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main(String[])
- Static method in class org.irisa.genouest.logol.dispatcher.
Dispatch
Entry point
main(String[])
- Static method in class org.irisa.genouest.logol.
Logol
Entry point of the program
main(String[])
- Static method in class org.irisa.genouest.logol.test.
PrologSuite
main(String[])
- Static method in class org.irisa.genouest.logol.test.
TestSuite
main(String[])
- Static method in class org.irisa.genouest.logol.utils.converter.
FastaConverter
Fasta conversion from Logol result file
main(String[])
- Static method in class org.irisa.genouest.logol.utils.converter.
GFFConverter
GFF converter from Logol result file
main(String[])
- Static method in class org.irisa.genouest.logol.utils.
Converter
Deprecated.
main(String[])
- Static method in class org.irisa.genouest.logol.utils.
FastaConverter
Deprecated.
main(String[])
- Static method in class org.irisa.genouest.logol.utils.model.
ModelConverter
mainModels
- Static variable in class org.irisa.genouest.logol.
LogolVariable
mANY()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
map2predicate(String, int, String, boolean)
- Static method in class org.irisa.genouest.logol.types.
RepeatVariable
map2predicate(String, int)
- Static method in class org.irisa.genouest.logol.types.
ViewVariable
Same as map2predicate(String predicate,int id, String plist,boolean overlap) with overlap set to false and no postponed list
map2predicate(String, int, String)
- Static method in class org.irisa.genouest.logol.types.
ViewVariable
Same as map2predicate(String predicate,int id, String plist,boolean overlap) with overlap set to false
map2predicate(String, int, String, boolean)
- Static method in class org.irisa.genouest.logol.types.
ViewVariable
From a predicate or a list of predicate, create a new predicate and add it to a list of predicates.
map2predicate(String, int, String, boolean, String, String, String)
- Static method in class org.irisa.genouest.logol.types.
ViewVariable
From a predicate or a list of predicate, create a new predicate and add it to a list of predicates.
mapSequenceMatch(String, String, String)
- Method in class org.irisa.genouest.logol.utils.model.
ModelConverter
Maps a Logol Match to the initial model to show the result
matchedVariables
- Static variable in class org.irisa.genouest.logol.
LogolVariable
matrix()
- Method in class org.irisa.genouest.logol.parser.
logolParser
max
- Variable in class org.irisa.genouest.logol.parser.
logolParser.interval_return
max
- Variable in class org.irisa.genouest.logol.
StringConstraint
max
- Variable in class org.irisa.genouest.logol.
StructConstraint
MAXDISTANCE
- Static variable in class org.irisa.genouest.logol.
Constants
maxLength
- Static variable in class org.irisa.genouest.logol.
Treatment
Maximum length of a variable X
maxResultSize
- Static variable in class org.irisa.genouest.logol.
Treatment
Maximum length of a complete match
maxSpacerLength
- Static variable in class org.irisa.genouest.logol.
Treatment
Maximum length of a spacer .*
MergeNode
- Class in
org.irisa.genouest.logol.utils.model
Merge node, used after a Fork node to merge the branches of the OR conditions.
MergeNode()
- Constructor for class org.irisa.genouest.logol.utils.model.
MergeNode
mID()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
min
- Variable in class org.irisa.genouest.logol.parser.
logolParser.interval_return
min
- Variable in class org.irisa.genouest.logol.
StringConstraint
min
- Variable in class org.irisa.genouest.logol.
StructConstraint
MINDISTANCE
- Static variable in class org.irisa.genouest.logol.
Constants
minLength
- Static variable in class org.irisa.genouest.logol.
Treatment
Minimum length of a variable X
mINT()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
MINUS
- Static variable in class org.irisa.genouest.logol.utils.model.
Commons
mLOWID()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mModelName()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mNEWLINE()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mod
- Variable in class org.irisa.genouest.logol.
LogolVariable
model
- Variable in class org.irisa.genouest.logol.
