io.repseq.cli

Class FromFastaParametersAbstract

java.lang.Object

com.milaboratory.cli.ActionParameters

com.milaboratory.cli.ActionParametersWithOutput

io.repseq.cli.FromFastaParametersAbstract

Direct Known Subclasses:

FromFastaAction.ActionParameters, FromPaddedFastaAction.ActionParameters

public abstract class FromFastaParametersAbstract
extends com.milaboratory.cli.ActionParametersWithOutput

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	chain
java.lang.Integer	functionalityIndex
java.lang.String	functionalityRegexp
java.lang.String	geneFeature
java.lang.String	geneType
boolean	ignoreDuplicates
int	nameIndex
java.util.Map<java.lang.String,java.lang.String>	patterns
java.util.Map<java.lang.String,java.lang.String>	points
java.util.List<java.lang.String>	speciesNames
java.lang.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
FromFastaParametersAbstract()

Method Summary

Modifier and Type	Method and Description
abstract boolean	doEmbedSequences() Whether to embed sequence information into JSON output library file.
java.util.regex.Pattern	getFunctionalityRegexp()
GeneFeature	getGeneFeature()
GeneType	getGeneType()
boolean	getIgnoreDuplicates()
java.lang.String	getInput()
java.lang.String	getOutputFasta()
protected java.util.List<java.lang.String>	getOutputFiles()
java.lang.String	getOutputJSON()
abstract char	getPaddingCharacter()
abstract java.util.List<java.lang.String>	getParameters()
void	validate()

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

geneType

public java.lang.String geneType

ignoreDuplicates

public boolean ignoreDuplicates

speciesNames

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

nameIndex

public int nameIndex

functionalityIndex

public java.lang.Integer functionalityIndex

functionalityRegexp

public java.lang.String functionalityRegexp

chain

public java.lang.String chain

taxonId

public java.lang.Long taxonId

geneFeature

public java.lang.String geneFeature

points

public java.util.Map<java.lang.String,java.lang.String> points

patterns

public java.util.Map<java.lang.String,java.lang.String> patterns

Constructor Detail

FromFastaParametersAbstract

public FromFastaParametersAbstract()

Method Detail

getParameters

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

getIgnoreDuplicates

public boolean getIgnoreDuplicates()

getInput

public java.lang.String getInput()

getOutputFasta

public java.lang.String getOutputFasta()

getOutputJSON

public java.lang.String getOutputJSON()

doEmbedSequences

public abstract boolean doEmbedSequences()

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

getPaddingCharacter

public abstract char getPaddingCharacter()

getGeneFeature

public GeneFeature getGeneFeature()

getGeneType

public GeneType getGeneType()

getFunctionalityRegexp

public java.util.regex.Pattern getFunctionalityRegexp()

getOutputFiles

protected java.util.List<java.lang.String> getOutputFiles()

Specified by:

getOutputFiles in class com.milaboratory.cli.ActionParametersWithOutput

validate

public void validate()

Overrides:

validate in class com.milaboratory.cli.ActionParametersWithOutput