- NEEDED_BORDER_WIDTH - Static variable in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
-
- NEEDED_BORDER_WIDTH - Static variable in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
-
- NewAlignmentModelParameterMap - Class in info.bioinfweb.libralign.model.factory
-
Parameter map that stores information used to create new instances of alignment models by implementations
of
AlignmentModelFactory.
- NewAlignmentModelParameterMap() - Constructor for class info.bioinfweb.libralign.model.factory.NewAlignmentModelParameterMap
-
- newAminoAcidInstance(boolean) - Static method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet
-
Returns a new instance of this class containing all amino acid tokens (one letter codes),
including the gap token ('-') and ambiguity codes.
- newCharacterInstance(AlignmentModel<Character>) - Static method in class info.bioinfweb.libralign.model.implementations.decorate.DNAAlignmentModelDecorator
-
- newCharacterInstance(AlignmentModel<Character>) - Static method in class info.bioinfweb.libralign.model.implementations.decorate.RNAAlignmentModelDecorator
-
- newDNAInstance(boolean) - Static method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet
-
Returns a new instance of this class containing all nucleotide tokens, including
'T' and not 'U', the gap token ('-') and all IUPAC ambiguity codes.
- newGapInstance() - Static method in class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
-
- newInsertInstance(AlignmentModel<T>, String) - Static method in class info.bioinfweb.libralign.model.events.SequenceChangeEvent
-
- newInsertInstance(AlignmentModel<T>, String, int, Collection<? extends T>) - Static method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
-
Creates a new instance of this class that represents an insertion of a list of tokens.
- newInsertInstance(AlignmentModel<T>, String, int, T) - Static method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
-
Creates a new instance of this class that represents an insertion of a single token.
- newInstanceFromProfile(Profile<Sequence<C>, C>, String, CharacterStateSetType, boolean, SequenceIDManager, boolean) - Static method in class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel
-
Creates a new instance of this class and copies the sequences contained underlyingModel to it.
- newInstanceFromProfile(Profile<Sequence<C>, C>, String, CharacterStateSetType, boolean) - Static method in class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel
-
Creates a new instance of this class and copies the sequences contained underlyingModel to it.
- newMissingInformationInstance() - Static method in class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
-
- newNucleotideInstance(boolean) - Static method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet
-
Returns a new instance of this class containing all nucleotide tokens, including both
'T' and 'U', the gap token ('-') and all IUPAC ambiguity codes.
- newRemoveInstance(AlignmentModel<T>, String) - Static method in class info.bioinfweb.libralign.model.events.SequenceChangeEvent
-
- newRemoveInstance(AlignmentModel<T>, String, int, Collection<? extends T>) - Static method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
-
Creates a new instance of this class that represents a deletion of a list of tokens.
- newRemoveInstance(AlignmentModel<T>, String, int, T) - Static method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
-
Creates a new instance of this class that represents a deletion of a single token.
- newReplaceInstance(AlignmentModel<T>, String, int, Collection<? extends T>) - Static method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
-
Creates a new instance of this class that represents a replacement of a list of tokens.
- newReplaceInstance(AlignmentModel<T>, String, int, T) - Static method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
-
Creates a new instance of this class that represents a replacement of a single token.
- newRNAInstance(boolean) - Static method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet
-
Returns a new instance of this class containing all nucleotide tokens, including
'U' and not 'T', the gap token ('-') and all IUPAC ambiguity codes.
- next() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaIterator
-
- next() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubAreaIterator
-
- next() - Method in class info.bioinfweb.libralign.dataarea.DataAreaVisibleIterator
-
- next() - Method in class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator
-
- next() - Method in class info.bioinfweb.libralign.model.utils.CharSequenceTokenScanner
-
Returns the next token from parsed from the underlying character sequence.
- NO_SELECTION - Static variable in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection
-
- NoArgDataModelFactory<M extends DataModel> - Class in info.bioinfweb.libralign.model.data
-
Default data model factory implementation that is able to create instances of all data model
classes that offer a constructor with no arguments.
- NoArgDataModelFactory(Class<M>) - Constructor for class info.bioinfweb.libralign.model.data.NoArgDataModelFactory
-
Creates a new instance of this class.
- NucleotideTokenPainter - Class in info.bioinfweb.libralign.alignmentarea.tokenpainter
-
Token painter that paints nucleotides.
- NucleotideTokenPainter() - Constructor for class info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter
-
Creates a new instance of this class.
