public class ProjectTranscriptToChromosomeOptions extends JannovarAnnotationOptions
| Constructor and Description |
|---|
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, setUseThreeLetterAminoAcidCodegetFtpProxy, getHttpProxy, getHttpsProxy, getVerbosity, isReportProgress, setFtpProxy, setHttpProxy, setHttpsProxy, setReportProgress, setVerbositypublic ProjectTranscriptToChromosomeOptions()
public void setFromArgs(net.sourceforge.argparse4j.inf.Namespace args)
throws CommandLineParsingException
JannovarBaseOptionsNamespace objectsetFromArgs in class JannovarAnnotationOptionsargs - Namespace to get the option values fromCommandLineParsingException - on problems parsing a given URLpublic static void setupParser(net.sourceforge.argparse4j.inf.Subparsers subParsers)
ArgumentParsersubParsers - Subparsers to setuppublic 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 JannovarAnnotationOptionsCopyright © 2016. All rights reserved.