A B C E G H I L M O P R S T U V X

A

add(String, String) - Method in class edu.upenn.cis.taggers.frontend.Article
Add a field-value pair.
addSegment(String, int) - Method in class edu.upenn.cis.taggers.Tag
 
addTag(Tag) - Method in class edu.upenn.cis.taggers.TagList
 
Article - Class in edu.upenn.cis.taggers.frontend
An article is a collection of field names and values, in the order they were received.
Article(Tagger) - Constructor for class edu.upenn.cis.taggers.frontend.Article
 

B

BatchTagger - Class in edu.upenn.cis.taggers.frontend
Facilitates tagging of a batch of MEDLINE articles
BatchTagger() - Constructor for class edu.upenn.cis.taggers.frontend.BatchTagger
 
BioTokenizer - Class in edu.upenn.cis.tokenizers
A class to handle tokenization of biological text
BioTokenizer() - Constructor for class edu.upenn.cis.tokenizers.BioTokenizer
 

C

Constants - Class in edu.upenn.cis.taggers
 
Constants() - Constructor for class edu.upenn.cis.taggers.Constants
 
ContainsLowFreqTriGram - Class in edu.upenn.cis.taggers.gene
 
ContainsLowFreqTriGram(String, Reader, boolean) - Constructor for class edu.upenn.cis.taggers.gene.ContainsLowFreqTriGram
 
ContainsLowFreqTriGram(String, File, boolean) - Constructor for class edu.upenn.cis.taggers.gene.ContainsLowFreqTriGram
 
ContainsLowFreqTriGram(File, boolean) - Constructor for class edu.upenn.cis.taggers.gene.ContainsLowFreqTriGram
 
ContainsLowFreqTriGram(File) - Constructor for class edu.upenn.cis.taggers.gene.ContainsLowFreqTriGram
 

E

edu.upenn.cis.taggers - package edu.upenn.cis.taggers
 
edu.upenn.cis.taggers.frontend - package edu.upenn.cis.taggers.frontend
 
edu.upenn.cis.taggers.gene - package edu.upenn.cis.taggers.gene
 
edu.upenn.cis.taggers.malignancy - package edu.upenn.cis.taggers.malignancy
 
edu.upenn.cis.taggers.variation - package edu.upenn.cis.taggers.variation
 
edu.upenn.cis.tokenizers - package edu.upenn.cis.tokenizers
 

G

GeneSegmentationEvaluator - Class in edu.upenn.cis.taggers.gene
 
GeneSegmentationEvaluator(Object[], Object[]) - Constructor for class edu.upenn.cis.taggers.gene.GeneSegmentationEvaluator
 
GeneSegmentationOutput - Class in edu.upenn.cis.taggers.gene
This class should never be called directly; it exists as an auxiliary to GeneTagger.
GeneSegmentationOutput() - Constructor for class edu.upenn.cis.taggers.gene.GeneSegmentationOutput
 
GeneSentence2TokenSequence - Class in edu.upenn.cis.taggers.gene
 
GeneSentence2TokenSequence() - Constructor for class edu.upenn.cis.taggers.gene.GeneSentence2TokenSequence
 
GeneSentence2TokenSequence(boolean) - Constructor for class edu.upenn.cis.taggers.gene.GeneSentence2TokenSequence
 
GeneTagger - Class in edu.upenn.cis.taggers.gene
Tags genes within a body of text
GeneTagger(String) - Constructor for class edu.upenn.cis.taggers.gene.GeneTagger
Construct a new gene tagger -- read in the model and whatnot
GeneTrainer - Class in edu.upenn.cis.taggers.gene
 
GeneTrainer() - Constructor for class edu.upenn.cis.taggers.gene.GeneTrainer
 
getEndOffset() - Method in class edu.upenn.cis.taggers.Tag
 
getStartOffset() - Method in class edu.upenn.cis.taggers.Tag
 
getTag(int) - Method in class edu.upenn.cis.taggers.TagList
 
getTagList() - Method in class edu.upenn.cis.taggers.gene.GeneTagger
 
getTagList() - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 
getTagname() - Method in class edu.upenn.cis.taggers.Tag
 
getTokenEndIndex() - Method in class edu.upenn.cis.taggers.Tag
 
getTokenStartIndex() - Method in class edu.upenn.cis.taggers.Tag
 
getValue(String) - Method in class edu.upenn.cis.taggers.frontend.Article
Return the value associated with a field, or null if there isn't one If it's been tagged or modified in any way, gets the modified one.
GZIP_EXTENSION - Static variable in class edu.upenn.cis.taggers.Model
 

