Index (SearchGUI 4.3.17 API)

A B C D E F G H I L M N O P R S T U V W X
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AdvancedParametersDialog - Class in eu.isas.searchgui.gui: SearchGUI advanced settings dialog.
AdvancedParametersDialog(SearchGUI, boolean) - Constructor for class eu.isas.searchgui.gui.AdvancedParametersDialog: Creates a new AdvancedSettingsDialog.
AlignedListCellRenderer - Class in eu.isas.searchgui.gui: ListCellRenderer with alignment functionality.
AlignedListCellRenderer(int) - Constructor for class eu.isas.searchgui.gui.AlignedListCellRenderer: Creates a new AlignedListCellRenderer
ALL - Enum constant in enum eu.isas.searchgui.cmd.PathSettingsCLIParams
ANDROMEDA - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
ANDROMEDA_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
AndromedaProcessBuilder - Class in eu.isas.searchgui.processbuilders: ProcessBuilder for the Andromeda search engine.
AndromedaProcessBuilder(File, File, SearchParameters, File, File, File, WaitingHandler, ExceptionHandler, int) - Constructor for class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder: Constructor.

B

browseAndromedaLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the Andromeda location.
browseCometLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the Comet location.
browseDirecTagLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the DirecTag location.
browseMetaMorpheusLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the MetaMorpheus location.
browseMsAmandaLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the MS Amanda location.
browseMsgfLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the MS-GF+ location.
browseMyriMatchLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the MyriMatch location.
browseNovorLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the Novor location.
browseOMSSALocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the OMSSA location.
browseSageLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the Sage location.
browseSearchEngineLocationPressed(Advocate, String, String, JTextField) - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for a search engine location.
browseSearchEngineLocationPressed(Advocate, String, JTextField) - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for a search engine location.
browseTideLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the Tide location.
browseXTandemLocationPressed() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method should be called whenever 'browse' has been pressed for the X!Tandem location.

C

call() - Method in class eu.isas.searchgui.cmd.FastaCLI: Calling this method will run the configured FastaCLI process.
call() - Method in class eu.isas.searchgui.cmd.PathSettingsCLI: Sets the path settings and returns null.
call() - Method in class eu.isas.searchgui.cmd.SearchCLI: Calling this method will run the configured SearchCLI process.
cancelSearch() - Method in class eu.isas.searchgui.SearchHandler: Cancel the search.
checkForNewVersion() - Method in class eu.isas.searchgui.gui.SearchGUI: Check for new version.
checkForNewVersion(String) - Method in class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Check for new version.
checkMgfSize() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns if the mgf should be checked for size.
cmsFolder - Enum constant in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey: The folder to use for cms files.
COMET - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
COMET_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
CometProcessBuilder - Class in eu.isas.searchgui.processbuilders: ProcessBuilder for the Comet search engine.
CometProcessBuilder(File, File, SearchParameters, File, File, WaitingHandler, ExceptionHandler, int, Double) - Constructor for class eu.isas.searchgui.processbuilders.CometProcessBuilder: Constructor.
CONDA_APP_NAME - Static variable in class eu.isas.searchgui.SearchHandler: Name of SearchGUI's Conda package.
CONFIG_FOLDER - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
createDatabaseFile(File, File, File) - Static method in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder: Creates the database configuration file.
createEnzymesFile(File) - Static method in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder: Creates the enzyme configuration file.
createGenericFastaFile(File, File, WaitingHandler) - Static method in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder: Create the FASTA file.
createOptionsCLI(Options) - Static method in enum eu.isas.searchgui.cmd.FastaCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Method in class eu.isas.searchgui.cmd.IdentificationParametersCLI
createOptionsCLI(Options) - Static method in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in class eu.isas.searchgui.cmd.SearchCLIdentificationParametersCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum eu.isas.searchgui.cmd.SearchCLIParams: Creates the options for the command line interface based on the possible values.
createPtmFile(File, IdentificationParameters, File) - Static method in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder: Creates the Andromeda PTM file and saves the PTM indexes in the search parameters.

D

decoy - Enum constant in enum eu.isas.searchgui.cmd.FastaCLIParams
decoy_suffix - Enum constant in enum eu.isas.searchgui.cmd.FastaCLIParams
DEFAULT_DATA_FOLDER - Static variable in class eu.isas.searchgui.SearchHandler: The name of the folder where to save the spectrum and FASTA files.
DEFAULT_OUTPUT_FILE_NAME_ENDING - Static variable in class eu.isas.searchgui.SearchHandler: Default file name ending for a SearchGUI output.
description - Variable in enum eu.isas.searchgui.cmd.FastaCLIParams: Explanation for the CLI parameter.
description - Variable in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: The description of the command line option.
description - Variable in enum eu.isas.searchgui.cmd.SearchCLIParams: Explanation for the CLI parameter.
DIRECTAG - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
DIRECTAG_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
DirecTagProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class will set up and start a process to run DirecTag.
DirecTagProcessBuilder(File, File, int, File, SearchParameters, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.DirecTagProcessBuilder: Constructor.
downloadPeptideShaker() - Method in class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Download PeptideShaker.
DUPLICATE_TITLE_HANDLING - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams

E

editPathParameters() - Method in class eu.isas.searchgui.gui.SearchGUI: Opens a dialog allowing the setting of paths.
editProteoWizardInstallation() - Method in class eu.isas.searchgui.gui.SearchGUI: Opens a dialog allowing the edition of the ProteoWizard installation folder.
enableSearchEngines(boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class eu.isas.searchgui.gui.SearchGUI: Enable or disable the search engines.
endProcess() - Method in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder: Cancels the process.
endProcess() - Method in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: Ends the process.
eu.isas.searchgui - package eu.isas.searchgui: SearchGUI handler and wrapper.
eu.isas.searchgui.cmd - package eu.isas.searchgui.cmd: Command line related classes.
eu.isas.searchgui.gui - package eu.isas.searchgui.gui: GUI classes.
eu.isas.searchgui.parameters - package eu.isas.searchgui.parameters: Preference settings.
eu.isas.searchgui.processbuilders - package eu.isas.searchgui.processbuilders: The process builders.
eu.isas.searchgui.utilities - package eu.isas.searchgui.utilities: Utility classes used by the other classes.
exceptionHandler - Variable in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: The exception handler to manage exception.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder: The name of the Andromeda executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.CometProcessBuilder: The name of the Comet executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.DirecTagProcessBuilder: Title of the DirecTag executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder: The name of the makeblastdb executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder: The name of the MS Amanda executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.MsgfProcessBuilder: The name of the MS-GF+ executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.MyriMatchProcessBuilder: The name of the MyriMatch executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.NovorProcessBuilder: The name of the Novor executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder: The name of the OMSSA executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: The name of the X!Tandem executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.TideIndexProcessBuilder: The name of the Tide executable.
EXECUTABLE_FILE_NAME - Static variable in class eu.isas.searchgui.processbuilders.TideSearchProcessBuilder: The name of the Tide executable.
extractAndUpdatePathOptions(String[]) - Static method in class eu.isas.searchgui.cmd.PathSettingsCLI: If the arguments contains changes to the paths these arguments will be extracted and the paths updated, before the remaining non-path options are returned for further processing.

F

FASTA_FILE - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
FastaCLI - Class in eu.isas.searchgui.cmd: This class allows the user to work on the database in command line.
FastaCLI(String[]) - Constructor for class eu.isas.searchgui.cmd.FastaCLI: Construct a new FastaCLI runnable from a list of arguments.
FastaCLIInputBean - Class in eu.isas.searchgui.cmd: This class contains the information necessary for running the FastaCLI.
FastaCLIInputBean(CommandLine) - Constructor for class eu.isas.searchgui.cmd.FastaCLIInputBean: Constructor.
FastaCLIParams - Enum in eu.isas.searchgui.cmd: This class contains the parameters which can be used in the FASTA command line.

