Package com.compomics.cli.identification_parameters

Class IdentificationParametersInputBean

java.lang.Object
com.compomics.cli.identification_parameters.IdentificationParametersInputBean
public class IdentificationParametersInputBean extends Object
This class parses the parameters from a command line and stores them in a SearchParameters object.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • IdentificationParametersInputBean

      public IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine) throws IOException, ClassNotFoundException
      Takes all the arguments from a command line.
      Parameters:
      aLine - the command line
      Throws:
      IOException - if an IOException occurs
      ClassNotFoundException - if aClassNotFoundException ClassNotFoundException occurs

  • Method Details

    • isValidStartup

      public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine, boolean checkMandatoryParameters)
      Verifies the command line start parameters.
      Parameters:
      aLine - the command line to validate
      checkMandatoryParameters - if true, check if mandatory parameters are included
      Returns:
      true if the startup was valid

    • updateIdentificationParameters

      public void updateIdentificationParameters()
      Updates the identification parameters according to the command line.

    • setIdentificationParameters

      public void setIdentificationParameters(IdentificationParameters identificationParameters)
      Sets the identification parameters.
      Parameters:
      identificationParameters - the identification parameters

    • getIdentificationParameters

      public IdentificationParameters getIdentificationParameters()
      Returns the identification parameters.
      Returns:
      the identification parameters

    • getInputFile

      public File getInputFile()
      Returns the input parameters file.
      Returns:
      the input parameters file

    • getDestinationFile

      public File getDestinationFile()
      Returns the file where to save the identification parameters.
      Returns:
      the file where to save the identification parameters

    • isListMods

      public Boolean isListMods()
      Indicates whether the modifications should be printed.
      Returns:
      true if the modifications should be printed

    • isListEnzymes

      public Boolean isListEnzymes()
      Indicates whether the enzymes should be printed.
      Returns:
      true if the enzymes should be printed

    • isValidModifications

      public static boolean isValidModifications(org.apache.commons.cli.CommandLine aLine) throws IOException
      Verifies that modifications are correctly recognized.
      Parameters:
      aLine - the command line to validate
      Returns:
      true if the startup was valid
      Throws:
      IOException - if an IOException occurs