C-Index

A B C D E F G H I J K L M N O P Q R S T U V W Z

C

calculateConstituents(String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractBioPolymerTokenPainter: To be implemented by inherited classes to determine the non-ambiguous tokens that could be represented by the specified ambiguity code.
calculateConstituents(String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AminoAcidTokenPainter
calculateConstituents(String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter
calculateFont(Graphics2D, Rectangle2D, String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
calculateFontZoomFactor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Calculates the factor to multiply font heights with to fit to the current size of the owning component.
calculatePaintRange(TICPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
calculatePaintRange(TICPaintEvent) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
calculatePreferredWidth(TokenSet<?>) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
calculateTraceCurvesHeight() - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter: Returns the height that is used to paint the trace curves.
changeQualityOutputType() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Changes the current quality output type to the next value in the order defined by PherogramFormats.QualityOutputType.
CharacterTokenSet - Class in info.bioinfweb.libralign.model.tokenset: A token set consisting of characters.
CharacterTokenSet(CharacterStateSetType) - Constructor for class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet: Creates a new empty instance of this class.
CharacterTokenSet(CharacterStateSetType, CharSequence) - Constructor for class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet: Creates a new instance of this class where the initial tokens are determined by the characters in the specified character sequence.
CharacterTokenSet(CharacterTokenSet) - Constructor for class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet: A constructor used to clone instances of this class.
charAt(int) - Method in class info.bioinfweb.libralign.model.adapters.SingleCharSequenceAdapter: Returns the character representation of the token in the underlying data source at the specified position.
CharSequenceAdapter<T> - Class in info.bioinfweb.libralign.model.adapters: Adapter class that allows to access the contents of an implementation of AlignmentModel as a set of CharSequences or Strings.
CharSequenceAdapter(AlignmentModel<T>, boolean) - Constructor for class info.bioinfweb.libralign.model.adapters.CharSequenceAdapter: Creates a new instance of this class.
CharSequenceAlignmentModel - Class in info.bioinfweb.libralign.model.implementations: An implementation of AlignmentModel backed by a set of CharSequence implementations (e.g.
CharSequenceAlignmentModel(TokenSet<Character>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.CharSequenceAlignmentModel: Creates a new instance of this class using a possibly shared ID manager.
CharSequenceAlignmentModel(TokenSet<Character>) - Constructor for class info.bioinfweb.libralign.model.implementations.CharSequenceAlignmentModel: Creates a new instance of this class using its own ID manager.
CharSequenceTokenScanner<T> - Class in info.bioinfweb.libralign.model.utils: A scanner that can subsequently parse tokens from a character sequence consisting of concatenated token representations.
CharSequenceTokenScanner(CharSequence, TokenSet<T>, boolean, T) - Constructor for class info.bioinfweb.libralign.model.utils.CharSequenceTokenScanner: Creates a new instance of this class.
charSequenceToTokenList(CharSequence, TokenSet<T>) - Static method in class info.bioinfweb.libralign.model.utils.AlignmentModelUtils: Converts a character sequence to a sequence of tokens.
charSequenceToTokenList(CharSequence, TokenSet<T>, boolean, T) - Static method in class info.bioinfweb.libralign.model.utils.AlignmentModelUtils: Convenience method that uses CharSequenceTokenScanner to parse all tokens contained in the specified string and returns these as a list.
CharSet - Class in info.bioinfweb.libralign.dataarea.implementations.charset
CharSet(String, Color) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet
CharSetArea - Class in info.bioinfweb.libralign.dataarea.implementations.charset: A data area displaying different character sets associated with the current alignment, as they are e.g.
CharSetArea(AlignmentContentArea, AlignmentArea, CharSetDataModel) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea: Creates a new instance of this class.
CharSetArea(AlignmentContentArea, AlignmentArea) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea: Creates a new instance of this class with an empty data model.
CharSetChangeEvent - Class in info.bioinfweb.libralign.dataarea.implementations.charset.events: This event indicates that an instance of CharSet was added, removed or replaced in an instance of CharSetDataModel.
CharSetChangeEvent(CharSetDataModel, boolean, String, CharSet, CharSet, ListChangeType) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetChangeEvent
CharSetChangeEvent(CharSetDataModel, boolean, String, CharSet, boolean) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetChangeEvent
CharSetChangeEvent(CharSetDataModel, boolean, String, CharSet, CharSet) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetChangeEvent
CharSetColorChangeEvent - Class in info.bioinfweb.libralign.dataarea.implementations.charset.events: This event indicates that the color of an instance of CharSet has been changed.
CharSetColorChangeEvent(CharSetDataModel, boolean, String, CharSet, Color) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetColorChangeEvent
CharSetColumnChangeEvent - Class in info.bioinfweb.libralign.dataarea.implementations.charset.events: This event indicates that one or more neighboring columns have been added to or removed from an instance of CharSet.
CharSetColumnChangeEvent(CharSetDataModel, boolean, String, CharSet, boolean, int, int) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetColumnChangeEvent
CharSetDataAdapter - Class in info.bioinfweb.libralign.dataarea.implementations.charset: JPhyloIO data adapter implementation to write the contents of a CharSetDataModel.
CharSetDataAdapter(String, CharSetDataModel, String, URIOrStringIdentifier, URIOrStringIdentifier) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter: Creates a new instance of this class.
CharSetDataAdapter(String, CharSetDataModel, String) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter: Creates a new instance of this class that will not write character set colors.
CharSetDataModel - Class in info.bioinfweb.libralign.dataarea.implementations.charset: The data model for a CharSetArea.
CharSetDataModel() - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModel
CharSetDataModelChangeEvent - Class in info.bioinfweb.libralign.dataarea.implementations.charset.events: This is the base class of all events providing information on content changes changes of an instance of CharSetDataModel.
CharSetDataModelChangeEvent(CharSetDataModel, boolean, String, CharSet) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetDataModelChangeEvent
CharSetDataModelListener - Interface in info.bioinfweb.libralign.dataarea.implementations.charset: This interface should be implemented by classes which want to receive information on changes in an instance of CharSetDataModel and the CharSet instances within.
CharSetEventReader - Class in info.bioinfweb.libralign.dataarea.implementations.charset: Reads CharacterSetEvents from JPhyloIO into instances of CharSetDataModel.
CharSetEventReader(AlignmentDataReader, URIOrStringIdentifier) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetEventReader
CharSetEventReader(AlignmentDataReader) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetEventReader
CharSetNameArea - Class in info.bioinfweb.libralign.dataarea.implementations.charset: GUI component used to display the name labels of character sets displayed by CharSetArea.
CharSetNameArea(AlignmentLabelArea, CharSetArea) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetNameArea
CharSetRenamedEvent - Class in info.bioinfweb.libralign.dataarea.implementations.charset.events: This event indicates that the name of an instance of CharSet has been changed.
CharSetRenamedEvent(CharSetDataModel, boolean, String, CharSet, String) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetRenamedEvent
clear() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Clears this selection.
clear() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Clears the current selection.
clear() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionSynchronizer
clear() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
clear() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModel
clear() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet: This method is not supported by this implementation and will always throw an UnsupportedOperationException.
clone() - Method in class info.bioinfweb.libralign.model.events.AlignmentModelChangeEvent
clone() - Method in class info.bioinfweb.libralign.model.events.SequenceChangeEvent
clone() - Method in class info.bioinfweb.libralign.model.events.SequenceRenamedEvent
clone() - Method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
clone() - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet: Inherited classes have to overwrite this method and create a deep copy of AbstractTokenSet.getKeyMap().
clone() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet: Clones this instance.
clone() - Method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet: Clones this instance.
clone() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
clone() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.DoubleTokenSet
clone() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.FloatTokenSet
clone() - Method in class info.bioinfweb.libralign.model.tokenset.DefaultTokenSet
clone() - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Returns a deep copy of this instance.
cloneWithNewSource(AlignmentModel<T>) - Method in class info.bioinfweb.libralign.model.events.AlignmentModelChangeEvent: Creates a copy of this event with all properties set to identical values but with a different source.
cloneWithNewSource(AlignmentModel<T>) - Method in class info.bioinfweb.libralign.model.events.SequenceChangeEvent
cloneWithNewSource(AlignmentModel<T>) - Method in class info.bioinfweb.libralign.model.events.SequenceRenamedEvent
cloneWithNewSource(AlignmentModel<T>) - Method in class info.bioinfweb.libralign.model.events.TokenChangeEvent
COLOR_METADATA_ID_SUFFIX - Static variable in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter
COLOR_METADATA_LABEL - Static variable in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter
ColorOverlay - Interface in info.bioinfweb.libralign.alignmentarea.tokenpainter: Classes implementing this interface define areas in the alignment that should be overlain with a certain color.
columnByPaintX(double) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea: Returns the column containing the specified x coordinate.
columnOffsetForPartModel(int) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel: Returns the global index of the first column provided by the part model with the specified index.
columnOffsetForPartModel(AlignmentModel<?>) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel: Returns the global index of the first column provided by the specified part model.
compareTo(ContinuousToken<V>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
ConcatenatedAlignmentModel - Interface in info.bioinfweb.libralign.model.concatenated: Warning: This interface is currently a placeholder.
