A B C D E F G I J L M N O P Q R S T U V

A

AUTHOR - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

AUTHOR_LIST - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

B

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

Builds an ESearchURL

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

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

C

COMMON_NAME - Static variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

commonName - Variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider.TaxonomySummary

count - Variable in class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

Total number of results returned

D

DB - Static variable in class org.eaglei.search.provider.ncbi.EUtils

DEBUG - Static variable in class org.eaglei.search.provider.ncbi.NCBIDBProvider

DESC - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

desc - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

descrip - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

details - Variable in class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

XML Document that represent the associated eSummary or eFetch results.

E

EAGLEI_TOOL - Static variable in class org.eaglei.search.provider.ncbi.NCBIDBProvider

Name of tool for eagle-i that is passed to NCBI eUtils.

EFetch - Class in org.eaglei.search.provider.ncbi

Contains logic for using NCBI eFetch.

EFetch() - Constructor for class org.eaglei.search.provider.ncbi.EFetch

ENTREZ_GENE - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

entrezDB - Variable in class org.eaglei.search.provider.ncbi.NCBIDBProvider

ESearch - Class in org.eaglei.search.provider.ncbi

Contains logic for using NCBI ESearch.

ESearch() - Constructor for class org.eaglei.search.provider.ncbi.ESearch

ESearch.ESearchResult - Class in org.eaglei.search.provider.ncbi

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

ESearch.ESearchResult(Document) - Constructor for class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

Creates an ESearchResult from an XML Document.

ESummary - Class in org.eaglei.search.provider.ncbi

Contains logic for using NCBI EUtils.

ESummary() - Constructor for class org.eaglei.search.provider.ncbi.ESummary

ESummary.ESummaryResult - Class in org.eaglei.search.provider.ncbi

Simple representation of the result (a DocSum) from an eSummary search

ESummary.ESummaryResult(Node) - Constructor for class org.eaglei.search.provider.ncbi.ESummary.ESummaryResult

ESummary.Item - Class in org.eaglei.search.provider.ncbi

ESummary.Item() - Constructor for class org.eaglei.search.provider.ncbi.ESummary.Item

ESummary.ListItem - Class in org.eaglei.search.provider.ncbi

ESummary.ListItem() - Constructor for class org.eaglei.search.provider.ncbi.ESummary.ListItem

EUtils - Class in org.eaglei.search.provider.ncbi

Contains logic for using NCBI EUtils.

EUtils() - Constructor for class org.eaglei.search.provider.ncbi.EUtils

EUTILS_SUMMARY_URL - Static variable in class org.eaglei.search.provider.ncbi.ESummary

EUTILS_URL - Static variable in class org.eaglei.search.provider.ncbi.EUtils

executeNCBIRequest(String) - Static method in class org.eaglei.search.provider.ncbi.EUtils

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

F

fetch(ESearch.ESearchResult, String, String, int) - Static method in class org.eaglei.search.provider.ncbi.EFetch

Executes an NCBI search and then series of eFetch calls for the initial page of results.

FULL_JOURNAL_NAME - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

G

GENE - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

GENE_URL - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

getSummaries(ESearch.ESearchResult, String, String, int) - Static method in class org.eaglei.search.provider.ncbi.ESummary

Executes an NCBI search and then series of summary calls for the initial page of results.

I

id - Variable in class org.eaglei.search.provider.ncbi.ESummary.ESummaryResult

ID - Static variable in class org.eaglei.search.provider.ncbi.EUtils

id - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

id - Variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

id - Variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

id - Variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider.TaxonomySummary

ID_PARAM - Static variable in class org.eaglei.search.provider.ncbi.EUtils

IDLIST - Static variable in class org.eaglei.search.provider.ncbi.EUtils

ids - Variable in class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

IDs of result set.

IDXLINKS - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

items - Variable in class org.eaglei.search.provider.ncbi.ESummary.ESummaryResult

items - Variable in class org.eaglei.search.provider.ncbi.ESummary.ListItem

J

journal - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

L

label - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

label - Variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

label - Variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

label - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

label - Variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider.TaxonomySummary

LINKSTYPE - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

logger - Static variable in class org.eaglei.search.provider.ncbi.NCBIDBProvider

M

max - Variable in class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

Max number of results

MESH - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

MESH_TERMS - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

MESH_URL - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

meshTerm - Variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

meshTerms - Variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

N

name - Variable in class org.eaglei.search.provider.ncbi.ESummary.Item

name - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

NAME - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

NAME - Static variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

name - Variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

NCBI_MESH_NAME - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

NCBI_PROBE_NAME - Static variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

NCBI_PUBMED_NAME - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

NCBI_TAXONOMY_NAME - Static variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

NCBIDBProvider - Class in org.eaglei.search.provider.ncbi

Abstract class that provides search support via eUtils for a specific NCBI Entrez database.

NCBIDBProvider(String) - Constructor for class org.eaglei.search.provider.ncbi.NCBIDBProvider

Creates a new NCBIDBProvider that executes queries against NCBI.

NCBIGeneProvider - Class in org.eaglei.search.provider.ncbi.gene

Contains logic for querying NCBI Entrez Gene via EUtils.

