Uses of Class
info.bioinfweb.libralign.alignmentarea.AlignmentArea

Packages that use AlignmentArea

Package	Description
info.bioinfweb.libralign.actions
info.bioinfweb.libralign.alignmentarea	Contains basic implementations for displaying an alignment area.
info.bioinfweb.libralign.alignmentarea.content	Contains classes related to AlignmentContentArea which display the contents of an alignment.
info.bioinfweb.libralign.alignmentarea.label	Contains general classes implementing the labeling of sequences and data areas.
info.bioinfweb.libralign.alignmentarea.order
info.bioinfweb.libralign.alignmentarea.paintsettings	Contains classes managing the painting of the contents of AlignmentAreas.
info.bioinfweb.libralign.alignmentarea.selection	Contains classes necessary to perform the selection of rows and/or columns in an AlignmentArea.
info.bioinfweb.libralign.alignmentarea.tokenpainter	Contains implementations of TokenPainter
info.bioinfweb.libralign.dataarea	Contains DataArea from which all data areas used in LibrAlign must be inherited as well as related classes and a set of general data area implementations provided with LibrAlign which are located in the subpackage implementations.
info.bioinfweb.libralign.dataarea.implementations	Contains classes that implement a concrete data area.
info.bioinfweb.libralign.dataarea.implementations.charset	Contains data area related classes to display character sets of an alignment.
info.bioinfweb.libralign.dataarea.implementations.sequenceindex
info.bioinfweb.libralign.model.utils	Contains utility classes to be used with implementations of AlignmentModel.
info.bioinfweb.libralign.multiplealignments	Contains classes used in the implementation of MultipleAlignmentsContainer which allow to combine several AlignmentAreas.

Uses of AlignmentArea in info.bioinfweb.libralign.actions

Methods in info.bioinfweb.libralign.actions that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	AlignmentActionProvider.getAlignmentArea() Returns the view this instance is associated with.

Constructors in info.bioinfweb.libralign.actions with parameters of type AlignmentArea

Constructor and Description
AlignmentActionProvider(AlignmentArea alignmentArea) Creates a new instance of this class that is associated with the specified view and model.

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea

Methods in info.bioinfweb.libralign.alignmentarea that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	ScrollContainerSwingAlignmentArea.getIndependentComponent()
AlignmentArea	AbstractSWTAlignmentArea.getIndependentComponent()
AlignmentArea	DirectPaintingSWTAlignmentArea.getIndependentComponent()
AlignmentArea	DirectPaintingSWTAlignmentContentScroller.getIndependentComponent()

Constructors in info.bioinfweb.libralign.alignmentarea with parameters of type AlignmentArea

Constructor and Description
AbstractSWTAlignmentArea(AlignmentArea independentComponent, org.eclipse.swt.widgets.Composite parent, int style)
DirectPaintingSWTAlignmentArea(AlignmentArea ticComponent, org.eclipse.swt.widgets.Composite parent, int style)
DirectPaintingSWTAlignmentContentScroller(AlignmentArea ticComponent, org.eclipse.swt.widgets.Composite parent, int style)
ScrollContainerSwingAlignmentArea(AlignmentArea independentComponent)
ScrollContainerSWTAlignmentArea(AlignmentArea owner, org.eclipse.swt.widgets.Composite parent, int style) Creates a new instance of this class.

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea.content

Methods in info.bioinfweb.libralign.alignmentarea.content that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	AlignmentContentArea.getOwner()
AlignmentArea	CursorSelectionInputListener.getOwner()
AlignmentArea	AlignmentPaintEvent.getParentAlignmentArea() Returns the alignment area that contains the component that triggered this event.