G

generateTargetDecoyDatabase(FastaParameters, WaitingHandler) - Method in class eu.isas.searchgui.cmd.FastaCLI: Appends decoy sequences to the given target database file.
getAndromedaFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the Andromeda result file.
getAndromedaLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the Andromeda location.
getAndromedaLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the Andromeda location.
getAndromedaLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the Andromeda location.
getASelected() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Returns yes if the a ions are selected, no otherwise.
getBSelected() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Returns yes if the b ions are selected, no otherwise.
getCmsFile(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the cms file with the given name.
getCmsFiles() - Method in class eu.isas.searchgui.SearchHandler: Returns the list of cms files.
getCometFileName(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the name of the Comet result file.
getCometFileName(String, CometParameters) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the Comet result file.
getCometLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the Comet location.
getCometLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the Comet location.
getCometLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the Comet location.
getConfigFolder() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the config folder.
getConfigFolder() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the folder where the configuration files are stored.
getConfigFolder() - Static method in class eu.isas.searchgui.SearchHandler: Returns the folder where the configuration files are stored.
getCSelected() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Returns yes if the c ions are selected, no otherwise.
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.CometProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.DirecTagProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.MsConvertProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.MsgfProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.MyriMatchProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.NovorProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.PeptideShakerProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.SageProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: Returns the file name of the currently processed file.
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.ThermoRawFileParserProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.TideIndexProcessBuilder
getCurrentlyProcessedFileName() - Method in class eu.isas.searchgui.processbuilders.TideSearchProcessBuilder
getDecoySuffix() - Method in class eu.isas.searchgui.cmd.FastaCLIInputBean: Returns the tag added after adding decoy sequences to a FASTA file.
getDefaultOutputFile(File, boolean) - Static method in class eu.isas.searchgui.SearchHandler: Returns the default output file produced by SearchGUI.
getDefaultOutputFile(File, String, boolean) - Static method in class eu.isas.searchgui.SearchHandler: Returns the default output file produced by SearchGUI classified according to a classifier.
getDefaultOutputFileName() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the default output name.
getDefaultOutputFileName() - Static method in class eu.isas.searchgui.SearchHandler: Returns the default output file name.
getDescription() - Method in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey
getDirecTagFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the DirecTag result file.
getDirecTagLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the DirecTag location.
getDirecTagLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the DirecTag location.
getDirecTagLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the DirecTag location.
getDuplicateSpectrumTitleHandling() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns how duplicate spectrum titles are to be handled.
getErrorKeys(File) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Returns a list containing the keys of the paths where the tool is not able to write.
getExecutableFileName() - Static method in class eu.isas.searchgui.processbuilders.SageProcessBuilder: Returns the name of the Sage executable.
getExecutableFileName(boolean) - Static method in class eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder: Returns the name of the MetaMorpheus executable.
getExperimentLabel() - Method in class eu.isas.searchgui.SearchHandler: Returns the experiment label.
getFastaFile() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Return the FASTA file.
getFastaFile() - Method in class eu.isas.searchgui.SearchHandler: Returns the FASTA file.
getId() - Method in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey
getIdentificationParameters() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the identification parameters.
getIdentificationParameters() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the identification parameters.
getIdentificationParametersFile() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the identification parameters file.
getInputFile() - Method in class eu.isas.searchgui.cmd.FastaCLIInputBean: Returns the input file.
getInputFile(File) - Static method in class eu.isas.searchgui.SearchHandler: Returns the file where the paths to the spectrum and FASTA files are saved.
getIonId(String) - Method in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder: Returns the ion type.
getJarFilePath() - Method in class eu.isas.searchgui.cmd.FastaCLI: Returns the path to the jar file.
getJarFilePath() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the path to the jar file.
getJarFilePath() - Method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Returns the path to the jar file.
getJarFilePath() - Method in class eu.isas.searchgui.SearchGUIWrapper: Returns the path to the jar file.
getJarFilePath() - Static method in class eu.isas.searchgui.SearchHandler: Returns the path to the jar file.
getKeyFromId(String) - Static method in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey: Returns the key from its id.
getLastSelectedFolder() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the last selected folder.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class eu.isas.searchgui.gui.AlignedListCellRenderer
getLogFileMessage() - Static method in class eu.isas.searchgui.cmd.FastaCLI: Returns the "see the log file" message.
getLogFileMessage() - Static method in class eu.isas.searchgui.cmd.SearchCLI: Returns the "see the log file" message.
getLogFolder() - Method in class eu.isas.searchgui.cmd.PathSettingsCLIInputBean: Returns the folder where to save the log files.
getMakeblastdbFolder() - Static method in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder: Returns the folder containing the makeblastdb script.
getMakeblastdbLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the makeblastdb location.
getMakeblastdbLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the makeblastdb location.
getMakeblastdbLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the makeblastdb location.
getMascotFiles() - Method in class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Returns the Mascot files.
getMascotFiles() - Method in class eu.isas.searchgui.SearchHandler: Returns the Mascot files.
getMetaMorpheusFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the MetaMorpheus result file.
getMetaMorpheusLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the MetaMorpheus location.
getMetaMorpheusLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the MetaMorpheus location.
getMetaMorpheusLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the MetaMorpheus location.
getMgfFiles() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the spectra files selected.
getMgfMaxSize() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the max mgf file size before splitting.
getMgfNSpectra() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Get the max number of spectra in an mgf file.
getMissingSpectrumTitleHandling() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns how missing spectrum titles are to be handled.
getMsAmandaFileName(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the name of the MS Amanda result file.
getMsAmandaFileName(String, MsAmandaParameters) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the MS Amanda result file.
getMsAmandaLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the MS Amanda location.
getMsAmandaLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the MS Amanda location.
getMsAmandaLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the MS Amanda location.
getMsConvertParameters() - Method in class eu.isas.searchgui.SearchHandler: Returns the msconvert parameters.
getMsgfFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the MS-GF+ result file.
getMsgfLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the MS-GF+ location.
getMsgfLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the MS-GF+ location.
getMsgfLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the MS-GF+ location.
getMyriMatchFileName(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the name of the MyriMatch result file.
getMyriMatchFileName(String, MyriMatchParameters) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the MyriMatch result file.
getMyriMatchLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the MyriMatch location.
getMyriMatchLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the MyriMatch location.
getMyriMatchLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the MyriMatch location.
getNovorFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the Novor result file.
getNovorLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the Novor location.
getNovorLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the Novor location.
getNovorLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the Novor location.
getNThreads() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the number of threads to use.
getOMSSAFileName(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the name of the OMSSA result file.
getOMSSAFileName(String, OmssaParameters) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the OMSSA result file.
getOmssaLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the OMSSA location, null if none is set.
getOmssaLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the OMSSA location.
getOmssaLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the OMSSA location.
getOmssaUserModBloc(Modification, int, int) - Static method in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder: Returns an MSModSpec bloc as present in the OMSSA user modification files for a given PTM.
getOptionIDs() - Static method in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: Returns the list of supported command line options.
getOptionsAsString() - Static method in enum eu.isas.searchgui.cmd.FastaCLIParams: Returns the options as a string.
getOptionsAsString() - Method in class eu.isas.searchgui.cmd.IdentificationParametersCLI
getOptionsAsString() - Static method in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in class eu.isas.searchgui.cmd.SearchCLIdentificationParametersCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in enum eu.isas.searchgui.cmd.SearchCLIParams: Returns the options as a string.
getOutputDate() - Static method in class eu.isas.searchgui.SearchHandler: Returns the date as a string to be included in the output.
getOutputFolder() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the output folder.
getOutputFolder() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the output folder.
getOutputOption() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the output option chosen by the user.
getParametersOptionsAsString() - Static method in class eu.isas.searchgui.cmd.SearchCLIdentificationParametersCLIParams: Returns the options as a string.
getPathParameter(SearchGUIPathParameters.SearchGUIPathKey, File) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Returns the path according to the given key and path.
getPaths() - Method in class eu.isas.searchgui.cmd.PathSettingsCLIInputBean: Returns the specific paths provided by the user in a map: Path id > path.
getPathSettingsCLIInputBean() - Method in class eu.isas.searchgui.cmd.FastaCLIInputBean: Returns the path settings provided by the user.
getPathSettingsCLIInputBean() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the path settings provided by the user.
getPeakListFolder(File) - Method in class eu.isas.searchgui.SearchHandler: Returns the folder to use to store peak lists.
getPeptideShakerFile() - Method in class eu.isas.searchgui.SearchHandler: Returns the PeptideShaker file.
getPeptideShakerOutputFile() - Method in class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Returns the PeptideShaker output file as set by the user.
getProcessingParameters() - Method in class eu.isas.searchgui.SearchHandler: Returns the processing preferences.
getProjectName() - Method in class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Returns the project name as set by the user.
getRawFiles() - Method in class eu.isas.searchgui.SearchHandler: Returns the list of raw files.
getRefMass() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
getResultsFolder() - Method in class eu.isas.searchgui.SearchHandler: Returns the results folder.
getSageFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the Sage result file.
getSageLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the Sage location.
getSageLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the Sage location.
getSageLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the Sage location.
getSearchedModificationsIds(ArrayList<String>, OmssaParameters) - Method in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder: Returns an array of OMSSA indexes corresponding to the list of given modification names.
getSearchHandler() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns a reference to the SearchGUI command line interface.
getSpectrumFile(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the spectrum file with the given name.
getSpectrumFiles() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Return the spectrum files.
getSpectrumFiles() - Method in class eu.isas.searchgui.SearchHandler: Returns the list of mass spectrometry files.
getSpectrumFiles(String) - Static method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns a list of spectrum files as imported from the command line option.
getTargetDecoyFileNameTag() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the target-decoy file name tag.
getTempFolder() - Method in class eu.isas.searchgui.cmd.PathSettingsCLIInputBean: Returns the temp folder, an empty string if not set.
getTempFolderPath(File) - Static method in class eu.isas.searchgui.SearchHandler: Returns the folder to use for temporary files.
getTempSearchEngineFolderPath(File) - Static method in class eu.isas.searchgui.SearchHandler: Returns the folder to use for temporary search engine files.
getThermoRawFileParserParameters() - Method in class eu.isas.searchgui.SearchHandler: Returns the ThermoRawFileParser parameters.
getTideFileName(String) - Method in class eu.isas.searchgui.SearchHandler: Returns the name of the Tide result file.
getTideFileName(String, TideParameters) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the Tide result file.
getTideIndexLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the Tide index location.
getTideLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the Tide location.
getTideLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the Tide location.
getTideLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the Tide location.
getTips() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns the tips of the day.
getType() - Method in class eu.isas.searchgui.processbuilders.AndromedaProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.CometProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.DirecTagProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.MsConvertProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.MsgfProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.MyriMatchProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.NovorProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.PeptideShakerProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.SageProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: Returns the type of the process.
getType() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.ThermoRawFileParserProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.TideIndexProcessBuilder
getType() - Method in class eu.isas.searchgui.processbuilders.TideSearchProcessBuilder
getUtilitiesUserParameters() - Method in class eu.isas.searchgui.gui.SearchGUI
getVersion() - Method in class eu.isas.searchgui.utilities.Properties: Retrieves the version number set in the pom file.
getXSelected() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Returns yes if the x ions are selected, no otherwise.
getXTandemFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Returns the name of the X!Tandem result file if renamed.
getXTandemFiles(File, String) - Method in class eu.isas.searchgui.SearchHandler: Lists all the files which can be X!Tandem output for this spectrum file in the given folder.
getXtandemLocation() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns the X!Tandem location.
getXtandemLocation() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns the X! Tandem location.
getXtandemLocation() - Method in class eu.isas.searchgui.SearchHandler: Returns the X!Tandem location.
getYSelected() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Returns yes if the y ions are selected, no otherwise.
getZSelected() - Method in class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Returns yes if the z ions are selected, no otherwise.
Gptmd - Enum constant in enum eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder.MetaMorpheusTaskType

