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D

DASH_LENGTH_FACTOR - Static variable in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea

The length of a dash

DASH_STROKE - Static variable in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea

The stroke used to paint the dashes

DataArea - Class in info.bioinfweb.libralign.dataarea

All classes representing a data area in an AlignmentArea must be inherited from this class.

DataArea(AlignmentContentArea, AlignmentArea) - Constructor for class info.bioinfweb.libralign.dataarea.DataArea

Creates a new instance of this class.

DataAreaChangeEvent - Class in info.bioinfweb.libralign.dataarea

Event that is used to indicate a change of data areas displayed inside an AlignmentArea.

DataAreaChangeEvent(Object, boolean, ListChangeType, Collection<? extends DataArea>) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaChangeEvent

Creates a new event object.

DataAreaChangeEvent(Object, boolean, ListChangeType, DataArea) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaChangeEvent

Creates a new event object.

DataAreaChangeEventList - Class in info.bioinfweb.libralign.dataarea

A wrapper around any implementation of List that fires DataAreaChangeEvents.

DataAreaChangeEventList(List<DataArea>) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

This constructor is only meant to be used in DataAreaList.

DataAreaChangeEventList(DataAreaList, List<DataArea>) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

Creates a new instance of this class.

dataAreaInsertedRemoved(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea

dataAreaInsertedRemoved(DataAreaChangeEvent) - Method in interface info.bioinfweb.libralign.dataarea.DataAreasModelListener

dataAreaInsertedRemoved(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder

DataAreaList - Class in info.bioinfweb.libralign.dataarea

A list of DataArea that are displayed at a specified position in an AlignmentArea.

DataAreaList(DataAreasModel, DataAreaListType) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaList

Creates a new instance of this class for lists containing data areas displayed above or underneath the alignment.

DataAreaList(DataAreasModel, String) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaList

Creates a new instance of this class representing a list of data areas attached to one sequence of the alignment.

DataAreaList(DataAreasModel, DataAreaLocation) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaList

Creates a new instance of this class representing a list of data areas attached to one sequence of the alignment.

DataAreaListType - Enum in info.bioinfweb.libralign.dataarea

Enumerates the types locations a DataArea can have inside a AlignmentArea.

DataAreaLocation - Class in info.bioinfweb.libralign.dataarea

Specified the location of a DataArea.

DataAreaLocation(DataAreaListType) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaLocation

Creates a new instance of this class specifying locations above or underneath the alignment.

DataAreaLocation(String) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaLocation

Creates a new instance of this class specifying a location attached to one sequence of the alignment.

DataAreaSequenceChangeListener - Class in info.bioinfweb.libralign.dataarea

Helper class used by DataAreasModel to inform the data areas it contains about changes in the associated AlignmentModel.

DataAreaSequenceChangeListener(DataAreasModel) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener

Creates a new instance of this class.

DataAreasModel - Class in info.bioinfweb.libralign.dataarea

Manages the data areas attached to an AlignmentArea.

DataAreasModel(AlignmentArea) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreasModel

Creates a new instance of this class.

DataAreasModelListener - Interface in info.bioinfweb.libralign.dataarea

This interface should be implemented by classes that want to track changes of the data areas contained in a AlignmentArea.

dataAreaVisibilityChanged(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea

dataAreaVisibilityChanged(DataAreaChangeEvent) - Method in interface info.bioinfweb.libralign.dataarea.DataAreasModelListener

dataAreaVisibilityChanged(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder

DataAreaVisibleIterator - Class in info.bioinfweb.libralign.dataarea

Iterator that only returns visible data areas and skips all the others.

DataAreaVisibleIterator(Iterator<DataArea>) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaVisibleIterator

Creates a new instance of this class.

DataModel - Interface in info.bioinfweb.libralign.model.data

The interface that all classes providing data for DataArea implementations should implement.

DataModelEventReader<M extends DataModel> - Interface in info.bioinfweb.libralign.model.io

Interface to be implemented by all readers that process JPhyloIO events to read data to be stored in implementations of DataModel.

DataModelFactory<M extends DataModel> - Interface in info.bioinfweb.libralign.model.data

DataModelKey - Class in info.bioinfweb.libralign.model.io

Stores information to access a data model that has been read from a data source (e.g.

DataModelKey(String, String) - Constructor for class info.bioinfweb.libralign.model.io.DataModelKey

Creates a new instance of this class.

DataModelKey(String) - Constructor for class info.bioinfweb.libralign.model.io.DataModelKey

Creates a new instance of this class with no sequence ID.

DEFAULT_AMINO_ACID_CHARACTER_STATE_COUNT - Static variable in class info.bioinfweb.libralign.model.factory.StringAlignmentModelFactory

DEFAULT_CURSOR_LINE_WIDTH - Static variable in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings

The initial cursor line width.

DEFAULT_FIRST_INDEX - Static variable in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea

The default value returned by SequenceIndexArea.getFirstIndex() if it has not been changed.

DEFAULT_HEIGHT - Static variable in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

DEFAULT_HEIGHT_FACTOR - Static variable in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea

DEFAULT_HEIGHT_FACTOR - Static variable in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea

DEFAULT_ID_PREFIX - Static variable in class info.bioinfweb.libralign.model.implementations.SequenceIDManager

DEFAULT_INITIAL_CAPACITY - Static variable in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel

DEFAULT_NUCLEOTIDE_CHARACTER_STATE_COUNT - Static variable in class info.bioinfweb.libralign.model.factory.biojava.BioJava3NucleotideAlignmentModelFactory

DEFAULT_WIDTH - Static variable in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

DefaultLabelSubArea - Class in info.bioinfweb.libralign.alignmentarea.label

GUI component used to label AlignmentSubAreas that do not provide an own label component.

