Package org.utgenome.shell

Interface Summary

Create.ScaffoldFileFilter
ServerListener

Class Summary

AddAction	A UTGBShell sub-command for adding new action class
Clean	UTGB Shell Sub Command for cleaning target directory
Compile	A UTGBShell sub command for compiling java source codes with Maven
Create	Create sub command
Create.CreateAllScaffoldFileFilter
Deploy
Eclipse	A sub command to generate Eclipse project files
FastqRename
FastqToFasta	fastq2fasta command
FastqToSAM
GWT	A sub command for creating a GWT interface
GWTCompile
Illumina2Fastq
Import	import command
Keyword	keyword DB management tool
Maven	Maven utility
Maven.CommandExecutor
Pack	creating packed FASTA
POM	POM objects corresponds to a Maven project file (pom.xml)
POMProperties	This class is used for retrieving the revision value described in the pom.xml file
QSeqToFastq
Repair
Sam2Wig
SAMToFastq
ScaffoldGenerator	Scaffold generator
Sequence	Retrieve the genome sequence from the pack file
Server	A UTGB sub command for starting up a UTGB portable server
SVNAdd	Sub-command to add the current project to the subversion repository
Upgrade
UTGBPortable	The stand-alone UTGB server launcher
UTGBPortableConfig	The configuration parameters of the UTGBPortable
UTGBPortableWidget	GUI Panel of the UTGB Portable Server
UTGBShell	A command line client entry point
UTGBShell.UTGBShellOption
UTGBShellCommand	A base implementation of the UTGBShell's sub commands
UTGBShellCommandBase
WebBrowser	Open a given URL via OS's default web browser.

Enum Summary

Create.OverwriteMode
Import.FileType
Keyword.SubCommand
OSType	This class provides information of current OS type.
UTGBPortableWidget.MessageType

Exception Summary

UTGBShellException

Exception class for UTGBShell