com.pacbio.secondary.vis.io.gff.variants

Class GFFVariantsReader

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

com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

All Implemented Interfaces:

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

Direct Known Subclasses:

VCFMultiSampleReader, VCFReader

public class GFFVariantsReader
extends GFFDataModel

Author:

Marco Milletti

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.lang.String	genotype_tag
protected boolean	is_v13
protected int	NUM_RESULTS
protected static java.lang.String	VARIANT_DEF_TAG
protected static java.lang.String	VARIANT_DELETION_TYPE
protected static java.lang.String	VARIANT_INSERTION_TYPE
protected static java.lang.String	VARIANT_SUBST_TYPE
protected static java.lang.String[]	VARIANT_TYPES_LABELS
protected static java.lang.String	VARIANT_V12_GENOTYPE_TAG
protected static java.lang.String	VARIANT_V13_GENOTYPE_TAG
protected static java.lang.String	VARIANT_V13_TAG
protected static java.lang.String	VARIANT_V131_TAG
protected static java.lang.String	VARIANT_V133_FREQUENCY_TAG
protected static java.lang.String	VARIANT_V133_TAG
protected static java.lang.String	VARIANT_V140_TAG
protected static java.lang.String	VARIANT_V200_TAG
protected static java.lang.String	VARIANT_V210_TAG

Fields inherited from class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

data, fileName, min_max_values, valid

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

changeNotifier, data_type, mc

Constructor Summary

Constructors

Constructor and Description
GFFVariantsReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	getDataPointForInterval(VariableValuesDataRecord record, java.lang.String col)
static java.lang.String	getVariantLabel(Marker marker) returns a variant string from type
void	loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	readElements(VioletApp app, java.io.Reader reader) Loads variants info

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

clear, get, getDataInfo, getFileHeader, getFilePath, getMinMaxValues, getResults, invalidate, isValid, size, toCollection, 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

NUM_RESULTS

protected final int NUM_RESULTS

See Also:

Constant Field Values

VARIANT_DEF_TAG

protected static final java.lang.String VARIANT_DEF_TAG

See Also:

Constant Field Values

VARIANT_DELETION_TYPE

protected static final java.lang.String VARIANT_DELETION_TYPE

See Also:

Constant Field Values

VARIANT_INSERTION_TYPE

protected static final java.lang.String VARIANT_INSERTION_TYPE

See Also:

Constant Field Values

VARIANT_SUBST_TYPE

protected static final java.lang.String VARIANT_SUBST_TYPE

See Also:

Constant Field Values

VARIANT_TYPES_LABELS

protected static final java.lang.String[] VARIANT_TYPES_LABELS

VARIANT_V13_TAG

protected static final java.lang.String VARIANT_V13_TAG

See Also:

Constant Field Values

VARIANT_V12_GENOTYPE_TAG

protected static final java.lang.String VARIANT_V12_GENOTYPE_TAG

See Also:

Constant Field Values

VARIANT_V13_GENOTYPE_TAG

protected static final java.lang.String VARIANT_V13_GENOTYPE_TAG

See Also:

Constant Field Values

is_v13

protected boolean is_v13

genotype_tag

protected java.lang.String genotype_tag

VARIANT_V131_TAG

protected static final java.lang.String VARIANT_V131_TAG

See Also:

Constant Field Values

VARIANT_V133_TAG

protected static final java.lang.String VARIANT_V133_TAG

See Also:

Constant Field Values

VARIANT_V140_TAG

protected static final java.lang.String VARIANT_V140_TAG

See Also:

Constant Field Values

VARIANT_V200_TAG

protected static final java.lang.String VARIANT_V200_TAG

See Also:

Constant Field Values

VARIANT_V210_TAG

protected static final java.lang.String VARIANT_V210_TAG

See Also:

Constant Field Values

VARIANT_V133_FREQUENCY_TAG

protected static final java.lang.String VARIANT_V133_FREQUENCY_TAG

See Also:

Constant Field Values

Constructor Detail

GFFVariantsReader

public GFFVariantsReader()

Method Detail

loadFromReader

public void loadFromReader(java.io.Reader reader,
                  java.lang.String file_name,
                  VioletApp app)
                    throws java.io.IOException,
                           FileFormatException

Throws:

java.io.IOException

FileFormatException

readElements

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

Loads variants info

Specified by:

readElements in class GFFDataModel

Parameters:

app -

reader -

Returns:

number of contigs in data file

Throws:

java.io.IOException

FileFormatException

getDataPointForInterval

protected void getDataPointForInterval(VariableValuesDataRecord record,
                           java.lang.String col)

getVariantLabel

public static java.lang.String getVariantLabel(Marker marker)

returns a variant string from type

Parameters:

type -

Returns: