Package org.monarchinitiative.lirical.io.output

Class TsvDifferential

java.lang.Object

org.monarchinitiative.lirical.io.output.TsvDifferential

public class TsvDifferential
extends Object

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

Constructor Summary

Constructors

Constructor	Description
TsvDifferential(String sampleId, org.monarchinitiative.phenol.ontology.data.TermId diseaseId, String diseaseName, TestResult result, int rank, List<VisualizableVariant> variants)

Method Summary

Modifier and Type	Method	Description
double	getCompositeLR()
String	getDiseaseCurie()
String	getDiseaseName()
String	getEntrezGeneId()
String	getGeneSymbol()
String	getPosttestprob()
String	getPretestprob()
int	getRank()
String	getVarString()
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()

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

Constructor Details

TsvDifferential

public TsvDifferential(String sampleId,
 org.monarchinitiative.phenol.ontology.data.TermId diseaseId,
 String diseaseName,
 TestResult result,
 int rank,
 List<VisualizableVariant> variants)

Method Details

getVarString

public String getVarString()

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()