A B C D E F G H I J L M N O P Q R S T U V W

A

accept(String) - Method in class org.utgenome.shell.Create.CreateAllScaffoldFileFilter
 
accept(String) - Method in interface org.utgenome.shell.Create.ScaffoldFileFilter
 
adaptor - Variable in class org.utgenome.shell.db.bed.BEDParser
 
AddAction - Class in org.utgenome.shell
A UTGBShell subcommand for adding new action class
AddAction() - Constructor for class org.utgenome.shell.AddAction
 
addAttribute(BED2Silk.BEDHeaderAttribute) - Method in class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderDescription
 
addCDS(CDS) - Method in class org.utgenome.shell.db.Gene
 
addContext(String, String) - Method in class org.utgenome.shell.tomcat.TomcatServer
 
addExon(Exon) - Method in class org.utgenome.shell.db.Gene
 
addGene(BEDDatabaseGenerator.BEDGene) - Method in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.DBBuilder
 
addServerListener(ServerListener) - Method in class org.utgenome.shell.UTGBPortable
 
addTrack(BEDDatabaseGenerator.BEDTrack) - Method in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.DBBuilder
 
afterStart() - Method in interface org.utgenome.shell.ServerListener
 
afterStart() - Method in class org.utgenome.shell.UTGBPortableWidget
 
afterStop() - Method in interface org.utgenome.shell.ServerListener
 
afterStop() - Method in class org.utgenome.shell.UTGBPortableWidget
 
APP_FOLDER - Static variable in class org.utgenome.shell.UTGBShellSubCommandBase
 
Attribute - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Attribute - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
attribute() - Method in class org.utgenome.shell.db.bed.BEDParser
 
attributeValue() - Method in class org.utgenome.shell.db.bed.BEDParser
 

B

BED2Silk - Class in org.utgenome.shell.db.bed
 
BED2Silk(File) - Constructor for class org.utgenome.shell.db.bed.BED2Silk
 
BED2Silk(Reader) - Constructor for class org.utgenome.shell.db.bed.BED2Silk
 
BED2Silk.BEDHeaderAttribute - Class in org.utgenome.shell.db.bed
 
BED2Silk.BEDHeaderAttribute() - Constructor for class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderAttribute
 
BED2Silk.BEDHeaderDescription - Class in org.utgenome.shell.db.bed
 
BED2Silk.BEDHeaderDescription() - Constructor for class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderDescription
 
BED2SilkReader - Class in org.utgenome.shell.db.bed
 
BED2SilkReader(Reader) - Constructor for class org.utgenome.shell.db.bed.BED2SilkReader
 
BEDDatabaseGenerator - Class in org.utgenome.shell.db.bed
 
BEDDatabaseGenerator() - Constructor for class org.utgenome.shell.db.bed.BEDDatabaseGenerator
 
BEDDatabaseGenerator.BEDGene - Class in org.utgenome.shell.db.bed
 
BEDDatabaseGenerator.BEDGene() - Constructor for class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDGene
 
BEDDatabaseGenerator.BEDTrack - Class in org.utgenome.shell.db.bed
 
BEDDatabaseGenerator.BEDTrack() - Constructor for class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
BEDDatabaseGenerator.DBBuilder - Class in org.utgenome.shell.db.bed
 
BEDDatabaseGenerator.DBBuilder(Connection) - Constructor for class org.utgenome.shell.db.bed.BEDDatabaseGenerator.DBBuilder
 
BEDLexer - Class in org.utgenome.shell.db.bed
 
BEDLexer() - Constructor for class org.utgenome.shell.db.bed.BEDLexer
 
BEDLexer(CharStream) - Constructor for class org.utgenome.shell.db.bed.BEDLexer
 
BEDLexer(CharStream, RecognizerSharedState) - Constructor for class org.utgenome.shell.db.bed.BEDLexer
 
BEDParser - Class in org.utgenome.shell.db.bed
 
BEDParser(TokenStream) - Constructor for class org.utgenome.shell.db.bed.BEDParser
 
BEDParser(TokenStream, RecognizerSharedState) - Constructor for class org.utgenome.shell.db.bed.BEDParser
 
