org.expasy.mzjava.proteomics.io.ms.ident

Class AbstractPsmCsvReader

java.lang.Object

org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader

All Implemented Interfaces:

PsmReader

Direct Known Subclasses:

MaxQuantPsmReader, ProteinPilotPsmReader

public abstract class AbstractPsmCsvReader
extends Object
implements PsmReader

Abstract implementation of PsmReader with a default parse template method. Each step of this parsing will have to be defined by inherited classes.

Author:

fnikitin Date: 4/9/13

Constructor Summary

Constructors

Constructor and Description
AbstractPsmCsvReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected abstract Collection<String>	getAccessionNumbers(ResultSet results) Extract accession numbers
int	getLineNumber()
protected abstract SpectrumIdentifier	getSpectrumId(ResultSet results) Create a new SpectrumIdentifier from a given ResultSet
protected abstract com.google.common.base.Optional<PeptideMatch>	makePeptideMatch(ResultSet results) Create a new PeptideMatch from a given ResultSet
void	parse(File file, PSMReaderCallback callback) Parse file and call back PSMReaderCallback on each found PSM
void	parse(File file, String delimiter, PSMReaderCallback callback)
void	parse(InputStream inputStream, PSMReaderCallback callback) Parse inputStream and call back PSMReaderCallback on each found PSM
void	parse(Reader reader, PSMReaderCallback callback) Parse reader and call back PSMReaderCallback on each found PSM
protected abstract void	setValues(PeptideMatch peptideMatch, ResultSet results) Set PeptideMatch score values

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractPsmCsvReader

public AbstractPsmCsvReader()

Method Detail

parse

public void parse(File file,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse file and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

file - input file

callback - a PSMReaderCallback implementation

parse

public void parse(InputStream inputStream,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse inputStream and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

inputStream - input stream

callback - a PSMReaderCallback implementation

parse

public void parse(Reader reader,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse reader and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

reader - input stream

callback - a PSMReaderCallback implementation

parse

public void parse(File file,
         String delimiter,
         PSMReaderCallback callback)

getLineNumber

public final int getLineNumber()

getSpectrumId

protected abstract SpectrumIdentifier getSpectrumId(ResultSet results)
                                             throws SQLException

Create a new SpectrumIdentifier from a given ResultSet

Parameters:

results - the current results to extract identified spectrum infos from

Returns:

a new SpectrumIdentifier

Throws:

SQLException

getAccessionNumbers

protected abstract Collection<String> getAccessionNumbers(ResultSet results)
                                                   throws SQLException

Extract accession numbers

Parameters:

results - the ResultSet to extract accession numbers from

Returns:

a collection of accession number

Throws:

SQLException

makePeptideMatch

protected abstract com.google.common.base.Optional<PeptideMatch> makePeptideMatch(ResultSet results)
                                                                           throws SQLException

Create a new PeptideMatch from a given ResultSet

Parameters:

results - the current results to extract PSM infos from

Returns:

an optional PeptideMatch instance

Throws:

SQLException

setValues

protected abstract void setValues(PeptideMatch peptideMatch,
             ResultSet results)
                           throws SQLException

Set PeptideMatch score values

Parameters:

peptideMatch - the peptide match to set values

results - the ResultSet to extract score values from

Throws:

SQLException