org.expasy.mzjava.proteomics.io.ms.spectrum

Class MspReader

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader

org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader

All Implemented Interfaces:

IterativeReader<PeptideConsensusSpectrum>

public class MspReader
extends MsLibReader

An IterativeReader that can read nist msp files. See http://peptide.nist.gov/

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MspReader.Builder

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

Method Summary

Methods

Modifier and Type	Method and Description
static MspReader.Builder	newBuilder(File file, PeakList.Precision precision) Factory method to create a Builder for creating a MspReader to read an msp file from file
static MspReader.Builder	newBuilder(Reader reader, URI source, PeakList.Precision precision) Factory method to create a Builder for creating a MspReader to read an msp file from the reader

Methods inherited from class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader

handlePeakLine, handleTagLine, handleUnknownLine, parseHeader, parseNextEntry, parseUnknownTag

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

acceptUnsortedSpectra, addPeaksToSpectrum, addPeakToSpectrum, close, getContext, getHeader, hasNext, init, next

Methods inherited from class java.lang.Object

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

Method Detail

newBuilder

public static MspReader.Builder newBuilder(File file,
                           PeakList.Precision precision)
                                    throws IOException

Factory method to create a Builder for creating a MspReader to read an msp file from file

Parameters:

file - the file that is to be read

Returns:

the new Builder

Throws:

IOException

newBuilder

public static MspReader.Builder newBuilder(Reader reader,
                           URI source,
                           PeakList.Precision precision)

Factory method to create a Builder for creating a MspReader to read an msp file from the reader

Parameters:

reader - the reader that is to be read

source - the source of the spectra

Returns:

the new Builder