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A
AA_TYPE
- Static variable in class org.genepi.means.
GenericReader
AbstractParser
- Class in
org.genepi.mean.parser
AbstractParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
AbstractParser
actionPerformed(ActionEvent)
- Method in class org.genepi.swing.
GlassPane
actionPerformed(ActionEvent)
- Method in class org.genepi.swing.
TimeLineView
actionPerformed(ActionEvent)
- Method in class org.genepi.swing.
ZoomableIntervalView
addDomain(String, Domain)
- Method in interface org.blackbox.model.
Blackboard
Add a new domain in the blackboard.
addDomain(String, Domain)
- Method in class org.blackbox.shell.
BBX_Blackboard
addDomain(String, String)
- Method in class org.genepi.
Configuration
addDomain(Domain)
- Method in class org.genepi.swing.
BlackboardView
addDomain(Domain)
- Method in class org.genepi.swing.
GenericViews
addDomain(TimeLine)
- Method in class org.genepi.swing.
TimeLinePane
addDomain(TimeLine)
- Method in class org.genepi.swing.
ZoomableIntervalView
addInterval(Interval)
- Method in class org.genepi.swing.
TimeLineView
addKS(KnowledgeSource)
- Method in class org.genepi.
Configuration
addLayoutComponent(String, Component)
- Method in class org.genepi.swing.
TimeLineLayout
Adds the specified component with the specified name to the layout.
addLayoutComponent(Component, Object)
- Method in class org.genepi.swing.
TimeLineLayout
Adds the specified component to the layout, using the specified constraint object.
addMean(Task)
- Method in class org.genepi.
Pipeline
Ajoute un moyen (une methode ) au pipline.
addObserver(ModelObserver)
- Method in class org.blackbox.model.
Hypothesis
addObserver(ModelObserver)
- Method in interface org.blackbox.model.
ObservableEntity
Add a new observer.
addObserver(Observer)
- Method in interface org.blackbox.model.
PatternMatcher
addObserver(ModelObserver)
- Method in class org.blackbox.shell.
ObserverPatternImpl
addObserver(ModelObserver)
- Method in class org.blackbox.test.
SimpleKS
addObserver(ModelObserver)
- Method in class org.genepi.
Pipeline
addObserver(Observer)
- Method in class org.genepi.rete.
ReteMatcher
addPredicate(Predicate)
- Method in class org.blackbox.model.
KnowledgeSource
addRule(Rule)
- Method in class org.blackbox.shell.
BBX_KSFarm
addVar(String)
- Method in class org.blackbox.model.
Pattern
afterExec()
- Method in class org.genepi.
Task
Methode executee apres le declenchement du moyens: placer ici ls routine de lebeation des ressources.
Agenda
- Interface in
org.blackbox.model
AgendaView
- Class in
org.genepi.swing
AgendaView()
- Constructor for class org.genepi.swing.
AgendaView
AgendaView(Agenda)
- Constructor for class org.genepi.swing.
AgendaView
annot
- Variable in class org.genepi.mean.parser.
AbstractParser
AppMenuBar
- Class in
org.genepi
JMenubar for app main JFrame.
AppMenuBar(JFrame)
- Constructor for class org.genepi.
AppMenuBar
AppWindow
- Class in
org.genepi
Genepi main window.
AppWindow()
- Constructor for class org.genepi.
AppWindow
arrayToString(Object[], String)
- Static method in class org.blackbox.util.
StringUtil
ARROW
- Static variable in class org.genepi.swing.
IntervalView
asFloat(String)
- Static method in class org.genepi.means.
MeansUtil
asInt(String)
- Static method in class org.genepi.means.
MeansUtil
assertHypothesis(Hypothesis)
- Method in class org.blackbox.domains.
BlackHole
assertHypothesis(Hypothesis)
- Method in class org.blackbox.domains.
List
assertHypothesis(Hypothesis)
- Method in class org.blackbox.domains.
TimeLine
assertHypothesis(Hypothesis)
- Method in interface org.blackbox.model.
Domain
Assert a new hypothesis in this domain.
asString()
- Method in class org.blackbox.shell.
BBX_SetOf
asTab()
- Method in class org.blackbox.shell.
BBX_Annotation
atExit()
- Method in class org.blackbox.model.
Controller
Called after execution.
atExit()
- Method in class org.blackbox.shell.
BBX_Controller
When dove cry...
atInit()
- Method in class org.blackbox.model.
Controller
Called before execution starts.
atInit()
- Method in class org.blackbox.shell.
BBX_Controller
Called at init.
ATTR_BB_LEVEL_MNEMO
- Static variable in class org.genepi.parser.
Keywords
ATTR_BB_LEVEL_TYPE
- Static variable in class org.genepi.parser.
Keywords
ATTR_CONFIG_NAME
- Static variable in class org.genepi.parser.
Keywords
ATTR_KS_ASSERT
- Static variable in class org.genepi.parser.
Keywords
ATTR_KS_DESC
- Static variable in class org.genepi.parser.
Keywords
ATTR_KS_NAME
- Static variable in class org.genepi.parser.
Keywords
ATTR_KS_SALIENCE
- Static variable in class org.genepi.parser.
Keywords
ATTR_PROJECT_BDIR
- Static variable in class org.genepi.parser.
Keywords
ATTR_RSRC_MNEMO
- Static variable in class org.genepi.parser.
Keywords
ATTR_RSRC_TYPE
- Static variable in class org.genepi.parser.
Keywords
ATTR_RSRC_VALUE
- Static variable in class org.genepi.parser.
Keywords
ATTR_SELECT_COND
- Static variable in class org.genepi.parser.
Keywords
ATTR_SELECT_CUTOFF
- Static variable in class org.genepi.parser.
Keywords
ATTR_VAR_LIST
- Static variable in class org.genepi.parser.
Keywords
attrAlpha(String)
- Method in class org.genepi.means.
Loader
attrCovmin(String)
- Method in class org.genepi.means.
SIMIResolver
attrDomain(String)
- Method in class org.genepi.means.
PostInterGenic
attrDomain(String)
- Method in class org.genepi.means.
RepostHypothesis
attrFilename(String)
- Method in class org.genepi.means.
Loader
attrFileName(String)
- Method in class org.genepi.means.
PublishFile
attrFormat(String)
- Method in class org.genepi.means.
Loader
attrFrom(String)
- Method in class org.genepi.means.
Zoom
attrIdentity(String)
- Method in class org.genepi.means.
SIMIResolver
attrLimitRes(String)
- Method in class org.genepi.means.
Blastp
attrLimitRes(String)
- Method in class org.genepi.means.
Blastx
attrList(String)
- Method in class org.genepi.means.
PostInterGenic
attrList(String)
- Method in class org.genepi.means.
RepostHypothesis
attrMessage(String)
- Method in class org.genepi.means.
WriteLn
attrMinLen(String)
- Method in class org.genepi.means.
ProkovCds
attrMinLen(String)
- Method in class org.genepi.means.
ProkovCds2
attrMinLen(String)
- Method in class org.genepi.means.
ProkovOrf
attrNot(String)
- Method in class org.genepi.means.
Filter
attrOperator(String)
- Method in class org.genepi.means.
Filter
attrOrder(String)
- Method in class org.genepi.means.
ProkovLearn
attrPath(String)
- Method in class org.genepi.means.
Loader
attrPath(String)
- Method in class org.genepi.means.
PublishFile
attrPattern(String)
- Method in class org.genepi.means.
RbsFinder
attrRbsRegionLen(String)
- Method in class org.genepi.means.
RbsFinder
attrSet(String)
- Method in class org.genepi.means.
Salience
attrSlot(String)
- Method in class org.genepi.means.
Filter
attrTo(String)
- Method in class org.genepi.means.
Zoom
attrTokenName(String)
- Method in class org.genepi.means.
PublishToken
attrUsMinLen(String)
- Method in class org.genepi.means.
Termit
attrValue(String)
- Method in class org.genepi.means.
Filter
B
bb
- Variable in class org.blackbox.model.
Controller
BBX_Agenda
- Class in
org.blackbox.shell
BBX_Agenda()
- Constructor for class org.blackbox.shell.
BBX_Agenda
BBX_Annotation
- Class in
org.blackbox.shell
BBX_Annotation(HSequence, Domain, KnowledgeSource, Map, boolean, int, int)
- Constructor for class org.blackbox.shell.
BBX_Annotation
BBX_Blackboard
- Class in
org.blackbox.shell
BBX_Blackboard(Hashtable)
- Constructor for class org.blackbox.shell.
BBX_Blackboard
BBX_CONFIG_FILENAME
- Static variable in class org.genepi.
Resource
BBX_Controller
- Class in
org.blackbox.shell
BBX_Controller(Blackboard, KsFarm, PatternMatcher, Agenda)
- Constructor for class org.blackbox.shell.
BBX_Controller
BBX_EngineEvent
- Class in
org.blackbox.shell
BBX_EngineEvent(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_EngineEvent
BBX_Exception
- Exception in
org.blackbox.shell
Root of all package Exception
BBX_Exception()
- Constructor for exception org.blackbox.shell.
BBX_Exception
Constructs a bbx exception with no descriptive information.
