Package org.molgenis.vibe.cli.io.options_digestion

Class VibeOptions

java.lang.Object

org.molgenis.vibe.cli.io.options_digestion.VibeOptions

public class VibeOptions
extends Object

Abstract class to be used for options parsing. Includes some basic validations (such as whether input arguments refer to actual files).

Constructor Summary

Constructors

Constructor	Description
VibeOptions()

Method Summary

Modifier and Type	Method	Description
GenePrioritizedOutputFormatWriterFactory	getGenePrioritizedOutputFormatWriterFactory()
Path	getHpoOntology()
Integer	getOntologyMaxDistance()
OutputWriter	getOutputWriter()
Set<Phenotype>	getPhenotypes()
PhenotypesRetrieverFactory	getPhenotypesRetrieverFactory()
RunMode	getRunMode()
Path	getVibeTdb()
boolean	isVerbose()
void	printVerbose(String text)
protected void	setFileOutputWriter(String outputFile)	Wrapper for setFileOutputWriter(Path).
protected void	setFileOutputWriter(Path outputFile)	Sets the OutputWriter to a FileOutputWriter.
protected void	setFileOutputWriterForced(String outputFile)	Wrapper for setFileOutputWriterForced(Path).
protected void	setFileOutputWriterForced(Path outputFile)	Sets the OutputWriter to a FileOutputWriter.
protected void	setStdoutOutputWriter()	Sets the OutputWriter to an StdoutOutputWriter.
String	toString()
boolean	validate()	Checks whether the set variables adhere to the selected RunMode.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

VibeOptions

public VibeOptions()

Method Detail

getRunMode

public RunMode getRunMode()

isVerbose

public boolean isVerbose()

printVerbose

public void printVerbose(String text)

getHpoOntology

public Path getHpoOntology()

getVibeTdb

public Path getVibeTdb()

getPhenotypes

public Set<Phenotype> getPhenotypes()

getPhenotypesRetrieverFactory

public PhenotypesRetrieverFactory getPhenotypesRetrieverFactory()

getOntologyMaxDistance

public Integer getOntologyMaxDistance()

getGenePrioritizedOutputFormatWriterFactory

public GenePrioritizedOutputFormatWriterFactory getGenePrioritizedOutputFormatWriterFactory()

getOutputWriter

public OutputWriter getOutputWriter()

setFileOutputWriter

protected void setFileOutputWriter(String outputFile)
                            throws InvalidPathException,
                                   FileAlreadyExistsException

Wrapper for setFileOutputWriter(Path).

Parameters:

outputFile - the file path to write the output to

Throws:

InvalidPathException - if outputFile could not be converted to Path

FileAlreadyExistsException - if file already exists

setFileOutputWriter

protected void setFileOutputWriter(Path outputFile)
                            throws FileAlreadyExistsException

Sets the OutputWriter to a FileOutputWriter. Overrides any previously set OutputWriter.

Parameters:

outputFile - the file path to write the output to

Throws:

FileAlreadyExistsException - if file already exists

setFileOutputWriterForced

protected void setFileOutputWriterForced(String outputFile)
                                  throws InvalidPathException

Wrapper for setFileOutputWriterForced(Path).

Parameters:

outputFile - the file path to write the output to

Throws:

InvalidPathException - if outputFile could not be converted to Path

setFileOutputWriterForced

protected void setFileOutputWriterForced(Path outputFile)

Sets the OutputWriter to a FileOutputWriter. Overrides any previously set OutputWriter. If an existing file is given, it will be overwritten.

Parameters:

outputFile - the file path to write the output to

See Also:

FileOutputWriter.initialize()

setStdoutOutputWriter

protected void setStdoutOutputWriter()

Sets the OutputWriter to an StdoutOutputWriter. Overrides any previously set OutputWriter.

validate

public boolean validate()

Checks whether the set variables adhere to the selected RunMode. Can be used after processing of user input to validate if variables are set correctly (based on the specified RunMode).

Returns:

true if available variables adhere to RunMode, false if not

toString

public String toString()

Overrides:

toString in class Object