eu.isas.peptideshaker.cmd

Class CLIExportMethods

java.lang.Object

eu.isas.peptideshaker.cmd.CLIExportMethods

public class CLIExportMethods
extends Object

This class groups standard methods used by the different command line interfaces.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
CLIExportMethods()

Method Summary

Modifier and Type	Method and Description
static File	exportAccessions(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filteringPreferences) Exports the accessions as specified in the follow-up input bean.
static ArrayList<File>	exportDeepLC(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports files needed by DeepLC.
static void	exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler) Writes the documentation corresponding to an export given the command line arguments.
static File	exportInclusionList(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filterPreferences) Exports an inclusion list of the validated hits.
static ArrayList<File>	exportMs2pip(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports the files needed by ms2pip.
static void	exportMzId(MzidCLIInputBean mzidCLIInputBean, PsdbParent psbdParent, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports the project in the mzIdentML format.
static void	exportPercolator(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports the files needed by Percolator.
static File	exportProgenesis(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) Exports the identification in a Progenesis compatible format.
static File	exportProteinSequences(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filteringPreferences) Exports the protein details in FASTA format as specified in the follow-up input bean.
static File	exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports proteoforms.
static File	exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) Writes an export according to the command line settings contained in the reportCLIInputBean.
static ArrayList<File>	exportSpectra(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) Exports the spectra as specified in the follow-up input bean.
static ArrayList<File>	recalibrateSpectra(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) Recalibrates spectra as specified in the follow-up input bean.

Methods inherited from class java.lang.Object

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

Constructor Detail

CLIExportMethods

public CLIExportMethods()

Method Detail

recalibrateSpectra

public static ArrayList<File> recalibrateSpectra(FollowUpCLIInputBean followUpCLIInputBean,
                                                 com.compomics.util.experiment.identification.Identification identification,
                                                 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                                 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                 com.compomics.util.waiting.WaitingHandler waitingHandler)
                                          throws IOException

Recalibrates spectra as specified in the follow-up input bean.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

sequenceProvider - the sequence provider

spectrumProvider - The spectrum provider.

identificationParameters - the identification parameters

waitingHandler - a waiting handler to display progress

Returns:

ArrayList files containing the recalibrated spectra

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportSpectra

public static ArrayList<File> exportSpectra(FollowUpCLIInputBean followUpCLIInputBean,
                                            com.compomics.util.experiment.identification.Identification identification,
                                            com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                            com.compomics.util.waiting.WaitingHandler waitingHandler,
                                            com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
                                     throws IOException,
                                            SQLException,
                                            ClassNotFoundException,
                                            InterruptedException

Exports the spectra as specified in the follow-up input bean.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

spectrumProvider - The spectrum provider.

waitingHandler - a waiting handler to display progress

sequenceMatchingPreferences - the sequence matching preferences

Returns:

ArrayList files containing the spectra

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

InterruptedException - exception thrown whenever a threading issue occurred while interacting with the database

SQLException - exception thrown whenever an SQL exception occurred while interacting with the database

ClassNotFoundException - exception thrown whenever an exception occurred while deserializing an object

exportAccessions

public static File exportAccessions(FollowUpCLIInputBean followUpCLIInputBean,
                                    com.compomics.util.experiment.identification.Identification identification,
                                    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                    com.compomics.util.waiting.WaitingHandler waitingHandler,
                                    com.compomics.util.gui.filtering.FilterParameters filteringPreferences)
                             throws IOException

Exports the accessions as specified in the follow-up input bean.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

sequenceProvider - the FASTA sequence provider

waitingHandler - a waiting handler to display progress

filteringPreferences - the filtering preferences

Returns:

File file containing accessions

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportProteinSequences

public static File exportProteinSequences(FollowUpCLIInputBean followUpCLIInputBean,
                                          com.compomics.util.experiment.identification.Identification identification,
                                          com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                          com.compomics.util.waiting.WaitingHandler waitingHandler,
                                          com.compomics.util.gui.filtering.FilterParameters filteringPreferences)
                                   throws IOException

Exports the protein details in FASTA format as specified in the follow-up input bean.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

sequenceProvider - the FASTA sequence provider

waitingHandler - a waiting handler to display progress

filteringPreferences - the filtering preferences

Returns:

File file containing the protein details in FASTA format

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportProgenesis

public static File exportProgenesis(FollowUpCLIInputBean followUpCLIInputBean,
                                    com.compomics.util.experiment.identification.Identification identification,
                                    com.compomics.util.waiting.WaitingHandler waitingHandler,
                                    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                    com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
                             throws IOException

Exports the identification in a Progenesis compatible format.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

waitingHandler - a waiting handler to display progress

sequenceProvider - the sequence provider

proteinDetailsProvider - the protein details provider

sequenceMatchingPreferences - the sequence matching preferences

Returns:

File file containing the identification data in a Progenesis compatible format

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportProteoforms

public static File exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean,
                                     com.compomics.util.experiment.identification.Identification identification,
                                     com.compomics.util.waiting.WaitingHandler waitingHandler)

Exports proteoforms.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

waitingHandler - a waiting handler to display progress

Returns:

File file containing the proteoforms data

exportDeepLC

public static ArrayList<File> exportDeepLC(FollowUpCLIInputBean followUpCLIInputBean,
                                           com.compomics.util.experiment.identification.Identification identification,
                                           com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters,
                                           com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                           com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                           com.compomics.util.waiting.WaitingHandler waitingHandler)

Exports files needed by DeepLC.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

modificationParameters - The modification parameters.

sequenceMatchingParameters - The sequence matching parameters.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.

Returns:

The files created by the export.

exportMs2pip

public static ArrayList<File> exportMs2pip(FollowUpCLIInputBean followUpCLIInputBean,
                                           com.compomics.util.experiment.identification.Identification identification,
                                           com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
                                           com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                           com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                           com.compomics.util.waiting.WaitingHandler waitingHandler)

Exports the files needed by ms2pip.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

searchParameters - The search parameters.

sequenceMatchingParameters - The sequence matching parameters.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.

Returns:

The files created by the export.

exportPercolator

public static void exportPercolator(FollowUpCLIInputBean followUpCLIInputBean,
                                    com.compomics.util.experiment.identification.Identification identification,
                                    com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
                                    com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                    com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters,
                                    com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters,
                                    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                    com.compomics.util.waiting.WaitingHandler waitingHandler)

Exports the files needed by Percolator.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

searchParameters - The search parameters.

sequenceMatchingParameters - The sequence matching parameters.

annotationParameters - The annotation parameters.

modificationLocalizationParameters - The modification localization parameters.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.

exportInclusionList

public static File exportInclusionList(FollowUpCLIInputBean followUpCLIInputBean,
                                       com.compomics.util.experiment.identification.Identification identification,
                                       com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                       com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                       com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
                                       com.compomics.util.waiting.WaitingHandler waitingHandler,
                                       com.compomics.util.gui.filtering.FilterParameters filterPreferences)
                                throws IOException

Exports an inclusion list of the validated hits.

Parameters:

followUpCLIInputBean - the follow up input bean

identification - the identification

identificationFeaturesGenerator - the identification features generator

spectrumProvider - The spectrum provider.

searchParameters - the search parameters

waitingHandler - a waiting handler to display progress

filterPreferences - the filter preferences

Returns:

File file containing the inclusion list

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportReport

public static File exportReport(ReportCLIInputBean reportCLIInputBean,
                                String reportType,
                                String experiment,
                                ProjectDetails projectDetails,
                                com.compomics.util.experiment.identification.Identification identification,
                                com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                                com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                int nSurroundingAA,
                                com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences,
                                com.compomics.util.waiting.WaitingHandler waitingHandler)
                         throws IOException

Writes an export according to the command line settings contained in the reportCLIInputBean.

Parameters:

reportCLIInputBean - the command line settings

reportType - the report type

experiment - the experiment of the project

projectDetails - the project details of the project

identification - the identification of the project

geneMaps - the gene maps

identificationFeaturesGenerator - the identification features generator

identificationParameters - the identification parameters used

sequenceProvider - the sequence provider

proteinDetailsProvider - the protein details provider

spectrumProvider - The spectrum provider.

nSurroundingAA - the number of amino acids to export on the side of peptide sequences

spectrumCountingPreferences - the spectrum counting preferences

waitingHandler - waiting handler displaying feedback to the user

Returns:

File file containing the exported report

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportDocumentation

public static void exportDocumentation(ReportCLIInputBean reportCLIInputBean,
                                       String reportType,
                                       com.compomics.util.waiting.WaitingHandler waitingHandler)
                                throws IOException

Writes the documentation corresponding to an export given the command line arguments.

Parameters:

reportCLIInputBean - the command line arguments

reportType - the type of report of interest

waitingHandler - waiting handler displaying feedback to the user

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

exportMzId

public static void exportMzId(MzidCLIInputBean mzidCLIInputBean,
                              PsdbParent psbdParent,
                              com.compomics.util.waiting.WaitingHandler waitingHandler)
                       throws IOException

Exports the project in the mzIdentML format.

Parameters:

mzidCLIInputBean - the user input

psbdParent - a psbd file parent allowing accessing the information it contains

waitingHandler - a waiting handler allowing display of progress and interruption of the export

Throws:

IOException - exception thrown whenever an IO exception occurred while reading or writing to a file