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## R

readFasta(BufferedReader) - Static method in class org.irisa.genouest.logol.utils.MySequenceIterator
  Accessor to a Fasta reader
referenceID - Variable in class org.irisa.genouest.logol.LogolVariable
referenceModel - Variable in class org.irisa.genouest.logol.LogolVariable
removeChangeListener(ChangeListener) - Method in class org.irisa.genouest.logol.utils.MySequence
removeChangeListener(ChangeListener, ChangeType) - Method in class org.irisa.genouest.logol.utils.MySequence
removeFeature(Feature) - Method in class org.irisa.genouest.logol.utils.MySequence
repeat(int) - Method in class org.irisa.genouest.logol.parser.logolParser
repeatAccessors - Static variable in class org.irisa.genouest.logol.utils.model.Commons
REPEATCONSTRAINT - Static variable in class org.irisa.genouest.logol.Constants
RepeatNode - Class in org.irisa.genouest.logol.utils.model
  Repeat node
RepeatNode() - Constructor for class org.irisa.genouest.logol.utils.model.RepeatNode
repeatParam - Variable in class org.irisa.genouest.logol.LogolVariable
repeatPostpone() - Method in class org.irisa.genouest.logol.LogolVariable
  Checks for the postpone of checks for repeat quantity
repeatQuantity - Variable in class org.irisa.genouest.logol.LogolVariable
repeatType - Variable in class org.irisa.genouest.logol.LogolVariable
  Repeat type defines the test to apply between repeats 0 = undefined 1 = AND 2 = OVERLAP
RepeatVariable - Class in org.irisa.genouest.logol.types
  Class managing repeat variable types
RepeatVariable(int) - Constructor for class org.irisa.genouest.logol.types.RepeatVariable
reset() - Static method in class org.irisa.genouest.logol.Logol
reset() - Static method in class org.irisa.genouest.logol.LogolVariable
reset() - Static method in class org.irisa.genouest.logol.Treatment
reset() - Static method in class org.irisa.genouest.logol.types.ViewVariable
  Reset static variables
reset() - Static method in class org.irisa.genouest.logol.utils.model.Commons
  Reset variable maps
RNA - Static variable in class org.irisa.genouest.logol.Constants
rule() - Method in class org.irisa.genouest.logol.parser.logolParser
RuleNode - Class in org.irisa.genouest.logol.utils.model
  Rule node.
RuleNode() - Constructor for class org.irisa.genouest.logol.utils.model.RuleNode
run() - Method in class org.irisa.genouest.logol.SequenceAnalyser
runJobs(String) - Method in interface org.irisa.genouest.logol.dispatcher.JobManager
runJobs(String) - Method in class org.irisa.genouest.logol.dispatcher.LocalJobManager
  Executes the job as sequential treatment.
runJobs(String) - Method in class org.irisa.genouest.logol.dispatcher.SGEJobManager

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