io.repseq.cli

Class FromPaddedFastaAction.ActionParameters

java.lang.Object

com.milaboratory.cli.ActionParameters

com.milaboratory.cli.ActionParametersWithOutput

io.repseq.cli.FromFastaParametersAbstract

io.repseq.cli.FromPaddedFastaAction.ActionParameters

Enclosing class:

FromPaddedFastaAction

public static final class FromPaddedFastaAction.ActionParameters
extends FromFastaParametersAbstract

Field Summary

Fields

Modifier and Type	Field and Description
char	paddingCharacter
java.util.List<java.lang.String>	parameters

Fields inherited from class io.repseq.cli.FromFastaParametersAbstract

chain, functionalityIndex, functionalityRegexp, geneFeature, geneType, ignoreDuplicates, nameIndex, patterns, points, speciesNames, 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
ActionParameters()

Method Summary

Modifier and Type	Method and Description
boolean	doEmbedSequences() Whether to embed sequence information into JSON output library file.
char	getPaddingCharacter()
java.util.List<java.lang.String>	getParameters()
void	validate()

Methods inherited from class io.repseq.cli.FromFastaParametersAbstract

getFunctionalityRegexp, getGeneFeature, getGeneType, getIgnoreDuplicates, getInput, getOutputFasta, getOutputFiles, getOutputJSON

Methods inherited from class com.milaboratory.cli.ActionParametersWithOutput

handleExistenceOfOutputFile, isForceOverwrite

Methods inherited from class com.milaboratory.cli.ActionParameters

forceHideParameters, help

Methods inherited from class java.lang.Object

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

Field Detail

parameters

public java.util.List<java.lang.String> parameters

paddingCharacter

public char paddingCharacter

Constructor Detail

ActionParameters

public ActionParameters()

Method Detail

getParameters

public java.util.List<java.lang.String> getParameters()

Specified by:

getParameters in class FromFastaParametersAbstract

getPaddingCharacter

public char getPaddingCharacter()

Specified by:

getPaddingCharacter in class FromFastaParametersAbstract

doEmbedSequences

public boolean doEmbedSequences()

Description copied from class: FromFastaParametersAbstract

Whether to embed sequence information into JSON output library file. If this parameter is false: (1) if FromFastaParametersAbstract.getOutputFasta() is null, input files will be directly linked inside json library, (2) if FromFastaParametersAbstract.getOutputFasta() is defined, separate file will be created, and linked inside newly created JSON library.

Specified by:

doEmbedSequences in class FromFastaParametersAbstract

validate

public void validate()

Overrides:

validate in class FromFastaParametersAbstract