H

hasArgument - Variable in enum eu.isas.searchgui.cmd.FastaCLIParams: Boolean indicating whether the command option has argument.
hasInput() - Method in class eu.isas.searchgui.cmd.PathSettingsCLIInputBean: Indicates whether the user gave some path configuration input.

I

id - Variable in enum eu.isas.searchgui.cmd.FastaCLIParams: Short Id for the CLI parameter.
id - Variable in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: The id of the command line option.
id - Variable in enum eu.isas.searchgui.cmd.SearchCLIParams: Short Id for the CLI parameter.
IdentificationParametersCLI - Class in eu.isas.searchgui.cmd: The SearchParametersCLI allows creating search parameters files using command line arguments.
IdentificationParametersCLI(String[]) - Constructor for class eu.isas.searchgui.cmd.IdentificationParametersCLI: Construct a new SearchParametersCLI runnable from a list of arguments.
in - Enum constant in enum eu.isas.searchgui.cmd.FastaCLIParams
isAndromedaEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if Andromeda is to be used.
isAndromedaEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether Andromeda is enabled.
isAndromedaEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if Andromeda is to be used.
isCanceled() - Method in class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Indicates whether the user pushed on cancel.
isCometEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if Comet is to be used.
isCometEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether Comet is enabled.
isCometEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if Comet is to be used.
isDecoy() - Method in class eu.isas.searchgui.cmd.FastaCLIInputBean: Indicates whether decoy sequences shall be added.
isDirecTagEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if DirecTag is to be used.
isDirecTagEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether DirecTag is enabled.
isDirecTagEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if DirecTag is to be used.
isGzip() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Indicates whether identification files should be gzipped.
isMetaMorpheusEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if MetaMorpheus is to be used.
isMetaMorpheusEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether MetaMorpheus is enabled.
isMetaMorpheusEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if MetaMorpheus is to be used.
isMsAmandaEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if MS Amanda is to be used.
isMsAmandaEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether MS Amanda is enabled.
isMsAmandaEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if MS Amanda is to be used.
isMsgfEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if MS-GF+ is to be used.
isMsgfEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether MS-GF+ is enabled.
isMsgfEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if MS-GF+ is to be used.
isMyriMatchEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if MyriMatch is to be used.
isMyriMatchEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether MyriMatch is enabled.
isMyriMatchEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if MyriMatch is to be used.
isNovorEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if Novor is to be used.
isNovorEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether Novor is enabled.
isNovorEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if Novor is to be used.
isOmssaEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if OMSSA is to be used.
isOmssaEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether OMSSA is enabled.
isOmssaEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if OMSSA is to be used.
isOutputData() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Indicates whether input data should be included in the output when it is zipped.
isOutputDate() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Indicates whether the date should be included in the output name.
isPeptideShakerEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns a boolean indicating whether PeptideShaker was enabled.
isReporterEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns a boolean indicating whether Reporter was enabled.
isSageEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if Sage is to be used.
isSageEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether Sage is enabled.
isSageEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if Sage is to be used.
isTideEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if Tide is to be used.
isTideEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether Tide is enabled.
isTideEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if Tide is to be used.
isValidStartup(CommandLine) - Static method in class eu.isas.searchgui.cmd.FastaCLIInputBean: Verifies the command line start parameters.
isValidStartup(CommandLine) - Static method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Verifies the command line start parameters.
isXtandemEnabled() - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: Returns whether X! Tandem is enabled.
isXtandemEnabled() - Method in class eu.isas.searchgui.SearchHandler: Returns true if X!Tandem is to be used.
isXTandemEnabled() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if X!Tandem is to be used.

