Package org.monarchinitiative.lirical.io.output

Class DifferentialDiagnosis

java.lang.Object

org.monarchinitiative.lirical.io.output.DifferentialDiagnosis

public class DifferentialDiagnosis
extends Object

This class stores all the information we need for a detailed differential diagnosis -- the major candidates. It is intended to be used as a Java Bean for the FreeMarker HTML template.

Author:

Peter Robinson

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	EMPTY_STRING
protected final org.monarchinitiative.phenol.annotations.formats.GeneIdentifier	geneId
protected static final String	NOT_AVAILABLE
protected final String	sampleId
protected final List<VisualizableVariant>	variants

Method Summary

Modifier and Type	Method	Description
String	getAnchor()
double	getCompositeLR()
String	getDiseaseCurie()
String	getDiseaseName()
String	getEntrezGeneId()
String	getGeneSymbol()
String	getGeneUrl()
String	getGenotypeExplanation()
String	getPosttestprob()
String	getPretestprob()
int	getRank()
String	getSvg()
String	getUrl()
List<VisualizableVariant>	getVisualizableVariants()
boolean	hasGenotypeExplanation()
boolean	hasVariants()	The answer to this string is used by the FreeMarker template to determine whether or not to show a table with variants.
String	sampleId()
void	setAnchor(String a)

Methods inherited from class java.lang.Object

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

Field Details

EMPTY_STRING

protected static final String EMPTY_STRING

See Also:

• Constant Field Values

NOT_AVAILABLE

protected static final String NOT_AVAILABLE

See Also:

• Constant Field Values

sampleId

protected final String sampleId

geneId

protected final org.monarchinitiative.phenol.annotations.formats.GeneIdentifier geneId

variants

protected final List<VisualizableVariant> variants

Method Details

getSvg

public String getSvg()

getUrl

public String getUrl()

getGeneUrl

public String getGeneUrl()

getVisualizableVariants

public List<VisualizableVariant> getVisualizableVariants()

setAnchor

public void setAnchor(String a)

Parameters:

a - An HTML anchor that is used for the HTML template.

getAnchor

public String getAnchor()

Returns:

An HTML anchor that is used for the HTML template.

hasGenotypeExplanation

public boolean hasGenotypeExplanation()

getGenotypeExplanation

public String getGenotypeExplanation()

Returns:

An genotypeExplanation of how the genotype score was calculated (for the HTML template).

sampleId

public String sampleId()

getDiseaseName

public String getDiseaseName()

getDiseaseCurie

public String getDiseaseCurie()

getPretestprob

public String getPretestprob()

getPosttestprob

public String getPosttestprob()

getCompositeLR

public double getCompositeLR()

getEntrezGeneId

public String getEntrezGeneId()

getGeneSymbol

public String getGeneSymbol()

hasVariants

public boolean hasVariants()

The answer to this string is used by the FreeMarker template to determine whether or not to show a table with variants.

Returns:

"yes" if this differential diagnosis has variants.

getRank

public int getRank()