Serialized Form

Package de.julielab.genemapper

Class de.julielab.genemapper.Configuration extends de.julielab.geneexpbase.configuration.Configuration implements Serializable

serialVersionUID:

-1636778667307698253L

Class de.julielab.genemapper.SynHitSet extends TreeSet<de.julielab.geneexpbase.candidateretrieval.SynHit> implements Serializable

serialVersionUID:

-3948116045932952171L

Package de.julielab.genemapper.composites

Class de.julielab.genemapper.composites.CompositeToken extends Object implements Serializable

Serialized Fields

begin

int begin

end

int end

leftWs

boolean leftWs

plural

boolean plural

rightWs

boolean rightWs

tag

char tag

text

String text

Class de.julielab.genemapper.composites.ResolvedCompositeGeneName extends ArrayList<CompositeToken> implements Serializable

Serialized Fields

acronymForms

List<ResolvedCompositeGeneName> acronymForms

resolutionComponent

Class<? extends CompositePatternResolver> resolutionComponent

Package de.julielab.genemapper.disambig

Class de.julielab.genemapper.disambig.ContextScoreCacheKey extends Object implements Serializable

Serialized Fields

contextHash

byte[] contextHash

field

String field

ids

Collection<String> ids

loadFieldValue

boolean loadFieldValue

Package de.julielab.genemapper.evaluation.tools

Class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputList extends ArrayList<TAPEvaluator.TapInputLine> implements Serializable

Serialized Fields

listname

String listname

Class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResult extends HashMap<Integer,TAPEvaluator.TapResultList> implements Serializable

Class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultList extends ArrayList<TAPEvaluator.TapResultRecord> implements Serializable

Serialized Fields

listname

String listname

listresult

TAPEvaluator.TapResultRecord listresult

Package de.julielab.genemapper.filtering

Class de.julielab.genemapper.filtering.ChunkTypePipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

4802583029926447079L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.ContextPosPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-950513387211046959L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

addWord

boolean addWord

position

int position

prefix

String prefix

Class de.julielab.genemapper.filtering.ExperimentsPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-774615625199603297L

Class de.julielab.genemapper.filtering.GeneSequence2SingleGene extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

1L

Class de.julielab.genemapper.filtering.GeneSet2GeneSequence extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

1L

Class de.julielab.genemapper.filtering.LowerCasePipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-9008919110526729880L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.NextCharPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

3529841669747911491L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.NounPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-4682006591893008027L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.NumberClassPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

1L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

brief

boolean brief

prefix

String prefix

Class de.julielab.genemapper.filtering.PrevCharPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

1401083563798737535L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.RegExPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-3413642492165269351L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

feature

String feature

regex

Pattern regex

Class de.julielab.genemapper.filtering.TokenPrefixPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-7163636109881859558L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

prefixLength

int prefixLength

Class de.julielab.genemapper.filtering.WordClassPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

1L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

brief

boolean brief

featurePrefix

String featurePrefix

Package de.julielab.genemapper.filtering.families

Class de.julielab.genemapper.filtering.families.AcronymPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-9008919110526729880L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.families.ChemicalSuffix extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-3442366946904548L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.families.ContextEmbeddingPipe extends cc.mallet.pipe.Pipe implements Serializable

Class de.julielab.genemapper.filtering.families.ContextPosPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-950513387211046959L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

addWord

boolean addWord

position

int position

prefix

String prefix

Class de.julielab.genemapper.filtering.families.FamilyConfidencePipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-9008919110526729880L

Class de.julielab.genemapper.filtering.families.FamilyGenegroupProbabilityPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

familyProbFunction

Function<de.julielab.geneexpbase.genemodel.GeneMention,Double> familyProbFunction

Class de.julielab.genemapper.filtering.families.FamilyMatchPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

useFamilyMatchExactFeature

boolean useFamilyMatchExactFeature

useFamilyMatchFractionFeature

boolean useFamilyMatchFractionFeature

useFamilyMatchRankFeature

boolean useFamilyMatchRankFeature

useFamilyMatchScoreFeature

boolean useFamilyMatchScoreFeature

Class de.julielab.genemapper.filtering.families.GeneMention2Token extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

