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

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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