ConsensusSequenceArea - Class in info.bioinfweb.libralign.dataarea.implementations: A data area that displays the consensus sequence of an alignment.
ConsensusSequenceArea(AlignmentContentArea) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea: Creates a new instance of this class that uses the sequence data provider of the specified alignment area.
ConsensusSequenceArea(AlignmentContentArea, AlignmentArea) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea: Creates a new instance of this class that uses the specified sequence data provider.
contains(Object) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionSynchronizer
contains(Object) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
contains(Object) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet: This default implementation always returns true.
containsAll(Collection<?>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
containsAll(Collection<?>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet: This default implementation always returns true.
containsLongTokens(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
containsPartModel(AlignmentModel<?>) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel: Checks if the specified model is contained in this concatenated model.
containsSequence(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Checks if a sequence associated with the specified unique identifier is contained in this model.
containsSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel
containsSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
containsSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
containsSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
contentScrolled(TICScrollEvent) - Method in class info.bioinfweb.libralign.multiplealignments.HorizontalScrollingSynchronizer
ContinuousToken<V extends java.lang.Number & java.lang.Comparable<V>> - Class in info.bioinfweb.libralign.model.tokenset.continuous: A token class to represent continuous values.
ContinuousToken(V) - Constructor for class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
ContinuousToken(V, CharacterSymbolMeaning) - Constructor for class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
controlMoved(ControlEvent) - Method in class info.bioinfweb.libralign.alignmentarea.SWTScrollableResizeListener
controlResized(ControlEvent) - Method in class info.bioinfweb.libralign.alignmentarea.SWTScrollableResizeListener
convertDecoratedSequenceID(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator: Method used to convert a sequence ID used by the decorator to the according sequence ID used by the underlying model.
convertDecoratedToken(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator: Inherited classes should perform the token translation from a viewed to an underlying token by implementing this method.
convertDecoratedToken(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DNAAlignmentModelDecorator
convertDecoratedToken(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.RNAAlignmentModelDecorator
convertDecoratedTokenIndex(String, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
convertDecoratedTokens(String, int, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
convertSequenceChangeEvent(SequenceChangeEvent<U>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator: Converts a SequenceChangeEvent event from the decorated instance to an event object compatible with this instance.
convertSequenceRenamedEvent(SequenceRenamedEvent<U>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator: Converts a SequenceRenamedEvent event from the decorated instance to an event object compatible with this instance.
convertTokenChangeEvent(TokenChangeEvent<U>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator: Converts a token change event from the underlying (decorated) model to a collection of according change events to be used with this decorator.
convertTokenChangeEvent(TokenChangeEvent<U>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
convertUnderlyingSequenceID(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator: Method used to convert a sequence ID from the underlying model to the according sequence ID used by the decorator.
convertUnderlyingToken(String, int, U) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator: Inherited classes should perform the token translation from an underlying to a viewed token by implementing this method.
convertUnderlyingToken(String, int, U) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DNAAlignmentModelDecorator
convertUnderlyingToken(String, int, U) - Method in class info.bioinfweb.libralign.model.implementations.decorate.RNAAlignmentModelDecorator
convertUnderlyingTokenIndex(String, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
convertUnderlyingTokens(String, int, Collection<? extends U>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
copyBaseCallSequence(int, int) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea: Copies a part of the base call sequence from the underlying model to the editable sequence this data area is attached to.
countCompounds(C...) - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
countGaps(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.GapPattern: Counts the number of gaps located before the specified position.
countGapsBeforeCurveCenter() - Method in class info.bioinfweb.libralign.pherogram.distortion.GapPattern: Calculates the number of gaps that are located before the center of the trace curves belonging to the region this gap pattern belongs to.
createAddSequenceEdit(SwingConcreteAddSequenceEdit<T>) - Method in interface info.bioinfweb.libralign.model.implementations.swingundo.SwingEditFactory: This method is called if an edit object that inserts a new sequence shall be created.