BEDParser.attribute_return - Class in org.utgenome.shell.db.bed
 
BEDParser.attribute_return() - Constructor for class org.utgenome.shell.db.bed.BEDParser.attribute_return
 
BEDParser.attributeValue_return - Class in org.utgenome.shell.db.bed
 
BEDParser.attributeValue_return() - Constructor for class org.utgenome.shell.db.bed.BEDParser.attributeValue_return
 
BEDParser.description_return - Class in org.utgenome.shell.db.bed
 
BEDParser.description_return() - Constructor for class org.utgenome.shell.db.bed.BEDParser.description_return
 
BEDParser.descriptionName_return - Class in org.utgenome.shell.db.bed
 
BEDParser.descriptionName_return() - Constructor for class org.utgenome.shell.db.bed.BEDParser.descriptionName_return
 
beforeStart() - Method in interface org.utgenome.shell.ServerListener
 
beforeStart() - Method in class org.utgenome.shell.UTGBPortableWidget
 
beforeStop() - Method in interface org.utgenome.shell.ServerListener
 
beforeStop() - Method in class org.utgenome.shell.UTGBPortableWidget
 
buildGUI() - Method in class org.utgenome.shell.UTGBPortableWidget
 

C

CDS - Class in org.utgenome.shell.db
Coding Sequence (CDS)
CDS() - Constructor for class org.utgenome.shell.db.CDS
 
CDS(long, long) - Constructor for class org.utgenome.shell.db.CDS
 
Clean - Class in org.utgenome.shell
UTGB Shell Sub Command for cleaning target directory
Clean() - Constructor for class org.utgenome.shell.Clean
 
clearStatus() - Method in class org.utgenome.shell.UTGBPortableWidget
 
close() - Method in class org.utgenome.shell.db.bed.BED2SilkReader
 
color - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
color - Variable in class org.utgenome.shell.db.Locus
 
compareTo(Exon) - Method in class org.utgenome.shell.db.Exon
 
compareTo(UTGBShellSubCommand) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
Compile - Class in org.utgenome.shell
A UTGBShell sub command for compiling java source codes with Maven
Compile() - Constructor for class org.utgenome.shell.Compile
 
configFile - Variable in class org.utgenome.shell.UTGBShell.UTGBShellOption
 
coordinate - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDGene
 
copyFile(InputStream, File) - Static method in class org.utgenome.shell.ScaffoldGenerator
 
copyScaffold(String, String) - Method in class org.utgenome.shell.ScaffoldGenerator
Creates the folder structure for the Tomcat
Create - Class in org.utgenome.shell
Create sub command
Create() - Constructor for class org.utgenome.shell.Create
 
Create.CreateAllScaffoldFileFilter - Class in org.utgenome.shell
 
Create.CreateAllScaffoldFileFilter() - Constructor for class org.utgenome.shell.Create.CreateAllScaffoldFileFilter
 
Create.Opt - Enum in org.utgenome.shell
 
Create.OverwriteMode - Enum in org.utgenome.shell
 
Create.ScaffoldFileFilter - Interface in org.utgenome.shell
 
createContextXML(String, String, boolean) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
createEclipseLaunchFile(String, String, String) - Method in class org.utgenome.shell.ScaffoldGenerator
 
createFileFromTemplate(Class<?>, String, String, Properties) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
createFileFromTemplate(Class<?>, String, String, String, Properties, boolean) - Static method in class org.utgenome.shell.UTGBShellSubCommandBase
 
createGWTModuleScaffold(String, String) - Method in class org.utgenome.shell.ScaffoldGenerator
 
createProjectScaffold(String, String, String) - Method in class org.utgenome.shell.ScaffoldGenerator
 
createScaffold(String, String, String, String, Create.ScaffoldFileFilter) - Static method in class org.utgenome.shell.Create
 
createTitledBorder(String) - Static method in class org.utgenome.shell.UTGBPortableWidget
 

D

db - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
DBInfo - Class in org.utgenome.shell
An UTGB Shell subcommand that displays database information described in config/track-config.xml
DBInfo() - Constructor for class org.utgenome.shell.DBInfo
 
