Package org.monarchinitiative.lirical.io.output

Class LiricalTemplate

java.lang.Object

org.monarchinitiative.lirical.io.output.LiricalTemplate

Direct Known Subclasses:

HtmlTemplate, TsvTemplate

public abstract class LiricalTemplate
extends Object

This is the superclass for TsvTemplate and HtmlTemplate, and provides common methods for setting up the data prior to output as either tab-separated values (TSV) or HTML.

Author:

Peter Robinson

Field Summary

Fields

Modifier and Type	Field	Description
protected final freemarker.template.Configuration	cfg	FreeMarker configuration object.
protected static final String	EMPTY_STRING
protected final Map<org.monarchinitiative.phenol.ontology.data.TermId,Gene2Genotype>	geneById
protected Path	outputPath
protected final Map<String,Object>	templateData	Map of data that will be used for the FreeMark template.
protected List<String>	topDiagnosisAnchors	Anchors that are used in the HTML output to navigate to the top differential diagnoses.
protected Map<String,String>	topDiagnosisMap	This map contains the names of the top differential diagnoses that we will show as a list at the top of the page together with anchors to navigate to the detailed analysis.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	LiricalTemplate(org.monarchinitiative.phenol.ontology.data.MinimalOntology hpo, AnalysisData analysisData, AnalysisResultsMetadata resultsMetadata, OutputOptions outputOptions)

Method Summary

Modifier and Type	Method	Description
protected static Path	createOutputFile(Path outdir, String prefix, String format)
protected static void	mkdirIfNotExist(Path dir)
protected abstract String	outputFormatString()
protected String	shortName(String name)	Some of our name strings contain multiple synonyms.
protected Function<LiricalVariant,VisualizableVariant>	toVisualizableVariant()

Methods inherited from class java.lang.Object

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

Field Details

templateData

protected final Map<String,Object> templateData

Map of data that will be used for the FreeMark template.

cfg

protected final freemarker.template.Configuration cfg

FreeMarker configuration object.

EMPTY_STRING

protected static final String EMPTY_STRING

See Also:

• Constant Field Values

outputPath

protected Path outputPath

topDiagnosisMap

protected Map<String,String> topDiagnosisMap

This map contains the names of the top differential diagnoses that we will show as a list at the top of the page together with anchors to navigate to the detailed analysis.

topDiagnosisAnchors

protected List<String> topDiagnosisAnchors

Anchors that are used in the HTML output to navigate to the top differential diagnoses.

geneById

protected final Map<org.monarchinitiative.phenol.ontology.data.TermId,Gene2Genotype> geneById

Constructor Details

LiricalTemplate

protected LiricalTemplate(org.monarchinitiative.phenol.ontology.data.MinimalOntology hpo,
 AnalysisData analysisData,
 AnalysisResultsMetadata resultsMetadata,
 OutputOptions outputOptions)

Method Details

outputFormatString

protected abstract String outputFormatString()

shortName

protected String shortName(String name)

Some of our name strings contain multiple synonyms. This function removes all but the first.

createOutputFile

protected static Path createOutputFile(Path outdir,
 String prefix,
 String format)

mkdirIfNotExist

protected static void mkdirIfNotExist(Path dir)

toVisualizableVariant

protected Function<LiricalVariant,VisualizableVariant> toVisualizableVariant()