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 and 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 and 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 Detail

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 Detail

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