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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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