Package eu.isas.reporter.cli

Class ReporterCLIInputBean

java.lang.Object
eu.isas.reporter.cli.ReporterCLIInputBean
public class ReporterCLIInputBean extends Object
This class is used to verify that a command line is valid and parse its parameters.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Details

    • ReporterCLIInputBean

      public ReporterCLIInputBean(org.apache.commons.cli.CommandLine aLine) throws IOException, ClassNotFoundException
      Parses the arguments of a command line.
      Parameters:
      aLine - the command line
      Throws:
      IOException - thrown if an error occurred while reading the FASTA file
      ClassNotFoundException - thrown if the search parameters cannot be converted

  • Method Details

    • getPeptideShakerFile

      public File getPeptideShakerFile()
      Returns the PeptideShaker file.
      Returns:
      the PeptideShaker file

    • getOutputFile

      public File getOutputFile()
      Returns the output file where to save the project, null if not set.
      Returns:
      the output file

    • getIsotopesFile

      public File getIsotopesFile()
      Returns the isotope correction file, null if not set.
      Returns:
      the isotope correction file

    • getReferenceSamples

      public ArrayList<Integer> getReferenceSamples()
      Returns the list of reference samples indexed by ordered reagent mass, 1 is the first reagent.
      Returns:
      the list of reference samples indexed by ordered reagent mass, 1 is the first reagent

    • getnThreads

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

    • getReporterMethod

      public String getReporterMethod()
      Returns the name of the reporter methods provided by the user.
      Returns:
      the name of the reporter method

    • getReporterIonTolerance

      public Double getReporterIonTolerance()
      Returns the tolerance used for the reporter ion matching in the spectrum.
      Returns:
      the tolerance used for the reporter ion matching in the spectrum

    • getMostAccurate

      public Boolean getMostAccurate()
      Indicates whether the most accurate reporter ion should be used.
      Returns:
      a boolean indicating whether the most accurate reporter ion should be used

    • getReporterIonsLocation

      public ReporterIonsLocationType getReporterIonsLocation()
      Indicates whether the quantification peaks are in the same spectra as the identification peaks.
      Returns:
      a boolean indicating whether the quantification peaks are in the same spectra as the identification peaks

    • getPrecMzTolerance

      public Double getPrecMzTolerance()
      Returns the m/z tolerance to use for the precursor ion window.
      Returns:
      the m/z tolerance to use for the precursor ion window

    • getPrecMzTolerancePpm

      public Boolean getPrecMzTolerancePpm()
      Indicates whether the precursor ion window m/z tolerance is in ppm.
      Returns:
      a boolean indicating whether the window precursor ion m/z tolerance is in ppm

    • getPrecRtTolerance

      public Double getPrecRtTolerance()
      Returns the RT tolerance to use for the precursor ion window in seconds.
      Returns:
      the RT tolerance to use for the precursor ion window in seconds

    • getIdentificationParametersFile

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

    • getIgnoreNull

      public Boolean getIgnoreNull()
      Returns a boolean indicating whether peptides presenting null intensities should be ignored.
      Returns:
      a boolean indicating whether peptides presenting null intensities should be ignored

    • getIgnoreMc

      public Boolean getIgnoreMc()
      Returns a boolean indicating whether peptides presenting missed cleavages should be ignored.
      Returns:
      a boolean indicating whether peptides presenting missed cleavages should be ignored

    • getPercentile

      public Double getPercentile()
      Returns the percentile for ratio window estimation.
      Returns:
      the percentile for ratio window estimation

    • getResolution

      public Double getResolution()
      Returns the resolution for ratio estimation.
      Returns:
      the resolution for ratio estimation

    • getMinUnique

      public Integer getMinUnique()
      Returns the minimum number of unique peptides to consider only those for a protein group ratio estimation.
      Returns:
      the minimum number of unique peptides to consider only those for a protein group ratio estimation

    • getIgnoredPtms

      public ArrayList<String> getIgnoredPtms()
      Returns the list of PTMs to ignore.
      Returns:
      the list of PTMs to ignore

    • getValidationPsm

      public Integer getValidationPsm()
      Returns the validation level to use for PSMs.
      Returns:
      the validation level to use for PSMs

    • getValidationPeptide

      public Integer getValidationPeptide()
      Returns the validation level to use for peptides.
      Returns:
      the validation level to use for peptides

    • getValidationProtein

      public Integer getValidationProtein()
      Returns the validation level to use for proteins.
      Returns:
      the validation level to use for proteins

    • getPsmNormalizationType

      public NormalizationType getPsmNormalizationType()
      Returns the PSM normalization.
      Returns:
      the PSM normalization

    • getPeptideNormalizationType

      public NormalizationType getPeptideNormalizationType()
      Returns the peptide normalization.
      Returns:
      the peptide normalization

    • getProteinNormalizationType

      public NormalizationType getProteinNormalizationType()
      Returns the protein normalization.
      Returns:
      the protein normalization

    • getStableProteins

      public File getStableProteins()
      Returns the file containing the stable proteins.
      Returns:
      the file containing the stable proteins

    • getContaminants

      public File getContaminants()
      Returns the file containing the contaminants.
      Returns:
      the file containing the contaminants

    • 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

    • getIdentificationParameters

      public com.compomics.util.parameters.identification.IdentificationParameters getIdentificationParameters()
      Returns the identification parameters.
      Returns:
      the identification parameters

    • getPathSettingsCLIInputBean

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

    • getReportCLIInputBean

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