B C D E G I L M N O Q R S T

B

buildSearchURL(String, String, String, int, int) - Static method in class org.eaglei.search.provider.nif.NIFQueryUtil

buildServiceURL(String, List<String>, String, int, String) - Static method in class org.eaglei.search.provider.nif.NIFQueryUtil

Builds a query URL for executing an eUtils service that retrieves information for a set of IDs.

C

count - Variable in class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

Total number of results returned

count(SearchCountRequest) - Method in class org.eaglei.search.provider.nif.NIFSearchProvider

D

DB - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

DEBUG - Static variable in class org.eaglei.search.provider.nif.NIFSearchProvider

details - Variable in class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

XML Document that represent the associated eSummary or eFetch results.

E

eagleiOntModel - Variable in class org.eaglei.search.provider.nif.NIFSearchProvider

EUTILS_URL - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

executeNIFRequest(String) - Static method in class org.eaglei.search.provider.nif.NIFQueryUtil

Executes an NCBI request at the specified eUtils URL and returns the XML response as a DOM Document

G

getQuery(SearchRequest, boolean, Set<EIURI>, boolean) - Method in class org.eaglei.search.provider.nif.NIFSearchProvider

Generic query generation logic

getType(SearchRequest) - Static method in class org.eaglei.search.provider.nif.NIFSearchProvider

Gets the type from a SearchRequest.

I

ID - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

ID_PARAM - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

IDLIST - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

ids - Variable in class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

IDs of result set.

init() - Method in class org.eaglei.search.provider.nif.NIFSearchProvider

institutionRegistry - Variable in class org.eaglei.search.provider.nif.NIFSearchProvider

isType(EIURI, EIURI) - Method in class org.eaglei.search.provider.nif.NIFSearchProvider

Checks, with inference, if a given type is of another type.

L

logger - Static variable in class org.eaglei.search.provider.nif.NIFSearchProvider

M

max - Variable in class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

Max number of results

N

NIFQueryUtil - Class in org.eaglei.search.provider.nif

Contains logic for using NIF ESearch.

NIFQueryUtil() - Constructor for class org.eaglei.search.provider.nif.NIFQueryUtil

NIFQueryUtil.ESearchResult - Class in org.eaglei.search.provider.nif

Simple representation of an eSearch result and, optionally, the results of a subsequent set of sSummary or eFetch calls.

NIFQueryUtil.ESearchResult(Document) - Constructor for class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

Creates an ESearchResult from an XML Document.

NIFSearchProvider - Class in org.eaglei.search.provider.nif

Abstract implementation of the eagle-i SearchProvider interface that wraps an NCBIDBProvider.

NIFSearchProvider(EIOntModel, InstitutionRegistry) - Constructor for class org.eaglei.search.provider.nif.NIFSearchProvider

Creates a new NCBIDBProvider that executes queries against NCBI.

O

org.eaglei.search.provider.nif - package org.eaglei.search.provider.nif

Q

query(SearchRequest) - Method in class org.eaglei.search.provider.nif.NIFSearchProvider

queryTranslation - Variable in class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

Translation of the query

R

RETMAX - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

RETMODE - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

RETSTART - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

S

search(String, String, String, int, int) - Static method in class org.eaglei.search.provider.nif.NIFQueryUtil

Executes an NCBI search.

serializeDocument(Document) - Static method in class org.eaglei.search.provider.nif.NIFQueryUtil

Utility method to serialize an XML document.

start - Variable in class org.eaglei.search.provider.nif.NIFQueryUtil.ESearchResult

Start of the result set

T

TERM - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

TOOL - Static variable in class org.eaglei.search.provider.nif.NIFQueryUtil

B C D E G I L M N O Q R S T