Package com.compomics.software
Class ToolFactory
java.lang.Object
com.compomics.software.ToolFactory
public class ToolFactory extends Object
This class can be used to start compomics tools.
- Author:
- Marc Vaudel, Harald Barsnes
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Field Summary
Fields Modifier and Type Field Description static String
OUTPUT_FOLDER_OPTION
The command line argument for an output folder.static String
PEPTIDE_SHAKER_FILE_OPTION
The command line argument for a psdb file for PeptideShaker.static String
PEPTIDE_SHAKER_PX_ACCESSION_OPTION
The command line argument to open a given PX accession in PRIDE Reshake.static String
PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION
The command line argument to indicate that the PX accession to open in PRIDE Reshake is private.static String
PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION
The command line argument for the download folder for the URL for PeptideShaker.static String
PEPTIDE_SHAKER_URL_OPTION
The command line argument for a zipped psdb URL for PeptideShaker.static String
PROJEC_NAME_OPTION
The command line argument for the PeptideShaker project name.static String
SEARCHGUI_FASTA_FILE_OPTION
The command line argument for FASTA file for SearchGUI.static String
SEARCHGUI_PARAMETERS_FILE_OPTION
The command line argument for a parameters file for SearchGUI.static String
SEARCHGUI_RAW_FILE_OPTION
The command line argument for raw files for SearchGUI.static String
SEARCHGUI_SPECTRUM_FILE_OPTION
The command line argument for mgf files for SearchGUI.static String
SPECIES_OPTION
The command line argument for the species.static String
SPECIES_TYPE_OPTION
The command line argument for the species type. -
Constructor Summary
Constructors Constructor Description ToolFactory()
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Method Summary
Modifier and Type Method Description static void
startPeptideShaker(JFrame parent)
Starts PeptideShaker from the location of utilities preferences.static void
startPeptideShaker(JFrame parent, File psdbFile)
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
startReshake(JFrame parent, String pxAccession)
Starts PeptideShaker from the location of utilities preferences in the Reshake mode and attempts at selecting the given project.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 fastaFile, File searchParameters, File outputFolder, String species, String speciesType, String projectName)
Starts SearchGUI from the location of utilities preferences.
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Field Details
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PEPTIDE_SHAKER_FILE_OPTION
The command line argument for a psdb file for PeptideShaker.- See Also:
- Constant Field Values
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PEPTIDE_SHAKER_URL_OPTION
The command line argument for a zipped psdb URL for PeptideShaker.- See Also:
- Constant Field Values
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PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION
The command line argument for the download folder for the URL for PeptideShaker.- See Also:
- Constant Field Values
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PEPTIDE_SHAKER_PX_ACCESSION_OPTION
The command line argument to open a given PX accession in PRIDE Reshake.- See Also:
- Constant Field Values
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PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION
The command line argument to indicate that the PX accession to open in PRIDE Reshake is private. If not set public is assumed.- See Also:
- Constant Field Values
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SEARCHGUI_SPECTRUM_FILE_OPTION
The command line argument for mgf files for SearchGUI.- See Also:
- Constant Field Values
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SEARCHGUI_FASTA_FILE_OPTION
The command line argument for FASTA file for SearchGUI.- See Also:
- Constant Field Values
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SEARCHGUI_RAW_FILE_OPTION
The command line argument for raw files for SearchGUI.- See Also:
- Constant Field Values
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SEARCHGUI_PARAMETERS_FILE_OPTION
The command line argument for a parameters file for SearchGUI.- See Also:
- Constant Field Values
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OUTPUT_FOLDER_OPTION
The command line argument for an output folder.- See Also:
- Constant Field Values
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SPECIES_OPTION
The command line argument for the species.- See Also:
- Constant Field Values
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SPECIES_TYPE_OPTION
The command line argument for the species type.- See Also:
- Constant Field Values
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PROJEC_NAME_OPTION
The command line argument for the PeptideShaker project name.- See Also:
- Constant Field Values
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Constructor Details
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ToolFactory
public ToolFactory()
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Method Details
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startPeptideShaker
public static void startPeptideShaker(JFrame parent) throws IOException, ClassNotFoundException, InterruptedExceptionStarts PeptideShaker from the location of utilities preferences.- Parameters:
parent
- a frame to display the path setting dialog (can be null)- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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startPeptideShaker
public static void startPeptideShaker(JFrame parent, File psdbFile) throws IOException, ClassNotFoundException, InterruptedExceptionStarts PeptideShaker from the location of utilities preferences and opens the file given as argument. If null is given as file or if the file to open is not found, the tool will go for a default start.- Parameters:
parent
- a frame to display the path setting dialog (can be null)psdbFile
- the file to open (psdb format) (can be null)- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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startReshake
public static void startReshake(JFrame parent, String pxAccession) throws IOException, ClassNotFoundException, InterruptedExceptionStarts PeptideShaker from the location of utilities preferences in the Reshake mode and attempts at selecting the given project.- Parameters:
parent
- a frame to display the path setting dialog (can be null)pxAccession
- the ProteomeXchange accession of the project to open (can be null)- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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startPeptideShakerFromURL
public static void startPeptideShakerFromURL(JFrame parent, String zipUrl, String downloadUrlFolder) throws IOException, ClassNotFoundException, InterruptedExceptionStarts PeptideShaker from the location of utilities preferences and opens the file given as argument. If null is given as file or if the file to open is not found, the tool will go for a default start.- Parameters:
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 used- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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startReporter
public static void startReporter(JFrame parent) throws IOException, ClassNotFoundException, InterruptedExceptionStarts Reporter from the location of utilities preferences.- Parameters:
parent
- a frame to display the path setting dialog.- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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startSearchGUI
public static void startSearchGUI(JFrame parent) throws IOException, ClassNotFoundException, InterruptedExceptionStarts SearchGUI from the location of utilities preferences.- Parameters:
parent
- a frame to display the path setting dialog.- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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startSearchGUI
public static void startSearchGUI(JFrame parent, ArrayList<File> mgfFiles, ArrayList<File> rawFiles, File fastaFile, File searchParameters, File outputFolder, String species, String speciesType, String projectName) throws IOException, ClassNotFoundException, InterruptedExceptionStarts SearchGUI from the location of utilities preferences.- Parameters:
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)fastaFile
- the FASTA filesearchParameters
- 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)projectName
- the PeptideShaker project name- Throws:
IOException
- if an exception occurs while reading or writing a fileClassNotFoundException
- if an exception occurs while reading the user preferencesInterruptedException
- if a threading issue occurs
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