L

loadModifications(SearchParameters) - Static method in class eu.isas.searchgui.SearchHandler: Verifies that the modifications backed-up in the search parameters are loaded and returns an error message if one was already loaded, null otherwise.
loadPathParameterFromLine(String) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Loads a path to be set from a line.
loadPathParametersFromFile(File) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Loads the path preferences from a text file.
LOG_FOLDER - Enum constant in enum eu.isas.searchgui.cmd.PathSettingsCLIParams

M

main(String[]) - Static method in class eu.isas.searchgui.cmd.FastaCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.searchgui.cmd.IdentificationParametersCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.searchgui.cmd.PathSettingsCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.searchgui.cmd.SearchCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.searchgui.gui.SearchGUI: The main method used to start SearchGUI.
main(String[]) - Static method in class eu.isas.searchgui.SearchGUIWrapper: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.searchgui.SearchGUIZipFileChecker: Start SearchGUIZipFileChecker.
MAKEBLASTDB_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MakeblastdbProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class takes care of starting the Makeblastdb Process.
MakeblastdbProcessBuilder(String, File, File, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder: Constructor.
mandatory - Variable in enum eu.isas.searchgui.cmd.FastaCLIParams: Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum eu.isas.searchgui.cmd.SearchCLIParams: Boolean indicating whether the parameter is mandatory.
META_MORPHEUS - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
META_MORPHEUS_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MetaMorpheusProcessBuilder - Class in eu.isas.searchgui.processbuilders: ProcessBuilder for the MetaMorpheus search engine.
MetaMorpheusProcessBuilder(File, boolean, File, SearchParameters, File, int, File, File, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder: Constructor.
MetaMorpheusProcessBuilder.MetaMorpheusTaskType - Enum in eu.isas.searchgui.processbuilders: The available MetaMorpheus task types.
MGF_CHECK_SIZE - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MGF_MAX_SPECTRA - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MGF_SPLITTING_LIMIT - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MISSING_TITLE_HANDLING - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MODIFICATION_SEPARATOR - Static variable in class eu.isas.searchgui.gui.SearchGUI: Reference for the separation of modifications.
MODIFICATION_USE_SEPARATOR - Static variable in class eu.isas.searchgui.gui.SearchGUI: Reference for the separation of modification and its frequency.
MS_AMANDA - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MS_AMANDA_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
msAmandaErrorMessage - Static variable in class eu.isas.searchgui.gui.SearchGUI: The error message shown if there is an issue with the MS Amanda installation.
MsAmandaProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class will build files and start a process to perform an MS Amanda search.
MsAmandaProcessBuilder(File, File, File, File, String, SearchParameters, FastaParameters, WaitingHandler, ExceptionHandler, int) - Constructor for class eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder: Constructor.
MsConvertProcessBuilder - Class in eu.isas.searchgui.processbuilders: Process builder to run msconvert.
MsConvertProcessBuilder(File, File, MsConvertParameters, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.MsConvertProcessBuilder: Constructor for the process builder.
MSGF - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MSGF_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MsgfProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class will set up and start a process to perform an MS-GF+ search.
MsgfProcessBuilder(File, File, File, File, File, SearchParameters, WaitingHandler, ExceptionHandler, int, boolean) - Constructor for class eu.isas.searchgui.processbuilders.MsgfProcessBuilder: Constructor.
MYRIMATCH - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MYRIMATCH_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
MyriMatchProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class will set up and start a process to perform a MyriMatch search.
MyriMatchProcessBuilder(File, File, File, File, SearchParameters, WaitingHandler, ExceptionHandler, int) - Constructor for class eu.isas.searchgui.processbuilders.MyriMatchProcessBuilder: Constructor.

N

needsFormatting() - Method in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder: Checks if makeblastdb has already been run on this file.
NOVOR - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
NOVOR_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
NovorProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class will set up and start a process to run Novor.
NovorProcessBuilder(File, File, File, File, SearchParameters, boolean, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.NovorProcessBuilder: Constructor.

O

OMSSA - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OMSSA_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OmssaclProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class takes care of building the omssacl process.
OmssaclProcessBuilder(File, File, File, File, File, SearchParameters, WaitingHandler, ExceptionHandler, Double, int) - Constructor for class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder: Constructor.
organizeOutput(File, File, HashMap<String, HashMap<Integer, File>>, File, boolean) - Method in class eu.isas.searchgui.SearchHandler: Organizes the identification files in zip files according to the output option of the search handler.
OUTPUT_DATA - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OUTPUT_DATE - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OUTPUT_DEFAULT_NAME - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OUTPUT_FOLDER - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OUTPUT_GZIP - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OUTPUT_OPTION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
OUTPUT_TEMP_FOLDER_NAME - Static variable in class eu.isas.searchgui.SearchHandler: Folder where the output is stored before packaging.