NCBIGeneProvider() - Constructor for class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

NCBIGeneProvider.GeneSummary - Class in org.eaglei.search.provider.ncbi.gene

NCBIGeneProvider.GeneSummary(ESummary.ESummaryResult) - Constructor for class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

NCBIMeSHProvider - Class in org.eaglei.search.provider.ncbi.mesh

Contains logic for querying NCBI MeSH via EUtils.

NCBIMeSHProvider() - Constructor for class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

NCBIMeSHProvider.MeSHSummary - Class in org.eaglei.search.provider.ncbi.mesh

NCBIMeSHProvider.MeSHSummary(ESummary.ESummaryResult) - Constructor for class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

NCBIProbeProvider - Class in org.eaglei.search.provider.ncbi.probe

Contains logic for querying NCBI Probe via EUtils.

NCBIProbeProvider() - Constructor for class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

NCBIProbeProvider.ProbeSummary - Class in org.eaglei.search.provider.ncbi.probe

NCBIProbeProvider.ProbeSummary(ESummary.ESummaryResult) - Constructor for class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

NCBIPubMedProvider - Class in org.eaglei.search.provider.ncbi.pubmed

Contains logic for querying PubMed via NCBI EUtils.

NCBIPubMedProvider() - Constructor for class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

NCBIPubMedProvider.PubMedSummary - Class in org.eaglei.search.provider.ncbi.pubmed

NCBIPubMedProvider.PubMedSummary(ESummary.ESummaryResult) - Constructor for class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

NCBITaxonomyProvider - Class in org.eaglei.search.provider.ncbi.taxonomy

Contains logic for querying NCBI Taxonomy via EUtils.

NCBITaxonomyProvider() - Constructor for class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

NCBITaxonomyProvider.TaxonomySummary - Class in org.eaglei.search.provider.ncbi.taxonomy

NCBITaxonomyProvider.TaxonomySummary(ESummary.ESummaryResult) - Constructor for class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider.TaxonomySummary

O

org.eaglei.search.provider.ncbi - package org.eaglei.search.provider.ncbi

org.eaglei.search.provider.ncbi.gene - package org.eaglei.search.provider.ncbi.gene

org.eaglei.search.provider.ncbi.mesh - package org.eaglei.search.provider.ncbi.mesh

org.eaglei.search.provider.ncbi.probe - package org.eaglei.search.provider.ncbi.probe

org.eaglei.search.provider.ncbi.pubmed - package org.eaglei.search.provider.ncbi.pubmed

org.eaglei.search.provider.ncbi.taxonomy - package org.eaglei.search.provider.ncbi.taxonomy

orgname - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

ORGNAME - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

OTHER_ALIASES - Static variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider

otherAliases - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

P

parseESummaryResult(Document) - Static method in class org.eaglei.search.provider.ncbi.ESummary

Parses an eSummary XML result and returns the IDs.

pmid - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

PROBE - Static variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

PROBE_URL - Static variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

ptype - Variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

PTYPE - Static variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

PUBMED - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

PUBMED_URL - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

Q

query(String, int, int) - Method in class org.eaglei.search.provider.ncbi.NCBIDBProvider

queryTranslation - Variable in class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

Translation of the query

R

RETMAX - Static variable in class org.eaglei.search.provider.ncbi.EUtils

RETMODE - Static variable in class org.eaglei.search.provider.ncbi.EUtils

RETSTART - Static variable in class org.eaglei.search.provider.ncbi.EUtils

S

SCI_NAME - Static variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

sciName - Variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider.TaxonomySummary

SCOPE_NOTE - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

scopeNote - Variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

search(String, String, String, int, int) - Static method in class org.eaglei.search.provider.ncbi.ESearch

Executes an NCBI search.

serializeDocument(Document) - Static method in class org.eaglei.search.provider.ncbi.EUtils

Utility method to serialize an XML document.

so - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

SO - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

SOURCE - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

start - Variable in class org.eaglei.search.provider.ncbi.ESearch.ESearchResult

Start of the result set

STRING - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

T

TAX_ID - Static variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

TAXONOMY - Static variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

TAXONOMY_URL - Static variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider

TERM - Static variable in class org.eaglei.search.provider.ncbi.EUtils

title - Variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

TITLE - Static variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider

title - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

TITLE - Static variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider

TOOL - Static variable in class org.eaglei.search.provider.ncbi.EUtils

TREENUM - Static variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider

type - Variable in class org.eaglei.search.provider.ncbi.ESummary.Item

U

url - Variable in class org.eaglei.search.provider.ncbi.gene.NCBIGeneProvider.GeneSummary

url - Variable in class org.eaglei.search.provider.ncbi.mesh.NCBIMeSHProvider.MeSHSummary

url - Variable in class org.eaglei.search.provider.ncbi.probe.NCBIProbeProvider.ProbeSummary

url - Variable in class org.eaglei.search.provider.ncbi.pubmed.NCBIPubMedProvider.PubMedSummary

url - Variable in class org.eaglei.search.provider.ncbi.taxonomy.NCBITaxonomyProvider.TaxonomySummary

V

value - Variable in class org.eaglei.search.provider.ncbi.ESummary.Item

A B C D E F G I J L M N O P Q R S T U V