A B C D F G I M N O P R S U X
All Classes All Packages

A

accept(Representation) - Method in class org.bridgedb.server.Batch

Attributes - Class in org.bridgedb.server

Resource that handles the attributes queries

Attributes() - Constructor for class org.bridgedb.server.Attributes

AttributeSearch - Class in org.bridgedb.server

Resource that handles the xref queries

AttributeSearch() - Constructor for class org.bridgedb.server.AttributeSearch

AttributeSet - Class in org.bridgedb.server

AttributeSet() - Constructor for class org.bridgedb.server.AttributeSet

B

BackPageText - Class in org.bridgedb.server

Resource that handles the xref queries

BackPageText() - Constructor for class org.bridgedb.server.BackPageText

Batch - Class in org.bridgedb.server

Batch() - Constructor for class org.bridgedb.server.Batch

C

CONF_GDBS - Static variable in class org.bridgedb.server.IDMapperService

Config - Class in org.bridgedb.server

Config() - Constructor for class org.bridgedb.server.Config

configFile - Variable in class org.bridgedb.server.IDMapperService

Contents - Class in org.bridgedb.server

Contents() - Constructor for class org.bridgedb.server.Contents

createRoot() - Method in class org.bridgedb.server.IDMapperService

D

DataSources - Class in org.bridgedb.server

DataSources() - Constructor for class org.bridgedb.server.DataSources

doInit() - Method in class org.bridgedb.server.Attributes

doInit() - Method in class org.bridgedb.server.AttributeSearch

doInit() - Method in class org.bridgedb.server.BackPageText

doInit() - Method in class org.bridgedb.server.Batch

doInit() - Method in class org.bridgedb.server.DataSources

doInit() - Method in class org.bridgedb.server.FreeSearch

doInit() - Method in class org.bridgedb.server.IDMapperResource

doInit() - Method in class org.bridgedb.server.IsMappingSupported

doInit() - Method in class org.bridgedb.server.XrefExists

doInit() - Method in class org.bridgedb.server.Xrefs

F

FreeSearch - Class in org.bridgedb.server

Resource that handles the xref queries

FreeSearch() - Constructor for class org.bridgedb.server.FreeSearch

G

getAttributes() - Method in class org.bridgedb.server.Attributes

getBackPageText() - Method in class org.bridgedb.server.BackPageText

getConfig() - Method in class org.bridgedb.server.Config

getContents() - Method in class org.bridgedb.server.Contents

getDataSources() - Method in class org.bridgedb.server.DataSources

getGdbProvider() - Method in class org.bridgedb.server.IDMapperService

getIDMappers() - Method in class org.bridgedb.server.IDMapperResource

getNoMatchResult() - Method in class org.bridgedb.server.NoMatch

getPropertiesResult() - Method in class org.bridgedb.server.Properties

getSupportedDataSourceResult() - Method in class org.bridgedb.server.AttributeSet

getSupportedDataSourceResult() - Method in class org.bridgedb.server.SupportedSourceDataSources

getSupportedDataSourceResult() - Method in class org.bridgedb.server.SupportedTargetDataSources

getXrefs() - Method in class org.bridgedb.server.Xrefs

I

IDMapperResource - Class in org.bridgedb.server

Base resource implementation that provides methods shared between the idmapper resources (such as access to the IDMapper objects).

IDMapperResource() - Constructor for class org.bridgedb.server.IDMapperResource

IDMapperService - Class in org.bridgedb.server

Server component for ID mapping.

IDMapperService(File, boolean) - Constructor for class org.bridgedb.server.IDMapperService

isFreeSearchSupported() - Method in class org.bridgedb.server.IsFreeSearchSupported

isFreeSearchSupported() - Method in class org.bridgedb.server.XrefExists

IsFreeSearchSupported - Class in org.bridgedb.server

IsFreeSearchSupported() - Constructor for class org.bridgedb.server.IsFreeSearchSupported

isMappingSupported() - Method in class org.bridgedb.server.IsMappingSupported

IsMappingSupported - Class in org.bridgedb.server

IsMappingSupported() - Constructor for class org.bridgedb.server.IsMappingSupported

