org.proteios.io
Class PklFileReader

java.lang.Object
  org.proteios.io.PklFileReader

All Implemented Interfaces:

FileValidationInterface, PeakListFileInterface, SpectrumIdReaderInterface

public class PklFileReader
extends Object
implements PeakListFileInterface, SpectrumIdReaderInterface, FileValidationInterface

This class contains methods to access spectra from a PKL peak list file.

Author:

olle

Constructor Summary

PklFileReader()
Default constructor.

PklFileReader(InputStream inputStream)
Constructor that takes a PKL input stream as parameter.

Method Summary

InputStream	getInputStream() Get PKL input stream.
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.
List<String>	getSpectrumIdList() Get spectrum id list.
boolean	importable() Validates first line of input stream.
boolean	isSpectrumIdObtainedFromSpectrumOrderNumber() Specifies if the spectrum id values were obtained from the spectrum order numbers.
void	setInputStream(InputStream inputStream) Set PKL input stream.
boolean	valid() Validates PKL input stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

PklFileReader

public PklFileReader()

Default constructor.

PklFileReader

public PklFileReader(InputStream inputStream)

Constructor that takes a PKL input stream as parameter.

Parameters:

inputStream - InputStream PKL input stream.

Method Detail

getInputStream

public InputStream getInputStream()

Get PKL input stream.

Returns:

InputStream PKL input stream.

setInputStream

public void setInputStream(InputStream inputStream)

Set PKL input stream.

Parameters:

inputStream - InputStream PKL input stream.

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()

Validates PKL input stream.

Specified by:

valid in interface FileValidationInterface

Returns:

True if the PKL input stream is valid, else false

Throws:

BaseException - If there is an error

importable

public boolean importable()

Validates first line of input stream.

Specified by:

importable in interface FileValidationInterface

Returns:

True if the input stream is valid, else false