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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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