Package de.julielab.jules.ae.genemapping

Class MentionMappingResult

java.lang.Object

de.julielab.jules.ae.genemapping.MentionMappingResult

All Implemented Interfaces:

java.lang.Comparable<MentionMappingResult>

public class MentionMappingResult
extends java.lang.Object
implements java.lang.Comparable<MentionMappingResult>

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MentionMappingResult.MatchType
static class	MentionMappingResult.RejectionSynHit

Field Summary

Fields

Modifier and Type	Field	Description
int	ambiguityDegree
java.util.List<SynHit>	bestCandidate	The best candidate at the current time of the mapping process, defaults to REJECTION.
double	confidence
java.util.List<SynHit>	filteredCandidates	The candidates that have been filtered by some criterion in the attempt to eliminate bad candidates.
java.util.List<GeneIdCandidate>	geneIdCandidates	This field is set towards the end of the mapping/disambiguation process.
GeneMention	mappedMention
MentionMappingResult.MatchType	matchType
java.util.List<SynHit>	originalCandidates	The database candidates found for the name of this gene mention.
static java.util.List<SynHit>	REJECTION
java.util.List<SynHit>	resultEntries
java.util.List<SynHit>	semanticallyOrderedCandidates	This list contains the same elements as filteredCandidates but sorted for semantic score, after the respective external algorithm in a disambiguation class has set this field.

Constructor Summary

Constructors

Constructor	Description
MentionMappingResult()

Method Summary

Modifier and Type	Method	Description
int	compareTo(MentionMappingResult o)	The comparison is delegated to the order of the resultEntry SynHits.
long	getCandidateRetrievalTime()
long	getDisambiguationTime()
void	setCandidateRetrievalTime(long candidateRetrievalTime)
void	setDisambiguationTime(long disambiguationTime)

Methods inherited from class java.lang.Object

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

Field Detail

REJECTION

public static final java.util.List<SynHit> REJECTION

resultEntries

public java.util.List<SynHit> resultEntries

ambiguityDegree

public int ambiguityDegree

matchType

public MentionMappingResult.MatchType matchType

mappedMention

public GeneMention mappedMention

geneIdCandidates

public java.util.List<GeneIdCandidate> geneIdCandidates

This field is set towards the end of the mapping/disambiguation process. A list of gene IDs will have been identified that look like they could be apply the gene mention. The list should always be ordered descending in score, meaning that the first entry would be the best to choose.

If this is only one candidate, the mention is unambiguously mappable (which doesn't mean to 100% that the mapping will be correct, but all the hints we have point to this single candidate).

If there are multiple candidates, we still haven't finally decided to this point.

originalCandidates

public java.util.List<SynHit> originalCandidates

The database candidates found for the name of this gene mention. This is a list of database name matches ordered by the score that the specific database name matches the gene name.

filteredCandidates

public java.util.List<SynHit> filteredCandidates

The candidates that have been filtered by some criterion in the attempt to eliminate bad candidates. The list has to be set by an external algorithm and will be null before that.

semanticallyOrderedCandidates

public java.util.List<SynHit> semanticallyOrderedCandidates

This list contains the same elements as filteredCandidates but sorted for semantic score, after the respective external algorithm in a disambiguation class has set this field.

bestCandidate

public java.util.List<SynHit> bestCandidate

The best candidate at the current time of the mapping process, defaults to REJECTION.

confidence

public double confidence

Constructor Detail

MentionMappingResult

public MentionMappingResult()

Method Detail

compareTo

public int compareTo(MentionMappingResult o)

The comparison is delegated to the order of the resultEntry SynHits. Thus, we actually sort by SynHit.

Specified by:

compareTo in interface java.lang.Comparable<MentionMappingResult>

getCandidateRetrievalTime

public long getCandidateRetrievalTime()

setCandidateRetrievalTime

public void setCandidateRetrievalTime(long candidateRetrievalTime)

getDisambiguationTime

public long getDisambiguationTime()

setDisambiguationTime

public void setDisambiguationTime(long disambiguationTime)