Uses of Class
biolockj.exception.SequnceFormatException

Packages that use SequnceFormatException

Package	Description
biolockj.module	Pipeline modules are loaded based on the BioModules listed in the Config file. All modules (i.e., implement BioModule) are contained within this package or its sub-packages.
biolockj.module.implicit	The modules in this package are implicitly added to pipelines as needed. These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y.
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.
biolockj.util	Static utilities centralize and organize reusable core methods.

Uses of SequnceFormatException in biolockj.module

Methods in biolockj.module that throw SequnceFormatException

Modifier and Type	Method and Description
List<File>	SeqModuleImpl.getSeqFiles(Collection<File> files)
List<File>	SeqModule.getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

Uses of SequnceFormatException in biolockj.module.implicit

Methods in biolockj.module.implicit that throw SequnceFormatException

Modifier and Type	Method and Description
List<File>	Demultiplexer.getSeqFiles(Collection<File> files)
List<File>	RegisterNumReads.getSeqFiles(Collection<File> files)

Uses of SequnceFormatException in biolockj.module.seq

Methods in biolockj.module.seq that throw SequnceFormatException

Modifier and Type	Method and Description
List<File>	RarefySeqs.getSeqFiles(Collection<File> files)
List<File>	Multiplexer.getSeqFiles(Collection<File> files)
List<File>	TrimPrimers.getSeqFiles(Collection<File> files)
List<File>	AwkFastaConverter.getSeqFiles(Collection<File> files)
List<File>	SeqFileValidator.getSeqFiles(Collection<File> files)

Uses of SequnceFormatException in biolockj.util

Methods in biolockj.util that throw SequnceFormatException

Modifier and Type	Method and Description
static String	SeqUtil.getSampleId(File file)
static List<File>	SeqUtil.getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.