public class JannovarAnnotateCSVOptions extends JannovarAnnotationOptions
Constructor and Description |
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JannovarAnnotateCSVOptions() |
Modifier and Type | Method and Description |
---|---|
int |
getAlt() |
int |
getChr() |
String |
getCsv() |
org.apache.commons.csv.CSVFormat |
getFormat() |
int |
getPos() |
int |
getRef() |
boolean |
isHeader() |
void |
setFromArgs(net.sourceforge.argparse4j.inf.Namespace args)
Get values from
Namespace object |
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 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 int getChr()
public int getAlt()
public int getRef()
public String getCsv()
public int getPos()
public org.apache.commons.csv.CSVFormat getFormat()
public boolean isHeader()
public String toString()
toString
in class JannovarAnnotationOptions
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