H

HTML - Static variable in class edu.upenn.cis.taggers.frontend.Article
 
htmlCloseTags() - Method in class edu.upenn.cis.taggers.gene.GeneTagger
See Tagger for details
htmlCloseTags() - Method in class edu.upenn.cis.taggers.malignancy.MalignancyTagger
See Tagger for details
htmlCloseTags() - Method in interface edu.upenn.cis.taggers.Tagger
Returns a string array of the HTML tags that should follow each tagged entity.
htmlCloseTags() - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 
htmlHeader() - Method in class edu.upenn.cis.taggers.gene.GeneTagger
 
htmlHeader() - Method in class edu.upenn.cis.taggers.malignancy.MalignancyTagger
 
htmlHeader() - Method in interface edu.upenn.cis.taggers.Tagger
Returns the header that should be written to an HTML output file.
htmlHeader() - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 
htmlOpenTags() - Method in class edu.upenn.cis.taggers.gene.GeneTagger
See Tagger for details
htmlOpenTags() - Method in class edu.upenn.cis.taggers.malignancy.MalignancyTagger
See Tagger for details
htmlOpenTags() - Method in interface edu.upenn.cis.taggers.Tagger
Returns a string array of the HTML tags that should precede each tagged entity.
htmlOpenTags() - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 

I

InBracket - Class in edu.upenn.cis.taggers.gene
 
InBracket(String, boolean) - Constructor for class edu.upenn.cis.taggers.gene.InBracket
 
iterator() - Method in class edu.upenn.cis.taggers.TagList
 

L

loadAndRetrieveModel(String) - Static method in class edu.upenn.cis.taggers.Model
 
loadAndRetrieveModel(InputStream) - Static method in class edu.upenn.cis.taggers.Model
 
loadAndRetrieveModelFromClassPathResource(String, Class) - Static method in class edu.upenn.cis.taggers.Model
 
loadModel() - Static method in class edu.upenn.cis.taggers.gene.GeneTrainer
 
loadModel(String) - Static method in class edu.upenn.cis.taggers.gene.GeneTrainer
 
LoadModelException - Exception in edu.upenn.cis.taggers
 
LoadModelException(String) - Constructor for exception edu.upenn.cis.taggers.LoadModelException
 

M

main(String[]) - Static method in class edu.upenn.cis.taggers.frontend.BatchTagger
Loads the specified tagger with the specified model, and passes the input file through it to be tagged.
main(String[]) - Static method in class edu.upenn.cis.taggers.gene.GeneTrainer
 
main(String[]) - Static method in class edu.upenn.cis.taggers.malignancy.MalignancyTrainer
 
main(String[]) - Static method in class edu.upenn.cis.taggers.variation.VariationTrainer
 
MalignancySegmentationEvaluator - Class in edu.upenn.cis.taggers.malignancy
 
MalignancySegmentationEvaluator(String[], String[]) - Constructor for class edu.upenn.cis.taggers.malignancy.MalignancySegmentationEvaluator
 
MalignancyTagger - Class in edu.upenn.cis.taggers.malignancy
 
MalignancyTagger(String) - Constructor for class edu.upenn.cis.taggers.malignancy.MalignancyTagger
 
MalignancyTrainer - Class in edu.upenn.cis.taggers.malignancy
 
MalignancyTrainer() - Constructor for class edu.upenn.cis.taggers.malignancy.MalignancyTrainer
 
MaligSentence2TokenSequence - Class in edu.upenn.cis.taggers.malignancy
 
MaligSentence2TokenSequence() - Constructor for class edu.upenn.cis.taggers.malignancy.MaligSentence2TokenSequence
 
MaligSentence2TokenSequence(boolean) - Constructor for class edu.upenn.cis.taggers.malignancy.MaligSentence2TokenSequence
 
MEDLINE - Static variable in class edu.upenn.cis.taggers.frontend.Article
 
medlineTags() - Method in class edu.upenn.cis.taggers.gene.GeneTagger
See Tagger for details
medlineTags() - Method in class edu.upenn.cis.taggers.malignancy.MalignancyTagger
See Tagger for details
medlineTags() - Method in interface edu.upenn.cis.taggers.Tagger
Returns a string array of the MEDLINE tags that should be written to the MEDLINE file.
medlineTags() - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 
Model - Class in edu.upenn.cis.taggers
 
Model() - Constructor for class edu.upenn.cis.taggers.Model
 

O

output(Transducer, InstanceList) - Method in class edu.upenn.cis.taggers.malignancy.MalignancySegmentationEvaluator
 
output(Transducer, InstanceList) - Method in class edu.upenn.cis.taggers.variation.VariationSegmentationEvaluator
 
output(Transducer, InstanceList, Vector) - Method in class edu.upenn.cis.taggers.variation.VariationSegmentationEvaluator
 

P

pipe(Instance) - Method in class edu.upenn.cis.taggers.gene.ContainsLowFreqTriGram
 
pipe(Instance) - Method in class edu.upenn.cis.taggers.gene.GeneSentence2TokenSequence
 
pipe(Instance) - Method in class edu.upenn.cis.taggers.gene.InBracket
 
pipe(Instance) - Method in class edu.upenn.cis.taggers.malignancy.MaligSentence2TokenSequence
 
pipe(Instance) - Method in class edu.upenn.cis.taggers.variation.VariationRegexTrieLexiconMembership
 
pipe(Instance) - Method in class edu.upenn.cis.taggers.variation.VariationSentence2TokenSequence
 