LogolVariable
Model
- Class in
org.irisa.genouest.logol
Model()
- Constructor for class org.irisa.genouest.logol.
Model
model()
- Method in class org.irisa.genouest.logol.parser.
logolParser
model
- Variable in class org.irisa.genouest.logol.
VariableId
ModelConverter
- Class in
org.irisa.genouest.logol.utils.model
ModelConverter()
- Constructor for class org.irisa.genouest.logol.utils.model.
ModelConverter
ModelDefinitionException
- Exception in
org.irisa.genouest.logol.utils.model
Exception raised when decoding a model
ModelDefinitionException(String)
- Constructor for exception org.irisa.genouest.logol.utils.model.
ModelDefinitionException
ModelName
- Static variable in class org.irisa.genouest.logol.parser.
logolLexer
ModelName
- Static variable in class org.irisa.genouest.logol.parser.
logolParser
ModelNode
- Class in
org.irisa.genouest.logol.utils.model
Model node
ModelNode()
- Constructor for class org.irisa.genouest.logol.utils.model.
ModelNode
models
- Static variable in class org.irisa.genouest.logol.
Treatment
ModelVariable
- Class in
org.irisa.genouest.logol.types
Class managing model variable type
ModelVariable(int)
- Constructor for class org.irisa.genouest.logol.types.
ModelVariable
modifier
- Variable in class org.irisa.genouest.logol.
LogolVariable
Modifier
- Class in
org.irisa.genouest.logol
Modifier()
- Constructor for class org.irisa.genouest.logol.
Modifier
modifier()
- Method in class org.irisa.genouest.logol.parser.
logolParser
MODIFIERCOST
- Static variable in class org.irisa.genouest.logol.
Constants
MODIFIERCOST
- Static variable in class org.irisa.genouest.logol.
Modifier
MODIFIERMORPHMINUS
- Static variable in class org.irisa.genouest.logol.
Constants
MODIFIERMORPHMINUS
- Static variable in class org.irisa.genouest.logol.
Modifier
MODIFIERMORPHPLUS
- Static variable in class org.irisa.genouest.logol.
Constants
MODIFIERMORPHPLUS
- Static variable in class org.irisa.genouest.logol.
Modifier
modifierName
- Variable in class org.irisa.genouest.logol.
Modifier
morphism()
- Method in class org.irisa.genouest.logol.parser.
logolParser
morphism
- Static variable in class org.irisa.genouest.logol.utils.model.
Commons
moveFile(String, String)
- Static method in class org.irisa.genouest.logol.utils.
LogolUtils
Move a file to an other place or name
mSequence()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mSequenceDef()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT15()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT16()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT17()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT18()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT19()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT20()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT21()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT22()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT23()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT24()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT25()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT26()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT27()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT28()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT29()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT30()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT31()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT32()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT33()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT34()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT35()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT36()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT37()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT38()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT39()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT40()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT41()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT42()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT43()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT44()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT45()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT46()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT47()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT48()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT49()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT50()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT51()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mT52()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mTokens()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mVARIABLE()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mVARID()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
mWHITESPACE()
- Method in class org.irisa.genouest.logol.parser.
logolLexer
MyRevCompSequence
- Class in
org.irisa.genouest.logol.utils
Simple Sequence implementation to fix memory issues with BioJava DNATools functions.
MyRevCompSequence(Sequence)
- Constructor for class org.irisa.genouest.logol.utils.
MyRevCompSequence
MySequence
- Class in
org.irisa.genouest.logol.utils
Simple Sequence implementation to fix memory issues with BioJava DNATools functions.
MySequence()
- Constructor for class org.irisa.genouest.logol.utils.
MySequence
MySequence(String, String)
- Constructor for class org.irisa.genouest.logol.utils.
MySequence
MySequenceIterator
- Class in
org.irisa.genouest.logol.utils
Simple Sequence implementation to fix memory issues with BioJava DNATools functions.
MySequenceIterator()
- Constructor for class org.irisa.genouest.logol.utils.
MySequenceIterator
Overview
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