Constructors in info.bioinfweb.libralign.alignmentarea.content with parameters of type AlignmentArea

Constructor and Description
AlignmentContentArea(AlignmentArea owner) Creates a new instance of this class.
AlignmentPaintEvent(java.lang.Object source, AlignmentArea parentAlignmentArea, int firstColumn, int lastColumn, java.awt.Graphics2D graphics, java.awt.geom.Rectangle2D rectangle) Creates a new instance of this class.
AlignmentSubAreaIterator(AlignmentArea area)
CursorSelectionInputListener(AlignmentArea owner)

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea.label

Methods in info.bioinfweb.libralign.alignmentarea.label that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	AlignmentLabelArea.getOwner() Returns the alignment area that uses this instance.

Constructors in info.bioinfweb.libralign.alignmentarea.label with parameters of type AlignmentArea

Constructor and Description
AlignmentLabelArea(AlignmentArea owner) Creates a new instance of this class.

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea.order

Methods in info.bioinfweb.libralign.alignmentarea.order that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	SequenceOrder.getOwner()

Constructors in info.bioinfweb.libralign.alignmentarea.order with parameters of type AlignmentArea

Constructor and Description
SequenceOrder(AlignmentArea owner) Crates a new instance of this class and loads the names from the underlying data source of the specified owner, if it has a data source.

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea.paintsettings

Methods in info.bioinfweb.libralign.alignmentarea.paintsettings that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	PaintSettings.getOwner() Returns the alignment area using this instance.

Constructors in info.bioinfweb.libralign.alignmentarea.paintsettings with parameters of type AlignmentArea

Constructor and Description
PaintSettings(AlignmentArea owner) Creates a new instance of this class using default values for the properties.

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea.selection

Methods in info.bioinfweb.libralign.alignmentarea.selection that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	AlignmentCursor.getOwner()
AlignmentArea	SelectionModel.getOwner() Returns the alignment content area that uses this selection object.

Constructors in info.bioinfweb.libralign.alignmentarea.selection with parameters of type AlignmentArea

Constructor and Description
AlignmentCursor(AlignmentArea owner)
SelectionModel(AlignmentArea owner) Creates a new instance of this class.

Uses of AlignmentArea in info.bioinfweb.libralign.alignmentarea.tokenpainter

Methods in info.bioinfweb.libralign.alignmentarea.tokenpainter with parameters of type AlignmentArea

Modifier and Type	Method and Description
protected void	AbstractBioPolymerTokenPainter.doPaintToken(AlignmentArea alignmentArea, java.lang.String sequenceID, int columnIndex, java.lang.Object token, java.lang.String tokenRepresentation, java.awt.Graphics2D g, java.awt.geom.Rectangle2D paintArea, java.awt.Color selectionColor)
protected abstract void	AbstractTokenPainter.doPaintToken(AlignmentArea alignmentModel, java.lang.String sequenceID, int columnIndex, java.lang.Object token, java.lang.String tokenRepresentation, java.awt.Graphics2D g, java.awt.geom.Rectangle2D paintArea, java.awt.Color overlayColor) Method to be implemented by inherited classes performing the actual paint operation.
protected void	SingleColorTokenPainter.doPaintToken(AlignmentArea alignmentArea, java.lang.String sequenceID, int columnIndex, java.lang.Object token, java.lang.String tokenRepresentation, java.awt.Graphics2D g, java.awt.geom.Rectangle2D area, java.awt.Color selectionColor)
java.awt.Color	ColorOverlay.getColor(AlignmentArea alignmentArea, java.lang.String sequenceID, int columnIndex) Determines the color to overlay the specified cell of the alignment.
void	AbstractTokenPainter.paintToken(AlignmentArea alignmentArea, java.lang.String sequenceID, int columnIndex, java.awt.Graphics2D g, java.awt.geom.Rectangle2D paintArea, java.awt.Color selectionColor) Default implementation that delegates to #doPaintToken(AlignmentModel, Object, String, Graphics2D, Rectangle2D) and determines the string representation of the specified token from the token set of the specified alignment model.
void	TokenPainter.paintToken(AlignmentArea alignmentArea, java.lang.String sequenceID, int columnIndex, java.awt.Graphics2D g, java.awt.geom.Rectangle2D paintArea, java.awt.Color selectionColor) Paints a representation of the specified token filling up the specified area.