M

main(String[]) - Static method in class org.bridgedb.server.Server

multiDataSource(Representation) - Method in class org.bridgedb.server.Batch

N

NoMatch - Class in org.bridgedb.server

NoMatch() - Constructor for class org.bridgedb.server.NoMatch

O

oneDataSource(Representation) - Method in class org.bridgedb.server.Batch

org.bridgedb.server - package org.bridgedb.server

P

PAR_DATASOURCES - Static variable in class org.bridgedb.server.IDMapperService

PAR_DEST_SYSTEM - Static variable in class org.bridgedb.server.IDMapperService

PAR_ID - Static variable in class org.bridgedb.server.IDMapperService

PAR_ORGANISM - Static variable in class org.bridgedb.server.IDMapperService

PAR_QUERY - Static variable in class org.bridgedb.server.IDMapperService

PAR_SOURCE_SYSTEM - Static variable in class org.bridgedb.server.IDMapperService

PAR_SYSTEM - Static variable in class org.bridgedb.server.IDMapperService

PAR_TARGET_ATTR_NAME - Static variable in class org.bridgedb.server.IDMapperService

PAR_TARGET_LIMIT - Static variable in class org.bridgedb.server.IDMapperService

PAR_TARGET_SYSTEM - Static variable in class org.bridgedb.server.IDMapperService

parseDataSource(String) - Method in class org.bridgedb.server.Batch

parseDataSource(String) - Method in class org.bridgedb.server.IDMapperResource

Properties - Class in org.bridgedb.server

Properties() - Constructor for class org.bridgedb.server.Properties

R

run(int, File) - Method in class org.bridgedb.server.Server

Deprecated.

use run (port, configFile, transitive) instead

run(int, File, boolean) - Method in class org.bridgedb.server.Server

S

search() - Method in class org.bridgedb.server.AttributeSearch

search() - Method in class org.bridgedb.server.FreeSearch

Server - Class in org.bridgedb.server

Server() - Constructor for class org.bridgedb.server.Server

start() - Method in class org.bridgedb.server.IDMapperService

stop() - Method in class org.bridgedb.server.Server

SupportedSourceDataSources - Class in org.bridgedb.server

SupportedSourceDataSources() - Constructor for class org.bridgedb.server.SupportedSourceDataSources

SupportedTargetDataSources - Class in org.bridgedb.server

SupportedTargetDataSources() - Constructor for class org.bridgedb.server.SupportedTargetDataSources

U

URL_ATTRIBUTE_SEARCH - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for searching by attribute.

URL_ATTRIBUTE_SET - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting the supported attribute set.
/{organism}/attributeSet

URL_ATTRIBUTES - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting attributes of an xref.

URL_BACK_PAGE_TEXT - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting backpage HTML.
URL:
/{organism}/backPageText/{system}/{id}

URL_CONFIG - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting the server configuration.
/config

URL_CONTENTS - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting a list of species loaded in the server.
/contents

URL_DATASOURCES - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting the datasources.txt file

URL_HOME - Static variable in class org.bridgedb.server.IDMapperService

URL pattern to redirect to home page.
{blank}

URL_IS_FREE_SEARCH_SUPPORTED - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for finding out if free search is supported.
/{organism}/isFreeSearchSupported

URL_IS_MAPPING_SUPPORTED - Static variable in class org.bridgedb.server.IDMapperService

URL pattern to find out if a mapping is supported.
/{organism}/isMappingSupported/{source_system}/{target_system}

URL_NO_MATCH - Static variable in class org.bridgedb.server.IDMapperService

URL pattern to catch a misformed query.
{unmatched patter}

URL_PROPERTIES - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting IDMapper properties.

URL_SEARCH - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for searching xrefs.
/{organism}/search/{query}[?limit={limit}]

URL_SUPPORTED_SOURCE_DATASOURCES - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting the supported source datasources for this database.
/{organism}/sourceDataSources

URL_SUPPORTED_TARGET_DATASOURCES - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for getting the supported target datasources for this database.
/{organism}/targetDataSources

URL_XREF_EXISTS - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for finding out if an xref exists in the database.
/{organism}/xrefExists/{system}/{id}

URL_XREFS - Static variable in class org.bridgedb.server.IDMapperService

URL pattern for mapping xrefs.
/{organism}/xrefs/{system}/{id}[?dataSource={dsName}]

urlDecode(String) - Method in class org.bridgedb.server.IDMapperResource

Decode the parameter from the url to remove %20 etc.

X

XrefExists - Class in org.bridgedb.server

XrefExists() - Constructor for class org.bridgedb.server.XrefExists

Xrefs - Class in org.bridgedb.server

Resource that handles the xref queries

Xrefs() - Constructor for class org.bridgedb.server.Xrefs

A B C D F G I M N O P R S U X
All Classes All Packages