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

Class GFFDataModel

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.gff.GFFDataModel

All Implemented Interfaces:

IVariableResolutionDataModelServer, IChangeNotifier, java.lang.Iterable<VariableValuesDataRecord>

Direct Known Subclasses:

GFF3Reader, GFFModificationsReader, GFFSummaryReader, GFFVariantsReader, UCSCGTFReader

public abstract class GFFDataModel
extends VariableResolutionDataModel

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 java.util.ArrayList<VariableValuesDataRecord>	data
protected java.lang.String	fileName
protected VariableResolutionDataSetValues	min_max_values
protected boolean	valid

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

changeNotifier, data_type, mc

Constructor Summary

Constructors

Constructor and Description
GFFDataModel()

Method Summary

Methods

Modifier and Type	Method and Description
void	clear()
VariableValuesDataRecord	get(int idx)
java.util.LinkedList<java.lang.String>	getDataInfo()
java.util.LinkedList<java.lang.String>	getFileHeader()
java.util.LinkedList<java.lang.String>	getFilePath()
VariableResolutionDataSetValues	getMinMaxValues()
float[]	getResults(int idx)
protected void	invalidate()
boolean	isValid()
abstract int	readElements(VioletApp app, java.io.Reader reader)
int	size() Returns the overall number of markers.
java.util.Collection<VariableValuesDataRecord>	toCollection()
void	validate()

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

copyAsMarkerCollectionArray, detach, getNumItems, getResult, 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, 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

Field Detail

data

protected java.util.ArrayList<VariableValuesDataRecord> data

valid

protected boolean valid

fileName

protected java.lang.String fileName

min_max_values

protected VariableResolutionDataSetValues min_max_values

Constructor Detail

GFFDataModel

public GFFDataModel()

Method Detail

readElements

public abstract int readElements(VioletApp app,
               java.io.Reader reader)
                          throws java.io.IOException,
                                 FileFormatException

Throws:

java.io.IOException

FileFormatException

invalidate

protected void invalidate()

clear

public void clear()

isValid

public boolean isValid()

validate

public void validate()

getFilePath

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

Returns:

Returns the path of the loaded files.

get

public final VariableValuesDataRecord get(int idx)

toCollection

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

getFileHeader

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

Returns:

Returns the header of the loaded files.

getDataInfo

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

Returns:

Returns summary info of loaded data

size

public int size()

Description copied from interface: IVariableResolutionDataModelServer

Returns the overall number of markers.

Returns:

getResults

public float[] getResults(int idx)

Specified by:

getResults in interface IVariableResolutionDataModelServer

Overrides:

getResults in class VariableResolutionDataModel

getMinMaxValues

public VariableResolutionDataSetValues getMinMaxValues()