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S

saveAccessors - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
saveAny - Static variable in class org.irisa.genouest.logol.Treatment
Decides if previous spacer must be saved
saveAs - Variable in class org.irisa.genouest.logol.LogolVariable
 
SAVECONSTRAINT - Static variable in class org.irisa.genouest.logol.Constants
 
SAVESIGN - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
scout - Variable in class org.irisa.genouest.logol.parser.logolParser.stringConstraints_return
 
scout - Variable in class org.irisa.genouest.logol.parser.logolParser.structConstraints_return
 
sendMail(Properties, String[], String, String, String) - Static method in class org.irisa.genouest.logol.utils.LogolUtils
Sends a mail to a list of recipents
SEPARATOR - Static variable in class org.irisa.genouest.logol.Constants
 
seqString() - Method in class org.irisa.genouest.logol.utils.MySequence
 
Sequence - Static variable in class org.irisa.genouest.logol.parser.logolLexer
 
Sequence - Static variable in class org.irisa.genouest.logol.parser.logolParser
 
SequenceAnalyser - Class in org.irisa.genouest.logol
 
SequenceDef - Static variable in class org.irisa.genouest.logol.parser.logolLexer
 
SequenceDef - Static variable in class org.irisa.genouest.logol.parser.logolParser
 
SEQUENCELength - Static variable in class org.irisa.genouest.logol.Constants
 
sequences() - Method in class org.irisa.genouest.logol.parser.logolParser
 
setContent(String) - Method in class org.irisa.genouest.logol.utils.MySequence
 
setErrFile(String) - Static method in exception org.irisa.genouest.logol.GrammarException
 
setGrammarFile(String) - Static method in class org.irisa.genouest.logol.Logol
 
setHeader(String) - Method in class org.irisa.genouest.logol.utils.MySequence
 
setInstallPath(String) - Method in interface org.irisa.genouest.logol.dispatcher.JobManager
 
setInstallPath(String) - Method in class org.irisa.genouest.logol.dispatcher.LocalJobManager
 
setInstallPath(String) - Method in class org.irisa.genouest.logol.dispatcher.SGEJobManager
 
setInterval(String) - Method in class org.irisa.genouest.logol.Interval
 
setJobArgs(String) - Method in interface org.irisa.genouest.logol.dispatcher.JobManager
 
setJobArgs(String) - Method in class org.irisa.genouest.logol.dispatcher.LocalJobManager
Sets the arguments for the job execution.
setJobArgs(String) - Method in class org.irisa.genouest.logol.dispatcher.SGEJobManager
 
setOutputSeqName(String) - Static method in class org.irisa.genouest.logol.Logol
Sets output sequence name
setParseStep(int) - Static method in class org.irisa.genouest.logol.Treatment
Defines current step
setPosition(long) - Method in class org.irisa.genouest.logol.utils.MySequence
 
setPredCount(int) - Static method in class org.irisa.genouest.logol.types.ViewVariable
 
setShowComments(boolean) - Method in class org.irisa.genouest.logol.utils.model.AbstractNode
 
setShowComments(boolean) - Method in interface org.irisa.genouest.logol.utils.model.LogolInterfaceNode
Add comments to logol generated data or not
setTerminals(HashMap<String, String>) - Method in class org.irisa.genouest.logol.utils.model.AbstractNode
 
setTerminals(HashMap<String, String>) - Method in interface org.irisa.genouest.logol.utils.model.LogolInterfaceNode
Sets the list of predefined terminals
setUp() - Method in class org.irisa.genouest.logol.test.PrologTest
 
setUp() - Method in class org.irisa.genouest.logol.test.TestView
 
SGEJobManager - Class in org.irisa.genouest.logol.dispatcher
 
SGEJobManager() - Constructor for class org.irisa.genouest.logol.dispatcher.SGEJobManager
 
showUsage(Options) - Static method in class org.irisa.genouest.logol.utils.LogolUtils
Show on output stream the usage based on a list of options
singlesOnly - Static variable in class org.irisa.genouest.logol.Logol
 
sizeAccessors - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
spacer - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
spacerAccessors - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
SpacerNode - Class in org.irisa.genouest.logol.utils.model
Spacer node
SpacerNode() - Constructor for class org.irisa.genouest.logol.utils.model.SpacerNode
 
splitSequence(int, int, int, int, int) - Static method in class org.irisa.genouest.logol.utils.LogolUtils
Split a sequence in several sub sequences according to size and number of processor
StartNode - Class in org.irisa.genouest.logol.utils.model
Start node e.g.
StartNode() - Constructor for class org.irisa.genouest.logol.utils.model.StartNode
 
stc_cost - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
stc_dist - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
stg_begin - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
stg_content - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
stg_end - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
stg_save - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
stg_size - Static variable in class org.irisa.genouest.logol.utils.model.Commons
 
string() - Method in class org.irisa.genouest.logol.parser.logolParser
 
stringConstraint() - Method in class org.irisa.genouest.logol.parser.logolParser
 
StringConstraint - Class in org.irisa.genouest.logol
 
StringConstraint() - Constructor for class org.irisa.genouest.logol.StringConstraint
 
stringConstraints - Variable in class org.irisa.genouest.logol.LogolVariable
 
stringConstraints() - Method in class org.irisa.genouest.logol.parser.logolParser
 
stringVariable() - Method in class org.irisa.genouest.logol.parser.logolParser
 
stringVariableElement() - Method in class org.irisa.genouest.logol.parser.logolParser
 
structConstraint() - Method in class org.irisa.genouest.logol.parser.logolParser
 
StructConstraint - Class in org.irisa.genouest.logol
 
StructConstraint() - Constructor for class org.irisa.genouest.logol.StructConstraint
 
structConstraints - Variable in class org.irisa.genouest.logol.LogolVariable
 
structConstraints() - Method in class org.irisa.genouest.logol.parser.logolParser
 
structureValue() - Method in class org.irisa.genouest.logol.parser.logolParser
 
structureValues() - Method in class org.irisa.genouest.logol.parser.logolParser
 
subList(int, int) - Method in class org.irisa.genouest.logol.utils.MySequence
 
subStr(int, int) - Method in class org.irisa.genouest.logol.utils.MySequence
 
suffixSearchPath - Static variable in class org.irisa.genouest.logol.Treatment
Path to suffixSearch shell
symbolAt(int) - Method in class org.irisa.genouest.logol.utils.MySequence
 
synpred25() - Method in class org.irisa.genouest.logol.parser.logolParser
 
synpred25_fragment() - Method in class org.irisa.genouest.logol.parser.logolParser
 
synpred78() - Method in class org.irisa.genouest.logol.parser.logolParser
 
synpred78_fragment() - Method in class org.irisa.genouest.logol.parser.logolParser
 

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