Uses of AlignmentArea in info.bioinfweb.libralign.dataarea

Methods in info.bioinfweb.libralign.dataarea that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	DataArea.getLabeledAlignmentArea() Returns the alignment area that is labeled by this data area.
AlignmentArea	DataAreasModel.getOwner() Returns the alignment content area that uses this instance.

Constructors in info.bioinfweb.libralign.dataarea with parameters of type AlignmentArea

Constructor and Description
DataArea(AlignmentContentArea owner, AlignmentArea labeledArea) Creates a new instance of this class.
DataAreasModel(AlignmentArea owner) Creates a new instance of this class.

Uses of AlignmentArea in info.bioinfweb.libralign.dataarea.implementations

Constructors in info.bioinfweb.libralign.dataarea.implementations with parameters of type AlignmentArea

Constructor and Description
ConsensusSequenceArea(AlignmentContentArea owner, AlignmentArea labeledAlignmentArea) Creates a new instance of this class that uses the specified sequence data provider.
LabelDataArea(AlignmentContentArea owner, AlignmentArea labeledArea)
LabelDataArea(AlignmentContentArea owner, AlignmentArea labeledArea, java.lang.String text)
LabelDataArea(AlignmentContentArea owner, AlignmentArea labeledArea, java.lang.String text, boolean alignToFirstColumn, boolean alignToScrollPosition)

Uses of AlignmentArea in info.bioinfweb.libralign.dataarea.implementations.charset

Constructors in info.bioinfweb.libralign.dataarea.implementations.charset with parameters of type AlignmentArea

Constructor and Description
CharSetArea(AlignmentContentArea owner, AlignmentArea labeledAlignmentArea) Creates a new instance of this class with an empty data model.
CharSetArea(AlignmentContentArea owner, AlignmentArea labeledAlignmentArea, CharSetDataModel model) Creates a new instance of this class.

Uses of AlignmentArea in info.bioinfweb.libralign.dataarea.implementations.sequenceindex

Constructors in info.bioinfweb.libralign.dataarea.implementations.sequenceindex with parameters of type AlignmentArea

Constructor and Description
SequenceIndexArea(AlignmentContentArea owner, AlignmentArea labeledArea) Creates a new instance of this class.

Uses of AlignmentArea in info.bioinfweb.libralign.model.utils

Methods in info.bioinfweb.libralign.model.utils with parameters of type AlignmentArea

Modifier and Type	Method and Description
static java.lang.String	AlignmentModelUtils.selectionAsString(AlignmentArea area, boolean separateBySpace) Converts the current selection to a String.

Uses of AlignmentArea in info.bioinfweb.libralign.multiplealignments

Methods in info.bioinfweb.libralign.multiplealignments that return AlignmentArea

Modifier and Type	Method and Description
AlignmentArea	MultipleAlignmentsContainer.getFocusedAlignmentArea() Returns the alignment area contained in this component, that currently has the focus.
AlignmentArea	ToolkitSpecificMultipleAlignmentsContainer.getFocusedAlignmentArea() Returns the alignment area contained in this component, that currently has the focus.
AlignmentArea	SwingMultipleAlignmentsContainer.getFocusedAlignmentArea()
AlignmentArea	SWTMultipleAlignmentsContainer.getFocusedAlignmentArea()

Methods in info.bioinfweb.libralign.multiplealignments with parameters of type AlignmentArea

Modifier and Type	Method and Description
protected void	AlignmentAreaList.afterReplace(int index, AlignmentArea previousElement, AlignmentArea currentElement)

Method parameters in info.bioinfweb.libralign.multiplealignments with type arguments of type AlignmentArea

Modifier and Type	Method and Description
protected void	AlignmentAreaList.afterAdd(int index, java.util.Collection<? extends AlignmentArea> addedElements)
protected void	AlignmentAreaList.afterRemove(int index, java.util.Collection<? extends AlignmentArea> removedElements)
protected void	AlignmentAreaList.beforeAdd(int index, java.util.Collection<? extends AlignmentArea> addedElements)