Package eu.isas.peptideshaker.cmd

Class PeptideShakerCLIInputBean

java.lang.Object
eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean
public class PeptideShakerCLIInputBean extends Object
This class is a simple bean wrapping the CLI parameters provided in an Options instance.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • PeptideShakerCLIInputBean

      public PeptideShakerCLIInputBean(org.apache.commons.cli.CommandLine aLine) throws IOException, ClassNotFoundException
      Construct a PeptideShakerCLIInputBean from an Apache CLI instance.
      Parameters:
      aLine - the command line
      Throws:
      IOException - thrown of IOException occurs
      ClassNotFoundException - thrown of ClassNotFoundException occurs

    • PeptideShakerCLIInputBean

      public PeptideShakerCLIInputBean()
      Empty constructor for API usage via other tools.

  • Method Details

    • getProjectType

      public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()
      Returns the project type.
      Returns:
      the project type

    • getZipExport

      public File getZipExport()
      Returns the file where to export the project as zip file. Null if not set.
      Returns:
      the file where to export the project as zip file

    • getMgfExport

      public boolean getMgfExport()
      When exporting the project to a zip file, returns whether mgf file/s should be written apart from it, into the same folder.
      Returns:
      whether mgf file/s should be written apart from the zip file

    • getExperimentID

      public String getExperimentID()
      Returns the experiment name.
      Returns:
      the experiment name

    • setExperimentID

      public void setExperimentID(String experimentID)
      Sets the experiment name.
      Parameters:
      experimentID - the experiment name

    • getOutput

      public File getOutput()
      Returns the psdb output file. Null if not set.
      Returns:
      the psdb output file

    • setOutput

      public void setOutput(File output)
      Sets the psdb output file.
      Parameters:
      output - the psdb output file

    • getConfigFolder

      public File getConfigFolder()
      Returns the config folder. Null if not set.
      Returns:
      the config folder

    • setConfigFoler

      public void setConfigFoler(File config_folder)
      Sets the config folder.
      Parameters:
      config_folder - the config folder

    • getIdFiles

      public ArrayList<File> getIdFiles()
      Returns the identification files.
      Returns:
      the identification files

    • setIdFiles

      public void setIdFiles(ArrayList<File> idFiles)
      Sets the identification files.
      Parameters:
      idFiles - the identification files

    • getPrideFile

      public File getPrideFile()
      Returns the pride file.
      Returns:
      the pride file

    • setPrideFile

      public void setPrideFile(File prideFile)
      Sets the pride file.
      Parameters:
      prideFile - the pride file

    • getSpectrumFiles

      public ArrayList<File> getSpectrumFiles()
      Returns the spectrum files.
      Returns:
      the spectrum files

    • setSpectrumFiles

      public void setSpectrumFiles(ArrayList<File> spectrumFiles)
      Sets the spectrum files.
      Parameters:
      spectrumFiles - the spectrum files

    • getFastaFile

      public File getFastaFile()
      Returns the FASTA file.
      Returns:
      the FASTA file

    • setFastaFile

      public void setFastaFile(File fastaFile)
      Sets the FASTA file.
      Parameters:
      fastaFile - the FASTA file

    • getSpectrumFiles

      public static ArrayList<File> getSpectrumFiles(String optionInput) throws FileNotFoundException
      Returns a list of spectrum files as imported from the command line option.
      Parameters:
      optionInput - the command line option
      Returns:
      a list of file candidates
      Throws:
      FileNotFoundException - exception thrown whenever a file is not found

    • getIdentificationFiles

      public static ArrayList<File> getIdentificationFiles(String optionInput) throws FileNotFoundException
      Returns a list of identification files as imported from the command line option.
      Parameters:
      optionInput - the command line option
      Returns:
      a list of file candidates
      Throws:
      FileNotFoundException - exception thrown whenever a file is not found

    • isGUI

      public boolean isGUI()
      Indicates whether a GUI shall be used to display the progress.
      Returns:
      a boolean indicating whether a GUI shall be used to display the progress

    • getFollowUpCLIInputBean

      public FollowUpCLIInputBean getFollowUpCLIInputBean()
      Returns the follow-up options required.
      Returns:
      the follow-up options required

    • getReportCLIInputBean

      public ReportCLIInputBean getReportCLIInputBean()
      Returns the report export options required.
      Returns:
      the report export options required

    • getMzidCLIInputBean

      public MzidCLIInputBean getMzidCLIInputBean()
      Returns the mzid export options required.
      Returns:
      the mzid export options required

    • getPathSettingsCLIInputBean

      public PathSettingsCLIInputBean getPathSettingsCLIInputBean()
      Returns the path settings provided by the user.
      Returns:
      the path settings provided by the user

    • getIdentificationParametersInputBean

      public com.compomics.cli.identification_parameters.IdentificationParametersInputBean getIdentificationParametersInputBean()
      Returns the identification parameters provided by the user.
      Returns:
      the identification parameters provided by the user

    • getIdentificationParametersFile

      public File getIdentificationParametersFile()
      Returns the identification parameters file.
      Returns:
      the identification parameters file

    • getnThreads

      public Integer getnThreads()
      Returns the number of threads to use.
      Returns:
      the number of threads to use

    • getCachePercolatorFeatures

      public Boolean getCachePercolatorFeatures()
      Returns wether the user enabled the caching of Percolator features.
      Returns:
      A boolean indicating wether the user enabled the caching of Percolator features.

    • isValidStartup

      public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine) throws IOException
      Verifies the command line start parameters.
      Parameters:
      aLine - the command line to validate
      Returns:
      true if the startup was valid
      Throws:
      IOException - if the spectrum file(s) are not found