eu.isas.peptideshaker.followup

Class ProgenesisExport

java.lang.Object

eu.isas.peptideshaker.followup.ProgenesisExport

public class ProgenesisExport
extends Object

This class exports identifications for post-processing with Non-Linear Progenesis.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ProgenesisExport.ExportType Enum of the different types of export implemented.

Field Summary

Fields

Modifier and Type	Field and Description
static char	SEPARATOR The separator (tab by default).

Constructor Summary

Constructors

Constructor and Description
ProgenesisExport()

Method Summary

Modifier and Type

Method and Description

static void

writeProgenesisExport(File destinationFile, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.identification.Identification identification, ProgenesisExport.ExportType exportType, com.compomics.util.waiting.WaitingHandler waitingHandler, HashSet<String> targetedModifications, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) Writes a file containing the PSMs in a Progenesis compatible format.

Methods inherited from class java.lang.Object

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

Field Detail

SEPARATOR

public static final char SEPARATOR

The separator (tab by default).

See Also:

Constant Field Values

Constructor Detail

ProgenesisExport

public ProgenesisExport()

Method Detail

writeProgenesisExport

public static void writeProgenesisExport(File destinationFile,
                                         com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                         com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                         com.compomics.util.experiment.identification.Identification identification,
                                         ProgenesisExport.ExportType exportType,
                                         com.compomics.util.waiting.WaitingHandler waitingHandler,
                                         HashSet<String> targetedModifications,
                                         com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
                                  throws IOException

Writes a file containing the PSMs in a Progenesis compatible format.

Parameters:

destinationFile - the destination file

sequenceProvider - a sequence provider

proteinDetailsProvider - the protein details provider

identification - the identification

exportType - the type of export

waitingHandler - waiting handler displaying progress to the user and allowing canceling the process

targetedModifications - the modifications of interest in case of a PTM export. Ignored otherwise.

sequenceMatchingPreferences - the sequence matching preferences

Throws:

IOException - thrown if an error occurred while writing the file