com.pacbio.secondary.vis.data.variableresolution.model

Class VariableResolutionDataModelsMerger

java.lang.Object

com.pacbio.secondary.vis.data.base.BaseDataModel

com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger

All Implemented Interfaces:

IVariableResolutionDataModelServer, IChangeNotifier, java.lang.Iterable<VariableValuesDataRecord>, java.util.EventListener, javax.swing.event.ChangeListener

public class VariableResolutionDataModelsMerger
extends VariableResolutionDataModel
implements javax.swing.event.ChangeListener

Merges an array of VariableResolutionDataModelsMerger

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

BaseDataModel.eDataType

Field Summary

Fields inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

changeNotifier, data_type, mc

Constructor Summary

Constructors

Constructor and Description
VariableResolutionDataModelsMerger()

Method Summary

Methods

Modifier and Type	Method and Description
void	addModel(IVariableResolutionDataModelServer model)
void	clear()
void	detach()
VariableValuesDataRecord	get(int j)
java.util.LinkedList<java.lang.String>	getDataInfo()
java.util.LinkedList<java.lang.String>	getFileHeader()
java.util.LinkedList<java.lang.String>	getFilePath()
VariableResolutionDataSetValues	getMinMaxValues()
protected void	invalidate()
java.util.Iterator<VariableValuesDataRecord>	iterator()
void	setModels(java.util.List<IVariableResolutionDataModelServer> newModels)
int	size() Returns the overall number of markers.
void	stateChanged(javax.swing.event.ChangeEvent e)
java.util.Collection<VariableValuesDataRecord>	toCollection()
protected void	updateMinMaxValues(IVariableResolutionDataModelServer model)
protected void	validate()
protected void	validateold() Deprecated.

Methods inherited from class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

copyAsMarkerCollectionArray, getNumItems, getResult, getResults

Methods inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

addChangeListener, fireChangeEvent, getDataType, getDataTypeAsString, getMarkersForContig, getNumContigs, hasData, isMarkerType, isModificationsType, isReadsType, isSummaryType, isVariantsType, removeChangeListener, setTypeAndNumContigs

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.pacbio.secondary.vis.gui.evt.IChangeNotifier

addChangeListener, removeChangeListener

Constructor Detail

VariableResolutionDataModelsMerger

public VariableResolutionDataModelsMerger()

Method Detail

getMinMaxValues

public VariableResolutionDataSetValues getMinMaxValues()

Specified by:

getMinMaxValues in interface IVariableResolutionDataModelServer

clear

public void clear()

detach

public void detach()

Specified by:

detach in interface IVariableResolutionDataModelServer

Overrides:

detach in class VariableResolutionDataModel

setModels

public void setModels(java.util.List<IVariableResolutionDataModelServer> newModels)

addModel

public void addModel(IVariableResolutionDataModelServer model)

updateMinMaxValues

protected void updateMinMaxValues(IVariableResolutionDataModelServer model)

validate

protected void validate()

invalidate

protected void invalidate()

stateChanged

public void stateChanged(javax.swing.event.ChangeEvent e)

Specified by:

stateChanged in interface javax.swing.event.ChangeListener

get

public VariableValuesDataRecord get(int j)

Specified by:

get in interface IVariableResolutionDataModelServer

getFilePath

public java.util.LinkedList<java.lang.String> getFilePath()

Specified by:

getFilePath in interface IVariableResolutionDataModelServer

Returns:

Returns the path of the loaded files.

size

public int size()

Description copied from interface: IVariableResolutionDataModelServer

Returns the overall number of markers.

Specified by:

size in interface IVariableResolutionDataModelServer

Returns:

iterator

public java.util.Iterator<VariableValuesDataRecord> iterator()

Specified by:

iterator in interface java.lang.Iterable<VariableValuesDataRecord>

Overrides:

iterator in class VariableResolutionDataModel

toCollection

public java.util.Collection<VariableValuesDataRecord> toCollection()

Specified by:

toCollection in interface IVariableResolutionDataModelServer

getFileHeader

public java.util.LinkedList<java.lang.String> getFileHeader()

Specified by:

getFileHeader in interface IVariableResolutionDataModelServer

Returns:

Returns the header of the loaded files.

getDataInfo

public java.util.LinkedList<java.lang.String> getDataInfo()

Specified by:

getDataInfo in interface IVariableResolutionDataModelServer

Returns:

Returns summary info of loaded data

validateold

@Deprecated
protected void validateold()

Deprecated.

Does the whole merging work: 1. Find overlapping (corresponding regions) and perform a voting - that is count the numbers of models voting for +, 0, or - i.e. copy_number > 2, copy_number = 2, copy_number < 2 Indifferent regions are those for which no majority exists. In this case the copy_number is set to -1. A copy_number of 2 will be neutral for the voting (???).