Package com.compomics.software

Class ToolFactory

java.lang.Object
com.compomics.software.ToolFactory
public class ToolFactory extends Object
This class can be used to start compomics tools.
Author:
Marc Vaudel, Harald Barsnes

  • Field Details

    • PEPTIDE_SHAKER_FILE_OPTION

      public static final String PEPTIDE_SHAKER_FILE_OPTION
      The command line argument for a psdb file for PeptideShaker.
      See Also:

    • PEPTIDE_SHAKER_URL_OPTION

      public static final String PEPTIDE_SHAKER_URL_OPTION
      The command line argument for a zipped psdb URL for PeptideShaker.
      See Also:

    • PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION

      public static final String PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION
      The command line argument for the download folder for the URL for PeptideShaker.
      See Also:

    • PEPTIDE_SHAKER_PX_ACCESSION_OPTION

      public static final String PEPTIDE_SHAKER_PX_ACCESSION_OPTION
      The command line argument to open a given PX accession in PRIDE Reshake.
      See Also:

    • PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION

      public static final String PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION
      The command line argument to indicate that the PX accession to open in PRIDE Reshake is private. If not set public is assumed.
      See Also:

    • SEARCHGUI_SPECTRUM_FILE_OPTION

      public static final String SEARCHGUI_SPECTRUM_FILE_OPTION
      The command line argument for mgf files for SearchGUI.
      See Also:

    • SEARCHGUI_FASTA_FILE_OPTION

      public static final String SEARCHGUI_FASTA_FILE_OPTION
      The command line argument for FASTA file for SearchGUI.
      See Also:

    • SEARCHGUI_RAW_FILE_OPTION

      public static final String SEARCHGUI_RAW_FILE_OPTION
      The command line argument for raw files for SearchGUI.
      See Also:

    • SEARCHGUI_PARAMETERS_FILE_OPTION

      public static final String SEARCHGUI_PARAMETERS_FILE_OPTION
      The command line argument for a parameters file for SearchGUI.
      See Also:

    • OUTPUT_FOLDER_OPTION

      public static final String OUTPUT_FOLDER_OPTION
      The command line argument for an output folder.
      See Also:

    • SPECIES_OPTION

      public static final String SPECIES_OPTION
      The command line argument for the species.
      See Also:

    • SPECIES_TYPE_OPTION

      public static final String SPECIES_TYPE_OPTION
      The command line argument for the species type.
      See Also:

    • PROJECT_NAME_OPTION

      public static final String PROJECT_NAME_OPTION
      The command line argument for the PeptideShaker project name.
      See Also:

    • CONFIG_FOLDER

      public static final String CONFIG_FOLDER
      The command line argument for the config folder.
      See Also:

  • Constructor Details

    • ToolFactory

      public ToolFactory()

  • Method Details

    • startPeptideShaker

      public static void startPeptideShaker(JFrame parent) throws IOException, ClassNotFoundException, InterruptedException
      Starts PeptideShaker from the location of utilities preferences.
      Parameters:
      parent - a frame to display the path setting dialog (can be null)
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs

    • startPeptideShaker

      public static void startPeptideShaker(JFrame parent, File psdbFile) throws IOException, ClassNotFoundException, 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)
      psdbFile - the file to open (psdb format) (can be null)
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs

    • startReshake

      public static void startReshake(JFrame parent, String pxAccession) throws IOException, ClassNotFoundException, InterruptedException
      Starts PeptideShaker from the location of utilities preferences in the Reshake mode and attempts at selecting the given project.
      Parameters:
      parent - a frame to display the path setting dialog (can be null)
      pxAccession - the ProteomeXchange accession of the project to open (can be null)
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs

    • startPeptideShakerFromURL

      public static void startPeptideShakerFromURL(JFrame parent, String zipUrl, String downloadUrlFolder) throws IOException, ClassNotFoundException, 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)
      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 used
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs

    • startReporter

      public static void startReporter(JFrame parent) throws IOException, ClassNotFoundException, InterruptedException
      Starts Reporter from the location of utilities preferences.
      Parameters:
      parent - a frame to display the path setting dialog.
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs

    • startSearchGUI

      public static void startSearchGUI(JFrame parent) throws IOException, ClassNotFoundException, InterruptedException
      Starts SearchGUI from the location of utilities preferences.
      Parameters:
      parent - a frame to display the path setting dialog.
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs

    • startSearchGUI

      public static void startSearchGUI(JFrame parent, ArrayList<File> spectrumFiles, ArrayList<File> rawFiles, File fastaFile, File searchParameters, File outputFolder, File configFolder, String species, String speciesType, String projectName) throws IOException, ClassNotFoundException, InterruptedException
      Starts SearchGUI from the location of utilities preferences.
      Parameters:
      parent - a frame to display the path setting dialog.
      spectrumFiles - the spectrum files to search (can be null)
      rawFiles - the raw files to search (can be null)
      fastaFile - the FASTA file
      searchParameters - the search parameters as a file (can be null)
      outputFolder - the output folder (can be null)
      configFolder - the config folder (can be null)
      species - the species (can be null)
      speciesType - the species type (can be null)
      projectName - the PeptideShaker project name
      Throws:
      IOException - if an exception occurs while reading or writing a file
      ClassNotFoundException - if an exception occurs while reading the user preferences
      InterruptedException - if a threading issue occurs