eu.isas.peptideshaker.export

Class PSExportFactory

java.lang.Object

eu.isas.peptideshaker.export.PSExportFactory

All Implemented Interfaces:

com.compomics.util.io.export.ExportFactory

public class PSExportFactory
extends Object
implements com.compomics.util.io.export.ExportFactory

The PeptideShaker export factory.

Author:

Marc Vaudel, Harald Barsnes

Method Summary

Modifier and Type	Method and Description
void	addExportScheme(com.compomics.util.io.export.ExportScheme exportScheme)
String	getCommandLineOptions() Returns the list of implemented reports as command line option.
static String	getDefaultDocumentation(String exportName) Returns the default file name for the export of the documentation of the given report export type.
static com.compomics.util.io.export.ExportScheme	getDefaultExportScheme(String schemeName) Returns the desired default export scheme.
static String[]	getDefaultExportSchemesNames() Returns a list of the default export schemes.
static String	getDefaultReportName(String experiment, String exportName) Returns the default file name for the export of a report based on the project details
ArrayList<com.compomics.util.io.export.ExportFeature>	getExportFeatures(String sectionName, boolean includeSubFeatures)
com.compomics.util.io.export.ExportScheme	getExportScheme(String schemeName)
String	getExportTypeFromCommandLineOption(int commandLine) Returns the export type based on the number used in command line.
ArrayList<String>	getImplementedSections()
static PSExportFactory	getInstance() Static method to get the instance of the factory.
static String	getJsonFile() Returns the file where to save the implemented export schemes.
static String	getJsonFolder() Returns the folder where to save the implemented export schemes.
ArrayList<String>	getUserSchemesNames() Returns a list of the name of the available user schemes.
static PSExportFactory	loadFromFile(File file) Loads an export factory from a file.
void	removeExportScheme(String schemeName)
static void	saveFactory(PSExportFactory psExportFactory) Saves the factory in the user folder.
static void	setJsonFolder(String serializationFolder) Sets the file where to save the implemented export schemes.
static void	writeDocumentation(com.compomics.util.io.export.ExportScheme exportScheme, com.compomics.util.io.export.ExportFormat exportFormat, File destinationFile) Writes the documentation related to a report.
static void	writeExport(com.compomics.util.io.export.ExportScheme exportScheme, File destinationFile, com.compomics.util.io.export.ExportFormat exportFormat, boolean gzip, String experiment, ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, long[] proteinKeys, long[] peptideKeys, long[] psmKeys, int nSurroundingAA, 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, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) Writes the desired export in text format.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static PSExportFactory getInstance()

Static method to get the instance of the factory.

Returns:

the instance of the factory

saveFactory

public static void saveFactory(PSExportFactory psExportFactory)
                        throws IOException

Saves the factory in the user folder.

Parameters:

psExportFactory - the instance of the factory to save

Throws:

IOException - exception thrown whenever an error occurred while saving the PSExportFactory

loadFromFile

public static PSExportFactory loadFromFile(File file)
                                    throws IOException

Loads an export factory from a file. The file must be an export of the factory in the json format.

Parameters:

file - the file to load

Returns:

the export factory saved in file

Throws:

IOException - exception thrown whenever an error occurred while loading the file

getUserSchemesNames

public ArrayList<String> getUserSchemesNames()

Returns a list of the name of the available user schemes.

Returns:

a list of the implemented user schemes

getDefaultExportScheme

public static com.compomics.util.io.export.ExportScheme getDefaultExportScheme(String schemeName)

Returns the desired default export scheme. Null if not found.

Parameters:

schemeName - the name of the default export scheme

Returns:

the default export scheme

getExportScheme

public com.compomics.util.io.export.ExportScheme getExportScheme(String schemeName)

Specified by:

getExportScheme in interface com.compomics.util.io.export.ExportFactory

removeExportScheme

public void removeExportScheme(String schemeName)

Specified by:

removeExportScheme in interface com.compomics.util.io.export.ExportFactory

addExportScheme

public void addExportScheme(com.compomics.util.io.export.ExportScheme exportScheme)

Specified by:

addExportScheme in interface com.compomics.util.io.export.ExportFactory

getImplementedSections

public ArrayList<String> getImplementedSections()

Specified by:

getImplementedSections in interface com.compomics.util.io.export.ExportFactory

getExportFeatures

public ArrayList<com.compomics.util.io.export.ExportFeature> getExportFeatures(String sectionName,
                                                                               boolean includeSubFeatures)

Specified by:

getExportFeatures in interface com.compomics.util.io.export.ExportFactory

getDefaultExportSchemesNames

public static String[] getDefaultExportSchemesNames()

Returns a list of the default export schemes.

