Package org.monarchinitiative.lirical.core.likelihoodratio

Class LrWithExplanation

java.lang.Object

org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation

All Implemented Interfaces:

Comparable<LrWithExplanation>

public class LrWithExplanation
extends Object
implements Comparable<LrWithExplanation>

There are five possible ways that a query term can match a disease term. The likelihood ratio is calculated differently for each of these match types (see LrMatchType).This class captures sufficient information about each match to provide an explanation for the HTML output.

Author:

Peter Robinson

Method Summary

Modifier and Type	Method	Description
int	compareTo(LrWithExplanation that)	Sort the LrWithExplanation objects in decreasing order according to likelihood ratio score.
String	escapedExplanation()
String	explanation()
double	lr()
org.monarchinitiative.phenol.ontology.data.TermId	matchingTerm()
LrMatchType	matchType()
static LrWithExplanation	of(org.monarchinitiative.phenol.ontology.data.TermId q, org.monarchinitiative.phenol.ontology.data.TermId m, LrMatchType mt, double lr, String explanation)
org.monarchinitiative.phenol.ontology.data.TermId	queryTerm()

Methods inherited from class java.lang.Object

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

Method Details

of

public static LrWithExplanation of(org.monarchinitiative.phenol.ontology.data.TermId q,
 org.monarchinitiative.phenol.ontology.data.TermId m,
 LrMatchType mt,
 double lr,
 String explanation)

queryTerm

public org.monarchinitiative.phenol.ontology.data.TermId queryTerm()

matchingTerm

public org.monarchinitiative.phenol.ontology.data.TermId matchingTerm()

matchType

public LrMatchType matchType()

lr

public double lr()

explanation

public String explanation()

escapedExplanation

public String escapedExplanation()

Returns:

explanation text suitable for including in HTML documents

compareTo

public int compareTo(LrWithExplanation that)

Sort the LrWithExplanation objects in decreasing order according to likelihood ratio score. This will match the order of the bars in the SVG plot.

Specified by:

compareTo in interface Comparable<LrWithExplanation>

Parameters:

that - Other object

Returns:

integer indicating sort order