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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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