info.bioinfweb.libralign.dataarea

Class DataArea

java.lang.Object

info.bioinfweb.tic.TICComponent

info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

info.bioinfweb.libralign.dataarea.DataArea

All Implemented Interfaces:

AlignmentModelChangeListener

Direct Known Subclasses:

CharSetArea, ConsensusSequenceArea, LabelDataArea, PherogramArea, SequenceIndexArea

public abstract class DataArea
extends AlignmentSubArea
implements AlignmentModelChangeListener

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

Since:

0.0.0

Author:

Ben Stöver

Field Summary

Fields inherited from class info.bioinfweb.tic.TICComponent

DISPATCHER_MAP, repaintRequested

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
AlignmentArea	getLabeledAlignmentArea() Returns the alignment area that is labeled by this data area.
AlignmentModel<?>	getLabeledAlignmentModel() Convenience method that returns the alignment model of the labeled alignment area.
double	getLengthAfterEnd() Returns the length in pixels considering the current zoom factor this component needs to display data right of the last alignment column.
double	getLengthBeforeStart() Returns the length in pixels considering the current zoom factor this component needs to display data left of the first alignment column.
DataAreaList	getList() Returns the list this data area is contained in.
boolean	isVisible() Indicates whether this data area is currently faded in or out in the containing alignment area.
void	setList(DataAreaList list) Updates the list this element is contained in.
boolean	setVisible(boolean visible) Fades this data area in or out and lets the containing alignment area repaint, if necessary.
abstract java.util.Set<DataAreaListType>	validLocations() The result should enumerate all valid locations where the implementing data area is allowed to be located.

Methods inherited from class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

createLabelSubArea, getHeight, getLabelSubArea, getOwner, getSize, paint, paintPart, repaint

Methods inherited from class info.bioinfweb.tic.TICComponent

addKeyListener, addMouseListener, addMouseWheelListener, assignSize, dispatchEvent, getCurrentToolkit, getKeyListenersSet, getMouseListenersSet, getMouseWheelListenersSet, getSwingComponentClassName, getSwingComponentConstructorParameters, getSWTComponentClassName, getSWTComponentConstructorParameters, getToolkitComponent, hasDefinedSize, hasToolkitComponent, isUpdateOngoing, removeKeyListener, removeMouseListener, removeWheelMouseListener, setToolkitComponent, setUpdateOngoing

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface info.bioinfweb.libralign.model.AlignmentModelChangeListener

afterModelChanged, afterSequenceChange, afterSequenceRenamed, afterTokenChange

Constructor Detail

DataArea

public DataArea(AlignmentContentArea owner,
                AlignmentArea labeledArea)

Creates a new instance of this class.

Parameters:

owner - the alignment area that will contain this instance

labeledArea - the alignment area displays the sequence which is labeled by the new instance (If null is specified here, the parent alignment area of owner will be assumed.)

Method Detail

getLabeledAlignmentArea

public AlignmentArea getLabeledAlignmentArea()

Returns the alignment area that is labeled by this data area.

Note that inside a MultipleAlignmentsContainer a data area could be located in a different alignment area than the related alignment data. Therefore the returned instance is not necessarily identical with the instance returned by getOwner().getOwner().

Returns:

the labeled alignment area

See Also:

getLabeledAlignmentModel()

getLabeledAlignmentModel

public AlignmentModel<?> getLabeledAlignmentModel()

Convenience method that returns the alignment model of the labeled alignment area.

Returns:

the alignment model providing the sequence data related to the contents of this data area

See Also:

getLabeledAlignmentArea()

getList

public DataAreaList getList()

Returns the list this data area is contained in. This list defines whether this data area is located above or underneath the alignment or attached to a sequence.

setList

public void setList(DataAreaList list)

Updates the list this element is contained in.

Parameters:

list - the list that contains this element

isVisible

public boolean isVisible()

Indicates whether this data area is currently faded in or out in the containing alignment area.

It does not state whether this data area is contained a area of the alignment area that is currently visible on the screen.

Returns:

true if this data area is faded in, false if it is faded out

setVisible

public boolean setVisible(boolean visible)

Fades this data area in or out and lets the containing alignment area repaint, if necessary.

Parameters:

visible -

Returns:

true if the state of this element was changed, false otherwise

validLocations

public abstract java.util.Set<DataAreaListType> validLocations()

The result should enumerate all valid locations where the implementing data area is allowed to be located.

An implementation for a data area could be located everywhere could look like this:

return EnumSet.of(DataAreaListType.TOP, DataAreaListType.BOTTOM, DataAreaListType.SEQUENCE);

Returns:

a non-empty set of locations

getLengthBeforeStart

public double getLengthBeforeStart()

Returns the length in pixels considering the current zoom factor this component needs to display data left of the first alignment column.

Overwrite this method if your component displays additional information left of the alignment.

Returns:

This default implementation always returns 0.

getLengthAfterEnd

public double getLengthAfterEnd()

Returns the length in pixels considering the current zoom factor this component needs to display data right of the last alignment column.

Overwrite this method if your component displays additional information right of the alignment.

Returns:

This default implementation always returns 0.