public class ProjectTranscriptToChromosomeOptions extends JannovarAnnotationOptions
Constructor and Description |
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ProjectTranscriptToChromosomeOptions() |
Modifier and Type | Method and Description |
---|---|
String |
getPathInputText() |
String |
getPathOutputVCF() |
String |
getPathReferenceFASTA() |
void |
setFromArgs(net.sourceforge.argparse4j.inf.Namespace args)
Get values from
Namespace object |
void |
setPathInputText(String pathInputText) |
void |
setPathOutputVCF(String pathOutputVCF) |
void |
setPathReferenceFASTA(String pathReferenceFASTA) |
static void |
setupParser(net.sourceforge.argparse4j.inf.Subparsers subParsers)
Setup
ArgumentParser |
String |
toString() |
getDatabaseFilePath, isNt3PrimeShifting, isShowAll, isUseThreeLetterAminoAcidCode, setDatabaseFilePath, setNt3PrimeShifting, setShowAll, setupParser, setUseThreeLetterAminoAcidCode
getFtpProxy, getHttpProxy, getHttpsProxy, getVerbosity, isReportProgress, setFtpProxy, setHttpProxy, setHttpsProxy, setReportProgress, setVerbosity
public ProjectTranscriptToChromosomeOptions()
public static void setupParser(net.sourceforge.argparse4j.inf.Subparsers subParsers)
ArgumentParser
subParsers
- Subparsers
to setuppublic void setFromArgs(net.sourceforge.argparse4j.inf.Namespace args) throws CommandLineParsingException
JannovarBaseOptions
Namespace
objectsetFromArgs
in class JannovarAnnotationOptions
args
- Namespace
to get the option values fromCommandLineParsingException
- on problems parsing a given URLpublic String getPathReferenceFASTA()
public void setPathReferenceFASTA(String pathReferenceFASTA)
public String getPathInputText()
public void setPathInputText(String pathInputText)
public String getPathOutputVCF()
public void setPathOutputVCF(String pathOutputVCF)
public String toString()
toString
in class JannovarAnnotationOptions
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