Index

B C D E G H I M O S T
All Classes and Interfaces|All Packages|Serialized Form

B

biolark(URL) - Static method in class org.monarchinitiative.hpotextmining.core.miners.TermMiners

BiolarkResult - Class in org.monarchinitiative.hpotextmining.core.miners.biolark

The server performing text-mining analysis returns results as a collection of JSON objects.

BiolarkResult(int, int, int, String, String, BiolarkToken, boolean) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

Create instance from single response object.

BiolarkTermMiner - Class in org.monarchinitiative.hpotextmining.core.miners.biolark

This TermMiner uses Biolark web API to discover positions of HPO terms within provided query.

BiolarkTermMiner(URL) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkTermMiner

BiolarkTermMiner(URLConnection) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkTermMiner

BiolarkToken - Class in org.monarchinitiative.hpotextmining.core.miners.biolark

This class is an internal representation of a single HPO term within the HPO text-mining analysis.

BiolarkToken(String, String, Set<String>) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

Create BiolarkToken with following content.

C

compareByName() - Static method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

compareByStart() - Static method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

compareTo(SciGraphResult) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

Compare by the start position

ConnectionFactory(URL) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphTermMiner.ConnectionFactory

D

doMining(String) - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkTermMiner

Performs mining of the provided text using Biolark service; query String is sent to the Biolark API and the Thread is blocked until a JSON response is received.

doMining(String) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphTermMiner

Performs mining of the provided text using SciGraph service; query String is sent to the SciGraph API and the Thread is blocked until a JSON response is received.

doMining(String) - Method in interface org.monarchinitiative.hpotextmining.core.miners.TermMiner

Parse given query String and return set of SimpleMinedTerms representing HPO terms identified in the query.

E

equals(Object) - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

equals(Object) - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

equals(Object) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

equals(Object) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

G

getBegin() - Method in interface org.monarchinitiative.hpotextmining.core.miners.MinedTerm

getCategories() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

getEnd() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

getEnd() - Method in interface org.monarchinitiative.hpotextmining.core.miners.MinedTerm

getEnd() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

getId() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

Get HPO id for this term.

getId() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

getLabel() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

Get a label (term).

getLength() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

getOriginal_text() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

getSource() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

getStart() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

getStart() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

getSynonyms() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

Get a copy of the synonyms.

getTerm() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

getTermId() - Method in interface org.monarchinitiative.hpotextmining.core.miners.MinedTerm

getTerms() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

getToken() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

H

hashCode() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

hashCode() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

hashCode() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

hashCode() - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

HpoTextMiningException - Exception Class in org.monarchinitiative.hpotextmining.core

A checked exception thrown by HPO Text Mining widgets.

HpoTextMiningException() - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningException

HpoTextMiningException(String) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningException

HpoTextMiningException(String, Throwable) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningException

HpoTextMiningException(String, Throwable, boolean, boolean) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningException

HpoTextMiningException(Throwable) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningException

HpoTextMiningRuntimeException - Exception Class in org.monarchinitiative.hpotextmining.core

An unchecked exception thrown by HPO Text Mining widgets.

HpoTextMiningRuntimeException() - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningRuntimeException

HpoTextMiningRuntimeException(String) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningRuntimeException

HpoTextMiningRuntimeException(String, Throwable) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningRuntimeException

HpoTextMiningRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningRuntimeException

HpoTextMiningRuntimeException(Throwable) - Constructor for exception class org.monarchinitiative.hpotextmining.core.HpoTextMiningRuntimeException

I

isNegated() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

isPresent() - Method in interface org.monarchinitiative.hpotextmining.core.miners.MinedTerm

M

MinedTerm - Interface in org.monarchinitiative.hpotextmining.core.miners

O

of(int, int, String, boolean) - Static method in interface org.monarchinitiative.hpotextmining.core.miners.MinedTerm

org.monarchinitiative.hpotextmining.core - module org.monarchinitiative.hpotextmining.core

org.monarchinitiative.hpotextmining.core - package org.monarchinitiative.hpotextmining.core

org.monarchinitiative.hpotextmining.core.miners - package org.monarchinitiative.hpotextmining.core.miners

org.monarchinitiative.hpotextmining.core.miners.biolark - package org.monarchinitiative.hpotextmining.core.miners.biolark

org.monarchinitiative.hpotextmining.core.miners.scigraph - package org.monarchinitiative.hpotextmining.core.miners.scigraph

S

scigraph(URL) - Static method in class org.monarchinitiative.hpotextmining.core.miners.TermMiners

SciGraphResult - Class in org.monarchinitiative.hpotextmining.core.miners.scigraph

JSON Class representation of Monarch SciGraph text mining results.

SciGraphResult(SciGraphToken, int, int) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

SciGraphTermMiner - Class in org.monarchinitiative.hpotextmining.core.miners.scigraph

This class allows using Monarch SciGraph Server for text mining.

SciGraphTermMiner(URL) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphTermMiner

SciGraphTermMiner.ConnectionFactory - Class in org.monarchinitiative.hpotextmining.core.miners.scigraph

Each time the text mining is requested we send the query to the server using a new connection.

SciGraphToken - Class in org.monarchinitiative.hpotextmining.core.miners.scigraph

This class represent a "token" from SciGraph server.

SciGraphToken(String, List<String>, List<String>) - Constructor for class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

setCategories(List<String>) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

setEnd(int) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

setId(String) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

setLabel(String) - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

setStart(int) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

setTerms(List<String>) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphToken

setToken(SciGraphToken) - Method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

T

TermMiner - Interface in org.monarchinitiative.hpotextmining.core.miners

Classes implementing this interface are able to mine a set of MinedTerms from given query.

TermMinerException - Exception Class in org.monarchinitiative.hpotextmining.core.miners

TermMinerException() - Constructor for exception class org.monarchinitiative.hpotextmining.core.miners.TermMinerException

TermMinerException(String) - Constructor for exception class org.monarchinitiative.hpotextmining.core.miners.TermMinerException

TermMinerException(String, Throwable) - Constructor for exception class org.monarchinitiative.hpotextmining.core.miners.TermMinerException

TermMiners - Class in org.monarchinitiative.hpotextmining.core.miners

toBiolarkResult(SciGraphResult, String) - Static method in class org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphResult

Convert to BiolarkResult.

toString() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkResult

toString() - Method in class org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkToken

B C D E G H I M O S T
All Classes and Interfaces|All Packages|Serialized Form