Package eu.isas.peptideshaker.fileimport

Class FileImporter

java.lang.Object
eu.isas.peptideshaker.fileimport.FileImporter
public class FileImporter extends Object
This class is responsible for the import of identifications.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    FileImporter​(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, ProjectDetails projectDetails, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Constructor for the importer.

  • Method Summary

    Modifier and Type
    Method
    Description
    com.compomics.util.experiment.identification.protein_inference.FastaMapper
    getFastaMapper()
    Returns the fasta mapper.
    com.compomics.util.experiment.biology.genes.GeneMaps
    getGeneMaps()
    Returns the gene maps.
    InputMap
    getInputMap()
    Returns the input map.
    HashMap<String,​Integer>
    getProteinCount()
    Returns the occurrence of proteins.
    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
    getProteinDetailsProvider()
    Returns the details provider.
    com.compomics.util.experiment.io.biology.protein.SequenceProvider
    getSequenceProvider()
    Returns the sequence provider.
    int
    importFiles​(ArrayList<File> idFiles)
    Imports the identifications from the files.
    void
    importGenes()
    Imports the gene information for this project.
    void
    importPsms​(File idFile)
    Imports the PSMs from an identification file.
    void
    importSequences​(com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Imports sequences from a FASTA file and sets the sequence provider and protein details provider fields.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • FileImporter

      public FileImporter​(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, ProjectDetails projectDetails, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
      Constructor for the importer.
      Parameters:
      identification - The identification where to store the matches.
      processingParameters - The processing parameters.
      identificationParameters - The identification parameters.
      projectDetails - The project details.
      metrics - The metrics of the data set to be saved.
      spectrumProvider - The spectrum provider.
      waitingHandler - The handler displaying feedback to the user.
      exceptionHandler - The exception handler.

  • Method Details

    • importFiles

      public int importFiles​(ArrayList<File> idFiles)
      Imports the identifications from the files.
      Parameters:
      idFiles - the identification files
      Returns:
      0 if success, 1 if not

    • importPsms

      public void importPsms​(File idFile) throws IOException, InterruptedException, TimeoutException
      Imports the PSMs from an identification file.
      Parameters:
      idFile - the identification file
      Throws:
      IOException - exception thrown if an error occurred when parsing the file
      InterruptedException - Exception thrown if a thread is interrupted.
      TimeoutException - Exception thrown if the process timed out.

    • importSequences

      public void importSequences​(com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) throws IOException
      Imports sequences from a FASTA file and sets the sequence provider and protein details provider fields.
      Parameters:
      sequenceMatchingParameters - the sequence matching parameters
      searchParameters - the search parameters
      fastaParameters - the FASTA parameters
      peptideVariantsParameters - the peptide variants parameters set by the user
      waitingHandler - the handler displaying feedback to the user and allowing canceling the import
      exceptionHandler - handler for exceptions
      Throws:
      IOException - exception thrown if an error occurred while reading the FASTA file

    • importGenes

      public void importGenes()
      Imports the gene information for this project.

    • getGeneMaps

      public com.compomics.util.experiment.biology.genes.GeneMaps getGeneMaps()
      Returns the gene maps.
      Returns:
      the gene maps

    • getSequenceProvider

      public com.compomics.util.experiment.io.biology.protein.SequenceProvider getSequenceProvider()
      Returns the sequence provider.
      Returns:
      the sequence provider

    • getProteinDetailsProvider

      public com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider getProteinDetailsProvider()
      Returns the details provider.
      Returns:
      the details provider

    • getFastaMapper

      public com.compomics.util.experiment.identification.protein_inference.FastaMapper getFastaMapper()
      Returns the fasta mapper.
      Returns:
      the fasta mapper

    • getInputMap

      public InputMap getInputMap()
      Returns the input map.
      Returns:
      the input map

    • getProteinCount

      public HashMap<String,​Integer> getProteinCount()
      Returns the occurrence of proteins.
      Returns:
      the occurrence of proteins