io.repseq.cli

Class FromPaddedFastaAction.Params

java.lang.Object

com.milaboratory.cli.ActionParameters

com.milaboratory.cli.ActionParametersWithOutput

io.repseq.cli.FromPaddedFastaAction.Params

Enclosing class:

FromPaddedFastaAction

public static final class FromPaddedFastaAction.Params
extends com.milaboratory.cli.ActionParametersWithOutput

Field Summary

Fields

Modifier and Type	Field and Description
String	chain
Integer	functionalityIndex
String	functionalityRegexp
String	geneType
Boolean	ignoreDuplicates
int	nameIndex
char	paddingCharacter
List<String>	parameters
Map<String,String>	patterns
Map<String,String>	points
Long	taxonId

Fields inherited from class com.milaboratory.cli.ActionParametersWithOutput

force

Fields inherited from class com.milaboratory.cli.ActionParameters

help

Constructor Summary

Constructors

Constructor and Description
FromPaddedFastaAction.Params()

Method Summary

Methods

Modifier and Type	Method and Description
Pattern	getFunctionalityRegexp()
GeneType	getGeneType()
boolean	getIgnoreDuplicates()
String	getInput()
String	getOutputFasta()
protected List<String>	getOutputFiles()
String	getOutputJSON()
void	validate()

Methods inherited from class com.milaboratory.cli.ActionParametersWithOutput

isForceOverwrite

Methods inherited from class com.milaboratory.cli.ActionParameters

help

Methods inherited from class java.lang.Object

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

Field Detail

parameters

public List<String> parameters

paddingCharacter

public char paddingCharacter

geneType

public String geneType

ignoreDuplicates

public Boolean ignoreDuplicates

nameIndex

public int nameIndex

functionalityIndex

public Integer functionalityIndex

functionalityRegexp

public String functionalityRegexp

chain

public String chain

taxonId

public Long taxonId

points

public Map<String,String> points

patterns

public Map<String,String> patterns

Constructor Detail

FromPaddedFastaAction.Params

public FromPaddedFastaAction.Params()

Method Detail

getIgnoreDuplicates

public boolean getIgnoreDuplicates()

getInput

public String getInput()

getOutputFasta

public String getOutputFasta()

getOutputJSON

public String getOutputJSON()

getGeneType

public GeneType getGeneType()

getFunctionalityRegexp

public Pattern getFunctionalityRegexp()

getOutputFiles

protected List<String> getOutputFiles()

Specified by:

getOutputFiles in class com.milaboratory.cli.ActionParametersWithOutput

validate

public void validate()

Overrides:

validate in class com.milaboratory.cli.ActionParametersWithOutput