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AbstractAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations
This is the base class for all alignment models and alignment model decorators.
AbstractAlignmentModel() - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel
 
AbstractAlignmentModelDecorator<T,U> - Class in info.bioinfweb.libralign.model.implementations.decorate
Basic implementation of AlignmentModelView which delegates sequence specific methods (which are independent of the token type) to the underlying model.
AbstractAlignmentModelDecorator(TokenSet<T>, AlignmentModel<U>) - Constructor for class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
Creates a new instance of this class.
AbstractAlignmentModelFactory<T> - Class in info.bioinfweb.libralign.model.factory
Implements shared functionality for alignment model factories.
AbstractAlignmentModelFactory() - Constructor for class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory
Creates a new instance of this class without an shared sequence ID manager.
AbstractAlignmentModelFactory(T) - Constructor for class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory
Creates a new instance of this class without an shared sequence ID manager.
AbstractAlignmentModelFactory(SequenceIDManager, boolean, T) - Constructor for class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory
Creates a new instance of this class using a shared sequence ID manager.
AbstractAlignmentSubAreaComponent - Class in info.bioinfweb.libralign.alignmentarea.content
 
AbstractAlignmentSubAreaComponent(AlignmentSubArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AbstractAlignmentSubAreaComponent
Creates a new instance of this class.
AbstractBasicAlignmentModelView<T> - Class in info.bioinfweb.libralign.model.adapters
All classes implementing BasicAlignmentModelViews can inherit from this class, which implements the access to the underlying data source.
AbstractBasicAlignmentModelView(AlignmentModel<T>) - Constructor for class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView
 
AbstractBioPolymerTokenPainter - Class in info.bioinfweb.libralign.alignmentarea.tokenpainter
Implements shared functionality for painting nucleotide and amino acid tokens including their ambiguity codes.
AbstractBioPolymerTokenPainter() - Constructor for class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractBioPolymerTokenPainter
 
AbstractContinuousSet<T extends java.lang.Number & java.lang.Comparable<T>> - Class in info.bioinfweb.libralign.model.tokenset.continuous
Implements type independent functionality for continuous token sets.
AbstractContinuousSet() - Constructor for class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
 
AbstractDataModelEventReader<M extends DataModel> - Class in info.bioinfweb.libralign.model.io
Implements shared functionality for all classes reading data from JPhyloIO events into implementations of DataModel.
AbstractDataModelEventReader(AlignmentDataReader, DataModelFactory<M>) - Constructor for class info.bioinfweb.libralign.model.io.AbstractDataModelEventReader
Creates a new instance of this class.
AbstractIndexTranslator<T,D> - Class in info.bioinfweb.libralign.model.utils.indextranslation
 
AbstractIndexTranslator(AlignmentModel<T>, Set<T>) - Constructor for class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
 
AbstractListAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations
An abstract implementation of AlignmentModel using a map of lists to store alignment data.
AbstractListAlignmentModel(TokenSet<T>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.
AbstractListAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, int, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
Creates a new instance of this class.
AbstractMapBasedAlignmentModel<S,T> - Class in info.bioinfweb.libralign.model.implementations
Implements all methods dealing with the organization of the sequence set using some implementation of Map to identify the sequence object belonging to a sequence ID.
AbstractMapBasedAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, Map<String, S>, List<String>) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel
Creates a new instance of this class with a custom map and list implementation.
AbstractMapBasedAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, Map<String, S>) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel
Creates a new instance of this class with a custom map implementation.
AbstractMapBasedAlignmentModel(TokenSet<T>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel
Creates a new instance of this class relying on a HashMap.
AbstractSequenceIDIterator<P extends AlignmentModel> - Class in info.bioinfweb.libralign.model.implementations
Abstract implementation of an iterator returning the IDs of all sequences provided by an implementation of AlignmentModel.
AbstractSequenceIDIterator(P, Iterator<String>) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator
Creates a new instance of this class.
AbstractSingleSequenceDataAdapter<T> - Class in info.bioinfweb.libralign.model.adapters
Implements basic functionality of SingleSequenceDataAdapter.
AbstractSingleSequenceDataAdapter(AlignmentModel<T>, String, int, int) - Constructor for class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
Creates a new instance of this class.
AbstractSingleSequenceDataAdapter(AlignmentModel<T>, String) - Constructor for class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
Creates a new instance of this class which views the whole length of a sequence in the underlying data source.
AbstractSWTAlignmentArea - Class in info.bioinfweb.libralign.alignmentarea
Implements shared functionality of ScrollContainerSWTAlignmentArea and DirectPaintingSWTAlignmentArea.
AbstractSWTAlignmentArea(AlignmentArea, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.AbstractSWTAlignmentArea
 
