- 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
BasicAlignmentModelView
s 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- AlignmentArea(MultipleAlignmentsContainer) - Constructor for class info.bioinfweb.libralign.alignmentarea.AlignmentArea
-
- AlignmentAreaList - Class in info.bioinfweb.libralign.multiplealignments
-
- 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
-
- 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
-
- 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
-
- 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
-
- AlignmentModelException(AlignmentModel<?>) - Constructor for exception info.bioinfweb.libralign.model.exception.AlignmentModelException
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- AlignmentModelException(AlignmentModel<?>, String) - Constructor for exception info.bioinfweb.libralign.model.exception.AlignmentModelException
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- AlignmentModelFactory<T> - Interface in info.bioinfweb.libralign.model.factory
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Interface to be implemented by classes creating instance of implementations of
AlignmentModel
.
- AlignmentModelUtils - Class in info.bioinfweb.libralign.model.utils
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Provider general tool methods to be used with instances of
AlignmentModel
.
- AlignmentModelUtils() - Constructor for class info.bioinfweb.libralign.model.utils.AlignmentModelUtils
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- AlignmentModelView<T,U> - Interface in info.bioinfweb.libralign.model
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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
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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
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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
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- AlignmentSubArea - Class in info.bioinfweb.libralign.alignmentarea.content
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- AlignmentSubArea(AlignmentContentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea
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Creates a new instance of this class.
- AlignmentSubAreaInfo - Class in info.bioinfweb.libralign.alignmentarea.content
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- AlignmentSubAreaInfo(AlignmentSubArea, double) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaInfo
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- AlignmentSubAreaIterator - Class in info.bioinfweb.libralign.alignmentarea.content
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- AlignmentSubAreaIterator(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaIterator
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- AminoAcidTokenPainter - Class in info.bioinfweb.libralign.alignmentarea.tokenpainter
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Token painter that paints amino acids.
- AminoAcidTokenPainter() - Constructor for class info.bioinfweb.libralign.alignmentarea.tokenpainter.AminoAcidTokenPainter
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- appendPartModel(AlignmentModel<?>) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel
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Appends an additional part model at the end of this concatenated alignment.
- appendToken(String, T) - Method in interface info.bioinfweb.libralign.model.AlignmentModel
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Appends a token at the end of the sequence.
- appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
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- appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
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- appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
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- appendToken(String, T) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
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- appendTokens(String, Collection<? extends T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModel
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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
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- appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
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- appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
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- appendTokens(String, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
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- ArrayListAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations
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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
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- ArrayListAlignmentModel(TokenSet<T>) - Constructor for class info.bioinfweb.libralign.model.implementations.ArrayListAlignmentModel
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- ArrayListAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, int, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.ArrayListAlignmentModel
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Creates a new instance of this class.
- assignSize() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea
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- assignSize() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
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- assignSizeToAll() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
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- assignSizeToAll() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
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- assignSizeToAll() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
-