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

Class MsLibReader

java.lang.Object

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

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

All Implemented Interfaces:

IterativeReader<PeptideConsensusSpectrum>

Direct Known Subclasses:

MspReader, SptxtReader

public class MsLibReader
extends AbstractMsReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

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
MsLibReader(Reader reader, URI spectraSource, PeakList.Precision precision, SpectraLibCommentParser commentParser, AnnotationResolver annotationResolver, PeakProcessorChain<PepLibPeakAnnotation> processorChain, ModificationResolver modResolver)

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	handlePeakLine(LibrarySpectrumBuilder builder, String line) Handle peak line, which is any line that starts with a digit
protected boolean	handleTagLine(String tag, String value, LibrarySpectrumBuilder spectrumBuilder) Handle tag value line.
protected boolean	handleUnknownLine(LibrarySpectrumBuilder spectrum, String line) Handle line that is not a comment, begin ion, tag, peak or end ion
protected String	parseHeader(AbstractMsReader.ParseContext context) This is called on reader initialization.
protected PeptideConsensusSpectrum	parseNextEntry(AbstractMsReader.ParseContext context)
protected boolean	parseUnknownTag(String tag, String value, LibrarySpectrumBuilder spectrum) Called if there are any tags that are not handled by SptxtReader2 This is meant to be over ridden by subclasses that want to parse tags that the SptxtReader2 does not know about

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

MsLibReader

public MsLibReader(Reader reader,
           URI spectraSource,
           PeakList.Precision precision,
           SpectraLibCommentParser commentParser,
           AnnotationResolver annotationResolver,
           PeakProcessorChain<PepLibPeakAnnotation> processorChain,
           ModificationResolver modResolver)
            throws IOException

Throws:

IOException

Method Detail

parseHeader

protected String parseHeader(AbstractMsReader.ParseContext context)
                      throws IOException

Description copied from class: AbstractMsReader

This is called on reader initialization. Subclasses should parse any information that occurs before the first spectrum. The information can returned as a string

Specified by:

parseHeader in class AbstractMsReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

Parameters:

context - the parser context

Returns:

the data that is before the first spectrum

Throws:

IOException

parseNextEntry

protected PeptideConsensusSpectrum parseNextEntry(AbstractMsReader.ParseContext context)
                                           throws IOException

Specified by:

parseNextEntry in class AbstractMsReader<PepLibPeakAnnotation,PeptideConsensusSpectrum>

Returns:

the next T-object or null if no more object to read.

Throws:

IOException

handleTagLine

protected boolean handleTagLine(String tag,
                    String value,
                    LibrarySpectrumBuilder spectrumBuilder)

Handle tag value line. The tag and value is separated by =

Parameters:

spectrumBuilder - the spectrumBuilder currently being read

tag - the string from the start of the lien to the = character

value - the string from the character after the = to the end of the line

Returns:

true if the information in the line was processed, false otherwise

handlePeakLine

protected boolean handlePeakLine(LibrarySpectrumBuilder builder,
                     String line)

Handle peak line, which is any line that starts with a digit

Parameters:

builder - the builder currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

handleUnknownLine

protected boolean handleUnknownLine(LibrarySpectrumBuilder spectrum,
                        String line)

Handle line that is not a comment, begin ion, tag, peak or end ion

Parameters:

spectrum - the spectrum currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

parseUnknownTag

protected boolean parseUnknownTag(String tag,
                      String value,
                      LibrarySpectrumBuilder spectrum)

Called if there are any tags that are not handled by SptxtReader2 This is meant to be over ridden by subclasses that want to parse tags that the SptxtReader2 does not know about

Parameters:

tag - the characters in the line before the first =

value - the characters in the line after the first =

spectrum - the spectrum that is being read

Returns:

true of this handled the tag, false otherwise