AbstractTokenPainter - Class in info.bioinfweb.libralign.alignmentarea.tokenpainter
Implements shared functionality between implementations of TokenPainter.
AbstractTokenPainter() - Constructor for class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter
 
AbstractTokenReplacementAlignmentModelDecorator<T,U> - Class in info.bioinfweb.libralign.model.implementations.decorate
Abstract base class for implementations of AlignmentModelView that simply replace a set of tokens by other tokens of the same type.
AbstractTokenReplacementAlignmentModelDecorator(TokenSet<T>, AlignmentModel<U>) - Constructor for class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
Creates a new instance of this class.
AbstractTokenSet<T> - Class in info.bioinfweb.libralign.model.tokenset
An abstract implementation of TokenSet that provides a TreeMap used to map key characters to tokens and inherits from HashSet so also tokens that do not implement Comparable are supported.
AbstractTokenSet(CharacterStateSetType) - Constructor for class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
Creates a new empty instance of this class.
AbstractTokenSet(CharacterStateSetType, AbstractTokenSet<T>) - Constructor for class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
Copy constructor that copies all elements the contents of the key map from source to the new instance.
AbstractUndecoratedAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations
Implements general functionality for alignment models that are not decorators of other models.
AbstractUndecoratedAlignmentModel(TokenSet<T>) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
Creates a new instance of this class with its own instance of SequenceIDManager.
AbstractUndecoratedAlignmentModel(TokenSet<T>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
Creates a new instance of this class.
AbstractUnmodifyableAlignmentModel<S,T> - Class in info.bioinfweb.libralign.model.implementations
Implements basic functionality for a map based alignment model that uses unmodifiable sequence objects as its underlying data source.
AbstractUnmodifyableAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, Map<String, S>, List<String>) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
Creates a new instance of this class with a custom map and list implementation.
AbstractUnmodifyableAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, Map<String, S>) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
Creates a new instance of this class with a custom map and list implementation.
AbstractUnmodifyableAlignmentModel(TokenSet<T>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
Creates a new instance of this class relying on a TreeMap.
add(SelectionModel) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionSynchronizer
 
add(DataArea) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
Appends the specified data area to the end of this list.
add(int, DataArea) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
 
add(int, int) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet
 
add(ContinuousToken<T>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
This method is not supported by this implementation and will always throw an UnsupportedOperationException.
addAll(Collection<? extends DataArea>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
 
addAll(int, Collection<? extends DataArea>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
 
addAll(Collection<? extends ContinuousToken<T>>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
This method is not supported by this implementation and will always throw an UnsupportedOperationException.
addDataAreaList(DataAreaList) - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSwingAlignmentContentArea
 
addDataAreaList(DataAreaList) - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea
 
addDataModelReader(DataModelEventReader<?>) - Method in class info.bioinfweb.libralign.model.io.AlignmentDataReader
Adds the specified data model reader to this instance, if it is not already present.
addListener(PaintSettingsListener) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
Attaches a paint settings listener to this instance.
addListener(DataAreasModelListener) - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel
Adds a lister to this object that will be informed about future insertions or deletions of data areas.
addListener(EditSettingsListener) - Method in class info.bioinfweb.libralign.editsettings.EditSettings
 
addListener(PherogramComponentModelListener) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel
 
addPropertyChangeListener(PropertyChangeListener) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats
 
addSelectionListener(SelectionListener<GenericEventObject<SelectionModel>>) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel
Adds a lister to this object that will be informed about future changes of the selection.
addSequence(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel
Adds a new empty sequence to the underlying data source and generates an ID for it.
addSequence(String, String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel
Adds a new empty sequence to the underlying data source assigning the specified ID to it.
addSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
 
addSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
 
addSequence(String, S) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
Adds a the specified sequence to the underlying data source and generates an ID for it.
addSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
 
addSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
 
addSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
 
addSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
 
addSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
 
addSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
 
addSequence(String, S) - Method in interface info.bioinfweb.libralign.model.SequenceAccessAlignmentModel
Adds a the specified sequence to the underlying data source and generates an ID for it.
addSequenceName(String) - Method in class info.bioinfweb.libralign.model.implementations.SequenceIDManager
Adds a new empty sequence to the underlying data source and generates an ID for it.
addShiftChange(int, int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
 
addSpaceKeyForGaps() - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
 
adoptChildAreas() - Method in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
 
adoptChildAreas() - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
 
adoptChildAreas() - Method in interface info.bioinfweb.libralign.multiplealignments.ToolkitSpecificMultipleAlignmentsContainer
This method is used internally by MultipleAlignmentsContainer if the order or set of contained alignment areas changes and these changes shall be reflected by the underlying GUI component.
adoptFromOther(AlignmentCursor) - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor
 
adoptFromOther(OneDimensionalSelection) - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection
 
adoptFromOther(SelectionModel) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel
Adopts the selection from another instance.
afterAdd(int, Collection<? extends AlignmentArea>) - Method in class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList
 
afterAlignmentModelChanged() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList
This method is called by the owning alignment area to notify this object about a change of the associated alignment model.
afterCharSetChange(CharSetChangeEvent) - Method in interface info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModelListener
 
afterCharSetColorChange(CharSetColorChangeEvent) - Method in interface info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModelListener
 
afterCharSetColumnChange(CharSetColumnChangeEvent) - Method in interface info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModelListener
 
afterCharSetRenamed(CharSetRenamedEvent) - Method in interface info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModelListener
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
 
afterModelChanged(CharSetDataModel, CharSetDataModel) - Method in interface info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModelListener
Called if this listener was moved to another instance of CharSetArea.
afterModelChanged(AlignmentModel, AlignmentModel) - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.model.AlignmentModelChangeAdapter
 
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in interface info.bioinfweb.libralign.model.AlignmentModelChangeListener
Called if this listener was moved to another instance of AlignmentModel.
afterModelChanged(AlignmentModel<T>, AlignmentModel<U>) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder
 
afterRemove(int, Collection<? extends AlignmentArea>) - Method in class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList
 
afterReplace(int, AlignmentArea, AlignmentArea) - Method in class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
 
afterSequenceChange(SequenceChangeEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.model.AlignmentModelChangeAdapter
 
afterSequenceChange(SequenceChangeEvent<T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModelChangeListener
Called after a sequence has been inserted, removed or replaced.
afterSequenceChange(SequenceChangeEvent<T>) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
 
afterSequenceRenamed(SequenceRenamedEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.model.AlignmentModelChangeAdapter
 
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModelChangeListener
Called after a sequence was renamed.
afterSequenceRenamed(SequenceRenamedEvent<T>) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
 
afterTokenChange(TokenChangeEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea
 
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.model.AlignmentModelChangeAdapter
 
afterTokenChange(TokenChangeEvent<T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModelChangeListener
Called after a single token or a set of tokens has been inserted, removed or replaced.
afterTokenChange(TokenChangeEvent<T>) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder
 
AlignmentActionProvider<T> - Class in info.bioinfweb.libralign.actions
This class provides the business logic for user actions triggered through the view AlignmentContentArea to manipulate the associated models AlignmentModel and SelectionModel.
AlignmentActionProvider(AlignmentArea) - Constructor for class info.bioinfweb.libralign.actions.AlignmentActionProvider
Creates a new instance of this class that is associated with the specified view and model.
AlignmentArea - Class in info.bioinfweb.libralign.alignmentarea
Instances of this class act as GUI components that display a multiple sequence alignment including attached data areas.
AlignmentArea() - Constructor for class info.bioinfweb.libralign.alignmentarea.AlignmentArea
Creates a new instance of this class that shall not part of a MultipleAlignmentsContainer.
AlignmentArea(MultipleAlignmentsContainer) - Constructor for class info.bioinfweb.libralign.alignmentarea.AlignmentArea
Creates a new instance of this class to be inserted into a MultipleAlignmentsContainer.
AlignmentAreaList - Class in info.bioinfweb.libralign.multiplealignments
A list implementation MultipleAlignmentsContainer uses to manage its contained alignment areas.
AlignmentAreaList(MultipleAlignmentsContainer) - Constructor for class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList
 