Returns:

a list of the default export schemes

writeExport

public static void writeExport(com.compomics.util.io.export.ExportScheme exportScheme,
                               File destinationFile,
                               com.compomics.util.io.export.ExportFormat exportFormat,
                               boolean gzip,
                               String experiment,
                               ProjectDetails projectDetails,
                               com.compomics.util.experiment.identification.Identification identification,
                               com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                               com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                               long[] proteinKeys,
                               long[] peptideKeys,
                               long[] psmKeys,
                               int nSurroundingAA,
                               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,
                               com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences,
                               com.compomics.util.waiting.WaitingHandler waitingHandler)
                        throws IOException

Writes the desired export in text format. If an argument is not needed, provide null (at your own risks).

Parameters:

exportScheme - the scheme of the export

destinationFile - the destination file

exportFormat - the format of export to use

gzip - if true export text as gzipped file

experiment - the experiment corresponding to this project (mandatory for the Project section)

projectDetails - the project details (mandatory for the Project section)

identification - the identification (mandatory for the Protein, Peptide and PSM sections)

identificationFeaturesGenerator - the identification features generator (mandatory for the Protein, Peptide and PSM sections)

geneMaps - the gene maps

proteinKeys - the protein keys to export (mandatory for the Protein section)

peptideKeys - the peptide keys to export (mandatory for the Peptide section)

psmKeys - the keys of the PSMs to export (mandatory for the PSM section)

nSurroundingAA - the number of surrounding amino acids to export (mandatory for the Peptide section)

identificationParameters - the identification parameters

sequenceProvider - a provider for the protein sequences

proteinDetailsProvider - the protein details provider

spectrumProvider - the spectrum provider

spectrumCountingPreferences - the spectrum counting preferences (mandatory for the spectrum counting section)

waitingHandler - the waiting handler

Throws:

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

writeDocumentation

public static void writeDocumentation(com.compomics.util.io.export.ExportScheme exportScheme,
                                      com.compomics.util.io.export.ExportFormat exportFormat,
                                      File destinationFile)
                               throws IOException

Writes the documentation related to a report.

Parameters:

exportScheme - the export scheme of the report

exportFormat - the export format chosen by the user

destinationFile - the destination file where to write the documentation

Throws:

IOException - thrown if an IOException occurs

getCommandLineOptions

public String getCommandLineOptions()

Returns the list of implemented reports as command line option.

Returns:

the list of implemented reports

getDefaultReportName

public static String getDefaultReportName(String experiment,
                                          String exportName)

Returns the default file name for the export of a report based on the project details

Parameters:

experiment - the experiment of the project

exportName - the name of the report type

Returns:

the default file name for the export

getDefaultDocumentation

public static String getDefaultDocumentation(String exportName)

Returns the default file name for the export of the documentation of the given report export type.

Parameters:

exportName - the export name

Returns:

the default file name for the export

getExportTypeFromCommandLineOption

public String getExportTypeFromCommandLineOption(int commandLine)

Returns the export type based on the number used in command line.

Parameters:

commandLine - the number used in command line option. See getCommandLineOptions().

Returns:

the corresponding export name

getJsonFile

public static String getJsonFile()

Returns the file where to save the implemented export schemes.

Returns:

the file where to save the implemented export schemes

getJsonFolder

public static String getJsonFolder()

Returns the folder where to save the implemented export schemes.

Returns:

the folder where to save the implemented export schemes

setJsonFolder

public static void setJsonFolder(String serializationFolder)

Sets the file where to save the implemented export schemes.

Parameters:

serializationFolder - the folder where to save the implemented export schemes