info.bioinfweb.libralign.dataarea.implementations.pherogram

Class PherogramArea

java.lang.Object

info.bioinfweb.tic.TICComponent

info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

info.bioinfweb.libralign.dataarea.DataArea

info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea

All Implemented Interfaces:

AlignmentModelChangeListener, PherogramComponent

public class PherogramArea
extends DataArea
implements PherogramComponent

A data area displaying a trace file resulting from Sanger sequencing.

Since:

0.1.0

Author:

Ben Stöver

See Also:

PherogramView

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_HEIGHT_FACTOR

Fields inherited from class info.bioinfweb.tic.TICComponent

DISPATCHER_MAP, repaintRequested

Constructor Summary

Constructors

Constructor and Description
PherogramArea(AlignmentContentArea owner, PherogramAreaModel model) 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.
protected SimpleSequenceInterval	calculatePaintRange(TICPaintEvent e)
boolean	copyBaseCallSequence(int startBaseCallIndex, int endBaseCallIndex) Copies a part of the base call sequence from the underlying model to the editable sequence this data area is attached to.
double	getEditableTokenWidth() Returns the width of the token in the editable sequence at #getFirstSeqPos(), considering the current zoom factor.
PherogramFormats	getFormats() Returns the format object that is used to paint the displayed pherogram.
double	getHeight() Returns the height in pixels considering the current zoom factor this component needs.
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.
PherogramAreaModel	getModel() Returns the model providing the base call sequence, the trace curves and the cut positions.
TokenPainter	getRelatedTokenPainter()
double	getVerticalScale()
boolean	isUpdateEditableSequence() Indicates whether the editable sequence should be updated if the cut positions of the model are modified.
void	paintPart(AlignmentPaintEvent e) Implementations of this method perform the painting of a part of the component.
boolean	setLeftCutPositionBySelection() Tries to set the left border where the base call sequence is cut off according to the left end of the current selection.
boolean	setRightCutPositionBySelection() Tries to set the right border where the base call sequence is cut off according to the right end of the current selection.
void	setUpdateEditableSequence(boolean updateEditableSequence) Specifies whether updated of the editable sequence shall be performed by this class automatically, if the cut positions in the underlying model are changed.
void	setVerticalScale(double value) Sets the horizontal zoom factor that shall used for displaying the trace curves.
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, 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_HEIGHT_FACTOR

public static final int DEFAULT_HEIGHT_FACTOR

See Also:

Constant Field Values

Constructor Detail

PherogramArea

public PherogramArea(AlignmentContentArea owner,
                     PherogramAreaModel model)

Creates a new instance of this class.

Parameters:

owner - the alignment area that will be containing the returned data area instance

model - the provider for the pherogram data to be displayed by the returned instance (Note that each instance of this class needs a separate model instance. model can anyway be shared with instances of PherogramTraceCurveView.)

Throws:

java.lang.IllegalArgumentException - if model is already owned by another pherogram area

Method Detail

calculatePaintRange

protected SimpleSequenceInterval calculatePaintRange(TICPaintEvent e)

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

getModel

public PherogramAreaModel getModel()

Description copied from interface: PherogramComponent

Returns the model providing the base call sequence, the trace curves and the cut positions.

Specified by:

getModel in interface PherogramComponent

Returns:

the model instance or null if not model has been specified yet

isUpdateEditableSequence

public boolean isUpdateEditableSequence()

Indicates whether the editable sequence should be updated if the cut positions of the model are modified.

Note that such updates only affect parts of the editable sequence that are or were associated with the cut off parts of the pherogram. In a reverse complement operation the editable sequence between the cut positions will never be updated. This needs to be done in application code e.g. by calling copyBaseCallSequence(int, int).

Returns:

true if updated in the editable sequence are performed automatically, false otherwise

See Also:

copyBaseCallSequence(int, int)

setUpdateEditableSequence

public void setUpdateEditableSequence(boolean updateEditableSequence)

Specifies whether updated of the editable sequence shall be performed by this class automatically, if the cut positions in the underlying model are changed.

Parameters:

updateEditableSequence - Specify true here, if automatic updated shall be performed from now on or false if the editable sequence shall be left unchanged from now on

copyBaseCallSequence

public boolean copyBaseCallSequence(int startBaseCallIndex,
                                    int endBaseCallIndex)

Copies a part of the base call sequence from the underlying model to the editable sequence this data area is attached to.

Note that this method will do nothing, if this instance has not been attached to any sequence yet.

Parameters:

startBaseCallIndex - the index of the first position in the base call sequence to be copied

endBaseCallIndex - the index after the last position of the base call sequence to be copied

Returns:

true if the editable sequence was updated, false if this area is currently not attached to any sequence

See Also:

isUpdateEditableSequence()

setLeftCutPositionBySelection

public boolean setLeftCutPositionBySelection()

Tries to set the left border where the base call sequence is cut off according to the left end of the current selection. If the left cut position is changed, the first sequence position is moved accordingly, so that the visible part of the pherogram still correctly aligns to the editable sequence.

If the right cut position would be located left of the left cut position after this operation, it will be moved to baseCallIndex as well. Note that this method does not test if the sequence, this area is attached to, is contained in the selection. It just relies on the selected columns.

Returns:

true if the right cut position was changed according to the selection (or the right cut position), false if that was not possible because the current right end of the selection lies outside of the pherogram

setRightCutPositionBySelection

public boolean setRightCutPositionBySelection()

Tries to set the right border where the base call sequence is cut off according to the right end of the current selection.

If the left cut position would be located right of the right cut position after this operation, it will be moved to baseCallIndex as well. Note that this method does not test if the sequence, this area is attached to, is contained in the selection. It just relies on the selected columns.

Returns:

true if the right cut position was changed according to the selection (or the right cut position), false if that was not possible

getVerticalScale

public double getVerticalScale()

Specified by:

getVerticalScale in interface PherogramComponent

setVerticalScale

public void setVerticalScale(double value)

Description copied from interface: PherogramComponent

Sets the horizontal zoom factor that shall used for displaying the trace curves.

Specified by:

setVerticalScale in interface PherogramComponent

Parameters:

value - the new zoom factor (must be greater than zero)

getFormats

public PherogramFormats getFormats()

Description copied from interface: PherogramComponent

Returns the format object that is used to paint the displayed pherogram.

Specified by:

getFormats in interface PherogramComponent

Returns:

the layout object containing color and font definitions

getEditableTokenWidth

public double getEditableTokenWidth()

Returns the width of the token in the editable sequence at #getFirstSeqPos(), considering the current zoom factor.

Returns:

the width of a token in the associated part of the editable sequence

getRelatedTokenPainter

public TokenPainter getRelatedTokenPainter()

getLengthBeforeStart

public double getLengthBeforeStart()

Description copied from class: DataArea

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.

Overrides:

getLengthBeforeStart in class DataArea

Returns:

This default implementation always returns 0.

getLengthAfterEnd

public double getLengthAfterEnd()

Description copied from class: DataArea

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.

Overrides:

getLengthAfterEnd in class DataArea

Returns:

This default implementation always returns 0.

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.

Specified by:

afterSequenceChange in interface AlignmentModelChangeListener

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.

Specified by:

afterSequenceRenamed in interface AlignmentModelChangeListener

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.

Specified by:

afterTokenChange in interface AlignmentModelChangeListener

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.

Specified by:

afterModelChanged in interface AlignmentModelChangeListener

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