Deploy - Class in org.utgenome.shell
 
Deploy() - Constructor for class org.utgenome.shell.Deploy
 
description - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
Description - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Description - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
description() - Method in class org.utgenome.shell.db.bed.BEDParser
 
descriptionName() - Method in class org.utgenome.shell.db.bed.BEDParser
 
dfa12 - Variable in class org.utgenome.shell.db.bed.BEDLexer
 
dfa14 - Variable in class org.utgenome.shell.db.bed.BEDLexer
 
Digit - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Digit - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
dispose() - Method in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.DBBuilder
 
Dot - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Dot - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
Double - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Double - Static variable in class org.utgenome.shell.db.bed.BEDParser
 

E

Eclipse - Class in org.utgenome.shell
A sub command to generate Eclipse project files
Eclipse() - Constructor for class org.utgenome.shell.Eclipse
 
end - Variable in class org.utgenome.shell.db.Locus
 
EOF - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
EOF - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
Eq - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Eq - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
EscapeSequence - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
EscapeSequence - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
exec(String) - Static method in class org.utgenome.shell.Maven.CommandExecutor
 
exec(String, String[], File) - Static method in class org.utgenome.shell.Maven.CommandExecutor
 
execCommand(String, String[], File) - Method in class org.utgenome.shell.Maven.CommandExecutor
 
execute(String[]) - Method in class org.utgenome.shell.AddAction
 
execute(String[]) - Method in class org.utgenome.shell.Clean
 
execute(String[]) - Method in class org.utgenome.shell.Compile
 
execute(String[]) - Method in class org.utgenome.shell.Create
 
execute(String[]) - Method in class org.utgenome.shell.DBInfo
 
execute(String[]) - Method in class org.utgenome.shell.Deploy
 
execute(String[]) - Method in class org.utgenome.shell.Eclipse
 
execute(String[]) - Method in class org.utgenome.shell.GWT
 
execute(String[]) - Method in class org.utgenome.shell.Import
 
execute(String[]) - Method in class org.utgenome.shell.Maven
 
execute(String[]) - Method in class org.utgenome.shell.Query
 
execute(String[]) - Method in class org.utgenome.shell.Repair
 
execute(String[]) - Method in class org.utgenome.shell.Server
 
execute(String[]) - Method in class org.utgenome.shell.SVNAdd
 
execute(UTGBShell.UTGBShellOption, String[]) - Method in interface org.utgenome.shell.UTGBShellSubCommand
 
execute(String[]) - Method in interface org.utgenome.shell.UTGBShellSubCommand
 
execute(UTGBShell.UTGBShellOption, String[]) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
execute(String[]) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
Exon - Class in org.utgenome.shell.db
Exon
Exon() - Constructor for class org.utgenome.shell.db.Exon
 
Exon(long, long) - Constructor for class org.utgenome.shell.db.Exon
 
Exp - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Exp - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
EXPLODED_WEBAPP_DIR - Static variable in class org.utgenome.shell.UTGBShellSubCommandBase
 
explodeWar() - Static method in class org.utgenome.shell.Maven
 

F

findDir(String) - Method in class org.utgenome.shell.tomcat.TomcatServer
 
FOLLOW_attribute_in_description419 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_attributeValue_in_attribute461 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_descriptionName_in_description417 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_Eq_in_attribute459 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_Number_in_attributeValue488 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_QName_in_attribute457 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_QName_in_attributeValue480 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_QName_in_descriptionName443 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
FOLLOW_String_in_attributeValue484 - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
Frac - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Frac - Static variable in class org.utgenome.shell.db.bed.BEDParser
 

G

Gene - Class in org.utgenome.shell.db
Gene with Exon and CDS regions
Gene() - Constructor for class org.utgenome.shell.db.Gene
 
