Package eu.isas.peptideshaker.cmd

Command line usage.

Class Summary

Class	Description
CLIExportMethods	This class groups standard methods used by the different command line interfaces.
FollowUpCLI	Command line interface to run follow-up analysis on psdb files.
FollowUpCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
IdentificationParametersCLI	The SearchParametersCLI allows creating search parameters files using command line arguments.
MzidCLI	Command line interface to export mzid files from psdb files.
MzidCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
PathSettingsCLI	Allows the user to set the path settings in command line.
PathSettingsCLIInputBean	Parses the command line and retrieves the user input.
PeptideShakerCLI	A command line interface to run PeptideShaker.
PeptideShakerCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
PeptideShakerIdentificationParametersCLIParams	This class provides the parameters which can be used for the identification parameters cli in PeptideShaker.
ReportCLI	This class performs the command line export of reports in command line.
ReportCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
StirredCLI	Command line to manage the modifications.
StirredOptionsBean	This class parses the parameters from an ModificationsCLI.

Enum Summary

Enum	Description
FollowUpCLIParams	Enum class specifying the Command Line Parameters for follow up analysis.
MzidCLIParams	Enum class specifying the Command Line Parameters for mzid export.
PathSettingsCLIParams	Enum of the command line parameters for path setting.
PeptideShakerCLIParams	Enum class specifying the Command Line Parameters for PeptideShaker.
ReportCLIParams	This class provides the available reports as command line parameters.
StirredOptions	Enum class specifying the ModificationsCLI parameters.