5719493241780864829L

Class de.julielab.genemapper.filtering.families.GeneSet2Token extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

5719493241780864829L

Class de.julielab.genemapper.filtering.families.IsAPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.families.IsFamilyPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-9008919110526729880L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.families.LastWordPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

featureName

String featureName

useGeneset

boolean useGeneset

Class de.julielab.genemapper.filtering.families.LowerCaseBoWPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-9008919110526729880L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.families.MentionEnvironmentPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.families.MentionPrefixPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

6376862551856291001L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

NONSPEC_KINASE

String[] NONSPEC_KINASE

prefix

String prefix

Class de.julielab.genemapper.filtering.families.MentionTypeHint extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-163529848335469810L

Class de.julielab.genemapper.filtering.families.NoDbHitsPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.families.NonDescriptivePipe extends cc.mallet.pipe.Pipe implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.families.NormalizeFeaturesForGeneSetSize extends cc.mallet.pipe.Pipe implements Serializable

Class de.julielab.genemapper.filtering.families.PluralPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.families.PoSBoWPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-9008919110526729880L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.families.ProteinSymbols extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

-7211355932042290296L

Class de.julielab.genemapper.filtering.families.SetFeatureVectorToGeneSetPipe extends cc.mallet.pipe.Pipe implements Serializable

Class de.julielab.genemapper.filtering.families.SetInstanceSourceToGeneSetPipe extends cc.mallet.pipe.Pipe implements Serializable

Class de.julielab.genemapper.filtering.families.SpecifierDetectionPipe extends cc.mallet.pipe.Pipe implements Serializable

Class de.julielab.genemapper.filtering.families.SymbolPrefixPipe extends cc.mallet.pipe.Pipe implements Serializable

serialVersionUID:

6376862551856291001L

Serialized Fields

prefix

String prefix

Class de.julielab.genemapper.filtering.families.UnspecifiedPipe extends cc.mallet.pipe.Pipe implements Serializable

Serialized Fields

featureName

String featureName

Class de.julielab.genemapper.filtering.families.WordEmbeddingPipe extends cc.mallet.pipe.Pipe implements Serializable

Package de.julielab.genemapper.hpo

Class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute extends de.julielab.geneexpbase.hpo.HpoRoute implements Serializable

Serialized Fields

entityEvaluator

de.julielab.evaluation.entities.EntityEvaluator entityEvaluator

fullEvalData

Map<String,List<org.apache.commons.lang3.tuple.Pair<de.julielab.evaluation.entities.EvaluationData,de.julielab.evaluation.entities.EvaluationData>>> fullEvalData

fullRejectionEvalData

Map<String,List<org.apache.commons.lang3.tuple.Pair<de.julielab.evaluation.entities.EvaluationData,de.julielab.evaluation.entities.EvaluationData>>> fullRejectionEvalData

inspectionFilePrinter

de.julielab.geneexpbase.hpo.InspectionFilePrinter inspectionFilePrinter

Class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute extends de.julielab.geneexpbase.hpo.HpoRoute implements Serializable

Class de.julielab.genemapper.hpo.GenesetsOptimizationRoute extends de.julielab.geneexpbase.hpo.HpoRoute implements Serializable

Class de.julielab.genemapper.hpo.GNormPlusBC2TestRoute extends CandidateRetrievalOptimizationRoute implements Serializable

Package de.julielab.genemapper.utils

Class de.julielab.genemapper.utils.GeneMapperException extends de.julielab.geneexpbase.GeneExpException implements Serializable

serialVersionUID:

6797330793965474689L

Class de.julielab.genemapper.utils.GeneMapperInitializationException extends Exception implements Serializable

Class de.julielab.genemapper.utils.GeneMapperRuntimeException extends de.julielab.geneexpbase.GeneExpRuntimeException implements Serializable

Class de.julielab.genemapper.utils.MissingConfigurationException extends GeneMapperRuntimeException implements Serializable