Package eu.isas.peptideshaker.followup

Class InclusionListExport

java.lang.Object

eu.isas.peptideshaker.followup.InclusionListExport

public class InclusionListExport
extends Object

This class exports identifications in an inclusion list.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	InclusionListExport.ExportFormat	Enum of the different types of export implemented.
static enum	InclusionListExport.PeptideFilterType	Enum of the peptide filters implemented.

Constructor Summary

Constructors

Constructor	Description
InclusionListExport()

Method Summary

Modifier and Type	Method	Description
static void	exportInclusionList(File destinationFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, ArrayList<Integer> proteinFilters, ArrayList<InclusionListExport.PeptideFilterType> peptideFilters, InclusionListExport.ExportFormat exportFormat, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, double rtWindow, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filterPreferences)	Writes an inclusion list based on the validated PSMs of the validated peptides of the validated proteins.
static String	getProteinFiltersCommandLineOptions()	Returns a description of the command line arguments for the protein filters.

Methods inherited from class java.lang.Object

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

Constructor Details

InclusionListExport

public InclusionListExport()

Method Details

exportInclusionList

public static void exportInclusionList(File destinationFile,
 com.compomics.util.experiment.identification.Identification identification,
 com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 ArrayList<Integer> proteinFilters,
 ArrayList<InclusionListExport.PeptideFilterType> peptideFilters,
 InclusionListExport.ExportFormat exportFormat,
 com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
 double rtWindow,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.gui.filtering.FilterParameters filterPreferences)
                                throws IOException

Writes an inclusion list based on the validated PSMs of the validated peptides of the validated proteins.

Parameters:

destinationFile - the file where to write the inclusion list

identification - the identification object containing all matches and match parameters

identificationFeaturesGenerator - the identification features generator calculating identification metrics on the fly

spectrumProvider - the spectrum provider

proteinFilters - the inclusion list protein filters

peptideFilters - the inclusion list peptide filters

exportFormat - the export format

searchParameters - the identification parameters

rtWindow - the window to use for retention time

waitingHandler - waiting handler displaying progress to the user (can be null)

filterPreferences - the general filtering preferences of this project

Throws:

IOException - thrown if an error occurred while writing the file

getProteinFiltersCommandLineOptions

public static String getProteinFiltersCommandLineOptions()

Returns a description of the command line arguments for the protein filters.

Returns:

a description of the command line arguments