createContentScroller(Composite) - Method in class info.bioinfweb.libralign.alignmentarea.AbstractSWTAlignmentArea
createContentScroller(Composite) - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentArea
createContentScroller(Composite) - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSWTAlignmentArea
createDocumentAdapter(AlignmentModel<T>, String, boolean) - Static method in class info.bioinfweb.libralign.model.io.IOTools: Creates a document data adapter that allows to write the contents of model to a file using e.g.
createDocumentAdapter(AlignmentModel<T>, String) - Static method in class info.bioinfweb.libralign.model.io.IOTools: Creates a document data adapter that allows to write the contents of model to a file using e.g.
createDocumentAdapter(AlignmentModel<T>) - Static method in class info.bioinfweb.libralign.model.io.IOTools: Creates a document data adapter that allows to write the contents of model to a file using e.g.
createEdit(LibrAlignSwingAlignmentEdit<T>) - Method in interface info.bioinfweb.libralign.model.implementations.swingundo.SwingEditFactory: This method is called to create new edit objects (except if a new sequence shall be added).
createLabelSubArea(AlignmentLabelArea) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea: This method can be overwritten to provide a specific implementation for labeling the implementing data area.
createLabelSubArea(AlignmentLabelArea) - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceArea
createLabelSubArea(AlignmentLabelArea) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
createNewModel() - Method in interface info.bioinfweb.libralign.model.data.DataModelFactory
createNewModel() - Method in class info.bioinfweb.libralign.model.data.NoArgDataModelFactory
createNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory
createNewModel(NewAlignmentModelParameterMap) - Method in interface info.bioinfweb.libralign.model.factory.AlignmentModelFactory: Creates a new instance of an alignment model according to the specified parameters.
createNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.biojava.BioJava3AminoAcidAligmentModelFactory
createNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.biojava.BioJava3NucleotideAlignmentModelFactory
createNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.StringAlignmentModelFactory: Creates a new instance of PackedAlignmentModel if the number of tokens is specified (using NewAlignmentModelParameterMap.KEY_CHARACTER_STATE_COUNT) or ArrayListAlignmentModel if not.
createNewSequence(String, String, int) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel: This method is called by #createNewSequence(int, String) and must be implemented by inherited classes.
createNewSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
createNewSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel: Implementing classes must offer a way to create their custom instances of sequence objects overwriting this method.
createNewSequence(String, String, int) - Method in class info.bioinfweb.libralign.model.implementations.ArrayListAlignmentModel
createNewSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel
createNewSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.CharSequenceAlignmentModel: Returns an empty string as the new character sequence.
createNewSequence(String, String, int) - Method in class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel
createPherogramDistortion() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
createProbabilityLabelsList() - Static method in class info.bioinfweb.libralign.pherogram.PherogramUtils
createSequenceData(String) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
createSequenceData(String) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator
createToken(AlignmentModel<T>, String) - Method in class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory: Creates a token using TokenSet.tokenByRepresentation(String).
createToken(AlignmentModel<T>, String) - Method in interface info.bioinfweb.libralign.model.factory.AlignmentModelFactory: Creates a token object associated with the specified string representation.
createToken(AlignmentModel<AminoAcidCompound>, String) - Method in class info.bioinfweb.libralign.model.factory.biojava.BioJava3AminoAcidAligmentModelFactory: Creates the token using the token set of the specified alignment model.
createToken(AlignmentModel<NucleotideCompound>, String) - Method in class info.bioinfweb.libralign.model.factory.biojava.BioJava3NucleotideAlignmentModelFactory
createToken(AlignmentModel<Character>, String) - Method in class info.bioinfweb.libralign.model.factory.BioPolymerCharAlignmentModelFactory
createToken(AlignmentModel<String>, String) - Method in class info.bioinfweb.libralign.model.factory.StringAlignmentModelFactory: Creates the token using the token set of the specified alignment model.
createTraceCurveNucleotideList() - Static method in class info.bioinfweb.libralign.pherogram.PherogramUtils
CursorSelectionInputListener - Class in info.bioinfweb.libralign.alignmentarea.content: Mouse and key listener modifying the selection and cursor if a cursor is used.
CursorSelectionInputListener(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.CursorSelectionInputListener
CUT_COLOR_FACTOR - Static variable in class info.bioinfweb.libralign.pherogram.PherogramFormats: Used to calculate the default background color for the cut off areas.

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