Gene(long, long) - Constructor for class org.utgenome.shell.db.Gene
 
Gene(String, long, long) - Constructor for class org.utgenome.shell.db.Gene
 
generateServerURLLinkHTML() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getAjp13port() - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
getCatalinaBase() - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
getCDS() - Method in class org.utgenome.shell.db.Gene
 
getColor() - Method in class org.utgenome.shell.db.Locus
 
getContextPath() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getDatabaseAccess(ConnectionInfo) - Static method in class org.utgenome.shell.JDBCUtil
 
getDatabaseAccess(String, ConnectionInfo) - Static method in class org.utgenome.shell.JDBCUtil
 
getDetailedDescription() - Method in class org.utgenome.shell.AddAction
 
getDetailedDescription() - Method in class org.utgenome.shell.Clean
 
getDetailedDescription() - Method in class org.utgenome.shell.Compile
 
getDetailedDescription() - Method in class org.utgenome.shell.Create
 
getDetailedDescription() - Method in class org.utgenome.shell.DBInfo
 
getDetailedDescription() - Method in class org.utgenome.shell.Deploy
 
getDetailedDescription() - Method in class org.utgenome.shell.Eclipse
 
getDetailedDescription() - Method in class org.utgenome.shell.GWT
 
getDetailedDescription() - Method in class org.utgenome.shell.Import
 
getDetailedDescription() - Method in class org.utgenome.shell.Maven
 
getDetailedDescription() - Method in class org.utgenome.shell.Query
 
getDetailedDescription() - Method in class org.utgenome.shell.Repair
 
getDetailedDescription() - Method in class org.utgenome.shell.Server
 
getDetailedDescription() - Method in class org.utgenome.shell.SVNAdd
 
getDetailedDescription() - Method in interface org.utgenome.shell.UTGBShellSubCommand
 
getEnd() - Method in class org.utgenome.shell.db.Locus
 
getExon() - Method in class org.utgenome.shell.db.Gene
 
getGrammarFileName() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
getGrammarFileName() - Method in class org.utgenome.shell.db.bed.BEDParser
 
getName() - Method in class org.utgenome.shell.db.Locus
 
getOneLinerDescription() - Method in class org.utgenome.shell.AddAction
 
getOneLinerDescription() - Method in class org.utgenome.shell.Clean
 
getOneLinerDescription() - Method in class org.utgenome.shell.Compile
 
getOneLinerDescription() - Method in class org.utgenome.shell.Create
 
getOneLinerDescription() - Method in class org.utgenome.shell.DBInfo
 
getOneLinerDescription() - Method in class org.utgenome.shell.Deploy
 
getOneLinerDescription() - Method in class org.utgenome.shell.Eclipse
 
getOneLinerDescription() - Method in class org.utgenome.shell.GWT
 
getOneLinerDescription() - Method in class org.utgenome.shell.Import
 
getOneLinerDescription() - Method in class org.utgenome.shell.Maven
 
getOneLinerDescription() - Method in class org.utgenome.shell.Query
 
getOneLinerDescription() - Method in class org.utgenome.shell.Repair
 
getOneLinerDescription() - Method in class org.utgenome.shell.Server
 
getOneLinerDescription() - Method in class org.utgenome.shell.SVNAdd
 
getOneLinerDescription() - Method in interface org.utgenome.shell.UTGBShellSubCommand
 
getOptionList() - Method in class org.utgenome.shell.AddAction
 
getOptionList() - Method in class org.utgenome.shell.Clean
 
getOptionList() - Method in class org.utgenome.shell.Compile
 
getOptionList() - Method in class org.utgenome.shell.Create
 
getOptionList() - Method in class org.utgenome.shell.DBInfo
 
getOptionList() - Method in class org.utgenome.shell.Deploy
 
getOptionList() - Method in class org.utgenome.shell.Eclipse
 
getOptionList() - Method in class org.utgenome.shell.GWT
 
getOptionList() - Method in class org.utgenome.shell.Import
 
getOptionList() - Method in class org.utgenome.shell.Maven
 
getOptionList() - Method in class org.utgenome.shell.Query
 
getOptionList() - Method in class org.utgenome.shell.Repair
 
getOptionList() - Method in class org.utgenome.shell.Server
 
getOptionList() - Method in class org.utgenome.shell.SVNAdd
 
getOptionList() - Method in interface org.utgenome.shell.UTGBShellSubCommand
 
getOSType() - Static method in enum org.utgenome.shell.OSType
Gets the current OS type
getPath(File) - Static method in class org.utgenome.shell.ScaffoldGenerator
 
getPath(File) - Static method in class org.utgenome.shell.UTGBShellSubCommandBase
 
