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

Class VariableResolutionDataSet

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.VariableResolutionDataSet

All Implemented Interfaces:

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

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

A DataSlot encapsulates one or more GenericDataModel datasets with all configurations. It is a "Strategy" in the sense that it encapsulates different (transparent) data flows.

Nested Class Summary

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

BaseDataModel.eDataType

Field Summary

Fields

Modifier and Type	Field and Description
protected VariableResolutionDataModelsMerger	merger
protected VariableResolutionDataSetValues	min_max_values
protected IVariableResolutionDataModelServer	output
protected java.util.LinkedList<IVariableResolutionDataModelServer>	sourceModels
java.util.ArrayList<java.lang.Integer>	track_indexes
java.awt.Color	trackColor
protected boolean	valid

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

changeNotifier, data_type, mc

Constructor Summary

Constructors

Constructor and Description
VariableResolutionDataSet(BaseDataModel.eDataType data_type, int num_contigs)

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.lang.String	getDataTypeAsString()
java.util.LinkedList<java.lang.String>	getFileHeader()
java.util.LinkedList<java.lang.String>	getFilePath()
VariableResolutionDataSetValues	getMinMaxValues()
java.util.Collection<IVariableResolutionDataModelServer>	getModels()
java.lang.String	getName(boolean bShortFormat) returns filenames
void	replaceModel(IVariableResolutionDataModelServer model)
void	setTypeAndNumContigs(BaseDataModel.eDataType data_type, int num_chromosomes)
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)

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

copyAsMarkerCollectionArray, getNumItems, getResult, getResults, iterator

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

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

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

Field Detail

sourceModels

protected java.util.LinkedList<IVariableResolutionDataModelServer> sourceModels

output

protected IVariableResolutionDataModelServer output

merger

protected VariableResolutionDataModelsMerger merger

valid

protected boolean valid

min_max_values

protected VariableResolutionDataSetValues min_max_values

trackColor

public java.awt.Color trackColor

track_indexes

public java.util.ArrayList<java.lang.Integer> track_indexes

Constructor Detail

VariableResolutionDataSet

public VariableResolutionDataSet(BaseDataModel.eDataType data_type,
                         int num_contigs)

Parameters:

parameters -

data_type -

num_contigs -

Method Detail

replaceModel

public void replaceModel(IVariableResolutionDataModelServer model)

addModel

public void addModel(IVariableResolutionDataModelServer model)

updateMinMaxValues

protected void updateMinMaxValues(IVariableResolutionDataModelServer model)

clear

public void clear()

getModels

public java.util.Collection<IVariableResolutionDataModelServer> getModels()

setTypeAndNumContigs

public void setTypeAndNumContigs(BaseDataModel.eDataType data_type,
                        int num_chromosomes)

Overrides:

setTypeAndNumContigs in class BaseDataModel

getDataTypeAsString

public java.lang.String getDataTypeAsString()

detach

public void detach()

Specified by:

detach in interface IVariableResolutionDataModelServer

Overrides:

detach in class VariableResolutionDataModel

get

public VariableValuesDataRecord get(int j)

Specified by:

get in interface IVariableResolutionDataModelServer

size

public int size()

Description copied from interface: IVariableResolutionDataModelServer

Returns the overall number of markers.

Specified by:

size in interface IVariableResolutionDataModelServer

Returns:

toCollection

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

Specified by:

toCollection 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.

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

getName

public java.lang.String getName(boolean bShortFormat)

returns filenames

Parameters:

bShortFormat - true for file name only, false for full path

Returns:

stateChanged

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

Specified by:

stateChanged in interface javax.swing.event.ChangeListener

getMinMaxValues

public VariableResolutionDataSetValues getMinMaxValues()

Specified by:

getMinMaxValues in interface IVariableResolutionDataModelServer