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

Class ResultsPerGeneSeparatedValuesOutputFormatWriter

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

Direct Known Subclasses:

ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds, ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris

public abstract class ResultsPerGeneSeparatedValuesOutputFormatWriter
extends PrioritizedOutputFormatWriter<Gene>

Writer for writing Gene to a CSV file where a single line represent a Gene. A separate List defines the order of Genes in the output file.

Constructor Summary

Constructors

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

Method Summary

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

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

ResultsPerGeneSeparatedValuesOutputFormatWriter

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

Parameters:

writer - writer object to be used to write the data

collection - the data to be written

priority - defines the order in which the Genes are written

primarySeparator - highest level values separator

keyValuePairSeparator - separates different key-value pairs

keyValueSeparator - separates a key and value

valuesSeparator - separates the values from a key-value pair

Throws:

IllegalArgumentException - if any separator is equal to another separator

Method Detail

generateOutput

public void generateOutput()
                    throws IOException

Specified by:

generateOutput in class OutputFormatWriter

Throws:

IOException

writeGene

protected abstract String writeGene(Gene gene)
                             throws IOException

Defines how a Gene is written.

Parameters:

gene - the gene to be written

Throws:

IOException

writeGeneSymbol

protected abstract String writeGeneSymbol(Gene gene)
                                   throws IOException

Throws:

IOException

writeDisease

protected abstract String writeDisease(Disease disease)
                                throws IOException

Defines how a Disease is written.

Parameters:

disease - the disease to be written

Throws:

IOException

writeEvidence

protected abstract List<String> writeEvidence(List<PubmedEvidence> pubmedEvidenceList)
                                       throws IOException

Throws:

IOException