public class ToolFactory extends Object
Modifier and Type | Field and Description |
---|---|
static String |
outputFolderOption
The command line argument for an output folder.
|
static String |
peptideShakerFileOption
The command line argument for a cps file for PeptideShaker.
|
static String |
peptideShakerPxAccessionOption
The command line argument to open a given PX accession in PRIDE Reshake.
|
static String |
peptideShakerPxAccessionPrivateOption
The command line argument to indicate that the PX accession to open in
PRIDE Reshake is private.
|
static String |
peptideShakerUrlDownloadFolderOption
The command line argument for the download folder for the URL for
PeptideShaker.
|
static String |
peptideShakerUrlOption
The command line argument for a zipped cps URL for PeptideShaker.
|
static String |
searchGuiParametersFileOption
The command line argument for a parameters file for SearchGUI.
|
static String |
searchGuiRawFileOption
The command line argument for raw files for SearchGUI.
|
static String |
searchGuiSpectrumFileOption
The command line argument for mgf files for SearchGUI.
|
static String |
speciesOption
The command line argument for the species.
|
static String |
speciesTypeOption
The command line argument for the species type.
|
Constructor and Description |
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ToolFactory() |
Modifier and Type | Method and Description |
---|---|
static void |
startPeptideShaker(JFrame parent)
Starts PeptideShaker from the location of utilities preferences.
|
static void |
startPeptideShaker(JFrame parent,
File cpsFile)
Starts PeptideShaker from the location of utilities preferences and opens
the file given as argument.
|
static void |
startPeptideShakerFromURL(JFrame parent,
String zipUrl,
String downloadUrlFolder)
Starts PeptideShaker from the location of utilities preferences and opens
the file given as argument.
|
static void |
startReporter(JFrame parent)
Starts Reporter from the location of utilities preferences.
|
static void |
startSearchGUI(JFrame parent)
Starts SearchGUI from the location of utilities preferences.
|
static void |
startSearchGUI(JFrame parent,
ArrayList<File> mgfFiles,
ArrayList<File> rawFiles,
File searchParameters,
File outputFolder,
String species,
String speciesType)
Starts SearchGUI from the location of utilities preferences.
|
public static final String peptideShakerFileOption
public static final String peptideShakerUrlOption
public static final String peptideShakerUrlDownloadFolderOption
public static final String peptideShakerPxAccessionOption
public static final String peptideShakerPxAccessionPrivateOption
public static final String searchGuiSpectrumFileOption
public static final String searchGuiRawFileOption
public static final String searchGuiParametersFileOption
public static final String outputFolderOption
public static final String speciesOption
public static final String speciesTypeOption
public static void startPeptideShaker(JFrame parent) throws FileNotFoundException, IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog (can be null)FileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic static void startPeptideShaker(JFrame parent, File cpsFile) throws FileNotFoundException, IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog (can be null)cpsFile
- the file to open (cps format) (can be null)FileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic static void startPeptideShakerFromURL(JFrame parent, String zipUrl, String downloadUrlFolder) throws FileNotFoundException, IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog (can be null)zipUrl
- the URL with the zipped PeptideShaker project to open (can
be null)downloadUrlFolder
- the folder to download the project to, mandatory
if zipUrl is usedFileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic static void startReporter(JFrame parent) throws FileNotFoundException, IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog.FileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic static void startSearchGUI(JFrame parent) throws FileNotFoundException, IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog.FileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic static void startSearchGUI(JFrame parent, ArrayList<File> mgfFiles, ArrayList<File> rawFiles, File searchParameters, File outputFolder, String species, String speciesType) throws FileNotFoundException, IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog.mgfFiles
- the mgf files to search (can be null)rawFiles
- the raw files to search (can be null)searchParameters
- the search parameters as a file (can be null)outputFolder
- outputFolder the output folder (can be null)species
- the species (can be null)speciesType
- the species type (can be null)FileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occursCopyright © 2016. All rights reserved.