Package eu.isas.peptideshaker.cmd

Class FollowUpCLIInputBean

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

  • Constructor Details

    • FollowUpCLIInputBean

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

  • Method Details

    • getPsdbFile

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

    • getZipFile

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

    • getRecalibrationFolder

      public File getRecalibrationFolder()
      The folder where to export recalibrated spectra. Null if not set.
      Returns:
      the folder where to export recalibrated spectra

    • getRecalibrationMode

      public int getRecalibrationMode()
      The recalibration mode. 0 by default. See the FollowUpCLIParams for detailed description.
      Returns:
      the recalibration mode

    • getSpectrumExportFolder

      public File getSpectrumExportFolder()
      Returns the folder where to export the spectrum files. Null if not set.
      Returns:
      the folder where to export the spectrum files

    • getSpectrumExportTypeIndex

      public int getSpectrumExportTypeIndex()
      Returns the type of export needed for the spectra. 0 by default. See the FollowUpCLIParams for detailed description.
      Returns:
      the type of export needed for the spectra

    • getAccessionsExportFile

      public File getAccessionsExportFile()
      Returns the file where to export the accessions. Null if not set.
      Returns:
      the file where to export the accessions

    • getAccessionsExportTypeIndex

      public int getAccessionsExportTypeIndex()
      Returns the type of export needed for the accessions. 0 by default. See the FollowUpCLIParams for detailed description.
      Returns:
      the type of export needed for the accession

    • getProteinSequencesExportFile

      public File getProteinSequencesExportFile()
      Returns the file where to export the protein details. Null if not set.
      Returns:
      the file where to export the protein details

    • getProteinSequencesExportTypeIndex

      public int getProteinSequencesExportTypeIndex()
      Returns the type of export needed for the protein details. 0 by default. See the FollowUpCLIParams for detailed description.
      Returns:
      the type of export needed for the protein details

    • getProgenesisExportFile

      public File getProgenesisExportFile()
      Returns the Progenesis file. Null if not set.
      Returns:
      the Progenesis file

    • getProteoformsFile

      public File getProteoformsFile()
      Returns the proteoforms file. Null if not set.
      Returns:
      the proteoforms file

    • getDeepLcStem

      public String getDeepLcStem()
      Returns the stem to use for the path to DeepLC files.
      Returns:
      The stem to use for the path to DeepLC files.

    • getMs2pipFile

      public File getMs2pipFile()
      Returns the file where to write the peptides for ms2pip.
      Returns:
      The file where to write the peptides for ms2pip.

    • getMs2pipModels

      public String[] getMs2pipModels()
      Returns the models for which to write an ms2pip config file.
      Returns:
      The models for which to write an ms2pip config file.

    • getPercolatorRtFile

      public File getPercolatorRtFile()
      Returns the file with retention time values for Percolator.
      Returns:
      The file with retention time values for Percolator.

    • getPercolatorFragmentationFile

      public File getPercolatorFragmentationFile()
      Returns the file with fragmentation values for Percolator.
      Returns:
      The file with fragmentation values for Percolator.

    • getPercolatorFile

      public File getPercolatorFile()
      Returns the file where to write the training file for Percolator.
      Returns:
      The file where to write the training file for Percolator.

    • getRTObsPredsFile

      public File getRTObsPredsFile()
      Returns the file where to write the RT observed and predicted values.
      Returns:
      The file where to write the RT observed and predicted values.

    • getPeaksIntensitiesObsFile

      public File getPeaksIntensitiesObsFile()
      Returns the file where to write the peaks intensities observed values.
      Returns:
      The file where to write the RT observed and predicted values.

    • getPSMIDsPeaksExportFile

      public File getPSMIDsPeaksExportFile()
      Returns the file where to read the PSM ids for the peaks export.
      Returns:
      The file where to read the PSM ids for the peaks export.

    • getPercolatorBenchmarkResultsFile

      public File getPercolatorBenchmarkResultsFile()
      Returns the file containing Percolator results for all PSMs to get confidence levels.
      Returns:
      The file containing Percolator results for all PSMs to get confidence levels.

