A C D E F G H I J L M O P R S T V

A

accept(String) - Method in class org.molgenis.gavin.job.input.LineSink

annotateFile(MultipartFile, String) - Method in class org.molgenis.gavin.controller.GavinController

Starts a job to annotate a VCF file

AnnotatorRunner - Class in org.molgenis.gavin.job

AnnotatorRunner(VcfAttributes, EntityTypeFactory, AttributeFactory, EffectStructureConverter) - Constructor for class org.molgenis.gavin.job.AnnotatorRunner

C

CADDS - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

CaddVariant - Class in org.molgenis.gavin.job.input.model

CaddVariant() - Constructor for class org.molgenis.gavin.job.input.model.CaddVariant

call(Progress) - Method in class org.molgenis.gavin.job.GavinJob

cleanUp() - Method in class org.molgenis.gavin.controller.GavinController

Removes old files in the gavin working directory from the file store.

close() - Method in class org.molgenis.gavin.job.input.LineSink

COMMENTS - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

create(String, long, String, String, Double, Double) - Static method in class org.molgenis.gavin.job.input.model.CaddVariant

create(String, long, String, String, String) - Static method in class org.molgenis.gavin.job.input.model.VcfVariant

createJob(GavinJobExecution) - Method in class org.molgenis.gavin.job.GavinJobFactory

D

download(HttpServletResponse, String) - Method in class org.molgenis.gavin.controller.GavinController

Downloads the result of a gavin annotation job.

downloadErrorReport(HttpServletResponse, String) - Method in class org.molgenis.gavin.controller.GavinController

Downloads the error report of a gavin annotation job.

E

ERRORS - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

F

FILENAME - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

Files - Class in org.molgenis.gavin.job.input

Files methods, adapted to also work for GZIPInputStream.

Files() - Constructor for class org.molgenis.gavin.job.input.Files

findGavinJobExecution(String) - Method in class org.molgenis.gavin.job.GavinJobFactory

Retrieves a GavinJobExecution for anyone who has the identifier, without checking their permissions.

G

GAVIN_APP - Static variable in class org.molgenis.gavin.controller.GavinController

GAVIN_JOB_EXECUTION - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

GavinConfig - Class in org.molgenis.gavin.controller

GavinConfig() - Constructor for class org.molgenis.gavin.controller.GavinConfig

GavinController - Class in org.molgenis.gavin.controller

GavinController(ExecutorService, GavinJobFactory, GavinJobExecutionFactory, FileStore, UserAccountService, MenuReaderService, IdGenerator) - Constructor for class org.molgenis.gavin.controller.GavinController

gavinExecutors() - Method in class org.molgenis.gavin.controller.GavinConfig

GavinJob - Class in org.molgenis.gavin.job

GavinJob(Progress, TransactionTemplate, Authentication, String, FileStore, MenuReaderService, RepositoryAnnotator, RepositoryAnnotator, RepositoryAnnotator, RepositoryAnnotator, Parser, AnnotatorRunner, GavinJobExecution) - Constructor for class org.molgenis.gavin.job.GavinJob

GavinJobExecution - Class in org.molgenis.gavin.job

GavinJobExecution(Entity) - Constructor for class org.molgenis.gavin.job.GavinJobExecution

GavinJobExecution(EntityType) - Constructor for class org.molgenis.gavin.job.GavinJobExecution

GavinJobExecution(String, EntityType) - Constructor for class org.molgenis.gavin.job.GavinJobExecution

GavinJobExecutionFactory - Class in org.molgenis.gavin.job.meta

GavinJobExecutionMetaData - Class in org.molgenis.gavin.job.meta

GavinJobExecutionMetaData(IndexPackage, JobExecutionMetaData) - Constructor for class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

GavinJobFactory - Class in org.molgenis.gavin.job

GavinJobFactory(DataService, PlatformTransactionManager, UserDetailsService, JobExecutionUpdater, MailSender, FileStore, RepositoryAnnotator, RepositoryAnnotator, RepositoryAnnotator, EffectBasedAnnotator, MenuReaderService, Parser, AnnotatorRunner) - Constructor for class org.molgenis.gavin.job.GavinJobFactory

getAlt() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getAlt() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

getAnnotatorsWithMissingResources() - Method in class org.molgenis.gavin.job.GavinJobFactory

getChrom() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getChrom() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

getFilename() - Method in class org.molgenis.gavin.job.GavinJobExecution

getGavinJobExecution(String) - Method in class org.molgenis.gavin.controller.GavinController

