Package 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
    Description
    static enum 
    FastaExport.ExportType
    Enum of the different types of export implemented.

  • Constructor Summary

    Constructors
    Constructor
    Description
    FastaExport()
     

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • FastaExport

      public FastaExport()

  • Method Details

    • 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