A C E F G H I L M O P R S T V W
All Classes All Packages

A

APP_NAME - org.molgenis.vibe.cli.properties.VibeProperties

APP_VERSION - org.molgenis.vibe.cli.properties.VibeProperties

C

close() - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

close() - Method in interface org.molgenis.vibe.cli.io.output.target.OutputWriter

Closes output target.

COLON - org.molgenis.vibe.cli.io.output.ValuesSeparator

COMMA - org.molgenis.vibe.cli.io.output.ValuesSeparator

CommandLineOptionsParser - Class in org.molgenis.vibe.cli.io.options_digestion

Command line options parser.

create(OutputWriter, GeneDiseaseCollection, List<T>) - Method in interface org.molgenis.vibe.cli.io.output.format.PrioritizedOutputFormatWriterFactory

E

EQUALS - org.molgenis.vibe.cli.io.output.ValuesSeparator

F

FileOutputWriter - Class in org.molgenis.vibe.cli.io.output.target

Writer for writing output to a file.

FileOutputWriter(Path) - Constructor for class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

G

GenePrioritizedOutputFormatWriterFactory - Enum in org.molgenis.vibe.cli.io.output.format.gene_prioritized

A factory for Gene prioritized PrioritizedOutputFormatWriters.

generateOutput() - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.OrderedGenesOutputFormatWriter

generateOutput() - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

generateOutput() - Method in class org.molgenis.vibe.cli.io.output.format.OutputFormatWriter

GENES_FOR_PHENOTYPES - org.molgenis.vibe.cli.RunMode

GENES_FOR_PHENOTYPES_WITH_ASSOCIATED_PHENOTYPES - org.molgenis.vibe.cli.RunMode

getDescription() - Method in enum org.molgenis.vibe.cli.RunMode

getGenePrioritizedOutputFormatWriterFactory() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getHpoOntology() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getOntologyMaxDistance() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getOutputWriter() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getOutputWriter() - Method in class org.molgenis.vibe.cli.io.output.format.OutputFormatWriter

getPath() - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

getPhenotypes() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getPhenotypesRetrieverFactory() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getPriority() - Method in class org.molgenis.vibe.cli.io.output.format.PrioritizedOutputFormatWriter

getRunMode() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

getSeparator() - Method in enum org.molgenis.vibe.cli.io.output.ValuesSeparator

getValue() - Method in enum org.molgenis.vibe.cli.properties.VibeProperties

getVibeDatabase() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

H

HELP - org.molgenis.vibe.cli.RunMode

HYPHEN_MINUS - org.molgenis.vibe.cli.io.output.ValuesSeparator

I

initialize() - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

initialize() - Method in interface org.molgenis.vibe.cli.io.output.target.OutputWriter

Makes preparations for writing output to an output target.

isVerbose() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

L

loadProperties() - Static method in class org.molgenis.vibe.cli.properties.VibePropertiesLoader

M

main(String[]) - Static method in class org.molgenis.vibe.cli.VibeApplication

The main method for when used as a standalone application.

O

OrderedGenesOutputFormatWriter - Class in org.molgenis.vibe.cli.io.output.format.gene_prioritized

A very basic ordered genes output writer.

OrderedGenesOutputFormatWriter(OutputWriter, List<Gene>, ValuesSeparator) - Constructor for class org.molgenis.vibe.cli.io.output.format.gene_prioritized.OrderedGenesOutputFormatWriter

org.molgenis.vibe.cli - package org.molgenis.vibe.cli

org.molgenis.vibe.cli.io.options_digestion - package org.molgenis.vibe.cli.io.options_digestion

org.molgenis.vibe.cli.io.output - package org.molgenis.vibe.cli.io.output

org.molgenis.vibe.cli.io.output.format - package org.molgenis.vibe.cli.io.output.format

org.molgenis.vibe.cli.io.output.format.gene_prioritized - package org.molgenis.vibe.cli.io.output.format.gene_prioritized

org.molgenis.vibe.cli.io.output.target - package org.molgenis.vibe.cli.io.output.target

org.molgenis.vibe.cli.properties - package org.molgenis.vibe.cli.properties

OutputFormatWriter - Class in org.molgenis.vibe.cli.io.output.format

Abstract class defining a complete writer (using OutputWriter as target to write to).