AlignmentContentArea - Class in info.bioinfweb.libralign.alignmentarea.content
Toolkit independent component displaying the contents (not the labels) of a single alignment and its attached data areas.
AlignmentContentArea(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
Creates a new instance of this class.
AlignmentCursor - Class in info.bioinfweb.libralign.alignmentarea.selection
Represents the position and height of the cursor in an AlignmentArea.
AlignmentCursor(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor
 
AlignmentDataReader - Class in info.bioinfweb.libralign.model.io
Reads the contents of AlignmentModels and DataModels from a stream of JPhyloIO events.
AlignmentDataReader(JPhyloIOEventReader, AlignmentModelFactory<?>) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentDataReader
Creates a new instance of this class.
AlignmentDataReader(File, AlignmentModelFactory<?>) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentDataReader
Creates a new instance of this class.
AlignmentDataReader(InputStream, AlignmentModelFactory<?>) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentDataReader
Creates a new instance of this class.
AlignmentDataReader(File) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentDataReader
Creates a new instance of this class.
AlignmentDataReader(InputStream) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentDataReader
Creates a new instance of this class.
AlignmentLabelArea - Class in info.bioinfweb.libralign.alignmentarea.label
A toolkit independent GUI component displaying the sequence names in an AlignmentArea.
AlignmentLabelArea(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
Creates a new instance of this class.
AlignmentLabelSubArea - Class in info.bioinfweb.libralign.alignmentarea.label
All GUI components displaying labels to aligned sequences or data areas must be inherited from this class.
AlignmentLabelSubArea(AlignmentLabelArea, AlignmentSubArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubArea
Creates a new instance of this class.
AlignmentLabelSubAreaIterator - Class in info.bioinfweb.libralign.alignmentarea.label
 
AlignmentLabelSubAreaIterator(AlignmentSubAreaIterator) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubAreaIterator
 
AlignmentModel<T> - Interface in info.bioinfweb.libralign.model
Interface that allows LibrAlign GUI elements to access different types of alignment data sources.
AlignmentModelChangeAdapter - Class in info.bioinfweb.libralign.model
Provides empty implementations for all listener methods of AlignmentModelChangeListener.
AlignmentModelChangeAdapter() - Constructor for class info.bioinfweb.libralign.model.AlignmentModelChangeAdapter
 
AlignmentModelChangeEvent<T> - Class in info.bioinfweb.libralign.model.events
Event object that represents a change in the data provided by an implementation of AlignmentModel.
AlignmentModelChangeEvent(AlignmentModel<T>, String) - Constructor for class info.bioinfweb.libralign.model.events.AlignmentModelChangeEvent
Creates a new instance of this class.
AlignmentModelChangeListener - Interface in info.bioinfweb.libralign.model
This interface should be implemented by classes that want to track changes in the stored data of an implementation of AlignmentModel.
AlignmentModelDataAdapter<T> - Class in info.bioinfweb.libralign.model.io
An JPhyloIO data adapter that allows writing the contents of an implementation of AlignmentModel to an implementation of JPhyloIOEventWriter.
AlignmentModelDataAdapter(String, LinkedLabeledIDEvent, AlignmentModel<T>, boolean) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
Creates a new instance of this class.
AlignmentModelEventReader - Class in info.bioinfweb.libralign.model.io
Reads alignment models from a JPhyloIO event stream.
AlignmentModelEventReader() - Constructor for class info.bioinfweb.libralign.model.io.AlignmentModelEventReader
Creates a new instance of this class using StringAlignmentModelFactory as the default factory and DoubleAlignmentModelFactory as the factory for continuous data.
AlignmentModelEventReader(AlignmentModelFactory<?>) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentModelEventReader
Creates a new instance of this class with an empty factory map.
AlignmentModelEventReader(AlignmentModelFactory<?>, Map<CharacterStateSetType, AlignmentModelFactory>) - Constructor for class info.bioinfweb.libralign.model.io.AlignmentModelEventReader
Creates a new instance of this class.
AlignmentModelException - Exception in info.bioinfweb.libralign.model.exception
Base class of all exceptions that can be thrown by an AlignmentModel.
AlignmentModelException(AlignmentModel<?>) - Constructor for exception info.bioinfweb.libralign.model.exception.AlignmentModelException
 
