public class ToolFactory
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
outputFolderOption
The command line argument for an output folder
|
static java.lang.String |
peptideShakerFileOption
The command line argument for a cps file for PeptideShaker.
|
static java.lang.String |
searchGuiParametersFileOption
The command line argument for a parameters file for SearchGUI.
|
static java.lang.String |
searchGuiSpectrumFileOption
The command line argument for mgf files for SearchGUI.
|
Constructor and Description |
---|
ToolFactory() |
Modifier and Type | Method and Description |
---|---|
static void |
startPeptideShaker(javax.swing.JFrame parent)
Starts PeptideShaker from the location of utilities preferences.
|
static void |
startPeptideShaker(javax.swing.JFrame parent,
java.io.File cpsFile)
Starts PeptideShaker from the location of utilities preferences and opens
the file given as argument.
|
static void |
startRelims(javax.swing.JFrame parent)
Deprecated.
use PeptideShaker's own Reshake option instead.
|
static void |
startReporter(javax.swing.JFrame parent)
Starts Reporter from the location of utilities preferences.
|
static void |
startSearchGUI(javax.swing.JFrame parent)
Starts SearchGUI from the location of utilities preferences.
|
static void |
startSearchGUI(javax.swing.JFrame parent,
java.util.ArrayList<java.io.File> mgfFiles,
java.io.File searchParameters,
java.io.File outputFolder)
Starts SearchGUI from the location of utilities preferences.
|
public static final java.lang.String peptideShakerFileOption
public static final java.lang.String searchGuiSpectrumFileOption
public static final java.lang.String searchGuiParametersFileOption
public static final java.lang.String outputFolderOption
public static void startPeptideShaker(javax.swing.JFrame parent) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.InterruptedException
parent
- a frame to display the path setting dialog (can be null)java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
public static void startPeptideShaker(javax.swing.JFrame parent, java.io.File cpsFile) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.InterruptedException
parent
- a frame to display the path setting dialog (can be null)cpsFile
- the file to open (cps format) (can be null)java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
public static void startReporter(javax.swing.JFrame parent) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.InterruptedException
parent
- a frame to display the path setting dialog.java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
public static void startRelims(javax.swing.JFrame parent) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.InterruptedException
parent
- a frame to display the path setting dialog.java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
public static void startSearchGUI(javax.swing.JFrame parent) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.InterruptedException
parent
- a frame to display the path setting dialog.java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
public static void startSearchGUI(javax.swing.JFrame parent, java.util.ArrayList<java.io.File> mgfFiles, java.io.File searchParameters, java.io.File outputFolder) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.InterruptedException
parent
- a frame to display the path setting dialog.mgfFiles
- the mgf files to search (can be null)searchParameters
- the search parameters as a file (can be null)outputFolder
- outputFolder the output folderjava.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
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