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java.lang.Objectcom.compomics.software.ToolFactory
public class ToolFactory
This class can be used to start compomics tools.
Field Summary | |
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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 | |
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ToolFactory()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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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
Constructor Detail |
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public ToolFactory()
Method Detail |
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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)
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.InterruptedException
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