public class ToolFactory extends Object
Modifier and Type | Field and 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 and Description |
---|
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 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.
|
public static final String PEPTIDE_SHAKER_FILE_OPTION
public static final String PEPTIDE_SHAKER_URL_OPTION
public static final String PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION
public static final String PEPTIDE_SHAKER_PX_ACCESSION_OPTION
public static final String PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION
public static final String SEARCHGUI_SPECTRUM_FILE_OPTION
public static final String SEARCHGUI_FASTA_FILE_OPTION
public static final String SEARCHGUI_RAW_FILE_OPTION
public static final String SEARCHGUI_PARAMETERS_FILE_OPTION
public static final String OUTPUT_FOLDER_OPTION
public static final String SPECIES_OPTION
public static final String SPECIES_TYPE_OPTION
public static final String PROJEC_NAME_OPTION
public static void startPeptideShaker(JFrame parent) throws IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog (can be null)IOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occurspublic static void startPeptideShaker(JFrame parent, File psdbFile) throws IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog (can be null)psdbFile
- the file to open (psdb format) (can be null)IOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occurspublic static void startReshake(JFrame parent, String pxAccession) throws IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog (can be null)pxAccession
- the ProteomeXchange accession of the project to open (can be null)IOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occurspublic static void startPeptideShakerFromURL(JFrame parent, String zipUrl, String downloadUrlFolder) throws 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 usedIOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occurspublic static void startReporter(JFrame parent) throws IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog.IOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occurspublic static void startSearchGUI(JFrame parent) throws IOException, ClassNotFoundException, InterruptedException
parent
- a frame to display the path setting dialog.IOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occurspublic 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, 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)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 nameIOException
- if an exception occurs while reading or writing a
fileClassNotFoundException
- if an exception occurs while reading the
user preferencesInterruptedException
- if a threading issue occursCopyright © 2021. All rights reserved.