P

PathSettingsCLI - Class in eu.isas.searchgui.cmd: Allows the user to set the path settings in command line.
PathSettingsCLI(PathSettingsCLIInputBean) - Constructor for class eu.isas.searchgui.cmd.PathSettingsCLI: Constructor.
PathSettingsCLIInputBean - Class in eu.isas.searchgui.cmd: Parses the command line and retrieves the user input.
PathSettingsCLIInputBean(CommandLine) - Constructor for class eu.isas.searchgui.cmd.PathSettingsCLIInputBean: Construct a FollowUpCLIInputBean from an Apache CLI instance.
PathSettingsCLIParams - Enum in eu.isas.searchgui.cmd: Parameters for the path settings command line.
PeptideShakerParametersDialog - Class in eu.isas.searchgui.gui: A dialog for editing the PeptideShaker settings required when starting PeptideShaker from SearchGUI.
PeptideShakerParametersDialog(SearchGUI, boolean, ArrayList<File>) - Constructor for class eu.isas.searchgui.gui.PeptideShakerParametersDialog: Creates a new PeptideShakerSettingsDialog.
PeptideShakerProcessBuilder - Class in eu.isas.searchgui.processbuilders: This process builder runs PeptideShaker.
PeptideShakerProcessBuilder(WaitingHandler, ExceptionHandler, String, ArrayList<File>, File, ArrayList<File>, File, File, boolean, ProcessingParameters, boolean) - Constructor for class eu.isas.searchgui.processbuilders.PeptideShakerProcessBuilder: Constructor for the process builder.
Properties - Class in eu.isas.searchgui.utilities: This class provides the SearchGUI version number.
Properties() - Constructor for class eu.isas.searchgui.utilities.Properties: Creates a new empty Properties object.

R

redirectErrorStream(File) - Static method in class eu.isas.searchgui.cmd.SearchCLI: Redirects the error stream to the SearchGUI.log of a given folder.
REFERENCE_MASS - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
RENAME_XTANDEM_OUTPUT - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
renameXTandemFile() - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Returns true if the X! Tandem file should be renamed.
reportBothBestHitsForTD() - Method in class eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder: Returns true if target and decoy are ranked separately, false if shared rank.
restart() - Method in class eu.isas.searchgui.gui.SearchGUI
run() - Method in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

