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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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