public class JannovarAnnotationOptions extends JannovarBaseOptions
Constructor and Description |
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JannovarAnnotationOptions() |
Modifier and Type | Method and Description |
---|---|
String |
getDatabaseFilePath() |
boolean |
isNt3PrimeShifting() |
boolean |
isShowAll() |
boolean |
isUseThreeLetterAminoAcidCode() |
void |
setDatabaseFilePath(String databaseFilePath) |
void |
setFromArgs(net.sourceforge.argparse4j.inf.Namespace args)
Get values from
Namespace object |
void |
setNt3PrimeShifting(boolean nt3PrimeShifting) |
void |
setShowAll(boolean showAll) |
static void |
setupParser(net.sourceforge.argparse4j.inf.ArgumentParser subParser)
Setup
ArgumentParser |
void |
setUseThreeLetterAminoAcidCode(boolean useThreeLetterAminoAcidCode) |
String |
toString() |
getFtpProxy, getHttpProxy, getHttpsProxy, getVerbosity, isReportProgress, setFtpProxy, setHttpProxy, setHttpsProxy, setReportProgress, setVerbosity
public static void setupParser(net.sourceforge.argparse4j.inf.ArgumentParser subParser)
ArgumentParser
subParsers
- Subparsers
to setuppublic void setFromArgs(net.sourceforge.argparse4j.inf.Namespace args) throws CommandLineParsingException
JannovarBaseOptions
Namespace
objectsetFromArgs
in class JannovarBaseOptions
args
- Namespace
to get the option values fromCommandLineParsingException
- on problems parsing a given URLpublic boolean isUseThreeLetterAminoAcidCode()
public void setUseThreeLetterAminoAcidCode(boolean useThreeLetterAminoAcidCode)
public boolean isNt3PrimeShifting()
public void setNt3PrimeShifting(boolean nt3PrimeShifting)
public String getDatabaseFilePath()
public void setDatabaseFilePath(String databaseFilePath)
public boolean isShowAll()
public void setShowAll(boolean showAll)
public String toString()
toString
in class JannovarBaseOptions
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