Retrieves GavinJobExecution job.

getId() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

getInfo() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getInputFileExtension() - Method in class org.molgenis.gavin.job.GavinJobExecution

getLines(Path, Charset) - Static method in class org.molgenis.gavin.job.input.Files

getLineType() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getLineType() - Method in interface org.molgenis.gavin.job.input.model.Variant

getLineType() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

getLineTypes() - Method in class org.molgenis.gavin.job.GavinJobExecution

getPhred() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getPos() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getPos() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

getRawScore() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getRef() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

getRef() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

GZ - Static variable in class org.molgenis.gavin.controller.GavinController

H

handleFileNotFound(FileNotFoundException, HttpServletResponse) - Method in class org.molgenis.gavin.controller.GavinController

handleJobNotFound(JobNotFoundException, HttpServletResponse) - Method in class org.molgenis.gavin.controller.GavinController

handleRuntimeException(RuntimeException) - Method in class org.molgenis.gavin.controller.GavinController

I

INDELS_NOCADD - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

init(Model) - Method in class org.molgenis.gavin.controller.GavinController

Shows the gavin page.

init() - Method in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

INPUT_FILE_EXTENSION - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

isComment(String) - Method in class org.molgenis.gavin.job.input.Parser

Determines if a line is a comment line.

J

JobNotFoundException - Exception in org.molgenis.gavin.job

JobNotFoundException(String) - Constructor for exception org.molgenis.gavin.job.JobNotFoundException

L

LineSink - Class in org.molgenis.gavin.job.input

Writes lines to file.

LineSink(File) - Constructor for class org.molgenis.gavin.job.input.LineSink

LineType - Enum in org.molgenis.gavin.job.input.model

Type of input lines.

M

MAX_LINES - Static variable in class org.molgenis.gavin.job.input.Parser

O

org.molgenis.gavin.controller - package org.molgenis.gavin.controller

org.molgenis.gavin.job - package org.molgenis.gavin.job

org.molgenis.gavin.job.input - package org.molgenis.gavin.job.input

org.molgenis.gavin.job.input.model - package org.molgenis.gavin.job.input.model

org.molgenis.gavin.job.meta - package org.molgenis.gavin.job.meta

P

Parser - Class in org.molgenis.gavin.job.input

Parses input lines.

Parser() - Constructor for class org.molgenis.gavin.job.input.Parser

R

result(String, Model, HttpServletRequest) - Method in class org.molgenis.gavin.controller.GavinController

Shows result page for a job.

runAnnotator(RepositoryAnnotator, File, File, boolean) - Method in class org.molgenis.gavin.job.AnnotatorRunner

S

setFilename(String) - Method in class org.molgenis.gavin.job.GavinJobExecution

setInputFileExtension(String) - Method in class org.molgenis.gavin.job.GavinJobExecution

setLineTypes(Multiset<LineType>) - Method in class org.molgenis.gavin.job.GavinJobExecution

SKIPPEDS - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

T

toString() - Method in class org.molgenis.gavin.job.input.model.CaddVariant

toString() - Method in class org.molgenis.gavin.job.input.model.VcfVariant

transformLine(String, int, int, LineSink, LineSink) - Method in class org.molgenis.gavin.job.input.Parser

Transforms a single line.

tryParseVariant(String) - Method in class org.molgenis.gavin.job.input.Parser

Parses a line into a Variant.

tryTransform(File, File, File) - Method in class org.molgenis.gavin.job.input.Parser

Transforms gavin input file.

TSV - Static variable in class org.molgenis.gavin.controller.GavinController

TSV_GZ - Static variable in class org.molgenis.gavin.controller.GavinController

V

valueOf(String) - Static method in enum org.molgenis.gavin.job.input.model.LineType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.gavin.job.input.model.LineType

Returns an array containing the constants of this enum type, in the order they are declared.

Variant - Interface in org.molgenis.gavin.job.input.model

VCFS - Static variable in class org.molgenis.gavin.job.meta.GavinJobExecutionMetaData

VcfVariant - Class in org.molgenis.gavin.job.input.model

VcfVariant() - Constructor for class org.molgenis.gavin.job.input.model.VcfVariant

A C D E F G H I J L M O P R S T V