Package org.molgenis.vibe.cli.io.output.format.gene_prioritized

Class ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

java.lang.Object

org.molgenis.vibe.cli.io.output.format.OutputFormatWriter

org.molgenis.vibe.cli.io.output.format.PrioritizedOutputFormatWriter<Gene>

org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

public class ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris
extends ResultsPerGeneSeparatedValuesOutputFormatWriter

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

Constructor Summary

Constructors

Constructor	Description
ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris(OutputWriter writer, List<Gene> priority, GeneDiseaseCollection collection, ValuesSeparator primarySeparator, ValuesSeparator keyValuePairSeparator, ValuesSeparator keyValueSeparator, ValuesSeparator valuesSeparator)

Method Summary

Modifier and Type	Method	Description
protected String	writeDisease(Disease disease)	Defines how a Disease is written.
protected List<String>	writeEvidence(List<PubmedEvidence> pubmedEvidenceList)
protected String	writeGene(Gene gene)	Defines how a Gene is written.
protected String	writeGeneSymbol(Gene gene)

Methods inherited from class org.molgenis.vibe.cli.io.output.format.gene_prioritized.ResultsPerGeneSeparatedValuesOutputFormatWriter

generateOutput

Methods inherited from class org.molgenis.vibe.cli.io.output.format.PrioritizedOutputFormatWriter

getPriority

Methods inherited from class org.molgenis.vibe.cli.io.output.format.OutputFormatWriter

getOutputWriter, run

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

public ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris(OutputWriter writer,
                                                                List<Gene> priority,
                                                                GeneDiseaseCollection collection,
                                                                ValuesSeparator primarySeparator,
                                                                ValuesSeparator keyValuePairSeparator,
                                                                ValuesSeparator keyValueSeparator,
                                                                ValuesSeparator valuesSeparator)

Method Detail

writeGene

protected String writeGene(Gene gene)

Description copied from class: ResultsPerGeneSeparatedValuesOutputFormatWriter

Defines how a Gene is written.

Specified by:

writeGene in class ResultsPerGeneSeparatedValuesOutputFormatWriter

Parameters:

gene - the gene to be written

writeGeneSymbol

protected String writeGeneSymbol(Gene gene)

Specified by:

writeGeneSymbol in class ResultsPerGeneSeparatedValuesOutputFormatWriter

writeDisease

protected String writeDisease(Disease disease)

Description copied from class: ResultsPerGeneSeparatedValuesOutputFormatWriter

Defines how a Disease is written.

Specified by:

writeDisease in class ResultsPerGeneSeparatedValuesOutputFormatWriter

Parameters:

disease - the disease to be written

writeEvidence

protected List<String> writeEvidence(List<PubmedEvidence> pubmedEvidenceList)

Specified by:

writeEvidence in class ResultsPerGeneSeparatedValuesOutputFormatWriter