Package eu.isas.peptideshaker.cmd

Class ReportCLIInputBean

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

  • Constructor Details

    • ReportCLIInputBean

      public ReportCLIInputBean(org.apache.commons.cli.CommandLine aLine)
      Construct a ReportCLIInputBean from an Apache CLI instance.
      Parameters:
      aLine - the command line

  • Method Details

    • getPsdbFile

      public File getPsdbFile()
      Returns the psdb file from which the information can be obtained.
      Returns:
      the psdb file from which the information can be obtained

    • getZipFile

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

    • getReportOutputFolder

      public File getReportOutputFolder()
      Returns the report output folder.
      Returns:
      the output folder

    • setReportOutputFolder

      public void setReportOutputFolder(File outputFolder)
      Set the report output folder.
      Parameters:
      outputFolder - the report output folder

    • getReportNamePrefix

      public String getReportNamePrefix()
      Returns the report name prefix.
      Returns:
      the report name prefix

    • setReportNamePrefix

      public void setReportNamePrefix(String reportNamePrefix)
      Set the report name prefix.
      Parameters:
      reportNamePrefix - the report output folder

    • getReportTypes

      public ArrayList<String> getReportTypes()
      Returns the types of output required by the user.
      Returns:
      the types of output

    • getDocumentationTypes

      public ArrayList<String> getDocumentationTypes()
      Returns the type of documentation required by the user.
      Returns:
      the type of documentation types

    • exportNeeded

      public boolean exportNeeded()
      Indicates whether a report export is needed.
      Returns:
      true if a report export is needed

    • reportExportNeeded

      public boolean reportExportNeeded()
      Indicates whether a report export is required by the user.
      Returns:
      true if a report export is required

    • documentationExportNeeded

      public boolean documentationExportNeeded()
      Indicates whether a documentation export is required by the user.
      Returns:
      true if documentation export is require

    • getPathSettingsCLIInputBean

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

    • isGzip

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