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

Class ProteinPilotPsmReader

java.lang.Object

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

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

All Implemented Interfaces:

PsmReader

public class ProteinPilotPsmReader
extends AbstractPsmCsvReader

A peptide spectrum match reader for ProteinPilot Peptide Summary Overview tsv file.

Unknown modifications

By default, an IllegalStateException runtime exception is thrown if the reader meets an unknown modification. If this crash is not an option, user should give an implementation of UnknownModListener to the reader. The makePeptideMatch method will return Optional.absent()).

Author:

fnikitin, Oliver Horlacher

Date: 4/9/13

Constructor Summary

Constructors

Constructor and Description
ProteinPilotPsmReader() Default constructor with default resolver ProteinPilotModificationResolver
ProteinPilotPsmReader(ModificationResolver modResolver)

Method Summary

Methods

Modifier and Type	Method and Description
protected Collection<String>	getAccessionNumbers(ResultSet results) Extract accession numbers
protected SpectrumIdentifier	getSpectrumId(ResultSet results) Create a new SpectrumIdentifier from a given ResultSet
protected com.google.common.base.Optional<PeptideMatch>	makePeptideMatch(ResultSet results) Create a new PeptideMatch from a given ResultSet
void	setUnknownModListener(UnknownModListener listener) Set the UnknownModListener
protected void	setValues(PeptideMatch peptideMatch, ResultSet results) Set PeptideMatch score values

Methods inherited from class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader

getLineNumber, parse, parse, parse, parse

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinPilotPsmReader

public ProteinPilotPsmReader()

Default constructor with default resolver ProteinPilotModificationResolver

ProteinPilotPsmReader

public ProteinPilotPsmReader(ModificationResolver modResolver)

Parameters:

modResolver - the modification resolver

Method Detail

setUnknownModListener

public void setUnknownModListener(UnknownModListener listener)

Set the UnknownModListener

Parameters:

listener - the listener that handle unknown modifications

getSpectrumId

protected SpectrumIdentifier getSpectrumId(ResultSet results)
                                    throws SQLException

Description copied from class: AbstractPsmCsvReader

Create a new SpectrumIdentifier from a given ResultSet

Specified by:

getSpectrumId in class AbstractPsmCsvReader

Parameters:

results - the current results to extract identified spectrum infos from

Returns:

a new SpectrumIdentifier

Throws:

SQLException

getAccessionNumbers

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

Description copied from class: AbstractPsmCsvReader

Extract accession numbers

Specified by:

getAccessionNumbers in class AbstractPsmCsvReader

Parameters:

results - the ResultSet to extract accession numbers from

Returns:

a collection of accession number

Throws:

SQLException

makePeptideMatch

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

Description copied from class: AbstractPsmCsvReader

Create a new PeptideMatch from a given ResultSet

Specified by:

makePeptideMatch in class AbstractPsmCsvReader

Parameters:

results - the current results to extract PSM infos from

Returns:

an optional PeptideMatch instance

Throws:

SQLException

setValues

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

Description copied from class: AbstractPsmCsvReader

Set PeptideMatch score values

Specified by:

setValues in class AbstractPsmCsvReader

Parameters:

peptideMatch - the peptide match to set values

results - the ResultSet to extract score values from

Throws:

SQLException