getPort() - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
getPortNumber() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getProgramInfo() - Static method in class org.utgenome.shell.UTGBShell
 
getProjectConfigDir() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getProjectResourcePath(String) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
getProjectRoot() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getProperties() - Method in class org.utgenome.shell.POM
 
getRevision() - Method in class org.utgenome.shell.POM
Retrieves Subversion's revision number from the pom.xml file
getRevision() - Method in class org.utgenome.shell.POMProperties
 
getRevision() - Static method in class org.utgenome.shell.UTGBShell
 
getServerURL() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getStart() - Method in class org.utgenome.shell.db.Locus
 
getStrand() - Method in class org.utgenome.shell.db.Locus
 
getTokenNames() - Method in class org.utgenome.shell.db.bed.BEDParser
 
getTree() - Method in class org.utgenome.shell.db.bed.BEDParser.attribute_return
 
getTree() - Method in class org.utgenome.shell.db.bed.BEDParser.attributeValue_return
 
getTree() - Method in class org.utgenome.shell.db.bed.BEDParser.description_return
 
getTree() - Method in class org.utgenome.shell.db.bed.BEDParser.descriptionName_return
 
getTreeAdaptor() - Method in class org.utgenome.shell.db.bed.BEDParser
 
getVersion() - Method in class org.utgenome.shell.POM
 
getVersion() - Static method in class org.utgenome.shell.UTGBShell
 
getWebAppDir() - Method in class org.utgenome.shell.UTGBPortableConfig
 
getWorkingDir() - Method in class org.utgenome.shell.UTGBPortableConfig
 
globalOption - Variable in class org.utgenome.shell.UTGBShellSubCommandBase
 
group - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
GWT - Class in org.utgenome.shell
A sub command for creating a GWT interface
GWT() - Constructor for class org.utgenome.shell.GWT
 

H

HexDigit - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
HexDigit - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
htmlUrl - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 

I

Import - Class in org.utgenome.shell
import command
Import() - Constructor for class org.utgenome.shell.Import
 
Int - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Int - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
Integer - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Integer - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
isDisplayHelp() - Method in class org.utgenome.shell.UTGBPortableConfig
 
isInProjectRoot() - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
isMavenInstalled() - Static method in class org.utgenome.shell.Maven
 
isUseGUI() - Method in class org.utgenome.shell.UTGBPortableConfig
 
isVerbose() - Method in class org.utgenome.shell.UTGBPortableConfig
 
itemRgb - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 

J

JDBCUtil - Class in org.utgenome.shell
Utilities for connecting DMBS through JDBC
JDBCUtil() - Constructor for class org.utgenome.shell.JDBCUtil
 

L

loadTrackConfiguration() - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
loadUsage(String) - Static method in class org.utgenome.shell.UTGBShellSubCommandBase
 
Locus - Class in org.utgenome.shell.db
Locus on a genome sequence
Locus() - Constructor for class org.utgenome.shell.db.Locus
 
Locus(long, long) - Constructor for class org.utgenome.shell.db.Locus
 
Locus(String, long, long) - Constructor for class org.utgenome.shell.db.Locus
 

M

main(String[]) - Static method in class org.utgenome.shell.tomcat.TomcatServer
entry point for running Tomcat from CUI
main(String[]) - Static method in class org.utgenome.shell.UTGBPortable
entry point of the UTGBServer
main(String[]) - Static method in class org.utgenome.shell.UTGBPortableWidget
 
main(String[]) - Static method in class org.utgenome.shell.UTGBShell
 
Maven - Class in org.utgenome.shell
Maven utility
Maven() - Constructor for class org.utgenome.shell.Maven
 
maven(String) - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
Maven.CommandExecutor - Class in org.utgenome.shell
 
