public class PeptideShakerCLIInputBean extends Object
| Constructor and Description |
|---|
PeptideShakerCLIInputBean()
Empty constructor for API usage via other tools.
|
PeptideShakerCLIInputBean(org.apache.commons.cli.CommandLine aLine)
Construct a PeptideShakerCLIInputBean from an Apache CLI instance.
|
| Modifier and Type | Method and Description |
|---|---|
String |
getExperimentID()
Returns the experiment name.
|
File |
getFastaFile()
Returns the FASTA file.
|
FollowUpCLIInputBean |
getFollowUpCLIInputBean()
Returns the follow-up options required.
|
static ArrayList<File> |
getIdentificationFiles(String optionInput)
Returns a list of identification files as imported from the command line
option.
|
File |
getIdentificationParametersFile()
Returns the identification parameters file.
|
com.compomics.cli.identification_parameters.IdentificationParametersInputBean |
getIdentificationParametersInputBean()
Returns the identification parameters provided by the user.
|
ArrayList<File> |
getIdFiles()
Returns the identification files.
|
boolean |
getMgfExport()
When exporting the project to a zip file, returns whether mgf file/s
should be written apart from it, into the same folder.
|
MzidCLIInputBean |
getMzidCLIInputBean()
Returns the mzid export options required.
|
Integer |
getnThreads()
Returns the number of threads to use.
|
File |
getOutput()
Returns the psdb output file.
|
PathSettingsCLIInputBean |
getPathSettingsCLIInputBean()
Returns the path settings provided by the user.
|
File |
getPrideFile()
Returns the pride file.
|
com.compomics.util.parameters.peptide_shaker.ProjectType |
getProjectType()
Returns the project type.
|
ReportCLIInputBean |
getReportCLIInputBean()
Returns the report export options required.
|
ArrayList<File> |
getSpectrumFiles()
Returns the spectrum files.
|
static ArrayList<File> |
getSpectrumFiles(String optionInput)
Returns a list of spectrum files as imported from the command line
option.
|
File |
getZipExport()
Returns the file where to export the project as zip file.
|
boolean |
isGUI()
Indicates whether a GUI shall be used to display the progress.
|
static boolean |
isValidStartup(org.apache.commons.cli.CommandLine aLine)
Verifies the command line start parameters.
|
void |
setExperimentID(String experimentID)
Sets the experiment name.
|
void |
setFastaFile(File fastaFile)
Sets the FASTA file.
|
void |
setIdFiles(ArrayList<File> idFiles)
Sets the identification files.
|
void |
setOutput(File output)
Sets the psdb output file.
|
void |
setPrideFile(File prideFile)
Sets the pride file.
|
void |
setSpectrumFiles(ArrayList<File> spectrumFiles)
Sets the spectrum files.
|
public PeptideShakerCLIInputBean(org.apache.commons.cli.CommandLine aLine)
throws IOException,
ClassNotFoundException
aLine - the command lineIOException - thrown of IOException occursClassNotFoundException - thrown of ClassNotFoundException occurspublic PeptideShakerCLIInputBean()
public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()
public File getZipExport()
public boolean getMgfExport()
public String getExperimentID()
public void setExperimentID(String experimentID)
experimentID - the experiment namepublic File getOutput()
public void setOutput(File output)
output - the psdb output filepublic ArrayList<File> getIdFiles()
public void setIdFiles(ArrayList<File> idFiles)
idFiles - the identification filespublic File getPrideFile()
public void setPrideFile(File prideFile)
prideFile - the pride filepublic ArrayList<File> getSpectrumFiles()
public void setSpectrumFiles(ArrayList<File> spectrumFiles)
spectrumFiles - the spectrum filespublic File getFastaFile()
public void setFastaFile(File fastaFile)
fastaFile - the FASTA filepublic static ArrayList<File> getSpectrumFiles(String optionInput) throws FileNotFoundException
optionInput - the command line optionFileNotFoundException - exception thrown whenever a file is not
foundpublic static ArrayList<File> getIdentificationFiles(String optionInput) throws FileNotFoundException
optionInput - the command line optionFileNotFoundException - exception thrown whenever a file is not
foundpublic boolean isGUI()
public FollowUpCLIInputBean getFollowUpCLIInputBean()
public ReportCLIInputBean getReportCLIInputBean()
public MzidCLIInputBean getMzidCLIInputBean()
public PathSettingsCLIInputBean getPathSettingsCLIInputBean()
public com.compomics.cli.identification_parameters.IdentificationParametersInputBean getIdentificationParametersInputBean()
public File getIdentificationParametersFile()
public Integer getnThreads()
public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine)
throws IOException
aLine - the command line to validateIOException - if the spectrum file(s) are not foundCopyright © 2021. All rights reserved.