OutputFormatWriter(OutputWriter) - Constructor for class org.molgenis.vibe.cli.io.output.format.OutputFormatWriter

OutputWriter - Interface in org.molgenis.vibe.cli.io.output.target

Superclass for the different types of output writers.

P

parse(String[]) - Static method in class org.molgenis.vibe.cli.io.options_digestion.CommandLineOptionsParser

Digests the command line arguments and stores this in a newly created VibeOptions instance.

parse(String[], VibeOptions) - Static method in class org.molgenis.vibe.cli.io.options_digestion.CommandLineOptionsParser

Digests the command line arguments and stores this in the supplied VibeOptions instance.

printHelpMessage() - Static method in class org.molgenis.vibe.cli.io.options_digestion.CommandLineOptionsParser

Prints the help message to stdout.

printUnexpectedExceptionOccurred() - Static method in class org.molgenis.vibe.cli.VibeApplication

printVerbose(String) - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

PrioritizedOutputFormatWriter<T extends BiologicalEntity> - Class in org.molgenis.vibe.cli.io.output.format

An OutputFormatWriter that writes in a specific format: where the results are prioritized based on a BiologicalEntity.

PrioritizedOutputFormatWriter(OutputWriter, List<T>) - Constructor for class org.molgenis.vibe.cli.io.output.format.PrioritizedOutputFormatWriter

PrioritizedOutputFormatWriterFactory<T extends BiologicalEntity> - Interface in org.molgenis.vibe.cli.io.output.format

Interface describing the required methods for all PrioritizedOutputFormatWriter factories.

R

REGULAR_ID - org.molgenis.vibe.cli.io.output.format.gene_prioritized.GenePrioritizedOutputFormatWriterFactory

REGULAR_URI - org.molgenis.vibe.cli.io.output.format.gene_prioritized.GenePrioritizedOutputFormatWriterFactory

ResultsPerGeneSeparatedValuesOutputFormatWriter - Class in org.molgenis.vibe.cli.io.output.format.gene_prioritized

Writer for writing Gene to a CSV file where a single line represent a Gene.

ResultsPerGeneSeparatedValuesOutputFormatWriter(OutputWriter, List<Gene>, GeneDiseaseCollection, ValuesSeparator, ValuesSeparator, ValuesSeparator, ValuesSeparator) - Constructor for class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds - Class in org.molgenis.vibe.cli.io.output.format.gene_prioritized

A ResultsPerGeneSeparatedValuesOutputFormatWriter where Entity.getId() is used for generating the output.

ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds(OutputWriter, List<Gene>, GeneDiseaseCollection, ValuesSeparator, ValuesSeparator, ValuesSeparator, ValuesSeparator) - Constructor for class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds

ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris - Class in org.molgenis.vibe.cli.io.output.format.gene_prioritized

A ResultsPerGeneSeparatedValuesOutputFormatWriter where Entity.getUri() is used for generating the output.

ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris(OutputWriter, List<Gene>, GeneDiseaseCollection, ValuesSeparator, ValuesSeparator, ValuesSeparator, ValuesSeparator) - Constructor for class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

run() - Method in class org.molgenis.vibe.cli.io.output.format.OutputFormatWriter

run(VibeOptions) - Method in enum org.molgenis.vibe.cli.RunMode

runMode(VibeOptions, Stopwatch) - Method in enum org.molgenis.vibe.cli.RunMode

RunMode - Enum in org.molgenis.vibe.cli

Describes what the application should do.

S

SEMICOLON - org.molgenis.vibe.cli.io.output.ValuesSeparator

setFileOutputWriter(String) - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

Wrapper for VibeOptions.setFileOutputWriter(Path).

setFileOutputWriter(Path) - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

Sets the OutputWriter to a FileOutputWriter.

setFileOutputWriterForced(String) - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

Wrapper for VibeOptions.setFileOutputWriterForced(Path).

setFileOutputWriterForced(Path) - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

Sets the OutputWriter to a FileOutputWriter.

setStdoutOutputWriter() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

Sets the OutputWriter to an StdoutOutputWriter.