AlignmentModelException(AlignmentModel<?>, String) - Constructor for exception info.bioinfweb.libralign.model.exception.AlignmentModelException
 
AlignmentModelFactory<T> - Interface in info.bioinfweb.libralign.model.factory
Interface to be implemented by classes creating instance of implementations of AlignmentModel.
AlignmentModelUtils - Class in info.bioinfweb.libralign.model.utils
Provider general tool methods to be used with instances of AlignmentModel.
AlignmentModelUtils() - Constructor for class info.bioinfweb.libralign.model.utils.AlignmentModelUtils
 
AlignmentModelView<T,U> - Interface in info.bioinfweb.libralign.model
This interface should be implemented by all classes which return the contents of another implementation of AlignmentModel in a modified way.
AlignmentModelWriteType - Enum in info.bioinfweb.libralign.model
Specifies if whole sequences or single tokens can be edited in the underlying data source of the implementation of an AlignmentModel.
AlignmentPaintEvent - Class in info.bioinfweb.libralign.alignmentarea.content
Event object used by AlignmentSubArea that provides information on the area of a component displaying a part of an alignment to be painted and the graphics context.
AlignmentPaintEvent(Object, AlignmentArea, int, int, Graphics2D, Rectangle2D) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentPaintEvent
Creates a new instance of this class.
AlignmentSourceNotWritableException - Exception in info.bioinfweb.libralign.model.exception
This exceptions is thrown if a modifying method of AlignmentModel is called which has a data source that is not writable.
AlignmentSourceNotWritableException(AlignmentModel<?>) - Constructor for exception info.bioinfweb.libralign.model.exception.AlignmentSourceNotWritableException
 
AlignmentSubArea - Class in info.bioinfweb.libralign.alignmentarea.content
All GUI components that are part of an AlignmentContentArea should inherit from this class.
AlignmentSubArea(AlignmentContentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea
Creates a new instance of this class.
AlignmentSubAreaInfo - Class in info.bioinfweb.libralign.alignmentarea.content
Stores a reference to an AlignmentSubArea and its y position relative to its parent AlignmentContentArea.
AlignmentSubAreaInfo(AlignmentSubArea, double) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaInfo
 
AlignmentSubAreaIterator - Class in info.bioinfweb.libralign.alignmentarea.content
Adapter class that converts an iterator of ToolkitComponent to an iterator of AlignmentSubAreas.
AlignmentSubAreaIterator(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaIterator
 
AminoAcidTokenPainter - Class in info.bioinfweb.libralign.alignmentarea.tokenpainter
Token painter that paints amino acids.
AminoAcidTokenPainter() - Constructor for class info.bioinfweb.libralign.alignmentarea.tokenpainter.AminoAcidTokenPainter
 
appendPartModel(AlignmentModel<?>) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel
Appends an additional part model at the end of this concatenated alignment.
appendToken(String, T) - Method in interface info.bioinfweb.libralign.model.AlignmentModel
Appends a token at the end of the sequence.
appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
 
appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
 
appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
 
appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
 
appendTokens(String, Collection<? extends T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModel
Appends a sequence of tokens starting at the end of the current sequence.
appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
 
appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
 
appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
 
appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
 
ArrayListAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations
An implementation of AlignmentModel using a map of array lists to store alignment data.
ArrayListAlignmentModel(TokenSet<T>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.ArrayListAlignmentModel
Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.
ArrayListAlignmentModel(TokenSet<T>) - Constructor for class info.bioinfweb.libralign.model.implementations.ArrayListAlignmentModel
Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.
ArrayListAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, int, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.ArrayListAlignmentModel
Creates a new instance of this class.
assignSize() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea
 
assignSize() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
 
assignSizeToAll() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
Calls the assignSize() method of the contained AlignmentContentArea, AlignmentLabelArea, their subcomponents and on this instance.
assignSizeToAll() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
 
assignSizeToAll() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
 
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