eu.isas.peptideshaker.followup

Class FastaExport

java.lang.Object

eu.isas.peptideshaker.followup.FastaExport

public class FastaExport
extends Object

Export proteins in the FASTA format.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

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

Constructor Summary

Constructors

Constructor and Description
FastaExport()

Method Summary

Modifier and Type	Method and Description
static void	export(File destinationFile, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.identification.Identification identification, FastaExport.ExportType exportType, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean accessionOnly) Exports the proteins of interest in a text file of the given format.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaExport

public FastaExport()

Method Detail

export

public static void export(File destinationFile,
                          com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                          com.compomics.util.experiment.identification.Identification identification,
                          FastaExport.ExportType exportType,
                          com.compomics.util.waiting.WaitingHandler waitingHandler,
                          boolean accessionOnly)

Exports the proteins of interest in a text file of the given format. Non validated protein mode iterates all proteins in the original FASTA file (size in the sequence factory). Validated protein mode iterates only validated proteins (size in the identification features generator).

Parameters:

destinationFile - the file where to write

sequenceProvider - the sequence provider

identification - the identification

exportType - the export type (see enum below)

waitingHandler - waiting handler used to display progress and cancel the process

accessionOnly - if true only the accession of the protein will be exported, if false the entire information in FASTA format