R

RAW_MODEL_EXTENSION - Static variable in class edu.upenn.cis.taggers.Model
 

S

SVUID_GENE_BIO_CREATIVE_SENTENCE_2_TOKEN_SEQUENCE - Static variable in class edu.upenn.cis.taggers.Constants
 
SVUID_GENE_CONTAINS_LOW_FREQ_TRIGRAM - Static variable in class edu.upenn.cis.taggers.Constants
 
SVUID_GENE_IN_BRACKET - Static variable in class edu.upenn.cis.taggers.Constants
 
SVUID_GENE_REGEX_TRIELEXICON_MEMBERSHIP - Static variable in class edu.upenn.cis.taggers.Constants
 
SVUID_VARIATION_REGEX_TRIELEXICON_MEMBERSHIP - Static variable in class edu.upenn.cis.taggers.Constants
 
SVUID_VARIATION_SENTENCE_2_TOKEN_SEQUENCE - Static variable in class edu.upenn.cis.taggers.Constants
 

T

tag(String) - Method in class edu.upenn.cis.taggers.frontend.Article
Tag the value associated with that field.
tag(String, Transducer, InstanceList) - Method in class edu.upenn.cis.taggers.gene.GeneSegmentationOutput
 
tag(String, Transducer, InstanceList, Vector) - Method in class edu.upenn.cis.taggers.gene.GeneSegmentationOutput
This class's only method.
tag(String) - Method in class edu.upenn.cis.taggers.gene.GeneTagger
Returns XML-tagged data
tag(String) - Method in class edu.upenn.cis.taggers.malignancy.MalignancyTagger
 
Tag - Class in edu.upenn.cis.taggers
 
Tag(String) - Constructor for class edu.upenn.cis.taggers.Tag
 
tag(String) - Method in interface edu.upenn.cis.taggers.Tagger
Returns the input String with xml tagging inline.
tag(String) - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 
Tagger - Interface in edu.upenn.cis.taggers
All taggers intended to be run on MEDLINE data should implement this interface.
TagList - Class in edu.upenn.cis.taggers
 
TagList() - Constructor for class edu.upenn.cis.taggers.TagList
 
tokenize(String) - Method in class edu.upenn.cis.tokenizers.BioTokenizer
Returns a tokenized version of the passed String
toString(boolean) - Method in class edu.upenn.cis.taggers.frontend.Article
Returns this article in either MEDLINE or HTML format MEDLINE will use all the original strings, with additional tags (specified by the tagger) for the data.
toString() - Method in class edu.upenn.cis.taggers.Tag
 
toXML(String[]) - Method in class edu.upenn.cis.taggers.TagList
 

U

updateOffset(int, int) - Method in class edu.upenn.cis.taggers.Tag
 

V

VariationRegexTrieLexiconMembership - Class in edu.upenn.cis.taggers.variation
 
VariationRegexTrieLexiconMembership(String, Reader, boolean) - Constructor for class edu.upenn.cis.taggers.variation.VariationRegexTrieLexiconMembership
 
VariationRegexTrieLexiconMembership(String, File, boolean) - Constructor for class edu.upenn.cis.taggers.variation.VariationRegexTrieLexiconMembership
 
VariationRegexTrieLexiconMembership(File, boolean) - Constructor for class edu.upenn.cis.taggers.variation.VariationRegexTrieLexiconMembership
 
VariationRegexTrieLexiconMembership(File) - Constructor for class edu.upenn.cis.taggers.variation.VariationRegexTrieLexiconMembership
 
VariationSegmentationEvaluator - Class in edu.upenn.cis.taggers.variation
This class should never be called directly; it exists as an auxiliary to VariationTagger.
VariationSegmentationEvaluator(String[], String[]) - Constructor for class edu.upenn.cis.taggers.variation.VariationSegmentationEvaluator
 
VariationSentence2TokenSequence - Class in edu.upenn.cis.taggers.variation
 
VariationSentence2TokenSequence() - Constructor for class edu.upenn.cis.taggers.variation.VariationSentence2TokenSequence
 
VariationTagger - Class in edu.upenn.cis.taggers.variation
Tags variations (mutations and such) within a body of text
VariationTagger(String) - Constructor for class edu.upenn.cis.taggers.variation.VariationTagger
Construct a variationTagger
VariationTrainer - Class in edu.upenn.cis.taggers.variation
 
VariationTrainer() - Constructor for class edu.upenn.cis.taggers.variation.VariationTrainer
 

X

xmlTags() - Method in class edu.upenn.cis.taggers.gene.GeneTagger
See Tagger for details
xmlTags() - Method in class edu.upenn.cis.taggers.malignancy.MalignancyTagger
See Tagger for details
xmlTags() - Method in interface edu.upenn.cis.taggers.Tagger
Returns a string array of the xml tags this tagger may insert.
xmlTags() - Method in class edu.upenn.cis.taggers.variation.VariationTagger
 

A B C E G H I L M O P R S T U V X