All Classes and Interfaces

Class	Description
AdvancedParametersDialog	SearchGUI advanced settings dialog.
AlignedListCellRenderer	ListCellRenderer with alignment functionality.
AndromedaProcessBuilder	ProcessBuilder for the Andromeda search engine.
CometProcessBuilder	ProcessBuilder for the Comet search engine.
DirecTagProcessBuilder	This class will set up and start a process to run DirecTag.
FastaCLI	This class allows the user to work on the database in command line.
FastaCLIInputBean	This class contains the information necessary for running the FastaCLI.
FastaCLIParams	This class contains the parameters which can be used in the FASTA command line.
IdentificationParametersCLI	The SearchParametersCLI allows creating search parameters files using command line arguments.
MakeblastdbProcessBuilder	This class takes care of starting the Makeblastdb Process.
MetaMorpheusProcessBuilder	ProcessBuilder for the MetaMorpheus search engine.
MetaMorpheusProcessBuilder.MetaMorpheusTaskType	The available MetaMorpheus task types.
MsAmandaProcessBuilder	This class will build files and start a process to perform an MS Amanda search.
MsConvertProcessBuilder	Process builder to run msconvert.
MsgfProcessBuilder	This class will set up and start a process to perform an MS-GF+ search.
MyriMatchProcessBuilder	This class will set up and start a process to perform a MyriMatch search.
NovorProcessBuilder	This class will set up and start a process to run Novor.
OmssaclProcessBuilder	This class takes care of building the omssacl process.
PathSettingsCLI	Allows the user to set the path settings in command line.
PathSettingsCLIInputBean	Parses the command line and retrieves the user input.
PathSettingsCLIParams	Parameters for the path settings command line.
PeptideShakerParametersDialog	A dialog for editing the PeptideShaker settings required when starting PeptideShaker from SearchGUI.
PeptideShakerProcessBuilder	This process builder runs PeptideShaker.
Properties	This class provides the SearchGUI version number.
SageProcessBuilder	ProcessBuilder for the Sage search engine.
SearchCLI	This class can be used to control SearchGUI in command line.
SearchCLIdentificationParametersCLIParams	This class provides the parameters which can be used for the identification parameters cli in SearchGUI.
SearchCLIInputBean	The SearchCLIInputBean reads and stores command line options from a command line.
SearchCLIParams	Command line option parameters for SearchCLI.
SearchGUI	The main frame of SearchGUI.
SearchGUIPathParameters	This class sets the path preferences for the files to read/write
SearchGUIPathParameters.SearchGUIPathKey	Enum of the paths which can be set in SearchGUI.
SearchGUIProcessBuilder	A simple ancestor class to reduce code duplication in formatdb, omssacl and tandem process builders.
SearchGUIWrapper	A wrapper class used to start the jar file with parameters.
SearchGUIZipFileChecker	A wrapper class used to check if the jar file is attempted started from within an unzipped zip file.
SearchHandler	This class represents the search command line interface.
SoftwareLocationDialog	The search engines settings dialog.
TandemProcessBuilder	This class will build files and start a process to perform an X!Tandem search.
ThermoRawFileParserProcessBuilder	Process builder to run ThermoRawFileParser.
TideIndexProcessBuilder	ProcessBuilder for the Tide index generation.
TideSearchProcessBuilder	ProcessBuilder for the Tide search command.