eu.isas.peptideshaker.cmd

Class PeptideShakerCLIInputBean

java.lang.Object

eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean

public class PeptideShakerCLIInputBean
extends Object

This class is a simple bean wrapping the CLI parameters provided in an Options instance.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
PeptideShakerCLIInputBean() Empty constructor for API usage via other tools.
PeptideShakerCLIInputBean(org.apache.commons.cli.CommandLine aLine) Construct a PeptideShakerCLIInputBean from an Apache CLI instance.

Method Summary

Modifier and Type	Method and Description
String	getExperimentID() Returns the experiment name.
File	getFastaFile() Returns the FASTA file.
FollowUpCLIInputBean	getFollowUpCLIInputBean() Returns the follow-up options required.
static ArrayList<File>	getIdentificationFiles(String optionInput) Returns a list of identification files as imported from the command line option.
File	getIdentificationParametersFile() Returns the identification parameters file.
com.compomics.cli.identification_parameters.IdentificationParametersInputBean	getIdentificationParametersInputBean() Returns the identification parameters provided by the user.
ArrayList<File>	getIdFiles() Returns the identification files.
boolean	getMgfExport() When exporting the project to a zip file, returns whether mgf file/s should be written apart from it, into the same folder.
MzidCLIInputBean	getMzidCLIInputBean() Returns the mzid export options required.
Integer	getnThreads() Returns the number of threads to use.
File	getOutput() Returns the psdb output file.
PathSettingsCLIInputBean	getPathSettingsCLIInputBean() Returns the path settings provided by the user.
File	getPrideFile() Returns the pride file.
com.compomics.util.parameters.peptide_shaker.ProjectType	getProjectType() Returns the project type.
ReportCLIInputBean	getReportCLIInputBean() Returns the report export options required.
ArrayList<File>	getSpectrumFiles() Returns the spectrum files.
static ArrayList<File>	getSpectrumFiles(String optionInput) Returns a list of spectrum files as imported from the command line option.
File	getZipExport() Returns the file where to export the project as zip file.
boolean	isGUI() Indicates whether a GUI shall be used to display the progress.
static boolean	isValidStartup(org.apache.commons.cli.CommandLine aLine) Verifies the command line start parameters.
void	setExperimentID(String experimentID) Sets the experiment name.
void	setFastaFile(File fastaFile) Sets the FASTA file.
void	setIdFiles(ArrayList<File> idFiles) Sets the identification files.
void	setOutput(File output) Sets the psdb output file.
void	setPrideFile(File prideFile) Sets the pride file.
void	setSpectrumFiles(ArrayList<File> spectrumFiles) Sets the spectrum files.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideShakerCLIInputBean

public PeptideShakerCLIInputBean(org.apache.commons.cli.CommandLine aLine)
                          throws IOException,
                                 ClassNotFoundException

Construct a PeptideShakerCLIInputBean from an Apache CLI instance.

Parameters:

aLine - the command line

Throws:

IOException - thrown of IOException occurs

ClassNotFoundException - thrown of ClassNotFoundException occurs

PeptideShakerCLIInputBean

public PeptideShakerCLIInputBean()

Empty constructor for API usage via other tools.

Method Detail

getProjectType

public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()

Returns the project type.

Returns:

the project type

getZipExport

public File getZipExport()

Returns the file where to export the project as zip file. Null if not set.

Returns:

the file where to export the project as zip file

getMgfExport

public boolean getMgfExport()

When exporting the project to a zip file, returns whether mgf file/s should be written apart from it, into the same folder.

Returns:

whether mgf file/s should be written apart from the zip file

getExperimentID

public String getExperimentID()

Returns the experiment name.

Returns:

the experiment name

setExperimentID

public void setExperimentID(String experimentID)

Sets the experiment name.

Parameters:

experimentID - the experiment name

getOutput

public File getOutput()

Returns the psdb output file. Null if not set.

Returns:

the psdb output file

setOutput

public void setOutput(File output)

Sets the psdb output file.

Parameters:

output - the psdb output file

getIdFiles

public ArrayList<File> getIdFiles()

Returns the identification files.

Returns:

the identification files

setIdFiles

public void setIdFiles(ArrayList<File> idFiles)

Sets the identification files.

Parameters:

idFiles - the identification files

getPrideFile

public File getPrideFile()

Returns the pride file.

Returns:

the pride file

setPrideFile

public void setPrideFile(File prideFile)

Sets the pride file.

Parameters:

prideFile - the pride file

getSpectrumFiles

public ArrayList<File> getSpectrumFiles()

Returns the spectrum files.

Returns:

the spectrum files

setSpectrumFiles

public void setSpectrumFiles(ArrayList<File> spectrumFiles)

Sets the spectrum files.

Parameters:

spectrumFiles - the spectrum files

getFastaFile

public File getFastaFile()

Returns the FASTA file.

Returns:

the FASTA file

setFastaFile

public void setFastaFile(File fastaFile)

Sets the FASTA file.

Parameters:

fastaFile - the FASTA file

getSpectrumFiles

public static ArrayList<File> getSpectrumFiles(String optionInput)
                                        throws FileNotFoundException

Returns a list of spectrum files as imported from the command line option.

Parameters:

optionInput - the command line option

Returns:

a list of file candidates

Throws:

FileNotFoundException - exception thrown whenever a file is not found

getIdentificationFiles

public static ArrayList<File> getIdentificationFiles(String optionInput)
                                              throws FileNotFoundException

Returns a list of identification files as imported from the command line option.

Parameters:

optionInput - the command line option

Returns:

a list of file candidates

Throws:

FileNotFoundException - exception thrown whenever a file is not found

isGUI

public boolean isGUI()

Indicates whether a GUI shall be used to display the progress.

Returns:

a boolean indicating whether a GUI shall be used to display the progress

getFollowUpCLIInputBean

public FollowUpCLIInputBean getFollowUpCLIInputBean()

Returns the follow-up options required.

Returns:

the follow-up options required

getReportCLIInputBean

public ReportCLIInputBean getReportCLIInputBean()

Returns the report export options required.

Returns:

the report export options required

getMzidCLIInputBean

public MzidCLIInputBean getMzidCLIInputBean()

Returns the mzid export options required.

Returns:

the mzid export options required

getPathSettingsCLIInputBean

public PathSettingsCLIInputBean getPathSettingsCLIInputBean()

Returns the path settings provided by the user.

Returns:

the path settings provided by the user

getIdentificationParametersInputBean

public com.compomics.cli.identification_parameters.IdentificationParametersInputBean getIdentificationParametersInputBean()

Returns the identification parameters provided by the user.

Returns:

the identification parameters provided by the user

getIdentificationParametersFile

public File getIdentificationParametersFile()

Returns the identification parameters file.

Returns:

the identification parameters file

getnThreads

public Integer getnThreads()

Returns the number of threads to use.

Returns:

the number of threads to use

isValidStartup

public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine)
                              throws IOException

Verifies the command line start parameters.

Parameters:

aLine - the command line to validate

Returns:

true if the startup was valid

Throws:

IOException - if the spectrum file(s) are not found