info.bioinfweb.libralign.pherogram.model

Class PherogramAreaModel

java.lang.Object

info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

info.bioinfweb.libralign.pherogram.model.PherogramAreaModel

All Implemented Interfaces:

DataModel

public class PherogramAreaModel
extends PherogramComponentModel
implements DataModel

The data area model of a PherogramArea containing the pherogram source, as well as cut positions, the column where the pherogram is attached to the editable sequence and pherogram distortion information.

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
PherogramAreaModel(PherogramComponentModel model) Creates a new instance based on the specified pherogram component model instance.
PherogramAreaModel(PherogramProvider provider) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
void	addShiftChange(int baseCallIndex, int shiftChangeAddend)
PherogramAlignmentRelation	baseCallIndexByEditableIndex(int editableIndex)
ScaledPherogramDistortion	createPherogramDistortion()
void	deleteCutOffDistortions() Deletes all distortions of the base call sequence to the editable sequence in the cut off areas at the beginning and the end of the pherogram and moves PherogramArea#getFirstSeqPos() of the owner accordingly, so that the visible part of the pherogram still correctly aligns to the editable sequence.
PherogramAlignmentRelation	editableIndexByBaseCallIndex(int baseCallIndex) Returns the index in the editable alignment sequence that corresponds to the specified index in the base call sequence.
protected PherogramAlignmentRelation	getAlignmentRelation(int baseCallIndex)
int	getFirstSeqPos() Returns the position in the sequence this pherogram is attached to where the output of the visible part of the pherogram starts.
PherogramArea	getOwner() The pherogram area associated with this model.
int	getShiftChangeCount() Returns the number of shift changes that are currently contained in this model.
protected void	onSetLeftCutPosition(int oldBaseCallIndex, int newBaseCallIndex) Hook method to be implemented in inherited classes and called from within PherogramComponentModel.setLeftCutPosition(int).
protected void	onSetRightCutPosition(int oldBaseCallIndex, int newBaseCallIndex) Hook method to be implemented in inherited classes and called from within PherogramComponentModel.setRightCutPosition(int).
void	reverseComplement() Reverse complements the pherogram and swaps the left and right cut positions accordingly.
void	setFirstSeqLeftCutPos(int firstSeqPos, int leftCutPos) Allows to specify a new first sequence and left cut position at the same time.
void	setFirstSeqPos(int firstSeqPos) Sets the index in the sequence this pherogram is attached to where the displaying of the visible part of the pherogram starts.
void	setOwner(PherogramArea owner) Specifies a new owning pherogram area for this instance.
void	setShiftChange(int baseCallIndex, int shiftChange) Adds or replaces a change in the shift between the editable sequence in the alignment and the base call sequence.
int	shiftAtBaseCallIndex(int baseCallIndex)
java.util.ListIterator<ShiftChange>	shiftChangeIterator()
java.util.ListIterator<ShiftChange>	shiftChangeIterator(int listIndex)
java.util.ListIterator<ShiftChange>	shiftChangeIteratorByBaseCallIndex(int baseCallIndex)

Methods inherited from class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

addListener, fireLeftCutPositionChanged, firePherogramProviderChanged, fireRightCutPositionChanged, getLeftCutPosition, getPherogramProvider, getRightCutPosition, removeListener, setLeftCutPosition, setProvider, setRightCutPosition

Methods inherited from class java.lang.Object

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

Constructor Detail

PherogramAreaModel

public PherogramAreaModel(PherogramProvider provider)

Creates a new instance of this class.

Note that some methods of this class may throw NullPointerExceptions as long as no owner has been provided using setOwner(PherogramArea). Note that each PherogramArea needs to have its own model instance. It is not possible to share an instance between several pherogram areas. Anyway an unlimited number of instances of PherogramTraceCurveView can use an instance if this class at the same time and in addition to one pherogram model.

Parameters:

pherogramProvider - the pherogram provider

Throws:

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

PherogramAreaModel

public PherogramAreaModel(PherogramComponentModel model)

Creates a new instance based on the specified pherogram component model instance. (The underlying pherogram provider instance is shared and not deep copied.)

Note that some methods of this class may throw NullPointerExceptions as long as no owner has been provided using setOwner(PherogramArea). Note that each PherogramArea needs to have its own model instance. It is not possible to share an instance between several pherogram areas. Anyway an unlimited number of instances of PherogramTraceCurveView can use an instance if this class at the same time and in addition to one pherogram model.

Parameters:

model - the source pherogram component model

Throws:

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

Method Detail

getOwner

public PherogramArea getOwner()

The pherogram area associated with this model.

Returns:

the associated data area

setOwner

public void setOwner(PherogramArea owner)

Specifies a new owning pherogram area for this instance. This method will usually not need to be called from application code directly, since it is called in the constructor of PherogramArea.

Note that specifying a different pherogram area here, than the one that currently uses this instance is illegal and can lead to unexpected behavior of the displaying pherogram area.

Parameters:

owner - the pherogram area that uses this model

Throws:

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

getFirstSeqPos

public int getFirstSeqPos()

Returns the position in the sequence this pherogram is attached to where the output of the visible part of the pherogram starts.

Returns:

a valid index in the sequence carrying this data area

setFirstSeqPos

public void setFirstSeqPos(int firstSeqPos)

Sets the index in the sequence this pherogram is attached to where the displaying of the visible part of the pherogram starts.

Parameters:

firstSeqPos - the new index

getAlignmentRelation

protected PherogramAlignmentRelation getAlignmentRelation(int baseCallIndex)

Overrides:

getAlignmentRelation in class PherogramComponentModel

onSetLeftCutPosition

protected void onSetLeftCutPosition(int oldBaseCallIndex,
                                    int newBaseCallIndex)

Description copied from class: PherogramComponentModel

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

Overrides:

onSetLeftCutPosition in class PherogramComponentModel

onSetRightCutPosition

protected void onSetRightCutPosition(int oldBaseCallIndex,
                                     int newBaseCallIndex)

Description copied from class: PherogramComponentModel

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

Overrides:

onSetRightCutPosition in class PherogramComponentModel

setFirstSeqLeftCutPos

public void setFirstSeqLeftCutPos(int firstSeqPos,
                                  int leftCutPos)

Allows to specify a new first sequence and left cut position at the same time. This method shall be used if both valid values for both properties are defined (e.g. in an external data source like a file) and firstSeqPos shall not be moved accordingly when leftCutPos is set, like it is done in PherogramComponentModel.setLeftCutPosition(int).

Parameters:

firstSeqPos - the new index in the editable sequence to which the first nucleotide of the base call sequence that is not cut off is aligned

leftCutPos - the new left cut position

editableIndexByBaseCallIndex

public PherogramAlignmentRelation editableIndexByBaseCallIndex(int baseCallIndex)

Returns the index in the editable alignment sequence that corresponds to the specified index in the base call sequence.

Parameters:

baseCallIndex - the absolute index in the base call sequence

Returns:

the absolute index in the editable sequence or #GAP if the according position in the editable sequence has been deleted or #OUT_OF_RANGE if the specified base call index lies outside the range of the pherogram

baseCallIndexByEditableIndex

public PherogramAlignmentRelation baseCallIndexByEditableIndex(int editableIndex)

shiftAtBaseCallIndex

public int shiftAtBaseCallIndex(int baseCallIndex)

setShiftChange

public void setShiftChange(int baseCallIndex,
                           int shiftChange)

Adds or replaces a change in the shift between the editable sequence in the alignment and the base call sequence.

If a shiftChange of 0 is specified the entry in the underlying shift list will be deleted.

Parameters:

baseCallIndex - the first position in the base call sequence where the shift change shall be valid

shiftChange - a positive of negative for the the shift change (number of positions in the editable sequence)

addShiftChange

public void addShiftChange(int baseCallIndex,
                           int shiftChangeAddend)

shiftChangeIterator

public java.util.ListIterator<ShiftChange> shiftChangeIterator(int listIndex)

shiftChangeIterator

public java.util.ListIterator<ShiftChange> shiftChangeIterator()

shiftChangeIteratorByBaseCallIndex

public java.util.ListIterator<ShiftChange> shiftChangeIteratorByBaseCallIndex(int baseCallIndex)

getShiftChangeCount

public int getShiftChangeCount()

Returns the number of shift changes that are currently contained in this model.

Returns:

the number of shift changes

Since:

0.4.0

deleteCutOffDistortions

public void deleteCutOffDistortions()

Deletes all distortions of the base call sequence to the editable sequence in the cut off areas at the beginning and the end of the pherogram and moves PherogramArea#getFirstSeqPos() of the owner accordingly, so that the visible part of the pherogram still correctly aligns to the editable sequence.

This method is intended for internal use in LibrAlign and is called from within PherogramArea#setLeftCutPosition(int) and PherogramArea#setRightCutPosition(int). Usually there should be no need to call it in application code directly.

reverseComplement

public void reverseComplement()

Description copied from class: PherogramComponentModel

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

Overrides:

reverseComplement in class PherogramComponentModel

createPherogramDistortion

public ScaledPherogramDistortion createPherogramDistortion()