BBX_Exception(String)
- Constructor for exception org.blackbox.shell.
BBX_Exception
Constructs an exception with the given descriptive message.
BBX_Exception(String, Throwable)
- Constructor for exception org.blackbox.shell.
BBX_Exception
Constructs an exception with the given message and exception as a root cause.
BBX_Exception(Throwable)
- Constructor for exception org.blackbox.shell.
BBX_Exception
Constructs an exception with the given exception as a root cause.
BBX_File
- Class in
org.blackbox.shell
BBX_File(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_File
BBX_File(Domain, KnowledgeSource, String, String)
- Constructor for class org.blackbox.shell.
BBX_File
BBX_KSFarm
- Class in
org.blackbox.shell
BBX_KSFarm(List)
- Constructor for class org.blackbox.shell.
BBX_KSFarm
BBX_KSFarm()
- Constructor for class org.blackbox.shell.
BBX_KSFarm
BBX_Pattern
- Class in
org.blackbox.shell
BBX_Pattern(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_Pattern
BBX_SeqTool
- Class in
org.blackbox.shell
BBX_SeqTool()
- Constructor for class org.blackbox.shell.
BBX_SeqTool
BBX_Sequence
- Class in
org.blackbox.shell
BBX_Sequence(Sequence, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_Sequence
BBX_SetOf
- Class in
org.blackbox.shell
BBX_SetOf(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_SetOf
BBX_SetOfInterval
- Class in
org.blackbox.shell
BBX_SetOfInterval(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_SetOfInterval
BBX_ShellException
- Exception in
org.blackbox.shell
Runtime's exceptions.
BBX_ShellException()
- Constructor for exception org.blackbox.shell.
BBX_ShellException
Constructs a build exception with no descriptive information.
BBX_ShellException(String)
- Constructor for exception org.blackbox.shell.
BBX_ShellException
Constructs an exception with the given descriptive message.
BBX_ShellException(Throwable)
- Constructor for exception org.blackbox.shell.
BBX_ShellException
Constructs an exception with the given exception as a root cause.
BBX_ShellException(String, Throwable)
- Constructor for exception org.blackbox.shell.
BBX_ShellException
Constructs an exception with the given message and exception as a root cause.
BBX_SimpleInterval
- Class in
org.blackbox.shell
BBX_SimpleInterval(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.shell.
BBX_SimpleInterval
beforeExec()
- Method in class org.genepi.
Task
Methode executee avant le declenchement du moyens: placer ici ls routine d'initialisation.
beforeXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
Retourne l'intervalle de plus petite coordonnee de debut.
bigerXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
Retourne le plus grand des deux intervalles.
blackboard()
- Method in class org.blackbox.domains.
BlackHole
blackboard()
- Method in class org.blackbox.domains.
List
blackboard()
- Method in class org.blackbox.domains.
TimeLine
Blackboard
- Interface in
org.blackbox.model
blackboard()
- Method in interface org.blackbox.model.
Domain
Return the name of this domain.
BLACKBOARD_DB
- Static variable in class org.genepi.
Genepi
BlackboardShell
- Class in
org.genepi
Blackboard architecture.
BlackboardShell(String)
- Constructor for class org.genepi.
BlackboardShell
BlackboardShell(File)
- Constructor for class org.genepi.
BlackboardShell
BlackboardView
- Class in
org.genepi.swing
Event router.
BlackboardView()
- Constructor for class org.genepi.swing.
BlackboardView
BlackHole
- Class in
org.blackbox.domains
BlackHole()
- Constructor for class org.blackbox.domains.
BlackHole
Blastp
- Class in
org.genepi.means
Blastp()
- Constructor for class org.genepi.means.
Blastp
BlastParserM9
- Class in
org.genepi.mean.parser
BlastParserM9(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
BlastParserM9
Blastx
- Class in
org.genepi.means
Blastx()
- Constructor for class org.genepi.means.
Blastx
buildContent()
- Method in class org.genepi.
AppWindow
buildPanel()
- Method in class org.genepi.swing.
AgendaView
buildPanel()
- Method in class org.genepi.swing.
GenericViews
buildPanel()
- Method in class org.genepi.swing.
TimeLinePane
buildPanel()
- Method in class org.genepi.swing.
ZoomableIntervalView
buildTabbedPanel()
- Method in class org.genepi.
AppWindow
C
characters(char[], int, int)
- Method in class org.genepi.parser.
DefaultHandler
clear()
- Method in class org.genepi.swing.
Messager
clone()
- Method in class org.blackbox.model.
Context
clone()
- Method in class org.blackbox.model.
Hypothesis
clone()
- Method in class org.blackbox.shell.
BBX_Annotation
clone()
- Method in class org.blackbox.shell.
BBX_EngineEvent
clone()
- Method in class org.blackbox.shell.
BBX_File
clone()
- Method in class org.blackbox.shell.
BBX_Pattern
clone()
- Method in class org.blackbox.shell.
BBX_Sequence
clone()
- Method in class org.blackbox.shell.
BBX_SetOf
clone()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
clone()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
clone()
- Method in class org.blackbox.test.
SimpleHInterval
cmd
- Variable in class org.genepi.means.
TinaShell
columns
- Variable in class org.genepi.swing.
JMultiLineToolTip
compareTo(Object)
- Method in class org.blackbox.domains.
BlackHole
compareTo(Object)
- Method in class org.blackbox.domains.
List
compareTo(Object)
- Method in class org.blackbox.domains.
TimeLine
compareTo(Object)
- Method in class org.blackbox.hypothesis.
HAnnotation
compareTo(Object)
- Method in class org.blackbox.hypothesis.
HSequence
compareTo(Object)
- Method in class org.blackbox.model.
KSAR
compareTo(Object)
- Method in class org.blackbox.shell.
BBX_SetOfInterval
compareTo(Object)
- Method in class org.blackbox.shell.
BBX_SimpleInterval
compareTo(Object)
- Method in class org.blackbox.test.
SimpleHInterval
compile()
- Method in interface org.blackbox.model.
PatternMatcher
Prepare matcher.
compile()
- Method in class org.genepi.rete.
ReteMatcher
do build the network.
CONF_SHOW_AT_STARTUP
- Static variable in class org.genepi.
Resource
ConfigParser
- Class in
org.genepi.parser
ConfigParser(File, BlackboardShell)
- Constructor for class org.genepi.parser.
ConfigParser
Parseur du fichier de configuration.
Configuration
- Class in
org.genepi
Configuration()
- Constructor for class org.genepi.
Configuration
Console
- Class in
org.genepi.swing
Context
- Class in
org.blackbox.model
Context(Object[])
- Constructor for class org.blackbox.model.
Context
Context(List)
- Constructor for class org.blackbox.model.
Context
Context(Tuple)
- Constructor for class org.blackbox.model.
Context
ContextCondition
- Class in
org.blackbox.conditions
ContextCondition()
- Constructor for class org.blackbox.conditions.
ContextCondition
continuousXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
A et B sont continues ssi A touche B ou si B touche A
Controller
- Class in
org.blackbox.model
Controller()
- Constructor for class org.blackbox.model.
Controller
countHypothesis()
- Method in class org.blackbox.domains.
BlackHole
countHypothesis()
- Method in class org.blackbox.domains.
List
countHypothesis()
- Method in class org.blackbox.domains.
TimeLine
countHypothesis()
- Method in interface org.blackbox.model.
Domain
Count the number of hypothesis in thsi domain.
covmaxXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
Retourne le % de couverture de A sur B ssi A > B
covminXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
Retourne le % de couverture de A sur B ssi A < B
createToolTip()
- Method in class org.genepi.swing.
IntervalView
curEvent
- Variable in class org.blackbox.model.
Hypothesis
curEvent
- Variable in class org.blackbox.shell.
ObserverPatternImpl
curEvent
- Variable in class org.genepi.
Pipeline
D
db
- Variable in class org.genepi.means.
GenericReader
DEFAULT_HEIGHT
- Static variable in class org.genepi.swing.
IntervalView
DEFAULT_SAX_IPLM
- Static variable in class org.genepi.
Resource
DefaultHandler
- Class in
org.genepi.parser
DefaultHandler(DocumentHandler, Parser, Locator, BlackboardShell)
- Constructor for class org.genepi.parser.
DefaultHandler
deleteDomain(String)
- Method in interface org.blackbox.model.
Blackboard
Remove a domain from the Blackboard.
deleteDomain(String)
- Method in class org.blackbox.shell.
BBX_Blackboard
delObject(String, Object)
- Method in interface org.blackbox.model.
PatternMatcher
disptach remove hypothesis
delObject(String, Object)
- Method in class org.genepi.rete.
ReteMatcher
Push remove on the top of the network.
destinationDomain
- Variable in class org.blackbox.model.
KnowledgeSource
Type produit par cette source de connaissance.
dispatchComplet(String, String)
- Method in class org.genepi.mean.parser.
BlastParserM9
Alloc. d'une hypothese correspondante a un hit
dispatchComplet(String, String, String)
- Method in class org.genepi.mean.parser.
FastRnaParser
Fait suivre les informations necessaires a la creation d'un feature.
dispatchComplet(String, String, String, String)
- Method in class org.genepi.mean.parser.