SIMPLE - org.molgenis.vibe.cli.io.output.format.gene_prioritized.GenePrioritizedOutputFormatWriterFactory

StdoutOutputWriter - Class in org.molgenis.vibe.cli.io.output.target

Writer for writing output to stdout.

StdoutOutputWriter() - Constructor for class org.molgenis.vibe.cli.io.output.target.StdoutOutputWriter

T

TAB - org.molgenis.vibe.cli.io.output.ValuesSeparator

target() - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

target() - Method in interface org.molgenis.vibe.cli.io.output.target.OutputWriter

Returns a String describing the target to which the output is written (primarily for logging purposes).

target() - Method in class org.molgenis.vibe.cli.io.output.target.StdoutOutputWriter

toString() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

toString() - Method in enum org.molgenis.vibe.cli.io.output.ValuesSeparator

V

validate() - Method in class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

Checks whether the set variables adhere to the selected RunMode.

valueOf(String) - Static method in enum org.molgenis.vibe.cli.io.output.format.gene_prioritized.GenePrioritizedOutputFormatWriterFactory

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

valueOf(String) - Static method in enum org.molgenis.vibe.cli.io.output.ValuesSeparator

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

valueOf(String) - Static method in enum org.molgenis.vibe.cli.properties.VibeProperties

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

valueOf(String) - Static method in enum org.molgenis.vibe.cli.RunMode

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

values() - Static method in enum org.molgenis.vibe.cli.io.output.format.gene_prioritized.GenePrioritizedOutputFormatWriterFactory

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

values() - Static method in enum org.molgenis.vibe.cli.io.output.ValuesSeparator

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

values() - Static method in enum org.molgenis.vibe.cli.properties.VibeProperties

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

values() - Static method in enum org.molgenis.vibe.cli.RunMode

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

ValuesSeparator - Enum in org.molgenis.vibe.cli.io.output

Defines possible separators to be used.

VERSION - org.molgenis.vibe.cli.RunMode

VERTICAL_LINE - org.molgenis.vibe.cli.io.output.ValuesSeparator

VibeApplication - Class in org.molgenis.vibe.cli

The main application class.

VibeApplication() - Constructor for class org.molgenis.vibe.cli.VibeApplication

VibeOptions - Class in org.molgenis.vibe.cli.io.options_digestion

Abstract class to be used for options parsing.

VibeOptions() - Constructor for class org.molgenis.vibe.cli.io.options_digestion.VibeOptions

VibeProperties - Enum in org.molgenis.vibe.cli.properties

Properties (parsed by VibePropertiesLoader) stored in application.properties accessible anywhere in the app (so VibePropertiesLoader should always be used first to parse the properties).

VibePropertiesLoader - Class in org.molgenis.vibe.cli.properties

Loads the properties stored in application.properties for usage by VibeProperties.

W

write(String) - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

write(String) - Method in interface org.molgenis.vibe.cli.io.output.target.OutputWriter

Writes single piece of information to output target.

write(String) - Method in class org.molgenis.vibe.cli.io.output.target.StdoutOutputWriter

writeDisease(Disease) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

Defines how a Disease is written.

writeDisease(Disease) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds

writeDisease(Disease) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

writeEvidence(List<PubmedEvidence>) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

writeEvidence(List<PubmedEvidence>) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds

writeEvidence(List<PubmedEvidence>) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

writeGene(Gene) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

Defines how a Gene is written.

writeGene(Gene) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds

writeGene(Gene) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

writeGeneSymbol(Gene) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

writeGeneSymbol(Gene) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds

writeGeneSymbol(Gene) - Method in class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

writeHeader(String) - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

writeHeader(String) - Method in interface org.molgenis.vibe.cli.io.output.target.OutputWriter

Writes the header (if available) to the output target.

writeHeader(String) - Method in class org.molgenis.vibe.cli.io.output.target.StdoutOutputWriter

writeNewLine() - Method in class org.molgenis.vibe.cli.io.output.target.FileOutputWriter

writeNewLine() - Method in interface org.molgenis.vibe.cli.io.output.target.OutputWriter

Generates a newline (if possible) in the output target.

writeNewLine() - Method in class org.molgenis.vibe.cli.io.output.target.StdoutOutputWriter

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