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

Class SptxtReader

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.SptxtReader

All Implemented Interfaces:

IterativeReader<PeptideConsensusSpectrum>

public class SptxtReader
extends MsLibReader

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SptxtReader.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

Constructor Summary

Constructors

Constructor and Description
SptxtReader(File file, PeakList.Precision precision)

Method Summary

Methods

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

Constructor Detail

SptxtReader

public SptxtReader(File file,
           PeakList.Precision precision)
            throws IOException

Throws:

IOException

Method Detail

newBuilder

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

Factory method to create a Builder for creating a SptxtReader to read an sptxt file from file

Parameters:

file - the file that is to be read

Returns:

the new Builder

Throws:

IOException

newBuilder

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

Factory method to create a Builder for creating a SptxtReader to read an sptxt file from the reader

Parameters:

reader - the reader that is to be read

source - the source of the spectra

Returns:

the new Builder