info.bioinfweb.libralign.pherogram.model

Class PherogramComponentModel

java.lang.Object

info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

Direct Known Subclasses:

PherogramAreaModel

public class PherogramComponentModel
extends java.lang.Object

The model used by all views displaying pherograms.

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
PherogramComponentModel(PherogramComponentModel model) Creates a copy from the specified instance.
PherogramComponentModel(PherogramProvider pherogramProvider) Creates a new instance of this class without any cut off pherogram ends.
PherogramComponentModel(PherogramProvider pherogramProvider, int leftCutPosition, int rightCutPosition) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
void	addListener(PherogramComponentModelListener listener)
protected void	fireLeftCutPositionChanged(int oldValue, PherogramAlignmentRelation oldEditableIndex, boolean moreEventsUpcoming)
protected void	firePherogramProviderChanged(PherogramProvider oldProvider, boolean reverseComplemented, boolean moreEventsUpcoming)
protected void	fireRightCutPositionChanged(int oldValue, PherogramAlignmentRelation oldEditableIndex, boolean moreEventsUpcoming)
protected PherogramAlignmentRelation	getAlignmentRelation(int baseCallIndex)
int	getLeftCutPosition() Returns the first base call index of the pherogram which has not been cut off.
PherogramProvider	getPherogramProvider()
int	getRightCutPosition() Returns the first base call index of the pherogram that has been cut off (so that the length of the visible area of the pherogram can be calculated as getRightCutPosition() - getLeftCutPosition()).
protected void	onSetLeftCutPosition(int oldBaseCallIndex, int newBaseCallIndex) Hook method to be implemented in inherited classes and called from within setLeftCutPosition(int).
protected void	onSetRightCutPosition(int oldBaseCallIndex, int newBaseCallIndex) Hook method to be implemented in inherited classes and called from within setRightCutPosition(int).
void	removeListener(PherogramComponentModelListener listener)
void	reverseComplement() Reverse complements the pherogram and swaps the left and right cut positions accordingly.
void	setLeftCutPosition(int baseCallIndex) Sets a new cut position for the left border of the visible part of the pherogram.
void	setProvider(PherogramProvider pherogramProvider) Sets a new pherogram provider and fires according events.
void	setRightCutPosition(int baseCallIndex) Sets a new cut position for the right border of the visible part of the pherogram.

Methods inherited from class java.lang.Object

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

Constructor Detail

PherogramComponentModel

public PherogramComponentModel(PherogramProvider pherogramProvider)

Creates a new instance of this class without any cut off pherogram ends.

Parameters:

pherogramProvider - the pherogram provider

Throws:

java.lang.NullPointerException - if null is specified for pherogramProvider

PherogramComponentModel

public PherogramComponentModel(PherogramComponentModel model)

Creates a copy from the specified instance. (The underlying pherogram provider instance is shared and not deep copied.)

Parameters:

model - the instance to be copied

Throws:

java.lang.NullPointerException - if null is specified for model

PherogramComponentModel

public PherogramComponentModel(PherogramProvider pherogramProvider,
                               int leftCutPosition,
                               int rightCutPosition)

Creates a new instance of this class.

Parameters:

pherogramProvider - the pherogram provider

leftCutPosition - the index in the base call sequence where the pherogram shall be cut off at the left end

rightCutPosition - the index in the base call sequence where the pherogram shall be cut off at the right end

Throws:

java.lang.NullPointerException - if null is specified for pherogramProvider

java.lang.IndexOutOfBoundsException - if leftCutPosition is not between 0 and and rightCutPosition or rightCutPosition if not between leftCutPosition and the length of the base call sequence defined by pherogramProvider

Method Detail

getPherogramProvider

public PherogramProvider getPherogramProvider()

reverseComplement

public void reverseComplement()

Reverse complements the pherogram and swaps the left and right cut positions accordingly.

setProvider

public void setProvider(PherogramProvider pherogramProvider)

Sets a new pherogram provider and fires according events. The left and right cut positions are set to the ends of the base call sequences of the new provider.

Parameters:

pherogramProvider - the new provider for trace curves and the base call sequence

Throws:

java.lang.NullPointerException - if null is specified for pherogramProvider

getLeftCutPosition

public int getLeftCutPosition()

Returns the first base call index of the pherogram which has not been cut off.

Returns:

a base call index > 0

onSetLeftCutPosition

protected void onSetLeftCutPosition(int oldBaseCallIndex,
                                    int newBaseCallIndex)

Hook method to be implemented in inherited classes and called from within setLeftCutPosition(int).

Parameters:

oldBaseCallIndex -

newBaseCallIndex -

setLeftCutPosition

public void setLeftCutPosition(int baseCallIndex)

Sets a new cut position for the left border of the visible part of the pherogram.

If this method is called on an instance of PherogramAreaModel the property PherogramAreaModel.getFirstSeqPos() is moved accordingly, so that the pherogram does not move relative to the sequence. If this shall be avoided PherogramAreaModel.setFirstSeqLeftCutPos(int, int) should be used instead.

Parameters:

baseCallIndex - the index of the first nucleotide in the base call sequence that shall be visible

Throws:

java.lang.IndexOutOfBoundsException - if baseCallIndex is not between 0 and and getRightCutPosition()

See Also:

PherogramAreaModel.setFirstSeqLeftCutPos(int, int)

getRightCutPosition

public int getRightCutPosition()

Returns the first base call index of the pherogram that has been cut off (so that the length of the visible area of the pherogram can be calculated as getRightCutPosition() - getLeftCutPosition()).

Returns:

a base call index >= getLeftCutPosition()

onSetRightCutPosition

protected void onSetRightCutPosition(int oldBaseCallIndex,
                                     int newBaseCallIndex)

Hook method to be implemented in inherited classes and called from within setRightCutPosition(int).

Parameters:

oldBaseCallIndex -

newBaseCallIndex -

setRightCutPosition

public void setRightCutPosition(int baseCallIndex)

Sets a new cut position for the right border of the visible part of the pherogram.

Parameters:

baseCallIndex - the index of the first nucleotide after the visible part in the base call sequence

Throws:

java.lang.IndexOutOfBoundsException - if baseCallIndex if not between getLeftCutPosition() and the length of the base call sequence defined by getPherogramProvider()

addListener

public void addListener(PherogramComponentModelListener listener)

removeListener

public void removeListener(PherogramComponentModelListener listener)

getAlignmentRelation

protected PherogramAlignmentRelation getAlignmentRelation(int baseCallIndex)

fireLeftCutPositionChanged

protected void fireLeftCutPositionChanged(int oldValue,
                                          PherogramAlignmentRelation oldEditableIndex,
                                          boolean moreEventsUpcoming)

fireRightCutPositionChanged

protected void fireRightCutPositionChanged(int oldValue,
                                           PherogramAlignmentRelation oldEditableIndex,
                                           boolean moreEventsUpcoming)

firePherogramProviderChanged

protected void firePherogramProviderChanged(PherogramProvider oldProvider,
                                            boolean reverseComplemented,
                                            boolean moreEventsUpcoming)