Maven.CommandExecutor() - Constructor for class org.utgenome.shell.Maven.CommandExecutor
 
mDigit() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mDot() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mDouble() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mEq() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mEscapeSequence() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mExp() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mFrac() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mHexDigit() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mInt() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mInteger() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mkdirs(File) - Static method in class org.utgenome.shell.Create
Create directories including its parent folders if not exist
mkdirs(File) - Static method in class org.utgenome.shell.ScaffoldGenerator
Create directories including its parent folders if not exist
mNumber() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mQName() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mString() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mStringChar() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mStringChars() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mTokens() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mUnicodeChar() - Method in class org.utgenome.shell.db.bed.BEDLexer
 
mWhiteSpace() - Method in class org.utgenome.shell.db.bed.BEDLexer
 

N

name() - Method in class org.utgenome.shell.AddAction
 
name() - Method in class org.utgenome.shell.Clean
 
name() - Method in class org.utgenome.shell.Compile
 
name() - Method in class org.utgenome.shell.Create
 
name - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
Name - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Name - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
name - Variable in class org.utgenome.shell.db.Locus
 
name() - Method in class org.utgenome.shell.DBInfo
 
name() - Method in class org.utgenome.shell.Deploy
 
name() - Method in class org.utgenome.shell.Eclipse
 
name() - Method in class org.utgenome.shell.GWT
 
name() - Method in class org.utgenome.shell.Import
 
name() - Method in class org.utgenome.shell.Maven
 
name() - Method in class org.utgenome.shell.Query
 
name() - Method in class org.utgenome.shell.Repair
 
name() - Method in class org.utgenome.shell.Server
 
name() - Method in class org.utgenome.shell.SVNAdd
 
name() - Method in interface org.utgenome.shell.UTGBShellSubCommand
 
name() - Method in class org.utgenome.shell.UTGBShellSubCommandBase
 
Number - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Number - Static variable in class org.utgenome.shell.db.bed.BEDParser
 

O

offset - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
openURL(String) - Static method in class org.utgenome.shell.WebBrowser
 
org.utgenome.shell - package org.utgenome.shell
 
org.utgenome.shell.db - package org.utgenome.shell.db
 
org.utgenome.shell.db.bed - package org.utgenome.shell.db.bed
 
org.utgenome.shell.tomcat - package org.utgenome.shell.tomcat
 
OSType - Enum in org.utgenome.shell
This class provides information of current OS type.

P

POM - Class in org.utgenome.shell
POM objects corresponds to a Maven project file (pom.xml)
POM() - Constructor for class org.utgenome.shell.POM
 
POMProperties - Class in org.utgenome.shell
This class is used for retrieving the revision value described in the pom.xml file
POMProperties() - Constructor for class org.utgenome.shell.POMProperties
 
priority - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
projectDir - Variable in class org.utgenome.shell.UTGBShell.UTGBShellOption
 
pushStart() - Method in class org.utgenome.shell.UTGBPortableWidget
 

Q

QName - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
QName - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
Query - Class in org.utgenome.shell
An UTGBShell sub commands that performs query
Query() - Constructor for class org.utgenome.shell.Query
 

R

read(char[], int, int) - Method in class org.utgenome.shell.db.bed.BED2SilkReader
 
registerWAR(String, String) - Method in class org.utgenome.shell.tomcat.TomcatServer
 
Repair - Class in org.utgenome.shell
 
Repair() - Constructor for class org.utgenome.shell.Repair
 
rsync(File, File) - Static method in class org.utgenome.shell.Server
 
rsync(String, String) - Static method in class org.utgenome.shell.Server
 
runInCUIMode() - Method in class org.utgenome.shell.UTGBPortable
 
runInGUIMode() - Method in class org.utgenome.shell.UTGBPortable
 
runMaven(String) - Static method in class org.utgenome.shell.Maven
 
runMaven(String, File) - Static method in class org.utgenome.shell.Maven
 
runMaven(String[]) - Static method in class org.utgenome.shell.Maven
 
runMaven(String[], File) - Static method in class org.utgenome.shell.Maven
 

S

ScaffoldGenerator - Class in org.utgenome.shell
Scaffold generator
ScaffoldGenerator(String, Create.ScaffoldFileFilter) - Constructor for class org.utgenome.shell.ScaffoldGenerator
 
searchSubCommands() - Static method in class org.utgenome.shell.UTGBShell
search sub commands from the this package (org.utgenome.shell)
Server - Class in org.utgenome.shell
A UTGB sub command for starting up a UTGB portable server
Server() - Constructor for class org.utgenome.shell.Server
 
