com.compomics.software
Class ToolFactory

java.lang.Object
  extended by com.compomics.software.ToolFactory

public class ToolFactory
extends java.lang.Object

This class can be used to start compomics tools.

Author:
Marc Vaudel

Field Summary
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 Summary
ToolFactory()
           
 
Method Summary
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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

peptideShakerFileOption

public static final java.lang.String peptideShakerFileOption
The command line argument for a cps file for PeptideShaker.

See Also:
Constant Field Values

searchGuiSpectrumFileOption

public static final java.lang.String searchGuiSpectrumFileOption
The command line argument for mgf files for SearchGUI.

See Also:
Constant Field Values

searchGuiParametersFileOption

public static final java.lang.String searchGuiParametersFileOption
The command line argument for a parameters file for SearchGUI.

See Also:
Constant Field Values

outputFolderOption

public static final java.lang.String outputFolderOption
The command line argument for an output folder

See Also:
Constant Field Values
Constructor Detail

ToolFactory

public ToolFactory()
Method Detail

startPeptideShaker

public static void startPeptideShaker(javax.swing.JFrame parent)
                               throws java.io.FileNotFoundException,
                                      java.io.IOException,
                                      java.lang.ClassNotFoundException,
                                      java.lang.InterruptedException
Starts PeptideShaker from the location of utilities preferences.

Parameters:
parent - a frame to display the path setting dialog (can be null)
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException

startPeptideShaker

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
Starts 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)
cpsFile - the file to open (cps format) (can be null)
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException

startReporter

public static void startReporter(javax.swing.JFrame parent)
                          throws java.io.FileNotFoundException,
                                 java.io.IOException,
                                 java.lang.ClassNotFoundException,
                                 java.lang.InterruptedException
Starts Reporter from the location of utilities preferences.

Parameters:
parent - a frame to display the path setting dialog.
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException

startRelims

public static void startRelims(javax.swing.JFrame parent)
                        throws java.io.FileNotFoundException,
                               java.io.IOException,
                               java.lang.ClassNotFoundException,
                               java.lang.InterruptedException
Deprecated. use PeptideShaker's own Reshake option instead.

Starts Relims from the location of utilities preferences.

Parameters:
parent - a frame to display the path setting dialog.
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException

startSearchGUI

public static void startSearchGUI(javax.swing.JFrame parent)
                           throws java.io.FileNotFoundException,
                                  java.io.IOException,
                                  java.lang.ClassNotFoundException,
                                  java.lang.InterruptedException
Starts SearchGUI from the location of utilities preferences.

Parameters:
parent - a frame to display the path setting dialog.
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException

startSearchGUI

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
Starts 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)
searchParameters - the search parameters as a file (can be null)
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException


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