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M

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
 

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