org.proteios.io
Class PeakListFileImpl

java.lang.Object
  org.proteios.io.PeakListFileImpl

All Implemented Interfaces:

FileValidationInterface, PeakListFileInterface, SpectrumFileContactReaderInterface, SpectrumFileInstrumentReaderInterface, SpectrumIdReaderInterface

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

This class implements the PeakListFileInterface that defines methods to access spectra from an mzData file.

Author:

olle

Constructor Summary

PeakListFileImpl()
Default constructor.

PeakListFileImpl(InputStream xmlInputStream)
Constructor that takes an mzData XML input stream as parameter.

Method Summary

Iterator<SpectrumInterface>	getSpectrum(List<String> spectrumIds) Get an iterator for spectra with specified spectrum ids.
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 list of all mzData spectrum ids from input stream. the function will read through the entire file.
InputStream	getXMLInputStream() Get mzData 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 mzData XML input stream.
void	setXsdFilePath(String xsdFilePath) Set XSD schema file to validate against.
boolean	valid() Validates mzData XML input stream against current mzData XSD file.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeakListFileImpl

public PeakListFileImpl()

Default constructor.

PeakListFileImpl

public PeakListFileImpl(InputStream xmlInputStream)

Constructor that takes an mzData XML input stream as parameter.

Parameters:

xmlInputStream - InputStream mzData XML input stream.

Method Detail

getXMLInputStream

public InputStream getXMLInputStream()

Get mzData XML input stream.

Returns:

xmlFilePath InputStream mzData XML input stream.

setXMLInputStream

public void setXMLInputStream(InputStream xmlInputStream)

Set mzData XML input stream.

Parameters:

xmlInputStream - InputStream mzData 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.

valid

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

Validates mzData XML input stream against current mzData XSD file.

Specified by:

valid in interface FileValidationInterface

Returns:

True if the mzData 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

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 ids.

Specified by:

getSpectrum in interface PeakListFileInterface

Parameters:

spectrumIds - List list with spectrum ids.

Returns:

iterator for spectra with specified spectrum ids.

getSpectrumIdList

public List<String> getSpectrumIdList()

Get list of all mzData spectrum ids from input stream. the function will read through the entire file.

Specified by:

getSpectrumIdList in interface SpectrumIdReaderInterface

Returns:

List list of spectrum ids.

isSpectrumIdObtainedFromSpectrumOrderNumber

public boolean isSpectrumIdObtainedFromSpectrumOrderNumber()

Description copied from interface: SpectrumIdReaderInterface

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.

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.