- 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
-
- DataAreaChangeEventList(List<DataArea>) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
-
- 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.DataAreaModelListener
-
- dataAreaInsertedRemoved(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsEventForwarder
-
- DataAreaList - Class in info.bioinfweb.libralign.dataarea
-
- DataAreaList(DataAreaModel, 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(DataAreaModel, 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(DataAreaModel, 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
-
- DataAreaLocation - Class in info.bioinfweb.libralign.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.
- DataAreaModel - Class in info.bioinfweb.libralign.dataarea
-
- DataAreaModel(AlignmentArea) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaModel
-
Creates a new instance of this class.
- DataAreaModelListener - 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
.
- DataAreaSequenceChangeListener - Class in info.bioinfweb.libralign.dataarea
-
- DataAreaSequenceChangeListener(DataAreaModel) - Constructor for class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener
-
Creates a new instance of this class.
- dataAreaVisibilityChanged(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
-
- dataAreaVisibilityChanged(DataAreaChangeEvent) - Method in interface info.bioinfweb.libralign.dataarea.DataAreaModelListener
-
- dataAreaVisibilityChanged(DataAreaChangeEvent) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsEventForwarder
-
- 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
-
- DataModelReadInfo<M extends DataModel> - Class in info.bioinfweb.libralign.model.io
-
Stores information about a data model that has been read from a data source (e.g.
- DataModelReadInfo(M, AlignmentModel<?>, String) - Constructor for class info.bioinfweb.libralign.model.io.DataModelReadInfo
-
Creates a new instance of this class.
- DataModelReadInfo(M, AlignmentModel<?>) - Constructor for class info.bioinfweb.libralign.model.io.DataModelReadInfo
-
Creates a new instance of this class with no sequence ID.
- DataModelReadInfo(M) - Constructor for class info.bioinfweb.libralign.model.io.DataModelReadInfo
-
Creates a new instance of this class with associated aligmment model.
- 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
-
- 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
AlignmentSubArea
s 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.
- degapedIndex(String, int) - Method in class info.bioinfweb.libralign.model.utils.DegapedIndexCalculator
-
Calculates the ungapped index according to a position in the sequence containing gaps.
- DegapedIndexCalculator<T> - Class in info.bioinfweb.libralign.model.utils
-
Utility class that can calculate ungapped indices of sequences in an alignment model.
- DegapedIndexCalculator(AlignmentModel<T>, Set<T>) - Constructor for class info.bioinfweb.libralign.model.utils.DegapedIndexCalculator
-
Creates a new instance of this class.
- DegapedIndexCalculator(AlignmentModel<T>) - Constructor for class info.bioinfweb.libralign.model.utils.DegapedIndexCalculator
-
Creates a new instance of this class using a
HashSet
containing the gap token specified by the
token set of
model
.
- 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.
- 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
-
- 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
-
- 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
-
- DuplicateSequenceNameException - Exception in info.bioinfweb.libralign.model.exception
-
This exceptions is thrown if a sequence provided by an implementation of
AlignmentModel
shall be renamed and the a sequence with the new name is already present in the underlying data source.
- DuplicateSequenceNameException(AlignmentModel<?>, String) - Constructor for exception info.bioinfweb.libralign.model.exception.DuplicateSequenceNameException
-
Create a new instance of this class.