S

SAGE - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
SAGE_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
SageProcessBuilder - Class in eu.isas.searchgui.processbuilders: ProcessBuilder for the Sage search engine.
SageProcessBuilder(File, File, SearchParameters, File, File, String, WaitingHandler, ExceptionHandler, int) - Constructor for class eu.isas.searchgui.processbuilders.SageProcessBuilder: Constructor.
saveInputFile(File) - Method in class eu.isas.searchgui.SearchHandler: Save the input file.
Search - Enum constant in enum eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder.MetaMorpheusTaskType
SearchCLI - Class in eu.isas.searchgui.cmd: This class can be used to control SearchGUI in command line.
SearchCLI(String[]) - Constructor for class eu.isas.searchgui.cmd.SearchCLI: Construct a new SearchCLI runnable from a list of arguments.
SearchCLIdentificationParametersCLIParams - Class in eu.isas.searchgui.cmd: This class provides the parameters which can be used for the identification parameters cli in SearchGUI.
SearchCLIdentificationParametersCLIParams() - Constructor for class eu.isas.searchgui.cmd.SearchCLIdentificationParametersCLIParams
SearchCLIInputBean - Class in eu.isas.searchgui.cmd: The SearchCLIInputBean reads and stores command line options from a command line.
SearchCLIInputBean(CommandLine) - Constructor for class eu.isas.searchgui.cmd.SearchCLIInputBean: Parses the arguments of a command line.
SearchCLIParams - Enum in eu.isas.searchgui.cmd: Command line option parameters for SearchCLI.
SearchGUI - Class in eu.isas.searchgui.gui: The main frame of SearchGUI.
SearchGUI(ArrayList<File>, File, ArrayList<File>, File, File, File, String, String, String) - Constructor for class eu.isas.searchgui.gui.SearchGUI: Creates a SearchGUI dialog.
SEARCHGUI_CONFIGURATION_FILE - Static variable in class eu.isas.searchgui.SearchHandler: Default SearchGUI configurations.
SearchGUIPathParameters - Class in eu.isas.searchgui.parameters: This class sets the path preferences for the files to read/write
SearchGUIPathParameters() - Constructor for class eu.isas.searchgui.parameters.SearchGUIPathParameters
SearchGUIPathParameters.SearchGUIPathKey - Enum in eu.isas.searchgui.parameters: Enum of the paths which can be set in SearchGUI.
SearchGUIProcessBuilder - Class in eu.isas.searchgui.processbuilders: A simple ancestor class to reduce code duplication in formatdb, omssacl and tandem process builders.
SearchGUIProcessBuilder() - Constructor for class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: Empty constructor.
SearchGUIWrapper - Class in eu.isas.searchgui: A wrapper class used to start the jar file with parameters.
SearchGUIWrapper() - Constructor for class eu.isas.searchgui.SearchGUIWrapper: Starts the launcher by calling the launch method.
SearchGUIWrapper(String[]) - Constructor for class eu.isas.searchgui.SearchGUIWrapper: Starts the launcher by calling the launch method.
SearchGUIZipFileChecker - Class in eu.isas.searchgui: A wrapper class used to check if the jar file is attempted started from within an unzipped zip file.
SearchGUIZipFileChecker(String[]) - Constructor for class eu.isas.searchgui.SearchGUIZipFileChecker: Checks if the jar file is started from within an unzipped zip file.
SearchHandler - Class in eu.isas.searchgui: This class represents the search command line interface.
SearchHandler() - Constructor for class eu.isas.searchgui.SearchHandler: Empty default constructor.
SearchHandler(IdentificationParameters, File, File, String, ArrayList<File>, File, ArrayList<File>, File, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, File, File, File, File, File, File, File, File, File, File, File, File, File, File, ProcessingParameters) - Constructor for class eu.isas.searchgui.SearchHandler: Constructor for the SearchGUI command line interface.If the search engines folders are set to null the default search engine locations are used.
SearchHandler(IdentificationParameters, File, File, ArrayList<File>, File, ArrayList<File>, File, ProcessingParameters, MsFileHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.SearchHandler: Constructor for the SearchGUI command line interface.Uses the configuration file searchGUI_configuration.txt to get the default search engine locations and which search engines that are enabled.Mainly for use via the graphical UI.
setAllPathsIn(String) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Sets all the paths inside a given folder.
setAndromedaEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if Andromeda is to be used.
setAndromedaLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the Andromeda location.
setCheckMgfSize(boolean) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Set if the mgf should be checked for size.
setCloseProcessWhenDone(boolean) - Static method in class eu.isas.searchgui.SearchHandler: Set whether the process should be closed when completing or crashing.
setCmsFiles(ArrayList<File>) - Method in class eu.isas.searchgui.SearchHandler: Sets the list of cms files.
setCometEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if Comet is to be used.
setCometLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the Comet location.
setConfigFolder(File) - Method in class eu.isas.searchgui.gui.SearchGUI: Set the config folder.
setDefaultOutputFileName(String) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Sets the default output name.
setDefaultOutputFileName(String) - Static method in class eu.isas.searchgui.SearchHandler: Sets the default output file name.
setDirecTagEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if DirecTag is to be used.
setDirecTagLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the DirecTag location.
setDuplicateSpectrumTitleHandling(int) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Set how duplicate spectrum titles are to be handled.
setExperimentLabel(String) - Method in class eu.isas.searchgui.SearchHandler: Sets the the experiment label.
setFastaFile(File) - Method in class eu.isas.searchgui.SearchHandler: Set the FASTA file.
setIdentificationParameters(IdentificationParameters) - Method in class eu.isas.searchgui.gui.SearchGUI: Sets the search parameters.
setIdentificationParameters(IdentificationParameters) - Method in class eu.isas.searchgui.SearchHandler: Set the identification parameters.
setIdentificationParametersFile(File) - Method in class eu.isas.searchgui.SearchHandler: Set the identification parameters file.
setLastSelectedFolder(LastSelectedFolder) - Method in class eu.isas.searchgui.gui.SearchGUI: Set the last selected folder.
setLogFolder(File) - Method in class eu.isas.searchgui.SearchHandler: Sets the log folder.
setMakeblastdbLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the makeblastdb location.
setMascotFiles(ArrayList<File>) - Method in class eu.isas.searchgui.SearchHandler: Sets the mascot files.
setMetaMorpheusEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if MetaMorpheus is to be used.
setMetaMorpheusLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the MetaMorpheus location.
setMissingSpectrumTitleHandling(int) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Set how missing spectrum titles are to be handled.
setMsAmandaEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if MS Amanda is to be used.
setMsAmandaLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the MS Amanda location.
setMsConvertParameters(MsConvertParameters) - Method in class eu.isas.searchgui.SearchHandler: Sets the msconvert parameters.
setMsgfEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if MS-GF+ is to be used.
setMsgfLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the MS-GF+ location.
setMyriMatchEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if MyriMatch is to be used.
setMyriMatchLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the MyriMatch location.
setNovorEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if Novor is to be used.
setNovorLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the Novor location.
setOmssaEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if OMSSA is to be used.
setOmssaLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the OMSSA location.
setOutputTimeStamp(String) - Method in class eu.isas.searchgui.SearchHandler: Set the current output time stamp.
setParametersDisplayed(boolean) - Method in class eu.isas.searchgui.gui.SearchGUI: Set if the settings have been displayed.
setPathConfiguration() - Method in class eu.isas.searchgui.gui.SearchGUI: Sets the path configuration.
setPathParameter(PathKey, String) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Sets the path according to the given key and path.
setPathParameter(SearchGUIPathParameters.SearchGUIPathKey, String) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Sets the path according to the given key and path.
setPathSettings() - Method in class eu.isas.searchgui.cmd.PathSettingsCLI: Sets the path settings according to the pathSettingsCLIInputBean.
setPeptideShakerEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if PeptideShaker is to be run or not.
setPeptideShakerFile(File) - Method in class eu.isas.searchgui.SearchHandler: Sets the PeptideShaker file.
setProcessingParameters(ProcessingParameters) - Method in class eu.isas.searchgui.SearchHandler: Set the processing preferences.
setRawFiles(ArrayList<File>) - Method in class eu.isas.searchgui.SearchHandler: Sets the list of raw files.
setRefMass(Double) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Sets the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
setRenameXTandemFile(Boolean) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Set if the X! Tandem file should be renamed.
setReportBothBestHitsForTD(boolean) - Method in class eu.isas.searchgui.processbuilders.MsAmandaProcessBuilder: Set if target and decoy are ranked separately or shared.
setResultsFolder(File) - Method in class eu.isas.searchgui.SearchHandler: Set the results folder.
setSageEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if Sage is to be used.
setSageLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the Sage location.
setSpectrumFiles(ArrayList<File>) - Method in class eu.isas.searchgui.SearchHandler: Sets the list of mass spectrometry files.
setTargetDecoyFileNameTag(String) - Method in class eu.isas.searchgui.cmd.SearchCLIInputBean: Set the target-decoy file name tag.
setTempFolderPath(String) - Static method in class eu.isas.searchgui.SearchHandler: Sets the folder to use for temporary files.
setTempSearchEngineFolderPath(String) - Static method in class eu.isas.searchgui.SearchHandler: Sets the folder to use for temporary search engine files.
setThermoRawFileParserParameters(ThermoRawFileParserParameters) - Method in class eu.isas.searchgui.SearchHandler: Sets the ThermoRawFileParser parameters.
setTideEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if Tide is to be used.
setTideLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the Tide location.
settingsDisplayed() - Method in class eu.isas.searchgui.gui.SearchGUI: Returns true if the settings have been displayed.
setXtandemEnabled(boolean) - Method in class eu.isas.searchgui.SearchHandler: Set if X!Tandem is to be used.
setXtandemLocation(File) - Method in class eu.isas.searchgui.SearchHandler: Set the X!Tandem location.
SoftwareLocationDialog - Class in eu.isas.searchgui.gui: The search engines settings dialog.
SoftwareLocationDialog(SearchGUI, boolean) - Constructor for class eu.isas.searchgui.gui.SoftwareLocationDialog: Creates a new SearchEnginesSettingsDialog.
SPECTRUM_FILES - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
startProcess() - Method in class eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder: Starts the process of a process builder, gets the input stream from the process and shows it in a JTextArea.
startProcess() - Method in class eu.isas.searchgui.processbuilders.MsConvertProcessBuilder
startProcess() - Method in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: Starts the process of a process builder, gets the input stream from the process and shows it in a JEditorPane supporting HTML.
startProcess() - Method in class eu.isas.searchgui.processbuilders.ThermoRawFileParserProcessBuilder
startSearch() - Method in class eu.isas.searchgui.gui.SearchGUI: This method is called whenever the 'Search' button is pressed.
startSearch(WaitingHandler) - Method in class eu.isas.searchgui.SearchHandler: Start the search.

