com.pacbio.secondary.vis.io.vcf

Class VCFReader

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

com.pacbio.secondary.vis.io.vcf.VCFReader

All Implemented Interfaces:

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

public class VCFReader
extends GFFVariantsReader

Author:

mmilletti

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 boolean	is_vPacBio
protected static int	NUM_RESULTS
protected static java.lang.String	VCF_COVERAGE_TAG
protected static java.lang.String	VCF_PACBIO_TAG

Fields inherited from class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

genotype_tag, is_v13, VARIANT_DEF_TAG, VARIANT_DELETION_TYPE, VARIANT_INSERTION_TYPE, VARIANT_SUBST_TYPE, VARIANT_TYPES_LABELS, VARIANT_V12_GENOTYPE_TAG, VARIANT_V13_GENOTYPE_TAG, VARIANT_V13_TAG, VARIANT_V131_TAG, VARIANT_V133_FREQUENCY_TAG, VARIANT_V133_TAG, VARIANT_V140_TAG, VARIANT_V200_TAG, 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
VCFReader()

Method Summary

Methods

Modifier and Type	Method and Description
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.io.gff.variants.GFFVariantsReader

getDataPointForInterval, getVariantLabel

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 static final int NUM_RESULTS

See Also:

Constant Field Values

VCF_PACBIO_TAG

protected static final java.lang.String VCF_PACBIO_TAG

See Also:

Constant Field Values

VCF_COVERAGE_TAG

protected static final java.lang.String VCF_COVERAGE_TAG

See Also:

Constant Field Values

is_vPacBio

protected boolean is_vPacBio

Constructor Detail

VCFReader

public VCFReader()

Method Detail

loadFromReader

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

Overrides:

loadFromReader in class GFFVariantsReader

Throws:

java.io.IOException

FileFormatException

readElements

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

Description copied from class: GFFVariantsReader

Loads variants info

Overrides:

readElements in class GFFVariantsReader

Returns:

number of contigs in data file

Throws:

java.io.IOException

FileFormatException