GffParser
Alloc. d'une hypothese correspondante a un hit.
dispatchComplet(String, String, String)
- Method in class org.genepi.mean.parser.
TermitParser
Fait suivre les informations necessaires a la creation d'un feature.
distance(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
Retourne la distance qui separe ces deux intervalles.
DNA_TYPE
- Static variable in class org.genepi.means.
GenericReader
Document
- Class in
org.genepi
Document(File)
- Constructor for class org.genepi.
Document
Domain
- Interface in
org.blackbox.model
domainName()
- Method in class org.blackbox.domains.
BlackHole
domainName()
- Method in class org.blackbox.domains.
List
domainName()
- Method in class org.blackbox.domains.
TimeLine
domainName()
- Method in interface org.blackbox.model.
Domain
Return the name of this domain.
domainTable
- Variable in class org.genepi.
Configuration
doTest(Context)
- Method in class org.blackbox.conditions.
ContextCondition
doTest(Context)
- Method in class org.blackbox.conditions.
Include
doTest(Context)
- Method in class org.blackbox.conditions.
Meet
doTest(Context)
- Method in class org.blackbox.conditions.
No
doTest(Context)
- Method in class org.blackbox.conditions.
Overlap
doTest(Context)
- Method in class org.blackbox.conditions.
Yes
dotFile()
- Method in class org.genepi.rete.
ReteMatcher
E
empty()
- Method in interface org.blackbox.model.
Agenda
Anwser the question : is this queue empty.
empty()
- Method in class org.blackbox.shell.
BBX_Agenda
endElement(String)
- Method in class org.genepi.parser.
DefaultHandler
equalsXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
eval(Context)
- Method in class org.blackbox.model.
KnowledgeSource
Execution de l'expertise de cette source de connaissances.
eval(Context)
- Method in class org.blackbox.test.
SimpleKS
eval(Context)
- Method in class org.genepi.
Pipeline
Provoque l'evaluation(execution) de cette source de connaissances.
Event
- Class in
org.blackbox.model
Event(String, String, Object)
- Constructor for class org.blackbox.model.
Event
Create a new Event.
execute()
- Method in class org.genepi.means.
Filter
execute()
- Method in class org.genepi.means.
Loader
execute()
- Method in class org.genepi.means.
Null
execute()
- Method in class org.genepi.means.
Pack
execute()
- Method in class org.genepi.means.
PackInterval
execute()
- Method in class org.genepi.means.
PostInterGenic
execute()
- Method in class org.genepi.means.
PublishFile
execute()
- Method in class org.genepi.means.
PublishToken
execute()
- Method in class org.genepi.means.
RepostHypothesis
execute()
- Method in class org.genepi.means.
Salience
execute()
- Method in class org.genepi.means.
SIMIResolver
execute()
- Method in class org.genepi.means.
TinaShell
execute()
- Method in class org.genepi.means.
Touch
execute()
- Method in class org.genepi.means.
WriteLn
execute()
- Method in class org.genepi.means.
Zoom
execute()
- Method in class org.genepi.
Task
Implementation du comportement du moyen.
executeContext()
- Method in class org.blackbox.model.
KSAR
extractRecords()
- Method in class org.genepi.means.
Blastp
extractRecords()
- Method in class org.genepi.means.
Blastx
extractRecords()
- Method in class org.genepi.means.
FastRna
extractRecords()
- Method in class org.genepi.means.
ProkovCds
extractRecords()
- Method in class org.genepi.means.
ProkovCds2
extractRecords()
- Method in class org.genepi.means.
ProkovLearn
extractRecords()
- Method in class org.genepi.means.
ProkovOrf
extractRecords()
- Method in class org.genepi.means.
RbsFinder
Cette methode parse le fichier TINA resultat et instancie les intervalles correspondants
extractRecords()
- Method in class org.genepi.means.
Termit
extractRecords()
- Method in class org.genepi.means.
TinaShell
F
FastRna
- Class in
org.genepi.means
FastRna()
- Constructor for class org.genepi.means.
FastRna
FastRnaParser
- Class in
org.genepi.mean.parser
FastRnaParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
FastRnaParser
featureComplet(int, int, boolean)
- Method in class org.genepi.mean.parser.
AbstractParser
featureFrame(int, int, boolean, HSequence)
- Method in class org.blackbox.shell.
BBX_Annotation
FeatureHandler
- Interface in
org.genepi.mean.parser
featureReady(int, int, boolean, Hashtable)
- Method in interface org.genepi.mean.parser.
FeatureHandler
Cette methode est appelee par le parser pour recevoir le feature.
featureReady(int, int, boolean, Hashtable)
- Method in class org.genepi.means.
Blastp
RedŽfinition de l'interface FeatureHandler necessaire pour mapper les coordonnŽe proteique->nuclŽique (*3).
featureReady(int, int, boolean, Hashtable)
- Method in class org.genepi.means.
Blastx
RedŽfinition de l'interface FeatureHandler necessaire pour mapper les coordonnŽe proteique->nuclŽique (*3).
featureReady(int, int, boolean, Hashtable)
- Method in class org.genepi.means.
TinaShell
Filter
- Class in
org.genepi.means
Filter()
- Constructor for class org.genepi.means.
Filter
fixedwidth
- Variable in class org.genepi.swing.
JMultiLineToolTip
flush()
- Method in class org.genepi.
Task
focusContext(boolean)
- Method in class org.blackbox.model.
KSAR
FORMAT_EMBL
- Static variable in class org.genepi.means.
GenericReader
FORMAT_FASTA
- Static variable in class org.genepi.means.
GenericReader
FORMAT_GENPEPT
- Static variable in class org.genepi.means.
GenericReader
FORMAT_SWISS
- Static variable in class org.genepi.means.
GenericReader
formatAnnot(Map)
- Method in class org.genepi.swing.
HypothesisInspector
from
- Variable in class org.genepi.mean.parser.
AbstractParser
G
gainFocus()
- Method in class org.blackbox.model.
Hypothesis
gathering
- Variable in class org.blackbox.model.
Controller
Genepi
- Class in
org.genepi
Genepi()
- Constructor for class org.genepi.
Genepi
GENEPI_CONFIG_FILENAME
- Static variable in class org.genepi.
Resource
GENEPI_DEFAULT_BIG_BIG_FONT
- Static variable in class org.genepi.
Resource
GENEPI_DEFAULT_BIG_FONT
- Static variable in class org.genepi.
Resource
GENEPI_DEFAULT_FONT
- Static variable in class org.genepi.
Resource
GENEPI_PETITE_FONT
- Static variable in class org.genepi.
Resource
GENEPI_VERSION
- Static variable in class org.genepi.
Resource
GenericDomainView
- Class in
org.genepi.swing
generic Graphic & synchrone representation of an hypothesis domain
GenericDomainView(Domain)
- Constructor for class org.genepi.swing.
GenericDomainView
GenericReader
- Class in
org.genepi.means
GenericReader(String, String, String, KnowledgeSource)
- Constructor for class org.genepi.means.
GenericReader
GenericViews
- Class in
org.genepi.swing
Visualise all generic domain for a blackboard
GenericViews()
- Constructor for class org.genepi.swing.
GenericViews
getAgenda()
- Method in class org.genepi.
BlackboardShell
getAnnotations()
- Method in class org.blackbox.hypothesis.
HAnnotation
getArgNameAt(int)
- Method in class org.blackbox.model.
Context
getArgNames()
- Method in class org.blackbox.model.
Context
getArgValueAt(int)
- Method in class org.blackbox.model.
Context
getArgValues()
- Method in class org.blackbox.model.
Context
getBlack()
- Static method in class org.genepi.swing.
SwingUtils
getBlackboard()
- Method in class org.genepi.
BlackboardShell
getBlackboardShell()
- Method in class org.genepi.
Pipeline
getByType(String)
- Method in class org.blackbox.util.
Pair
getColumns()
- Method in class org.genepi.swing.
JMultiLineToolTip
getCondition()
- Method in class org.blackbox.model.
Pattern
getConfig()
- Method in class org.genepi.
BlackboardShell
getConfigFile()
- Method in class org.genepi.
Configuration
getConfiguration()
- Method in class org.genepi.
Task
getConsoleInstance()
- Static method in class org.genepi.swing.
Console
getController()
- Method in class org.blackbox.hypothesis.
HEngineEvent
getController()
- Method in class org.blackbox.shell.
BBX_EngineEvent
getCurrentSalience()
- Method in interface org.blackbox.model.
Agenda
getCurrentSalience()
- Method in class org.blackbox.shell.
BBX_Agenda
getDelay()
- Method in class org.genepi.swing.
GlassPane
getDestinationDomain()
- Method in class org.blackbox.model.
KnowledgeSource
getDomainOrigin()
- Method in class org.blackbox.model.
Hypothesis
getDriver(String)
- Static method in class org.genepi.
Resource
getEngine()
- Method in class org.genepi.
BlackboardShell
getEventBuffer()
- Method in interface org.blackbox.model.
Blackboard
Return the event buffer.
getEventBuffer()
- Method in class org.blackbox.shell.
BBX_Blackboard
getException()
- Method in exception org.blackbox.shell.
BBX_Exception
Returns the nested exception.
getException()
- Method in exception org.blackbox.shell.
BBX_ShellException
Returns the nested exception.
getException()
- Method in exception org.genepi.means.
MeanException
Returns the nested exception.
getException()
- Method in exception org.genepi.parser.
ParseException
Returns the nested exception.
getExecutionContext()
- Method in class org.blackbox.model.
KSAR
getFile()
- Method in class org.blackbox.hypothesis.
HFile
getFile()
- Method in class org.blackbox.shell.
BBX_File
getFixedWidth()
- Method in class org.genepi.swing.
JMultiLineToolTip
getFrame()
- Method in interface org.blackbox.model.
Interval
Frame of this interval.
getFrame()
- Method in class org.blackbox.shell.
BBX_Annotation
getFrame()
- Method in class org.blackbox.shell.
BBX_Pattern
getFrame()
- Method in class org.blackbox.shell.
BBX_Sequence
getFrame()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
getFrame()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
getFrame()
- Method in class org.blackbox.test.
SimpleHInterval
getFrame()
- Method in class org.blackbox.test.
SimpleInterval
getHead()
- Method in class org.blackbox.util.
Pair
getHypothesisMap()
- Method in class org.blackbox.model.
Context
getIconAsResource(String)
- Static method in class org.genepi.swing.
SwingUtils
Get required icon or image with specified url
getIconByURL(String)
- Static method in class org.genepi.swing.
SwingUtils
Get required icon or image with specified url
getInputs()
- Method in class org.genepi.
Task
getInstance()
- Static method in class org.genepi.swing.
Console
getInterval()
- Method in class org.genepi.swing.
IntervalView
getKnowledge()
- Method in class org.blackbox.model.
Hypothesis
getKS()
- Method in class org.blackbox.model.
KSAR
getKsCreator()
- Method in class org.blackbox.model.
Hypothesis
getKsFarm()
- Method in class org.genepi.
BlackboardShell
getLayoutAlignmentX(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Returns the alignment along the x axis.
getLayoutAlignmentY(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Returns the alignment along the y axis.
getLayoutSize(Container, boolean)
- Method in class org.genepi.swing.
TimeLineLayout
Algorithm for calculating layout size (minimum or preferred).
getLength()
- Method in interface org.blackbox.model.
Interval
Retourne la taille de cet intervalle.
getLength()
- Method in class org.blackbox.shell.
BBX_Annotation
getLength()
- Method in class org.blackbox.shell.
BBX_Pattern
getLength()
- Method in class org.blackbox.shell.
BBX_Sequence
getLength()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
getLength()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
getLength()
- Method in class org.blackbox.test.
SimpleHInterval
getLength()
- Method in class org.blackbox.test.
SimpleInterval
getList()
- Method in class org.blackbox.hypothesis.
HSetOf
getList()
- Method in class org.blackbox.shell.
BBX_SetOf
getList()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
getLocation()
- Method in exception org.genepi.parser.
ParseException
getMax()
- Method in interface org.blackbox.model.
Interval
Retourne la plus grande des deux coordonnees.
getMax()
- Method in class org.blackbox.shell.
BBX_Annotation
getMax()
- Method in class org.blackbox.shell.
BBX_Pattern
getMax()
- Method in class org.blackbox.shell.
BBX_Sequence
getMax()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
getMax()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
getMax()
- Method in class org.blackbox.test.
SimpleHInterval
getMax()
- Method in class org.blackbox.test.
SimpleInterval
getMaximumSize()
- Method in class org.genepi.swing.
IntervalView
getMessage()
- Method in class org.blackbox.model.
Event
getMin()
- Method in interface org.blackbox.model.
Interval
Retourne la plus petite des deux coordonnees.
getMin()
- Method in class org.blackbox.shell.
BBX_Annotation
getMin()
- Method in class org.blackbox.shell.
BBX_Pattern
getMin()
- Method in class org.blackbox.shell.
BBX_Sequence
getMin()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
getMin()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
getMin()
- Method in class org.blackbox.test.
SimpleHInterval
getMin()
- Method in class org.blackbox.test.
SimpleInterval
getMinimumSize()
- Method in class org.genepi.swing.
IntervalView
getModel()
- Method in class org.genepi.swing.
TimeLineView
Return the domain represented by the view
getName()
- Method in class org.blackbox.hypothesis.
HSequence
Name of this sequence.
getName()
- Method in class org.blackbox.model.
Pattern
getName()
- Method in class org.blackbox.shell.
BBX_Sequence
getNameSpace()
- Method in interface org.blackbox.model.
Blackboard
Return all the domain's ids in a list.
getNameSpace()
- Method in class org.blackbox.shell.
BBX_Blackboard
getNotifier()
- Method in class org.genepi.
AppWindow
getNotifier()
- Static method in class org.genepi.
Genepi
Return main notifier (c) beurk code
getOutputs()
- Method in class org.genepi.
Task
getOutputStream()
- Method in class org.genepi.swing.
Console
getOwningKS()
- Method in class org.genepi.
Task
getPath()
- Method in class org.blackbox.hypothesis.
HFile
getPath()
- Method in class org.blackbox.shell.
BBX_File
getPathPrefix()
- Method in class org.genepi.
Configuration
getPattern()
- Method in class org.blackbox.hypothesis.
HPattern
getPattern()
- Method in class org.blackbox.shell.
BBX_Pattern
getPatternMatcher()
- Method in class org.genepi.
BlackboardShell
getPipelineAsList()
- Method in class org.genepi.
Pipeline
getPredicates()
- Method in class org.blackbox.model.
KnowledgeSource
getPreferredSize()
- Method in class org.genepi.swing.
IntervalView
getProjectName()
- Method in class org.genepi.
Configuration
getPrototype()
- Method in class org.blackbox.model.
Pattern
getRange()
- Method in class org.blackbox.domains.
TimeLine
getRuleName()
- Method in class org.blackbox.model.
KnowledgeSource
getRules()
- Method in class org.blackbox.shell.
BBX_KSFarm
getSalience()
- Method in class org.blackbox.model.
KnowledgeSource
getSequence()
- Method in class org.blackbox.hypothesis.
HAnnotation
Retourne la sequence qui porte ce feature.
getSequence()
- Method in class org.blackbox.shell.
BBX_Annotation
getSequenceIterator()
- Method in class org.genepi.means.
GenericReader
getShell()
- Method in class org.genepi.
Document
getShell()
- Method in class org.genepi.
Pipeline
getSource()
- Method in class org.blackbox.model.
Event
getStrand()
- Method in interface org.blackbox.model.
Interval
Strand holding this interval.
getStrand()
- Method in class org.blackbox.shell.
BBX_Annotation
getStrand()
- Method in class org.blackbox.shell.
BBX_Pattern
getStrand()
- Method in class org.blackbox.shell.
BBX_Sequence
getStrand()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
getStrand()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
getStrand()
- Method in class org.blackbox.test.
SimpleHInterval
getStrand()
- Method in class org.blackbox.test.
SimpleInterval
getTabbedPane()
- Method in class org.genepi.
AppWindow
getTail()
- Method in class org.blackbox.util.
Pair
getTarget()
- Method in class org.genepi.swing.
HypothesisInspector
getTextOutput()
- Method in class org.genepi.
BlackboardShell
getTimeString(long)
- Static method in class org.blackbox.util.
StringUtil
getTimeString(long)
- Static method in class org.genepi.means.
MeansUtil
getType()
- Method in class org.blackbox.model.
Event
getTypes()
- Method in class org.blackbox.model.
Context
getViewer()
- Method in class org.genepi.swing.
HypothesisInspector
getWhite()
- Static method in class org.genepi.swing.
SwingUtils
GffParser
- Class in
org.genepi.mean.parser
GffParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
GffParser
GlassPane
- Class in
org.genepi.swing
This code drifts from MoveGlassPane by Jon Lipsky (more on MoveGlassPane http://blog.elevenworks.com).
GlassPane(JFrame)
- Constructor for class org.genepi.swing.
GlassPane
gw
- Static variable in class org.genepi.
Genepi
H
hand
- Variable in class org.genepi.mean.parser.
AbstractParser
handleOpenFile(File)
- Method in class org.genepi.
AppMenuBar
HAnnotation
- Class in
org.blackbox.hypothesis
HAnnotation(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HAnnotation
HeaderPanel
- Class in
org.genepi.swing
HeaderPanel(ImageIcon, String, String, String)
- Constructor for class org.genepi.swing.
HeaderPanel
HEngineEvent
- Class in
org.blackbox.hypothesis
HEngineEvent(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HEngineEvent
HFile
- Class in
org.blackbox.hypothesis
HFile(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HFile
HPattern
- Class in
org.blackbox.hypothesis
HPattern(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HPattern
HSequence
- Class in
org.blackbox.hypothesis
HSequence(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HSequence
HSetOf
- Class in
org.blackbox.hypothesis
HSetOf(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HSetOf
HSetOfInterval
- Class in
org.blackbox.hypothesis
HSetOfInterval(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HSetOfInterval
HSimpleInterval
- Class in
org.blackbox.hypothesis
HSimpleInterval(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.hypothesis.