    • getPSMIdentifiersFile

      public File getPSMIdentifiersFile()
      Returns the file containing Percolator results for all PSMs to get confidence levels.
      Returns:
      The file containing Percolator results for all PSMs to get confidence levels.

    • getProgenesisExportTypeIndex

      public int getProgenesisExportTypeIndex()
      Returns the type of export needed for the Progenesis export. 0 by default. See the FollowUpCLIParams for detailed description.
      Returns:
      the type of export needed for the Progenesis export

    • getProgenesisTargetedPTMs

      public HashSet<String> getProgenesisTargetedPTMs()
      Returns the list of PTMs targeted for the Progenesis PTM export. An empty list if none selected.
      Returns:
      the list of PTMs targeted for the Progenesis PTM export

    • getInclusionFile

      public File getInclusionFile()
      Returns the file for the inclusion list generation. null if not set.
      Returns:
      the file for the inclusion list generation. null if not set

    • getInclusionFormat

      public int getInclusionFormat()
      Returns the format for inclusion list generation.
      Returns:
      the format for inclusion list generation.

    • getInclusionProteinFilter

      public ArrayList<Integer> getInclusionProteinFilter()
      Returns the protein inference filters to use for inclusion list generation.
      Returns:
      the protein inference filters to use for inclusion list generation

    • getInclusionPeptideFilter

      public ArrayList<Integer> getInclusionPeptideFilter()
      Returns the peptide filters to use for inclusion list generation.
      Returns:
      the peptide filters to use for inclusion list generation

    • getInclusionRtWindow

      public Double getInclusionRtWindow()
      Returns the retention time window to use for inclusion list generation.
      Returns:
      the retention time window to use for inclusion list generation

    • followUpNeeded

      public boolean followUpNeeded()
      Indicates whether follow-up tasks are required.
      Returns:
      indicates whether follow-up tasks are required

    • recalibrationNeeded

      public boolean recalibrationNeeded()
      Indicates whether a recalibration is needed.
      Returns:
      whether a recalibration is needed

    • spectrumExportNeeded

      public boolean spectrumExportNeeded()
      Indicates whether a spectrum export is needed.
      Returns:
      whether a spectrum export is needed

    • accessionExportNeeded

      public boolean accessionExportNeeded()
      Indicates whether an accession export is needed.
      Returns:
      whether an accession export is needed

    • proteinSequencesExportNeeded

      public boolean proteinSequencesExportNeeded()
      Indicates whether protein details (in FASTA format) export is needed.
      Returns:
      whether protein details (in FASTA format) export is needed

    • progenesisExportNeeded

      public boolean progenesisExportNeeded()
      Indicates whether a Progenesis export is needed.
      Returns:
      whether a Progenesis export is needed

    • inclusionListNeeded

      public boolean inclusionListNeeded()
      Indicates whether an inclusion list generation is needed.
      Returns:
      whether an inclusion list generation is needed

    • proteoformsNeeded

      public boolean proteoformsNeeded()
      Indicates whether a list of proteoforms is needed.
      Returns:
      whether a list of proteoforms is needed

    • deepLcExportNeeded

      public boolean deepLcExportNeeded()
      Indicates whether DeepLC export is needed.
      Returns:
      whether DeepLC export is needed

    • ms2pipExportNeeded

      public boolean ms2pipExportNeeded()
      Indicates whether MS2PIP export is needed.
      Returns:
      whether MS2PIP export is needed

    • percolatorExportNeeded

      public boolean percolatorExportNeeded()
      Indicates whether Percolator export is needed.
      Returns:
      whether Percolator export is needed

    • RTValuesExportNeeded

      public boolean RTValuesExportNeeded()
      Indicates whether RT observed/predicted values export is needed.
      Returns:
      whether RT observed/predicted values export is needed

    • peaksIntensitiesObsExportNeeded

      public boolean peaksIntensitiesObsExportNeeded()
      Indicates whether peaks intensities observed/predicted values export is needed.
      Returns:
      whether peaks intensities observed/predicted values export is needed

    • PSMIdentifiersExportNeeded

      public boolean PSMIdentifiersExportNeeded()
      Indicates whether PSM identifiers export is needed.
      Returns:
      whether PSM identifiers export is needed

    • getPathSettingsCLIInputBean

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