Uses of Class
com.pacbio.secondary.vis.common.utils.exception.FileFormatException

Packages that use FileFormatException

Package	Description
com.pacbio.secondary.vis.data.db	Ideogram and genes collections support
com.pacbio.secondary.vis.data.variableresolution.model.gff	GFF3 variable resolution data model
com.pacbio.secondary.vis.io.epipro	Parser for epipro/unmapped reads data
com.pacbio.secondary.vis.io.gff	GFF3 reader support
com.pacbio.secondary.vis.io.gff.modifications	GFF3 Base Modifications Info support
com.pacbio.secondary.vis.io.gff.summary	GFF3 Summary Info support
com.pacbio.secondary.vis.io.gff.variants	GFF3 variants support
com.pacbio.secondary.vis.io.importer	Local and remote data files import support
com.pacbio.secondary.vis.io.motifs	Parser for Motifs files
com.pacbio.secondary.vis.io.ucsc.gtf.reader	Parser for UCSC generated gtf (gene transfer format) files
com.pacbio.secondary.vis.io.vcf	Parser for VCF (variants) files

Uses of FileFormatException in com.pacbio.secondary.vis.data.db

Methods in com.pacbio.secondary.vis.data.db that throw FileFormatException

Modifier and Type	Method and Description
boolean	GeneDB.read(ReferenceInfo reference, java.io.Reader reader, java.lang.String file_name, IProgressNotifier notifier) Loads a gene database from a stream.
boolean	IdeogramDB.readIdeogramData(java.io.Reader reader, IProgressNotifier notifier)

Uses of FileFormatException in com.pacbio.secondary.vis.data.variableresolution.model.gff

Methods in com.pacbio.secondary.vis.data.variableresolution.model.gff that throw FileFormatException

Modifier and Type	Method and Description
abstract int	GFFDataModel.readElements(VioletApp app, java.io.Reader reader)

Uses of FileFormatException in com.pacbio.secondary.vis.io.epipro

Methods in com.pacbio.secondary.vis.io.epipro that throw FileFormatException

Modifier and Type	Method and Description
void	EpiProReadsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
void	EpiProReadsReader.readElements(VioletApp app, java.io.Reader reader)

Uses of FileFormatException in com.pacbio.secondary.vis.io.gff

Methods in com.pacbio.secondary.vis.io.gff that throw FileFormatException

Modifier and Type	Method and Description
void	GFF3Reader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFF3Reader.readElements(VioletApp app, java.io.Reader reader) Loads a marker collection from a stream.

Uses of FileFormatException in com.pacbio.secondary.vis.io.gff.modifications

Methods in com.pacbio.secondary.vis.io.gff.modifications that throw FileFormatException

Modifier and Type	Method and Description
void	GFFModificationsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFFModificationsReader.readElements(VioletApp app, java.io.Reader reader) Loads base mods or motifs info

Uses of FileFormatException in com.pacbio.secondary.vis.io.gff.summary

Methods in com.pacbio.secondary.vis.io.gff.summary that throw FileFormatException

Modifier and Type	Method and Description
void	GFFSummaryReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFFSummaryReader.readElements(VioletApp app, java.io.Reader reader) Loads summary information

Uses of FileFormatException in com.pacbio.secondary.vis.io.gff.variants

Methods in com.pacbio.secondary.vis.io.gff.variants that throw FileFormatException

Modifier and Type	Method and Description
void	GFFVariantsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	GFFVariantsReader.readElements(VioletApp app, java.io.Reader reader) Loads variants info

Uses of FileFormatException in com.pacbio.secondary.vis.io.importer

Methods in com.pacbio.secondary.vis.io.importer that throw FileFormatException

Modifier and Type	Method and Description
protected boolean	ImportDataHelper.importCommonFileTypesFromReader(DataFileInfo.eFileType file_type, java.io.Reader reader, java.lang.String file_name) reads file types common to interactive and bkg loading
protected boolean	ImportDataHelper.importEpiProReadsFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importGFF3FileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importModificationsGFFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importMultiSampleVCFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importSummaryGFFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importUCSCGTFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importVariantsGFFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importVCFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	ImportDataHelper.importVioletHDFReadsFile(java.io.File file)

Uses of FileFormatException in com.pacbio.secondary.vis.io.motifs

Methods in com.pacbio.secondary.vis.io.motifs that throw FileFormatException

Modifier and Type	Method and Description
int	MotifsReader.loadFromFile(java.io.File file, VioletApp app)
int	MotifsReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	MotifsReader.readElements(VioletApp app, java.io.Reader reader)

Uses of FileFormatException in com.pacbio.secondary.vis.io.ucsc.gtf.reader

Methods in com.pacbio.secondary.vis.io.ucsc.gtf.reader that throw FileFormatException

Modifier and Type	Method and Description
void	UCSCGTFReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	UCSCGTFReader.readElements(VioletApp app, java.io.Reader reader) Loads a marker collection from a stream.

Uses of FileFormatException in com.pacbio.secondary.vis.io.vcf

Methods in com.pacbio.secondary.vis.io.vcf that throw FileFormatException

Modifier and Type	Method and Description
void	VCFMultiSampleReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
void	VCFReader.loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	VCFMultiSampleReader.readElements(VioletApp app, java.io.Reader reader)
int	VCFReader.readElements(VioletApp app, java.io.Reader reader)