HSimpleInterval
Hypothesis
- Class in
org.blackbox.model
Hypothesis(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.model.
Hypothesis
HypothesisInspector
- Class in
org.genepi.swing
Generic viewer 'decorator'.
HypothesisInspector(Object)
- Constructor for class org.genepi.swing.
HypothesisInspector
HypothesisInspector(Object, List)
- Constructor for class org.genepi.swing.
HypothesisInspector
I
ICON_ANIM_DLOG
- Static variable in class org.genepi.
Resource
ICON_MSG_16
- Static variable in class org.genepi.
Resource
ICON_OPEN_16
- Static variable in class org.genepi.
Resource
ICON_RUN_16
- Static variable in class org.genepi.
Resource
ICON_STEP_16
- Static variable in class org.genepi.
Resource
IMAGE_SPLASHSCREEN_FILENAME
- Static variable in class org.genepi.
Resource
Include
- Class in
org.blackbox.conditions
Allen intervals are included.
Include()
- Constructor for class org.blackbox.conditions.
Include
includeXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
INFOS_WARN
- Static variable in class org.genepi.parser.
Keywords
initBlackboard()
- Method in class org.genepi.
BlackboardShell
initEngine()
- Method in class org.genepi.
BlackboardShell
initKsFarm()
- Method in class org.genepi.
BlackboardShell
inputs
- Variable in class org.genepi.
Task
inspect()
- Method in class org.genepi.swing.
HypothesisInspector
inspectDomain(String)
- Method in interface org.blackbox.model.
Blackboard
Return the domain called name.
inspectDomain(String)
- Method in class org.blackbox.shell.
BBX_Blackboard
Interval
- Interface in
org.blackbox.model
IntervalUtil
- Class in
org.blackbox.util
Relation spaciales entre paires d'intervalles.
IntervalUtil()
- Constructor for class org.blackbox.util.
IntervalUtil
IntervalView
- Class in
org.genepi.swing
IntervalView(Interval, float)
- Constructor for class org.genepi.swing.
IntervalView
invalidateLayout(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Invalidates the layout, indicating that if the layout manager has cached information it should be discarded.
isFramed()
- Method in class org.blackbox.domains.
TimeLine
isFramed()
- Method in interface org.blackbox.model.
Interval
Return true if this interval is framed.
isFramed()
- Method in class org.blackbox.shell.
BBX_Annotation
isFramed()
- Method in class org.blackbox.shell.
BBX_Pattern
isFramed()
- Method in class org.blackbox.shell.
BBX_Sequence
isFramed()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
isFramed()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
isFramed()
- Method in class org.blackbox.test.
SimpleHInterval
isFramed()
- Method in class org.blackbox.test.
SimpleInterval
isFramed
- Variable in class org.genepi.means.
TinaShell
isOpaque()
- Method in class org.genepi.swing.
IntervalView
isOwningFocus()
- Method in class org.genepi.swing.
IntervalView
Return Focus status.
isRunning
- Variable in class org.blackbox.model.
KSAR
iterator()
- Method in class org.blackbox.domains.
BlackHole
iterator()
- Method in class org.blackbox.domains.
List
iterator()
- Method in class org.blackbox.domains.
TimeLine
iterator()
- Method in interface org.blackbox.model.
Agenda
Agenda iterator
iterator()
- Method in interface org.blackbox.model.
Blackboard
Return a new iterator on the content of this bb.
iterator()
- Method in interface org.blackbox.model.
Domain
Hypothesis iterator.
iterator()
- Method in interface org.blackbox.model.
KsFarm
Farm iterator.
iterator()
- Method in class org.blackbox.shell.
BBX_Agenda
iterator()
- Method in class org.blackbox.shell.
BBX_Blackboard
iterator()
- Method in class org.blackbox.shell.
BBX_KSFarm
itResults
- Variable in class org.genepi.means.
TinaShell
J
JMultiLineToolTip
- Class in
org.genepi.swing
JMultiLineToolTip()
- Constructor for class org.genepi.swing.
JMultiLineToolTip
K
Keywords
- Class in
org.genepi.parser
KnowledgeSource
- Class in
org.blackbox.model
KnowledgeSource()
- Constructor for class org.blackbox.model.
KnowledgeSource
KnowledgeSource(String, Domain)
- Constructor for class org.blackbox.model.
KnowledgeSource
KSAR
- Class in
org.blackbox.model
KSAR(KnowledgeSource, Context)
- Constructor for class org.blackbox.model.
KSAR
KsFarm
- Interface in
org.blackbox.model
ksLib
- Variable in class org.genepi.
Configuration
L
labelUpdate(Hypothesis)
- Method in class org.genepi.swing.
GenericDomainView
launchUI()
- Static method in class org.genepi.
Genepi
Do launch the ui.
laxIncludeXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
layoutContainer(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Lays out the container in the specified container.
libConds
- Static variable in class org.genepi.
Genepi
libMeans
- Static variable in class org.genepi.
Genepi
List
- Class in
org.blackbox.domains
List()
- Constructor for class org.blackbox.domains.
List
List(String)
- Constructor for class org.blackbox.domains.
List
listofMeans
- Variable in class org.genepi.
Pipeline
Loader
- Class in
org.genepi.means
Loader()
- Constructor for class org.genepi.means.
Loader
loadFasta(File)
- Method in class org.blackbox.domains.
TimeLine
Location
- Class in
org.genepi.parser
Stores the file name and line number in a file.
Location(String)
- Constructor for class org.genepi.parser.
Location
Creates a location consisting of a file name but no line number.
Location(String, int, int)
- Constructor for class org.genepi.parser.
Location
Creates a location consisting of a file name and line number.
locator
- Variable in class org.genepi.parser.
DefaultHandler
LongOrfParser
- Class in
org.genepi.mean.parser
LongOrfParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
LongOrfParser
lookupDomain(String)
- Method in interface org.blackbox.model.
Blackboard
Test if a Domain name is on ths Blackboard.
lookupDomain(String)
- Method in class org.blackbox.shell.
BBX_Blackboard
loseFocus()
- Method in class org.blackbox.model.
Hypothesis
lst
- Variable in class org.blackbox.shell.
BBX_SetOf
M
macOS
- Static variable in class org.genepi.
AppMenuBar
macOS
- Static variable in class org.genepi.
Resource
main(String[])
- Static method in class org.genepi.
Genepi
Starting point.
main(String[])
- Static method in class org.genepi.swing.
AgendaView
main(String[])
- Static method in class org.genepi.swing.
BlackboardView
main(String[])
- Static method in class org.genepi.swing.
GenericDomainView
main(String[])
- Static method in class org.genepi.swing.
GenericViews
main(String[])
- Static method in class org.genepi.swing.
GlassPane
main(String[])
- Static method in class org.genepi.swing.
IntervalView
main(String[])
- Static method in class org.genepi.swing.
SplashScreen
main(String[])
- Static method in class org.genepi.swing.
TimeLinePane
main(String[])
- Static method in class org.genepi.swing.
TimeLineView
main(String[])
- Static method in class org.genepi.swing.
ZoomableIntervalView
makePath()
- Static method in class org.genepi.means.
MeansUtil
manageAgenda()
- Method in interface org.blackbox.model.
Agenda
When called this fn (re)-arrays the agenda if necessary.
manageAgenda()
- Method in class org.blackbox.shell.
BBX_Agenda
mask
- Variable in class org.genepi.
AppMenuBar
matcher
- Variable in class org.blackbox.model.
Controller
MAX_SALIENCE
- Static variable in interface org.blackbox.model.
Agenda
maximumLayoutSize(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Returns the maximum size of this component.
MeanException
- Exception in
org.genepi.means
Runtime's exceptions.
MeanException()
- Constructor for exception org.genepi.means.
MeanException
Constructs a build exception with no descriptive information.
MeanException(String)
- Constructor for exception org.genepi.means.
MeanException
Constructs an exception with the given descriptive message.
MeanException(Throwable)
- Constructor for exception org.genepi.means.
MeanException
Constructs an exception with the given exception as a root cause.
MeanException(String, Throwable)
- Constructor for exception org.genepi.means.
MeanException
Constructs an exception with the given message and exception as a root cause.
MEANS_LST_FILENAME
- Static variable in class org.genepi.
Resource
MeansUtil
- Class in
org.genepi.means
MeansUtil()
- Constructor for class org.genepi.means.
MeansUtil
Meet
- Class in
org.blackbox.conditions
Allen intervals are included.
Meet()
- Constructor for class org.blackbox.conditions.
Meet
meetsXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
message(String)
- Method in class org.genepi.
Task
Messager
- Class in
org.genepi.swing
Messager()
- Constructor for class org.genepi.swing.
Messager
MIN_WIDTH
- Static variable in class org.genepi.swing.
IntervalView
minimumLayoutSize(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Calculates the minimum size dimensions for the specified panel given the components in the specified parent container.
ModelObserver
- Interface in
org.blackbox.model
Observer are notified of changes issued in Observable objects.
muteObject(String, Object)
- Method in interface org.blackbox.model.
PatternMatcher
muteObject(String, Object)
- Method in class org.genepi.rete.
ReteMatcher
Push mute on the top of the network.
N
newObject(String, Object)
- Method in interface org.blackbox.model.
PatternMatcher
Dispatch new hypothesis.
newObject(String, Object)
- Method in class org.genepi.rete.
ReteMatcher
Push add on the top of the network.
No
- Class in
org.blackbox.conditions
Ne couche jammais :(
No()
- Constructor for class org.blackbox.conditions.
No
notify(String)
- Method in class org.genepi.swing.
GlassPane
notifyObservers()
- Method in class org.blackbox.model.
Hypothesis
notifyObservers()
- Method in class org.blackbox.shell.
ObserverPatternImpl
notifyObservers()
- Method in class org.genepi.
Pipeline
Null
- Class in
org.genepi.means
Null()
- Constructor for class org.genepi.means.
Null
O
ObservableEntity
- Interface in
org.blackbox.model
"Observer" design pattern modify to feet our needs.
ObservableStream
- Class in
org.genepi.swing
ObservableStream()
- Constructor for class org.genepi.swing.
ObservableStream
ObserverPatternImpl
- Class in
org.blackbox.shell
Implementation of the Observale pattern for a container.
ObserverPatternImpl()
- Constructor for class org.blackbox.shell.
ObserverPatternImpl
open()
- Method in class org.genepi.
AppMenuBar
org.blackbox.conditions
- package org.blackbox.conditions
org.blackbox.domains
- package org.blackbox.domains
org.blackbox.hypothesis
- package org.blackbox.hypothesis
org.blackbox.model
- package org.blackbox.model
org.blackbox.shell
- package org.blackbox.shell
org.blackbox.test
- package org.blackbox.test
org.blackbox.util
- package org.blackbox.util
org.genepi
- package org.genepi
org.genepi.mean.parser
- package org.genepi.mean.parser
org.genepi.means
- package org.genepi.means
org.genepi.parser
- package org.genepi.parser
org.genepi.rete
- package org.genepi.rete
org.genepi.swing
- package org.genepi.swing
outputs
- Variable in class org.genepi.
Task
Overlap
- Class in
org.blackbox.conditions
Allen intervals are included.
Overlap()
- Constructor for class org.blackbox.conditions.
Overlap
overlapXY(Interval, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
P
Pack
- Class in
org.genepi.means
Pack()
- Constructor for class org.genepi.means.
Pack
PackInterval
- Class in
org.genepi.means
PackInterval()
- Constructor for class org.genepi.means.
PackInterval
paintComponent(Graphics)
- Method in class org.genepi.swing.
Console
paintComponent(Graphics)
- Method in class org.genepi.swing.
GlassPane
paintComponent(Graphics)
- Method in class org.genepi.swing.
HeaderPanel
paintComponent(Graphics)
- Method in class org.genepi.swing.
IntervalView
paintComponent(Graphics)
- Method in class org.genepi.swing.
TimeLineView
Pair
- Class in
org.blackbox.util
Pair(Object, Object)
- Constructor for class org.blackbox.util.
Pair
Pair(Object[])
- Constructor for class org.blackbox.util.
Pair
parent
- Variable in class org.genepi.swing.
TimeLineView
parentHandler
- Variable in class org.genepi.parser.
DefaultHandler
parse()
- Method in class org.genepi.mean.parser.
AbstractParser
parse()
- Method in class org.genepi.mean.parser.
BlastParserM9
parse()
- Method in class org.genepi.mean.parser.
FastRnaParser
parse()
- Method in class org.genepi.mean.parser.
GffParser
parse()
- Method in class org.genepi.mean.parser.
LongOrfParser
parse()
- Method in class org.genepi.mean.parser.
ProkovParser
parse()
- Method in class org.genepi.mean.parser.
RbsFinderParser
parse()
- Method in class org.genepi.mean.parser.
TermitParser
parse()
- Method in class org.genepi.parser.
ConfigParser
Parses le fichier de connaissances.
parseAndAlloc()
- Method in class org.genepi.
BlackboardShell
parseAndLoadGenepiRC()
- Static method in class org.genepi.
Resource
parseAndloadMeans(Class)
- Static method in class org.genepi.
Resource
parseAndLoadPreCond(Class)
- Static method in class org.genepi.
Resource
ParseException
- Exception in
org.genepi.parser
Les instances de cette classe represente un erreur lors du parsing du fichier de connaissance.
ParseException()
- Constructor for exception org.genepi.parser.
ParseException
Constructs a build exception with no descriptive information.
ParseException(String)
- Constructor for exception org.genepi.parser.
ParseException
Constructs an exception with the given descriptive message.
ParseException(String, Throwable)
- Constructor for exception org.genepi.parser.
ParseException
Constructs an exception with the given message and exception as a root cause.
ParseException(String, Throwable, Location)
- Constructor for exception org.genepi.parser.
ParseException
Constructs an exception with the given message and exception as a root cause and a location in a file.
ParseException(Throwable)
- Constructor for exception org.genepi.parser.
ParseException
Constructs an exception with the given exception as a root cause.
ParseException(String, Location)
- Constructor for exception org.genepi.parser.
ParseException
Constructs an exception with the given descriptive message and a location in a file.
parseGffLine(String)
- Method in class org.genepi.mean.parser.
GffParser
Parser de fichier Gff resultat de l'execution d'un externe.
parseHits(TinaRecord, Iterator)
- Method in class org.genepi.mean.parser.
BlastParserM9
Parser de fichier TINA resulat de l'execution d'un BLAST.
parser
- Variable in class org.genepi.parser.
DefaultHandler
Pattern
- Class in
org.blackbox.model
Pattern(String, Condition)
- Constructor for class org.blackbox.model.
Pattern
PatternMatcher
- Interface in
org.blackbox.model
Match Event -> KSAR.
peekKSAR()
- Method in interface org.blackbox.model.
Agenda
Peek the best next KSAR (this one which is located at the top of the agenda).
peekKSAR()
- Method in class org.blackbox.shell.
BBX_Agenda
Pipeline
- Class in
org.genepi
Pipeline(BlackboardShell)
- Constructor for class org.genepi.
Pipeline
popKSAR()
- Method in interface org.blackbox.model.
Agenda
Remove the top of the agenda.
popKSAR()
- Method in class org.blackbox.shell.
BBX_Agenda
PostInterGenic
- Class in
org.genepi.means
PostInterGenic()
- Constructor for class org.genepi.means.
PostInterGenic
PRECOND_LST_FILENAME
- Static variable in class org.genepi.
Resource
preferredLayoutSize(Container)
- Method in class org.genepi.swing.
TimeLineLayout
Calculates the preferred size dimensions for the specified panel given the components in the specified parent container.
prepare()
- Method in class org.genepi.means.
Blastp
Dump des donnees en entree en TINA.
prepare()
- Method in class org.genepi.means.
Blastx
Dump des donnees en entree en TINA.
prepare()
- Method in class org.genepi.means.
FastRna
prepare()
- Method in class org.genepi.means.
ProkovCds
prepare()
- Method in class org.genepi.means.
ProkovCds2
prepare()
- Method in class org.genepi.means.
ProkovLearn
prepare()
- Method in class org.genepi.means.
ProkovOrf
prepare()
- Method in class org.genepi.means.
RbsFinder
Dump le tina en entree
prepare()
- Method in class org.genepi.means.
Termit
prepare()
- Method in class org.genepi.means.
TinaShell
process()
- Method in class org.genepi.
Task
Cycle d'execution compend : before, execute puis after
processStep()
- Method in class org.blackbox.shell.
BBX_Controller
Trigger an engine new step in non-interactive mode.
progName
- Variable in class org.genepi.means.
TinaShell
project
- Variable in class org.genepi.parser.
DefaultHandler
ProkovCds
- Class in
org.genepi.means
ProkovCds()
- Constructor for class org.genepi.means.
ProkovCds
ProkovCds2
- Class in
org.genepi.means
ProkovCds2()
- Constructor for class org.genepi.means.
ProkovCds2
ProkovLearn
- Class in
org.genepi.means
ProkovLearn()
- Constructor for class org.genepi.means.
ProkovLearn
ProkovOrf
- Class in
org.genepi.means
ProkovOrf()
- Constructor for class org.genepi.means.
ProkovOrf
ProkovParser
- Class in
org.genepi.mean.parser
ProkovParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
ProkovParser
PublishFile
- Class in
org.genepi.means
PublishFile()
- Constructor for class org.genepi.means.
PublishFile
PublishToken
- Class in
org.genepi.means
PublishToken()
- Constructor for class org.genepi.means.
PublishToken
pushKSAR(KSAR)
- Method in interface org.blackbox.model.
Agenda
Add a new KSAR to execution list.
pushKSAR(KSAR)
- Method in class org.blackbox.shell.
BBX_Agenda
R
RbsFinder
- Class in
org.genepi.means
RbsFinder()
- Constructor for class org.genepi.means.
RbsFinder
RbsFinderParser
- Class in
org.genepi.mean.parser
RbsFinderParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
RbsFinderParser
records
- Variable in class org.genepi.mean.parser.
AbstractParser
removeDomain(Domain)
- Method in class org.genepi.swing.
BlackboardView
removeDomain(Domain)
- Method in class org.genepi.swing.
GenericViews
removeDomain(TimeLine)
- Method in class org.genepi.swing.
TimeLinePane
removeDomain(TimeLine)
- Method in class org.genepi.swing.
ZoomableIntervalView
removeInterval(Interval)
- Method in class org.genepi.swing.
TimeLineView
removeLayoutComponent(Component)
- Method in class org.genepi.swing.
TimeLineLayout
Removes the specified component from the layout.
removeObserver(ModelObserver)
- Method in class org.blackbox.model.
Hypothesis
removeObserver(ModelObserver)
- Method in interface org.blackbox.model.
ObservableEntity
Remove an observer.
removeObserver(Observer)
- Method in interface org.blackbox.model.
PatternMatcher
removeObserver(ModelObserver)
- Method in class org.blackbox.shell.
ObserverPatternImpl
removeObserver(ModelObserver)
- Method in class org.blackbox.test.
SimpleKS
removeObserver(ModelObserver)
- Method in class org.genepi.
Pipeline
removeObserver(Observer)
- Method in class org.genepi.rete.
ReteMatcher
RepostHypothesis
- Class in
org.genepi.means
RepostHypothesis()
- Constructor for class org.genepi.means.
RepostHypothesis
reScale(float, Interval)
- Static method in class org.blackbox.util.
IntervalUtil
Resource
- Class in
org.genepi
Resource()
- Constructor for class org.genepi.
Resource
ReteMatcher
- Class in
org.genepi.rete
ReteMatcher(KsFarm)
- Constructor for class org.genepi.rete.
ReteMatcher
Build a new rete pattern matcher.
retractHypothesis(Hypothesis)
- Method in class org.blackbox.domains.
BlackHole
retractHypothesis(Hypothesis)
- Method in class org.blackbox.domains.
List
retractHypothesis(Hypothesis)
- Method in class org.blackbox.domains.
TimeLine
retractHypothesis(Hypothesis)
- Method in interface org.blackbox.model.
Domain
Retract an hypothesis in this domain.
reverseComplement(String, String, Sequence)
- Static method in class org.blackbox.shell.
BBX_SeqTool
right(String, int, char)
- Static method in class org.blackbox.util.
StringUtil
RNA_TYPE
- Static variable in class org.genepi.means.
GenericReader
ROOT_DIR
- Static variable in class org.genepi.
Resource
S
salience
- Variable in class org.blackbox.model.
KSAR
Salience
- Class in
org.genepi.means
Salience()
- Constructor for class org.genepi.means.
Salience
saveAsFasta(File)
- Method in class org.blackbox.domains.
TimeLine
saveAsGFF(File)
- Method in class org.blackbox.domains.
TimeLine
saveAsTab()
- Method in class org.blackbox.shell.
BBX_SetOf
Tab dump.
sens
- Variable in class org.genepi.mean.parser.
AbstractParser
seqdb
- Variable in class org.genepi.means.
GenericReader
seqMother
- Variable in class org.genepi.means.
TinaShell
seqString()
- Method in interface org.blackbox.model.
Interval
String representation for this interval.
seqString()
- Method in class org.blackbox.shell.
BBX_Annotation
seqString()
- Method in class org.blackbox.shell.
BBX_Pattern
seqString()
- Method in class org.blackbox.shell.
BBX_Sequence
seqString()
- Method in class org.blackbox.shell.
BBX_SetOfInterval
seqString()
- Method in class org.blackbox.shell.
BBX_SimpleInterval
seqString()
- Method in class org.blackbox.test.
SimpleHInterval
seqString()
- Method in class org.blackbox.test.
SimpleInterval
setAgenda(Agenda)
- Method in class org.genepi.swing.
AgendaView
setBlackboard(Blackboard)
- Method in class org.blackbox.domains.
BlackHole
setBlackboard(Blackboard)
- Method in class org.blackbox.domains.
List
setBlackboard(Blackboard)
- Method in class org.blackbox.domains.
TimeLine
setBlackboard(Blackboard)
- Method in interface org.blackbox.model.
Domain
Set the name of this domain.
setBlackboard(Blackboard)
- Method in class org.genepi.
BlackboardShell
setBlackboard(Blackboard)
- Method in class org.genepi.swing.
BlackboardView
setBottom(String)
- Method in class org.genepi.swing.
HeaderPanel
setColumns(int)
- Method in class org.genepi.swing.
JMultiLineToolTip
setConfig(Configuration)
- Method in class org.genepi.
BlackboardShell
setConfigFile(File)
- Method in class org.genepi.
Configuration
setConfiguration(Configuration)
- Method in class org.genepi.
Task
setConstraints(Component, Interval)
- Method in class org.genepi.swing.
TimeLineLayout
setController(Controller)
- Method in class org.blackbox.hypothesis.
HEngineEvent
setController(Controller)
- Method in class org.blackbox.shell.
BBX_EngineEvent
setCurrentSalienceTo(int)
- Method in interface org.blackbox.model.
Agenda
setCurrentSalienceTo(int)
- Method in class org.blackbox.shell.
BBX_Agenda
setDelay(int)
- Method in class org.genepi.swing.
GlassPane
setDestination(String)
- Method in class org.genepi.
Pipeline
setDestinationDomain(Domain)
- Method in class org.blackbox.model.
KnowledgeSource
setDomainName(String)
- Method in class org.blackbox.domains.
BlackHole
setDomainName(String)
- Method in class org.blackbox.domains.
List
setDomainName(String)
- Method in class org.blackbox.domains.
TimeLine
setDomainName(String)
- Method in interface org.blackbox.model.
Domain
Set the name of this domain.
setDomainOrigin(Domain)
- Method in class org.blackbox.model.
Hypothesis
setEnableFrame(boolean)
- Method in class org.blackbox.test.
SimpleHInterval
setEngine(Controller)
- Method in class org.genepi.
BlackboardShell
setFile(String)
- Method in class org.blackbox.hypothesis.
HFile
setFile(String)
- Method in class org.blackbox.shell.
BBX_File
setFixedWidth(int)
- Method in class org.genepi.swing.
JMultiLineToolTip
setFocus(boolean)
- Method in class org.genepi.swing.
IntervalView
Set focus status.
setFramed(boolean)
- Method in class org.blackbox.shell.
BBX_Annotation
setFullScreen()
- Method in class org.genepi.
AppWindow
setHead(Object)
- Method in class org.blackbox.util.
Pair
setInputs(Context)
- Method in class org.genepi.
Task
setKnowledge(Object)
- Method in class org.blackbox.model.
Hypothesis
setKsCreator(KnowledgeSource)
- Method in class org.blackbox.model.
Hypothesis
setKsFarm(KsFarm)
- Method in class org.genepi.
BlackboardShell
setList(List)
- Method in class org.blackbox.hypothesis.
HSetOf
setList(List)
- Method in class org.blackbox.shell.
BBX_SetOf
setList(List)
- Method in class org.blackbox.shell.
BBX_SetOfInterval
setLocation(Location)
- Method in exception org.genepi.parser.
ParseException
setMessage(Object)
- Method in class org.blackbox.model.
Event
setOutput()
- Method in class org.genepi.swing.
Console
setOwningKS(Pipeline)
- Method in class org.genepi.
Task
setPath(String)
- Method in class org.blackbox.hypothesis.
HFile
setPath(String)
- Method in class org.blackbox.shell.
BBX_File
setPathPrefix(String)
- Method in class org.genepi.
Configuration
setProjectName(String)
- Method in class org.genepi.
Configuration
setRuleName(String)
- Method in class org.blackbox.model.
KnowledgeSource
setSalience(int)
- Method in class org.blackbox.model.
KnowledgeSource
setScale(float)
- Method in class org.genepi.swing.
TimeLineLayout
setScale(float)
- Method in class org.genepi.swing.
TimeLinePane
setScale(double)
- Method in class org.genepi.swing.
TimeLineView
setScriptName()
- Method in class org.genepi.means.
Blastp
setScriptName()
- Method in class org.genepi.means.
Blastx
setScriptName()
- Method in class org.genepi.means.
FastRna
setScriptName()
- Method in class org.genepi.means.
ProkovCds
setScriptName()
- Method in class org.genepi.means.
ProkovCds2
setScriptName()
- Method in class org.genepi.means.
ProkovLearn
setScriptName()
- Method in class org.genepi.means.
ProkovOrf
setScriptName()
- Method in class org.genepi.means.
RbsFinder
setScriptName()
- Method in class org.genepi.means.
Termit
setScriptName()
- Method in class org.genepi.means.
TinaShell
setShell(BlackboardShell)
- Method in class org.genepi.
Pipeline
setSource(String)
- Method in class org.blackbox.model.
Event
setStrand(boolean)
- Method in class org.blackbox.shell.
BBX_SetOfInterval
setStrand(boolean)
- Method in class org.blackbox.shell.
BBX_SimpleInterval
setTail(Object)
- Method in class org.blackbox.util.
Pair
setTarget(Object)
- Method in class org.genepi.swing.
HypothesisInspector
setTextOutput(Messager)
- Method in class org.genepi.
