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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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