Package de.julielab.genemapper.evaluation.tools

Class TAPEvaluator

java.lang.Object

de.julielab.genemapper.evaluation.tools.TAPEvaluator

public class TAPEvaluator
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	TAPEvaluator.TapInputLine
static class	TAPEvaluator.TapInputList
static class	TAPEvaluator.TapResult
static class	TAPEvaluator.TapResultList
static class	TAPEvaluator.TapResultRecord

Field Summary

Fields

Modifier and Type	Field	Description
static File	TAP_EXEC
static File	TAP_EXEC_WORKING_DIR
File	tapInputDir
File	tapStatsDir

Constructor Summary

Constructors

Constructor	Description
TAPEvaluator()
TAPEvaluator(File tapStatsDir)
TAPEvaluator(File tapInputDir, File tapStatsDir)

Method Summary

Modifier and Type	Method	Description
TAPEvaluator.TapResult	evaluate(String evaluationRunId, com.google.common.collect.Multimap<String,String> gold, com.google.common.collect.Multimap<String,de.julielab.geneexpbase.genemodel.GeneMention> predicted, Function<de.julielab.geneexpbase.candidateretrieval.SynHit,Double> confidenceFunction)	Writes the TAP input file from the given gold and predicted data and runs the TAP evaluation script via evaluate(String, File, File)-
TAPEvaluator.TapResult	evaluate(String evaluationRunId, File tapInputDir, File tapInputFile)	Carries out the evaluation on the tapInputFile.
List<TAPEvaluator.TapInputList>	makeTapInputLists(String evaluationRunId, com.google.common.collect.Multimap<String,String> gold, com.google.common.collect.Multimap<String,de.julielab.geneexpbase.genemodel.GeneMention> predicted, Function<de.julielab.geneexpbase.candidateretrieval.SynHit,Double> confidenceFunction)	Creates a representation of TAP input lists.
void	setK(String[] k)	Sets the evaluation points in number of errors.
void	writeTapInputFile(File tapInputFile, String evaluationRunId, com.google.common.collect.Multimap<String,String> gold, com.google.common.collect.Multimap<String,de.julielab.geneexpbase.genemodel.GeneMention> predicted, Function<de.julielab.geneexpbase.candidateretrieval.SynHit,Double> confidenceFunction)	Writes TAP input list data created by makeTapInputLists(String, Multimap, Multimap, Function) to tapInputFile.

Methods inherited from class java.lang.Object

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

Field Detail

TAP_EXEC_WORKING_DIR

public static final File TAP_EXEC_WORKING_DIR

TAP_EXEC

public static final File TAP_EXEC

tapInputDir

public File tapInputDir

tapStatsDir

public File tapStatsDir

Constructor Detail

TAPEvaluator

public TAPEvaluator()

TAPEvaluator

public TAPEvaluator(File tapInputDir,
                    File tapStatsDir)

TAPEvaluator

public TAPEvaluator(File tapStatsDir)

Method Detail

setK

public void setK(String[] k)

Sets the evaluation points in number of errors.

Parameters:

k -

evaluate

public TAPEvaluator.TapResult evaluate(String evaluationRunId,
                                       com.google.common.collect.Multimap<String,String> gold,
                                       com.google.common.collect.Multimap<String,de.julielab.geneexpbase.genemodel.GeneMention> predicted,
                                       Function<de.julielab.geneexpbase.candidateretrieval.SynHit,Double> confidenceFunction)
                                throws IOException

Writes the TAP input file from the given gold and predicted data and runs the TAP evaluation script via evaluate(String, File, File)-

Parameters:

evaluationRunId -

gold -

predicted -

confidenceFunction -

Returns:

Throws:

IOException

evaluate

public TAPEvaluator.TapResult evaluate(String evaluationRunId,
                                       File tapInputDir,
                                       File tapInputFile)
                                throws IOException

Carries out the evaluation on the tapInputFile.

Parameters:

evaluationRunId -

tapInputDir -

tapInputFile -

Returns:

Throws:

IOException

makeTapInputLists

public List<TAPEvaluator.TapInputList> makeTapInputLists(String evaluationRunId,
                                                         com.google.common.collect.Multimap<String,String> gold,
                                                         com.google.common.collect.Multimap<String,de.julielab.geneexpbase.genemodel.GeneMention> predicted,
                                                         Function<de.julielab.geneexpbase.candidateretrieval.SynHit,Double> confidenceFunction)

Creates a representation of TAP input lists. Each list is sorted ascending according to the passed confidence function.

The input lists are sorted by the name of the lists in the returned value.

Parameters:

evaluationRunId -

gold -

predicted -

confidenceFunction -

Returns:

writeTapInputFile

public void writeTapInputFile(File tapInputFile,
                              String evaluationRunId,
                              com.google.common.collect.Multimap<String,String> gold,
                              com.google.common.collect.Multimap<String,de.julielab.geneexpbase.genemodel.GeneMention> predicted,
                              Function<de.julielab.geneexpbase.candidateretrieval.SynHit,Double> confidenceFunction)
                       throws IOException

Writes TAP input list data created by makeTapInputLists(String, Multimap, Multimap, Function) to tapInputFile.

Parameters:

tapInputFile -

evaluationRunId -

gold -

predicted -

confidenceFunction -

Throws:

IOException