DefaultLabelSubArea(AlignmentLabelArea, AlignmentSubArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.DefaultLabelSubArea

DefaultTokenSet<T> - Class in info.bioinfweb.libralign.model.tokenset

Basic implementation of a discrete token set.

DefaultTokenSet(CharacterStateSetType) - Constructor for class info.bioinfweb.libralign.model.tokenset.DefaultTokenSet

Returns a new instance of this class.

DelegatedAlignmentModelView<T> - Class in info.bioinfweb.libralign.model.implementations.decorate

Implementation of AlignmentModelView that delegates all methods to the underlying model and uses the same token type as the underlying model.

DelegatedAlignmentModelView(AlignmentModel<T>) - Constructor for class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView

deleteBackwards() - Method in class info.bioinfweb.libralign.actions.AlignmentActionProvider

Removes the currently selected tokens from the underlying AlignmentModel.

deleteCutOffDistortions() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel

Deletes all distortions of the base call sequence to the editable sequence in the cut off areas at the beginning and the end of the pherogram and moves PherogramArea#getFirstSeqPos() of the owner accordingly, so that the visible part of the pherogram still correctly aligns to the editable sequence.

deleteForward() - Method in class info.bioinfweb.libralign.actions.AlignmentActionProvider

Removes the currently selected tokens from the underlying AlignmentModel.

deleteSelection() - Method in class info.bioinfweb.libralign.actions.AlignmentActionProvider

Deletes the currently selected tokens.

descriptionByToken(C) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet

descriptionByToken(Character) - Method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet

In this default implementation the description is equal the character itself.

descriptionByToken(ContinuousToken<T>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet

descriptionByToken(T) - Method in class info.bioinfweb.libralign.model.tokenset.DefaultTokenSet

descriptionByToken(T) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet

An description of the specified token (e.g.

determineUseSubcomponents(Object[]) - Static method in class info.bioinfweb.libralign.alignmentarea.GUITools

Used by AlignmentArea and AlignmentContentArea to determine whether to create subcomponents for each sequence and data area or not for SWT.

DirectPaintingSWTAlignmentArea - Class in info.bioinfweb.libralign.alignmentarea

A toolkit-specific alignment area that implements scrolling via direct painting for SWT.

DirectPaintingSWTAlignmentArea(AlignmentArea, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentArea

DirectPaintingSWTAlignmentContentScroller - Class in info.bioinfweb.libralign.alignmentarea

Extends DirectPaintingSWTScrollContainer from TIC with some LibrAlign specific functionality to allow direct scrolling of an AlignmentContentArea.

DirectPaintingSWTAlignmentContentScroller(AlignmentArea, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentContentScroller

DIVIDER_WIDTH - Static variable in class info.bioinfweb.libralign.alignmentarea.AlignmentArea

Defines the width of the divider of the GUI components for the head, content, and bottom area.

DNAAlignmentModelDecorator<T,U> - Class in info.bioinfweb.libralign.model.implementations.decorate

Shows the underlying nucleotide data source as a DNA sequence, i.e.

DNAAlignmentModelDecorator(TokenSet<T>, AlignmentModel<U>) - Constructor for class info.bioinfweb.libralign.model.implementations.decorate.DNAAlignmentModelDecorator

doAddSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel

doAddSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

This method is called by AbstractUndecoratedAlignmentModel.addSequence(String) if #isReadOnly() returns false.

doCreateNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory

doCreateNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.BioPolymerCharAlignmentModelFactory

doCreateNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.continuous.DoubleAlignmentModelFactory

doCreateNewModel(NewAlignmentModelParameterMap) - Method in class info.bioinfweb.libralign.model.factory.continuous.FloatAlignmentModelFactory

doPaintToken(AlignmentArea, String, int, Object, String, Graphics2D, Rectangle2D, Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractBioPolymerTokenPainter

doPaintToken(AlignmentArea, String, int, Object, String, Graphics2D, Rectangle2D, Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter

Method to be implemented by inherited classes performing the actual paint operation.

doPaintToken(AlignmentArea, String, int, Object, String, Graphics2D, Rectangle2D, Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

doRemove() - Method in class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator

Overwrite this method to perform implementation specific remove operations.

doRemoveSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel

doRemoveSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

This method is called by #removeSequence(int) if #isReadOnly() returns false.

doRenameSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

This method is called by #renameSequence(int, String) if #isReadOnly() returns false and the specified sequence is contained in this model.

DOUBLE_MAX_REPRESENTATION_LENGTH - Static variable in class info.bioinfweb.libralign.model.tokenset.continuous.DoubleTokenSet

DoubleAlignmentModelFactory - Class in info.bioinfweb.libralign.model.factory.continuous

Factory that creates ArrayListAlignmentModels with Double values as tokens.

DoubleAlignmentModelFactory() - Constructor for class info.bioinfweb.libralign.model.factory.continuous.DoubleAlignmentModelFactory

DoubleTokenSet - Class in info.bioinfweb.libralign.model.tokenset.continuous

Implementation of a token set containing all possible double values.

DoubleTokenSet() - Constructor for class info.bioinfweb.libralign.model.tokenset.continuous.DoubleTokenSet

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