FollowUpCLIInputBean (PeptideShaker 2.2.2 API)

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 Summary

Constructors
Constructor and Description

FollowUpCLIInputBean(org.apache.commons.cli.CommandLine aLine)
Construct a FollowUpCLIInputBean from an Apache CLI instance.

Constructors
Constructor and Description
`FollowUpCLIInputBean(org.apache.commons.cli.CommandLine aLine)` Construct a FollowUpCLIInputBean from an Apache CLI instance.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`accessionExportNeeded()` Indicates whether an accession export is needed.
`boolean`	`deepLcExportNeeded()` Indicates whether DeepLC export is needed.
`boolean`	`followUpNeeded()` Indicates whether follow-up tasks are required.
`File`	`getAccessionsExportFile()` Returns the file where to export the accessions.
`int`	`getAccessionsExportTypeIndex()` Returns the type of export needed for the accessions.
`String`	`getDeepLcStem()` Returns the stem to use for the path to DeepLC files.
`File`	`getInclusionFile()` Returns the file for the inclusion list generation.
`int`	`getInclusionFormat()` Returns the format for inclusion list generation.
`ArrayList<Integer>`	`getInclusionPeptideFilter()` Returns the peptide filters to use for inclusion list generation.
`ArrayList<Integer>`	`getInclusionProteinFilter()` Returns the protein inference filters to use for inclusion list generation.
`Double`	`getInclusionRtWindow()` Returns the retention time window to use for inclusion list generation.
`File`	`getMs2pipFile()` Returns the file where to write the peptides for ms2pip.
`String[]`	`getMs2pipModels()` Returns the models for which to write an ms2pip config file.
`PathSettingsCLIInputBean`	`getPathSettingsCLIInputBean()` Returns the path settings provided by the user.
`File`	`getPercolatorFile()` Returns the file where to write the training file for Percolator.
`File`	`getPercolatorFragmentationFile()` Returns the file with fragmentation values for Percolator.
`File`	`getPercolatorRtFile()` Returns the file with retention time values for Percolator.
`File`	`getProgenesisExportFile()` Returns the Progenesis file.
`int`	`getProgenesisExportTypeIndex()` Returns the type of export needed for the Progenesis export.
`HashSet<String>`	`getProgenesisTargetedPTMs()` Returns the list of PTMs targeted for the Progenesis PTM export.
`File`	`getProteinSequencesExportFile()` Returns the file where to export the protein details.
`int`	`getProteinSequencesExportTypeIndex()` Returns the type of export needed for the protein details.
`File`	`getProteoformsFile()` Returns the proteoforms file.
`File`	`getPsdbFile()` The psdb file selected by the user.
`File`	`getRecalibrationFolder()` The folder where to export recalibrated spectra.
`int`	`getRecalibrationMode()` The recalibration mode.
`File`	`getSpectrumExportFolder()` Returns the folder where to export the spectrum files.
`int`	`getSpectrumExportTypeIndex()` Returns the type of export needed for the spectra.
`File`	`getZipFile()` The zip file selected by the user.
`boolean`	`inclusionListNeeded()` Indicates whether an inclusion list generation is needed.
`boolean`	`ms2pipExportNeeded()` Indicates whether DeepLC export is needed.
`boolean`	`percolatorExportNeeded()` Indicates whether DeepLC export is needed.
`boolean`	`progenesisExportNeeded()` Indicates whether a Progenesis export is needed.
`boolean`	`proteinSequencesExportNeeded()` Indicates whether protein details (in FASTA format) export is needed.
`boolean`	`proteoformsNeeded()` Indicates whether a list of proteoforms is needed.
`boolean`	`recalibrationNeeded()` Indicates whether a recalibration is needed.
`boolean`	`spectrumExportNeeded()` Indicates whether a spectrum export is needed.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - FollowUpCLIInputBean
```
public FollowUpCLIInputBean(org.apache.commons.cli.CommandLine aLine)
```
    Construct a FollowUpCLIInputBean from an Apache CLI instance.
    
    Parameters:
    
    aLine - the command line
- Method Detail
  - 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.
  - 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 DeepLC export is needed.
    
    Returns:
    
    whether DeepLC export is needed
  - percolatorExportNeeded
```
public boolean percolatorExportNeeded()
```
    Indicates whether DeepLC export is needed.
    
    Returns:
    
    whether DeepLC export is needed
  - getPathSettingsCLIInputBean
```
public PathSettingsCLIInputBean getPathSettingsCLIInputBean()
```
    Returns the path settings provided by the user.
    
    Returns:
    
    the path settings provided by the user

Class FollowUpCLIInputBean

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FollowUpCLIInputBean

Method Detail

getPsdbFile

getZipFile

getRecalibrationFolder

getRecalibrationMode

getSpectrumExportFolder

getSpectrumExportTypeIndex

getAccessionsExportFile

getAccessionsExportTypeIndex

getProteinSequencesExportFile

getProteinSequencesExportTypeIndex

getProgenesisExportFile

getProteoformsFile

getDeepLcStem

getMs2pipFile

getMs2pipModels

getPercolatorRtFile

getPercolatorFragmentationFile

getPercolatorFile

getProgenesisExportTypeIndex

getProgenesisTargetedPTMs

getInclusionFile

getInclusionFormat

getInclusionProteinFilter

getInclusionPeptideFilter

getInclusionRtWindow

followUpNeeded

recalibrationNeeded

spectrumExportNeeded

accessionExportNeeded

proteinSequencesExportNeeded

progenesisExportNeeded

inclusionListNeeded

proteoformsNeeded

deepLcExportNeeded

ms2pipExportNeeded

percolatorExportNeeded

getPathSettingsCLIInputBean