info.bioinfweb.libralign.dataarea.implementations.sequenceindex

Class SequenceIndexArea

java.lang.Object

info.bioinfweb.tic.TICComponent

info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

info.bioinfweb.libralign.dataarea.DataArea

info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea

All Implemented Interfaces:

AlignmentModelChangeListener

public class SequenceIndexArea
extends DataArea

A data area displaying the indices of aligned sequences.

You would usually use this component in the head area of an AlignmentArea but it is possible to insert it at any position.

The labeling interval if this area is calculated from the space needed to label the highest index in the associated alignment model. Note that due to rounding effects the label interval may vary by one depending on the zoom factor.

Since:

0.2.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static double	DASH_LENGTH_FACTOR The length of a dash
static java.awt.Stroke	DASH_STROKE The stroke used to paint the dashes
static int	DEFAULT_FIRST_INDEX The default value returned by getFirstIndex() if it has not been changed.
static double	LABEL_LEFT_DISTANCE_FACTOR The distance of the labels to their dash
static double	LABEL_TOP_DISTANCE_FACTOR The distance of the labels to the border of the component
static double	LABELED_DASH_LENGTH_FACTOR The length of a dash with a label

Fields inherited from class info.bioinfweb.tic.TICComponent

DISPATCHER_MAP, repaintRequested

Constructor Summary

Constructors

Constructor and Description
SequenceIndexArea(AlignmentContentArea owner) Creates a new instance of this class using the parent alignment area of owner as the labeled area.
SequenceIndexArea(AlignmentContentArea owner, AlignmentArea labeledArea) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
<T,U> void	afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current) Called if this listener was moved to another instance of AlignmentModel.
<T> void	afterSequenceChange(SequenceChangeEvent<T> e) Called after a sequence has been inserted, removed or replaced.
<T> void	afterSequenceRenamed(SequenceRenamedEvent<T> e) Called after a sequence was renamed.
<T> void	afterTokenChange(TokenChangeEvent<T> e) Called after a single token or a set of tokens has been inserted, removed or replaced.
int	getFirstIndex() Returns the index that will be displayed for the first column of the alignment area.
double	getHeight() Returns the height in pixels considering the current zoom factor this component needs.
void	paintPart(AlignmentPaintEvent e) Implementations of this method perform the painting of a part of the component.
void	setFirstIndex(int firstIndex) Sets a new index that will be displayed for the first column of the alignment area.
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.dataarea.DataArea

getLabeledAlignmentArea, getLabeledAlignmentModel, getLengthAfterEnd, getLengthBeforeStart, getList, isVisible, setList, setVisible

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

createLabelSubArea, getLabelSubArea, getOwner, getSize, paint, 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

Field Detail

DEFAULT_FIRST_INDEX

public static final int DEFAULT_FIRST_INDEX

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

See Also:

Constant Field Values

DASH_STROKE

public static final java.awt.Stroke DASH_STROKE

The stroke used to paint the dashes

DASH_LENGTH_FACTOR

public static final double DASH_LENGTH_FACTOR

The length of a dash

See Also:

Constant Field Values

LABELED_DASH_LENGTH_FACTOR

public static final double LABELED_DASH_LENGTH_FACTOR

The length of a dash with a label

See Also:

Constant Field Values

LABEL_TOP_DISTANCE_FACTOR

public static final double LABEL_TOP_DISTANCE_FACTOR

The distance of the labels to the border of the component

See Also:

Constant Field Values

LABEL_LEFT_DISTANCE_FACTOR

public static final double LABEL_LEFT_DISTANCE_FACTOR

The distance of the labels to their dash

See Also:

Constant Field Values

Constructor Detail

SequenceIndexArea

public SequenceIndexArea(AlignmentContentArea owner,
                         AlignmentArea labeledArea)

Creates a new instance of this class.

Parameters:

owner - the alignment area that is going to contain this data area

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.)

SequenceIndexArea

public SequenceIndexArea(AlignmentContentArea owner)

Creates a new instance of this class using the parent alignment area of owner as the labeled area.

Parameters:

owner - the alignment area that is going to contain this data area

Method Detail

paintPart

public void paintPart(AlignmentPaintEvent e)

Description copied from class: AlignmentSubArea

Implementations of this method perform the painting of a part of the component. It is used when an AlignmentArea is set to contain no subcomponents but to paint its contents directly.

This default implementation always throws an UnsupportedOperationException. Note that therefore inherited classes must either overwrite this method or #createComponent() in order to return an instance there that does not delegate to this method.

Note that the aim of this method is to allow painting very wide components, which may have a width larger than Integer.MAX_VALUE. Therefore painting coordinates are stored as double values (using Graphics2D and Rectangle2D.Double). Implementations should not calculate pixel coordinates as ints at any time to avoid overflows, but only use double (or possibly long if necessary).

Overrides:

paintPart in class AlignmentSubArea

Parameters:

e - the paint event providing information on the area to be painted, the graphics context and tool methods.

validLocations

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

Description copied from class: DataArea

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);

Specified by:

validLocations in class DataArea

Returns:

a non-empty set of locations

getFirstIndex

public int getFirstIndex()

Returns the index that will be displayed for the first column of the alignment area.

The default value is 1. Note that the methods of AlignmentArea and associated classes will always use 0 as the index of the first column no matter which value is set here. It is used for the GUI output of this data area only.

Returns:

the displayed index of the first column

setFirstIndex

public void setFirstIndex(int firstIndex)

Sets a new index that will be displayed for the first column of the alignment area.

The methods of AlignmentArea and associated classes will always use 0 as the index of the first column no matter which value is specified here. It is used for the GUI output of this data area only.

Parameters:

firstIndex - the new index display for the first column

getHeight

public double getHeight()

Description copied from class: AlignmentSubArea

Returns the height in pixels considering the current zoom factor this component needs.

Specified by:

getHeight in class AlignmentSubArea

Returns:

a double value > 0

afterSequenceChange

public <T> void afterSequenceChange(SequenceChangeEvent<T> e)

Description copied from interface: AlignmentModelChangeListener

Called after a sequence has been inserted, removed or replaced.

Parameters:

e - the event object containing information on the change

afterSequenceRenamed

public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e)

Description copied from interface: AlignmentModelChangeListener

Called after a sequence was renamed.

Parameters:

e - the event object containing information on the change

afterTokenChange

public <T> void afterTokenChange(TokenChangeEvent<T> e)

Description copied from interface: AlignmentModelChangeListener

Called after a single token or a set of tokens has been inserted, removed or replaced.

Parameters:

e - the event object containing information on the change

afterModelChanged

public <T,U> void afterModelChanged(AlignmentModel<T> previous,
                                    AlignmentModel<U> current)

Description copied from interface: AlignmentModelChangeListener

Called if this listener was moved to another instance of AlignmentModel.

This happens if the alignment model of an AlignmentArea was changed.

Parameters:

previous - the alignment model this listener was attached to before the event happened

current - the new alignment model this listener is attached to now