ServerListener - Interface in org.utgenome.shell
 
setAjp13port(int) - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
setButtonMargin(JButton) - Static method in class org.utgenome.shell.UTGBPortableWidget
 
setCatalinaBase(String) - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
setColor(String) - Method in class org.utgenome.shell.db.Locus
 
setConfiguration(TomcatServerConfiguration) - Method in class org.utgenome.shell.tomcat.TomcatServer
 
setEnd(long) - Method in class org.utgenome.shell.db.Locus
 
setName(String) - Method in class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderAttribute
 
setName(String) - Method in class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderDescription
 
setName(String) - Method in class org.utgenome.shell.db.Locus
 
setPort(int) - Method in class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
setProperties(POMProperties) - Method in class org.utgenome.shell.POM
 
setRevision(String) - Method in class org.utgenome.shell.POMProperties
 
setStart(long) - Method in class org.utgenome.shell.db.Locus
 
setStatus(UTGBPortableWidget.MessageType, String) - Method in class org.utgenome.shell.UTGBPortableWidget
 
setStrand(String) - Method in class org.utgenome.shell.db.Locus
 
setTomcatServerLauncher(TomcatServerLauncher) - Method in class org.utgenome.shell.UTGBPortableWidget
 
setTreeAdaptor(TreeAdaptor) - Method in class org.utgenome.shell.db.bed.BEDParser
 
setValue(String) - Method in class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderAttribute
 
setVersion(String) - Method in class org.utgenome.shell.POM
 
SRC_FOLDER - Static variable in class org.utgenome.shell.UTGBShellSubCommandBase
 
start - Variable in class org.utgenome.shell.db.Locus
 
start() - Method in class org.utgenome.shell.tomcat.TomcatServer
Starts the tomcat server
start() - Method in class org.utgenome.shell.UTGBPortable
Starts the web server
start(int, TimeUnit) - Method in class org.utgenome.shell.UTGBPortable
 
startTomcatServer(UTGBPortableConfig) - Method in class org.utgenome.shell.UTGBPortable
starts the Tomcat server
stop() - Method in class org.utgenome.shell.tomcat.TomcatServer
Stops the tomcat server
stopTomcatServer(UTGBPortableConfig) - Method in class org.utgenome.shell.UTGBPortable
stops the Tomcat server
strand - Variable in class org.utgenome.shell.db.Locus
 
String - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
String - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
StringChar - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
StringChar - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
StringChars - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
StringChars - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
subCommandTable - Static variable in class org.utgenome.shell.UTGBShell
 
SVNAdd - Class in org.utgenome.shell
Subcommand to add the current project to the subversion repository
SVNAdd() - Constructor for class org.utgenome.shell.SVNAdd
 
svnAddDir(String, boolean) - Method in class org.utgenome.shell.SVNAdd
 
svnAddFile(String) - Method in class org.utgenome.shell.SVNAdd
 
svnIgnore(String, String, boolean) - Method in class org.utgenome.shell.SVNAdd
 

T

tokenNames - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
TomcatServer - Class in org.utgenome.shell.tomcat
Embedded Tomcat Server
TomcatServer(int) - Constructor for class org.utgenome.shell.tomcat.TomcatServer
Creates a TomcatServer instance with the specified port
TomcatServer(TomcatServerConfiguration) - Constructor for class org.utgenome.shell.tomcat.TomcatServer
Configures the tomcat server
TomcatServer.Opt - Class in org.utgenome.shell.tomcat
 
TomcatServer.Opt() - Constructor for class org.utgenome.shell.tomcat.TomcatServer.Opt
 
