com.pacbio.secondary.vis.data.base

Class BaseDataModel

java.lang.Object

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

Direct Known Subclasses:

EpiProReadsReader, VariableResolutionDataModel

public class BaseDataModel
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BaseDataModel.eDataType

Field Summary

Fields

Modifier and Type	Field and Description
protected ChangeNotifier	changeNotifier
protected BaseDataModel.eDataType	data_type
protected MarkerCollection[]	mc

Constructor Summary

Constructors

Constructor and Description
BaseDataModel(BaseDataModel.eDataType data_type, int num_chromosomes)

Method Summary

Methods

Modifier and Type	Method and Description
void	addChangeListener(javax.swing.event.ChangeListener listener)
protected void	fireChangeEvent()
BaseDataModel.eDataType	getDataType()
static java.lang.String	getDataTypeAsString(BaseDataModel.eDataType data) static method
MarkerCollection	getMarkersForContig(int contig)
int	getNumContigs()
boolean	hasData()
boolean	isMarkerType() returns true if this is marker type
boolean	isModificationsType() returns true if this is base mods data type
boolean	isReadsType() returns true if this is reads type or unmapped read type
boolean	isSummaryType() returns true if this is summary type
boolean	isVariantsType() returns true if this is variants or vcf data type
void	removeChangeListener(javax.swing.event.ChangeListener listener)
void	setTypeAndNumContigs(BaseDataModel.eDataType data_type, int num_contigs)

Methods inherited from class java.lang.Object

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

Field Detail

data_type

protected BaseDataModel.eDataType data_type

mc

protected MarkerCollection[] mc

changeNotifier

protected ChangeNotifier changeNotifier

Constructor Detail

BaseDataModel

public BaseDataModel(BaseDataModel.eDataType data_type,
             int num_chromosomes)

Method Detail

setTypeAndNumContigs

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

addChangeListener

public void addChangeListener(javax.swing.event.ChangeListener listener)

removeChangeListener

public void removeChangeListener(javax.swing.event.ChangeListener listener)

fireChangeEvent

protected void fireChangeEvent()

getNumContigs

public int getNumContigs()

hasData

public boolean hasData()

getMarkersForContig

public MarkerCollection getMarkersForContig(int contig)

getDataType

public BaseDataModel.eDataType getDataType()

isReadsType

public boolean isReadsType()

returns true if this is reads type or unmapped read type

Parameters:

data -

Returns:

isVariantsType

public boolean isVariantsType()

returns true if this is variants or vcf data type

Parameters:

data -

Returns:

isModificationsType

public boolean isModificationsType()

returns true if this is base mods data type

Parameters:

data -

Returns:

isSummaryType

public boolean isSummaryType()

returns true if this is summary type

Parameters:

data -

Returns:

isMarkerType

public boolean isMarkerType()

returns true if this is marker type

Parameters:

data -

Returns:

getDataTypeAsString

public static java.lang.String getDataTypeAsString(BaseDataModel.eDataType data)

static method

Parameters:

data -

Returns: