org.mulinlab.varnote.cmdline.tools

Class Intersect

java.lang.Object

org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

org.mulinlab.varnote.cmdline.abstractclass.RunProgram

org.mulinlab.varnote.cmdline.abstractclass.QueryProgram

org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

org.mulinlab.varnote.cmdline.tools.Intersect

public final class Intersect
extends QueryFileProgram

Field Summary

Fields

Modifier and Type	Field and Description
boolean	isRemoveComment
int	outModeValue
OutputArgumentCollection	outputArguments

Fields inherited from class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

inputArguments, runArguments

Fields inherited from class org.mulinlab.varnote.cmdline.abstractclass.QueryProgram

dbArguments

Fields inherited from class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

islog, USE_JDK_INFLATER

Fields inherited from class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

help

Constructor Summary

Constructors

Constructor and Description
Intersect()

Method Summary

Modifier and Type	Method and Description
protected int	doWork()

Methods inherited from class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

getFormat, getQueryFilePath

Methods inherited from class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

onShutdown, onStartup

Methods inherited from class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

customCommandLineValidation, getCommandLineParser, getUsage, getVersion, instanceMain, parseArgs, runTool

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

outputArguments

@ArgumentCollection
public final OutputArgumentCollection outputArguments

isRemoveComment

@Argument(shortName="RC",
          fullName="is-remove-comment",
          optional=true,
          doc="A flag to determine whether or not to remove the comment lines(start with \'@\') in the output file. Note that the comment lines are required for the VarNote Annotation program.")
public boolean isRemoveComment

outModeValue

@Argument(shortName="OM",
          fullName="out-mode",
          optional=true,
          doc="Output recording mode (default 2). 0 for \"only output query records\"; 1 for \"only output matched database records\"; 2 for \"output both query records and matched database records\"")
public int outModeValue

Constructor Detail

Intersect

public Intersect()

Method Detail

doWork

protected int doWork()

Specified by:

doWork in class CMDProgram