TomcatServerConfiguration - Class in org.utgenome.shell.tomcat
Configuration bean for the TomcatServer.
TomcatServerConfiguration() - Constructor for class org.utgenome.shell.tomcat.TomcatServerConfiguration
 
toSilk(PrintWriter) - Method in class org.utgenome.shell.db.bed.BED2Silk
 
toSilk() - Method in class org.utgenome.shell.db.bed.BED2Silk
 
toSQLiteDB(Reader, String) - Static method in class org.utgenome.shell.db.bed.BEDDatabaseGenerator
 
toString() - Method in class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderAttribute
 
toString() - Method in class org.utgenome.shell.db.bed.BED2Silk.BEDHeaderDescription
 
toString() - Method in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDGene
 
toString() - Method in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
toString() - Method in class org.utgenome.shell.db.CDS
 
toString() - Method in class org.utgenome.shell.UTGBPortableConfig
 

U

UnicodeChar - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
UnicodeChar - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
updateLink() - Method in class org.utgenome.shell.UTGBPortableWidget
 
url - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
useGUI - Variable in class org.utgenome.shell.UTGBShell.UTGBShellOption
 
useScore - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 
UTGBPortable - Class in org.utgenome.shell
The stand-alone UTGB server launcher
UTGBPortable(String[]) - Constructor for class org.utgenome.shell.UTGBPortable
Create an instance of the UTGBServer
UTGBPortable(UTGBPortableConfig) - Constructor for class org.utgenome.shell.UTGBPortable
 
UTGBPortableConfig - Class in org.utgenome.shell
The configuration parameters of the UTGBPortable
UTGBPortableConfig() - Constructor for class org.utgenome.shell.UTGBPortableConfig
 
UTGBPortableConfig(int, String, String) - Constructor for class org.utgenome.shell.UTGBPortableConfig
 
UTGBPortableWidget - Class in org.utgenome.shell
GUI Panel of the UTGB Portable Server
UTGBPortableWidget() - Constructor for class org.utgenome.shell.UTGBPortableWidget
 
UTGBPortableWidget(UTGBPortableConfig) - Constructor for class org.utgenome.shell.UTGBPortableWidget
 
UTGBPortableWidget.MessageType - Enum in org.utgenome.shell
 
UTGBShell - Class in org.utgenome.shell
A command line client entry point
UTGBShell() - Constructor for class org.utgenome.shell.UTGBShell
 
UTGBShell.UTGBShellOption - Class in org.utgenome.shell
 
UTGBShell.UTGBShellOption() - Constructor for class org.utgenome.shell.UTGBShell.UTGBShellOption
 
UTGBShellException - Exception in org.utgenome.shell
 
UTGBShellException() - Constructor for exception org.utgenome.shell.UTGBShellException
 
UTGBShellException(String, Throwable) - Constructor for exception org.utgenome.shell.UTGBShellException
 
UTGBShellException(String) - Constructor for exception org.utgenome.shell.UTGBShellException
 
UTGBShellException(Throwable) - Constructor for exception org.utgenome.shell.UTGBShellException
 
UTGBShellSubCommand - Interface in org.utgenome.shell
A common interface of UTGB Shell subcommands
UTGBShellSubCommandBase - Class in org.utgenome.shell
A common implementation of the UTGBShell's sub commands
UTGBShellSubCommandBase() - Constructor for class org.utgenome.shell.UTGBShellSubCommandBase
 
UTGBShellWidget - Class in org.utgenome.shell
A GUI Interface of the UTGB Shell
UTGBShellWidget() - Constructor for class org.utgenome.shell.UTGBShellWidget
 

V

Value - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
Value - Static variable in class org.utgenome.shell.db.bed.BEDParser
 
valueOf(String) - Static method in enum org.utgenome.shell.Create.Opt
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.utgenome.shell.Create.OverwriteMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.utgenome.shell.OSType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.utgenome.shell.UTGBPortableWidget.MessageType
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.utgenome.shell.Create.Opt
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.utgenome.shell.Create.OverwriteMode
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.utgenome.shell.OSType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.utgenome.shell.UTGBPortableWidget.MessageType
Returns an array containing the constants of this enum type, in the order they're declared.
visibility - Variable in class org.utgenome.shell.db.bed.BEDDatabaseGenerator.BEDTrack
 

W

WEBAPP_FOLDER - Static variable in class org.utgenome.shell.UTGBShellSubCommandBase
 
WebBrowser - Class in org.utgenome.shell
Open a given URL via OS's default web browser.
WebBrowser() - Constructor for class org.utgenome.shell.WebBrowser
 
WhiteSpace - Static variable in class org.utgenome.shell.db.bed.BEDLexer
 
WhiteSpace - Static variable in class org.utgenome.shell.db.bed.BEDParser
 

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