HtmlTemplate (LIRICAL 2.0.3-SNAPSHOT API)

java.lang.Object

org.monarchinitiative.lirical.io.output.LiricalTemplate

org.monarchinitiative.lirical.io.output.HtmlTemplate

public class HtmlTemplate extends LiricalTemplate

This class coordinates getting the data from the analysis into the FreeMark org.monarchinitiative.lirical.output templates.

Author:: Peter Robinson

Field Summary

Fields

Modifier and Type

Field

Description

protected Set<String>

symbolsWithoutGeneIds

There are gene symbols returned by Jannovar for which we cannot find a geneId.

Fields inherited from class org.monarchinitiative.lirical.io.output.LiricalTemplate
cfg, EMPTY_STRING, geneById, outputPath, templateData, topDiagnosisAnchors, topDiagnosisMap
Method Summary

Modifier and Type

Method

Description

void

outputFile()

protected String

outputFormatString()

Methods inherited from class org.monarchinitiative.lirical.io.output.LiricalTemplate
createOutputFile, mkdirIfNotExist, shortName, toVisualizableVariant

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- symbolsWithoutGeneIds
  
  protected Set<String> symbolsWithoutGeneIds
  
  There are gene symbols returned by Jannovar for which we cannot find a geneId. This issues seems to be related to the input files used by Jannovar from UCSC ( knownToLocusLink.txt.gz has links between ucsc ids, e.g., uc003fts.3, and NCBIGene ids (earlier known as locus link), e.g., 1370).
Method Details
- outputFile
  
  public void outputFile()
- outputFormatString
  
  protected String outputFormatString()
  
  Specified by:
  
  outputFormatString in class LiricalTemplate