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