Package eu.isas.peptideshaker.cmd

Class MzidCLIInputBean

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

  • Constructor Details

    • MzidCLIInputBean

      public MzidCLIInputBean(org.apache.commons.cli.CommandLine aLine)
      Parses a MzidCLI command line and stores the input in the attributes.
      Parameters:
      aLine - a MzidCLI command line

  • Method Details

    • getPsdbFile

      public File getPsdbFile()
      Returns the psdb file.
      Returns:
      the psdb file

    • getZipFile

      public File getZipFile()
      The zip file selected by the user. Null if not set.
      Returns:
      zip file selected by the user

    • getContactFirstName

      public String getContactFirstName()
      Returns the contact first name.
      Returns:
      the contact first name

    • getContactLastName

      public String getContactLastName()
      Returns the contact last name.
      Returns:
      the contact last name

    • getContactEmail

      public String getContactEmail()
      Returns the contact email.
      Returns:
      the contact email

    • getContactAddress

      public String getContactAddress()
      Returns the contact address.
      Returns:
      the contact address

    • getContactUrl

      public String getContactUrl()
      Returns the contact URL.
      Returns:
      the contact URL

    • getOrganizationName

      public String getOrganizationName()
      Returns the organization name.
      Returns:
      the organization name

    • getOrganizationMail

      public String getOrganizationMail()
      Returns the organization mail.
      Returns:
      the organization mail

    • getOrganizationAddress

      public String getOrganizationAddress()
      Returns the organization address.
      Returns:
      the organization address

    • getOrganizationUrl

      public String getOrganizationUrl()
      Returns the organization URL.
      Returns:
      the organization URL

    • getOutputFile

      public File getOutputFile()
      Returns the file where to mzIdentML export will be stored.
      Returns:
      the file where to mzIdentML export will be stored

    • getIncludeProteinSequences

      public boolean getIncludeProteinSequences()
      Returns true if the protein sequences are to be included in the mzid export.
      Returns:
      true if the protein sequences are to be included in the mzid export

    • getMzIdentMLVersion

      public com.compomics.util.experiment.io.identification.MzIdentMLVersion getMzIdentMLVersion()
      Returns the mzIdentML version to use for this file.
      Returns:
      the mzIdentML version to use for this file

    • getPathSettingsCLIInputBean

      public PathSettingsCLIInputBean getPathSettingsCLIInputBean()
      Returns the path settings input.
      Returns:
      the path settings input

    • isGzip

      public boolean isGzip()
      Returns a boolean indicating whether the export should be gzipped.
      Returns:
      a boolean indicating whether the export should be gzipped