T

TandemProcessBuilder - Class in eu.isas.searchgui.processbuilders: This class will build files and start a process to perform an X!Tandem search.
TandemProcessBuilder(File, File, File, File, String, SearchParameters, WaitingHandler, ExceptionHandler, int) - Constructor for class eu.isas.searchgui.processbuilders.TandemProcessBuilder: Constructor.
TARGET_DECOY_TAG - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
tempDirectory - Enum constant in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey: Directory where SearchGUI temporary files should be stored.
tempSearchEngineDirectory - Enum constant in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey: Folder where search engine temporary files should be stored.
ThermoRawFileParserProcessBuilder - Class in eu.isas.searchgui.processbuilders: Process builder to run ThermoRawFileParser.
ThermoRawFileParserProcessBuilder(File, File, File, ThermoRawFileParserParameters, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.ThermoRawFileParserProcessBuilder: Constructor for the process builder.
THREADS - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
TIDE - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
TIDE_INDEX_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
TIDE_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
TideIndexProcessBuilder - Class in eu.isas.searchgui.processbuilders: ProcessBuilder for the Tide index generation.
TideIndexProcessBuilder(File, File, File, File, SearchParameters, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.searchgui.processbuilders.TideIndexProcessBuilder: Constructor.
TideSearchProcessBuilder - Class in eu.isas.searchgui.processbuilders: ProcessBuilder for the Tide search command.
TideSearchProcessBuilder(File, File, File, SearchParameters, File, WaitingHandler, ExceptionHandler, int) - Constructor for class eu.isas.searchgui.processbuilders.TideSearchProcessBuilder: Constructor.
TITLED_BORDER_HORIZONTAL_PADDING - Static variable in class eu.isas.searchgui.gui.SearchGUI: The horizontal padding used before and after the text in the titled borders.
toString() - Method in class eu.isas.searchgui.cmd.PathSettingsCLI

U

USE_LOG_FOLDER - Enum constant in enum eu.isas.searchgui.cmd.PathSettingsCLIParams
useLogFile() - Method in class eu.isas.searchgui.cmd.PathSettingsCLIInputBean: Return true if a log file is to be used.

V

validateAdvancedParametersInput(boolean) - Method in class eu.isas.searchgui.gui.AdvancedParametersDialog: Inspects the parameters validity.
validateParametersInput(boolean) - Method in class eu.isas.searchgui.gui.SearchGUI: Inspects the parameter validity.
validateSearchEngineFolder(File, String) - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method validates whether the specified folder is the root folder if the given search engine.
validateSearchEngineFolder(File, String, String) - Method in class eu.isas.searchgui.gui.SoftwareLocationDialog: This method validates whether the specified folder is the root folder of the given search engine.
validateSearchEngineInstallation(Advocate, File, boolean) - Static method in class eu.isas.searchgui.gui.SearchGUI: Tries to validate the search engine installation by running the executable.
validateSearchEngines(boolean) - Method in class eu.isas.searchgui.gui.SearchGUI: Validate that the search engines work.
valueOf(String) - Static method in enum eu.isas.searchgui.cmd.FastaCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.searchgui.cmd.SearchCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder.MetaMorpheusTaskType: Returns the enum constant of this type with the specified name.
values() - Static method in enum eu.isas.searchgui.cmd.FastaCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.searchgui.cmd.PathSettingsCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.searchgui.cmd.SearchCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.searchgui.parameters.SearchGUIPathParameters.SearchGUIPathKey: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.searchgui.processbuilders.MetaMorpheusProcessBuilder.MetaMorpheusTaskType: Returns an array containing the constants of this enum type, in the order they are declared.
verifySpectrumFileNames() - Method in class eu.isas.searchgui.gui.SearchGUI: Verifies that all spectrum files have different names and displays a warning with the first conflict encountered.

W

waitingHandler - Variable in class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder: The waiting handler to display the feedback.
writeConfigurationToFile(SimpleFileWriter, File) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Writes all path configurations to the given file.
writeConfigurationToFile(File, File) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Writes all path configurations to the given file.
writeDbProperties(FastaSummary, FastaParameters) - Method in class eu.isas.searchgui.cmd.FastaCLI: Writes the database properties to System.out.
writeOmssaUserModificationsFile(File, IdentificationParameters, File) - Static method in class eu.isas.searchgui.processbuilders.OmssaclProcessBuilder: Writes the OMSSA modification file corresponding to the PTMs loaded in the factory in the given file.
writePathToFile(SimpleFileWriter, SearchGUIPathParameters.SearchGUIPathKey, File) - Static method in class eu.isas.searchgui.parameters.SearchGUIPathParameters: Writes the path of interest using the provided buffered writer.

X

XTANDEM - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams
XTANDEM_LOCATION - Enum constant in enum eu.isas.searchgui.cmd.SearchCLIParams

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