BlackboardShell
setTop(String)
- Method in class org.genepi.swing.
HeaderPanel
setType(String)
- Method in class org.blackbox.model.
Event
setViewer(JTextComponent)
- Method in class org.genepi.swing.
HypothesisInspector
shell
- Variable in class org.genepi.
Document
shell
- Variable in class org.genepi.
Pipeline
shellCommand
- Variable in class org.genepi.means.
TinaShell
SIMIResolver
- Class in
org.genepi.means
SIMIResolver()
- Constructor for class org.genepi.means.
SIMIResolver
SimpleHInterval
- Class in
org.blackbox.test
Convenient class for debuging / dev.
SimpleHInterval(Object, Domain, KnowledgeSource)
- Constructor for class org.blackbox.test.
SimpleHInterval
SimpleInterval
- Class in
org.blackbox.test
Convenient class for debuging / dev.
SimpleInterval(Interval)
- Constructor for class org.blackbox.test.
SimpleInterval
SimpleInterval(int, int)
- Constructor for class org.blackbox.test.
SimpleInterval
SimpleInterval()
- Constructor for class org.blackbox.test.
SimpleInterval
SimpleInterval(int)
- Constructor for class org.blackbox.test.
SimpleInterval
SimpleKS
- Class in
org.blackbox.test
SimpleKS(String, Domain)
- Constructor for class org.blackbox.test.
SimpleKS
size()
- Method in interface org.blackbox.model.
Agenda
Return current number of ksar occurences in this queue.
size()
- Method in interface org.blackbox.model.
KsFarm
The number of rules in this farm.
size()
- Method in class org.blackbox.shell.
BBX_Agenda
size()
- Method in class org.blackbox.shell.
BBX_KSFarm
solve()
- Method in class org.blackbox.model.
Controller
Solve.
solve()
- Method in class org.blackbox.shell.
BBX_Controller
sp
- Static variable in class org.genepi.
Genepi
SplashScreen
- Class in
org.genepi.swing
A JWindow based splashscreen.
SplashScreen()
- Constructor for class org.genepi.swing.
SplashScreen
Build a new Splashscreen.
SplashScreen(String)
- Constructor for class org.genepi.swing.
SplashScreen
startElement(String, AttributeList)
- Method in class org.genepi.parser.
DefaultHandler
stepByStep()
- Method in class org.blackbox.model.
Controller
Interactive solve.
stepByStep()
- Method in class org.blackbox.shell.
BBX_Controller
Trigger an engine new step in interactive mode.
STR_NULL_TYPE
- Static variable in class org.genepi.parser.
Keywords
strConfDir
- Static variable in class org.genepi.
Resource
streamChanged()
- Method in class org.genepi.swing.
Console
streamChanged()
- Method in interface org.genepi.swing.
StreamObserver
StreamObserver
- Interface in
org.genepi.swing
StringUtil
- Class in
org.blackbox.util
StringUtil()
- Constructor for class org.blackbox.util.
StringUtil
subSequence(int, int, String, String, Sequence)
- Static method in class org.blackbox.shell.
BBX_SeqTool
SwingUtils
- Class in
org.genepi.swing
Misc utils related to swing objects.
SwingUtils()
- Constructor for class org.genepi.swing.
SwingUtils
switchColor()
- Static method in class org.genepi.swing.
SwingUtils
syncDisplay()
- Method in class org.genepi.swing.
BlackboardView
syncDisplay()
- Method in class org.genepi.swing.
TimeLineView
Synchronization between the content of the domain and its representation.
T
TAG_DEF_BB
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_CONTROL
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_KS
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_KS_PIPELINE
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_KS_SELECT
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_KS_VAR_LIST
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_LEVEL
- Static variable in class org.genepi.parser.
Keywords
TAG_DEF_PROJECT
- Static variable in class org.genepi.parser.
Keywords
Task
- Class in
org.genepi
Task()
- Constructor for class org.genepi.
Task
taste(Tuple)
- Method in class org.blackbox.conditions.
ContextCondition
Termit
- Class in
org.genepi.means
Termit()
- Constructor for class org.genepi.means.
Termit
TermitParser
- Class in
org.genepi.mean.parser
TermitParser(FeatureHandler, Iterator)
- Constructor for class org.genepi.mean.parser.
TermitParser
TimeLine
- Class in
org.blackbox.domains
TimeLine()
- Constructor for class org.blackbox.domains.
TimeLine
TimeLine(String)
- Constructor for class org.blackbox.domains.
TimeLine
TimeLine(boolean)
- Constructor for class org.blackbox.domains.
TimeLine
TimeLine(String, boolean)
- Constructor for class org.blackbox.domains.
TimeLine
TimeLineLayout
- Class in
org.genepi.swing
The
TimeLineLayout
class is a layout manager that lays out a container's components on a TimeLine grid.
TimeLineLayout(Container)
- Constructor for class org.genepi.swing.
TimeLineLayout
Creates a map layout with the given grid size and padding.
TimeLineLayout(Container, float)
- Constructor for class org.genepi.swing.
TimeLineLayout
TimeLinePane
- Class in
org.genepi.swing
Visualise all interval for a blackboard
TimeLinePane()
- Constructor for class org.genepi.swing.
TimeLinePane
TimeLineView
- Class in
org.genepi.swing
Graphic representation of a 'timeline' domain
TimeLineView(TimeLine, Color)
- Constructor for class org.genepi.swing.
TimeLineView
TinaShell
- Class in
org.genepi.means
TinaShell()
- Constructor for class org.genepi.means.
TinaShell
to
- Variable in class org.genepi.mean.parser.
AbstractParser
toArray()
- Method in interface org.blackbox.model.
KsFarm
Return all Rules in an array.
toArray()
- Method in class org.blackbox.shell.
BBX_KSFarm
toString()
- Method in class org.blackbox.domains.
BlackHole
toString()
- Method in class org.blackbox.domains.
List
toString()
- Method in class org.blackbox.domains.
TimeLine
toString()
- Method in class org.blackbox.model.
Event
String rep of this class
toString()
- Method in class org.blackbox.model.
KnowledgeSource
Q&D display
toString()
- Method in class org.blackbox.model.
KSAR
toString()
- Method in class org.blackbox.model.
Pattern
toString()
- Method in class org.blackbox.shell.
BBX_Annotation
GFF compliant toString.
toString()
- Method in class org.blackbox.shell.
BBX_EngineEvent
toString()
- Method in exception org.blackbox.shell.
BBX_Exception
toString()
- Method in class org.blackbox.shell.
BBX_File
toString()
- Method in class org.blackbox.shell.
BBX_Pattern
toString()
- Method in class org.blackbox.shell.
BBX_Sequence
toString()
- Method in class org.blackbox.shell.
BBX_SetOf
toString()
- Method in exception org.blackbox.shell.
BBX_ShellException
toString()
- Method in class org.blackbox.test.
SimpleHInterval
toString()
- Method in class org.blackbox.util.
Pair
toString()
- Method in exception org.genepi.means.
MeanException
toString()
- Method in class org.genepi.parser.
Location
Returns the file name, line number and a trailing space.
toString()
- Method in exception org.genepi.parser.
ParseException
Touch
- Class in
org.genepi.means
Touch()
- Constructor for class org.genepi.means.
Touch
translate(String, String, Sequence)
- Static method in class org.blackbox.shell.
BBX_SeqTool
U
UNKNOWN_LOCATION
- Static variable in class org.genepi.parser.
Location
unPair()
- Method in class org.blackbox.util.
Pair
unSign(Tuple)
- Static method in class org.blackbox.model.
Context
update(ObservableEntity, Event)
- Method in interface org.blackbox.model.
ModelObserver
Action to performed when catching an update event on Observable.
update(Object)
- Method in class org.blackbox.shell.
BBX_Agenda
update(ObservableEntity, Event)
- Method in class org.genepi.swing.
AgendaView
update(ObservableEntity, Event)
- Method in class org.genepi.swing.
BlackboardView
update(ObservableEntity, Event)
- Method in class org.genepi.swing.
GenericDomainView
update(ObservableEntity, Event)
- Method in class org.genepi.swing.
IntervalView
update(ObservableEntity, Event)
- Method in class org.genepi.swing.
TimeLineView
updateUI()
- Method in class org.genepi.swing.
JMultiLineToolTip
userLog()
- Method in class org.genepi.
Pipeline
W
welcome()
- Static method in class org.genepi.swing.
Console
write(byte[], int, int)
- Method in class org.genepi.swing.
ObservableStream
WriteLn
- Class in
org.genepi.means
WriteLn()
- Constructor for class org.genepi.means.
WriteLn
writeMessage(String)
- Method in class org.genepi.swing.
Messager
Y
Yes
- Class in
org.blackbox.conditions
Couche le premier soir ;)
Yes()
- Constructor for class org.blackbox.conditions.
Yes
Z
Zoom
- Class in
org.genepi.means
Zoom()
- Constructor for class org.genepi.means.
Zoom
zoom(int)
- Method in class org.genepi.swing.
ZoomableIntervalView
ZoomableIntervalView
- Class in
org.genepi.swing
ZoomableIntervalView()
- Constructor for class org.genepi.swing.
ZoomableIntervalView
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