath()

Get XSD schema file to validate against.

Returns:

xsdFilePath String with path for XSD schema file.

setXsdFilePath

public void setXsdFilePath(String xsdFilePath)

Set XSD schema file to validate against.

Parameters:

xsdFilePath - String with path for XSD schema file.

getSpectrum

public SpectrumInterface getSpectrum(String spectrumId)

Get the spectrum data for specified spectrum id.

Specified by:

getSpectrum in interface PeakListFileInterface

Parameters:

spectrumId - String spectrum id.

Returns:

spectrum with specified spectrum id.

getSpectrum

public Iterator<SpectrumInterface> getSpectrum(List<String> spectrumIds)

Get an iterator for spectra with specified spectrum id values.

Specified by:

getSpectrum in interface PeakListFileInterface

Parameters:

spectrumIds - List list with spectrum id values.

Returns:

iterator for spectra with specified spectrum id values.

getSpectrumIdList

public List<String> getSpectrumIdList()

Get spectrum id list.

Specified by:

getSpectrumIdList in interface SpectrumIdReaderInterface

Returns:

List List with spectrum id values.

isSpectrumIdObtainedFromSpectrumOrderNumber

public boolean isSpectrumIdObtainedFromSpectrumOrderNumber()

Specifies if the spectrum id values were obtained from the spectrum order numbers.

Specified by:

isSpectrumIdObtainedFromSpectrumOrderNumber in interface SpectrumIdReaderInterface

Returns:

boolean True if the spectrum id values were obtained from spectrum order numbers, else false.

valid

public boolean valid()
              throws javax.xml.stream.XMLStreamException,
                     SAXException

Validates mzML XML input stream against current mzML XSD file.

Specified by:

valid in interface FileValidationInterface

Returns:

True if the mzML XML input stream is valid, else false

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

SAXException

importable

public boolean importable()

Validates first element of input stream.

Specified by:

importable in interface FileValidationInterface

Returns:

True if the input stream is valid, else false

getSpectrumContact

public SpectrumFileContact getSpectrumContact()

Get the spectrum contact data.

Specified by:

getSpectrumContact in interface SpectrumFileContactReaderInterface

Returns:

SpectrumContact The spectrum contact data.

getSpectrumFileInstrumentList

public List<SpectrumFileInstrumentInterface> getSpectrumFileInstrumentList()

Get the spectrum file instrument list.

Specified by:

getSpectrumFileInstrumentList in interface SpectrumFileInstrumentReaderInterface

Returns:

List The spectrum file instrument list.