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B

BridgeDBException - Exception in org.bridgedb.utils

BridgeDBException(String) - Constructor for exception org.bridgedb.utils.BridgeDBException

See Exception (String).

BridgeDBException(String, Throwable) - Constructor for exception org.bridgedb.utils.BridgeDBException

See Exception(String, Throwable).

BridgeDBException(String, Throwable, String) - Constructor for exception org.bridgedb.utils.BridgeDBException

See Exception(String, Throwable).

BridgeDBException(IDMapperException) - Constructor for exception org.bridgedb.utils.BridgeDBException

See Exception(Throwable).

C

CodeMapper - Interface in org.bridgedb.pairs

CONFIG_FILE_NAME - Static variable in class org.bridgedb.utils.ConfigReader

CONFIG_FILE_PATH_PROPERTY - Static variable in class org.bridgedb.utils.ConfigReader

CONFIG_FILE_PATH_SOURCE_PROPERTY - Static variable in class org.bridgedb.utils.ConfigReader

ConfigReader - Class in org.bridgedb.utils

ConfigReader() - Constructor for class org.bridgedb.utils.ConfigReader

configureLogger() - Static method in class org.bridgedb.utils.ConfigReader

convertToBridgeDB(IDMapperException) - Static method in exception org.bridgedb.utils.BridgeDBException

E

equals(Object) - Method in class org.bridgedb.pairs.IdSysCodePair

error(String) - Static method in class org.bridgedb.utils.Reporter

error(String, Exception) - Static method in class org.bridgedb.utils.Reporter

G

getId() - Method in class org.bridgedb.pairs.IdSysCodePair

getInputStream(String) - Static method in class org.bridgedb.utils.ConfigReader

getProperties() - Static method in class org.bridgedb.utils.ConfigReader

getProperties(String) - Static method in class org.bridgedb.utils.ConfigReader

getProperty(String) - Static method in class org.bridgedb.utils.ConfigReader

getSysCode() - Method in class org.bridgedb.pairs.IdSysCodePair

H

hashCode() - Method in class org.bridgedb.pairs.IdSysCodePair

I

IdSysCodePair - Class in org.bridgedb.pairs

A thin wrapper around two String which represent the Id and dataSourceCode parts of a potential Xref.

IdSysCodePair(String, String) - Constructor for class org.bridgedb.pairs.IdSysCodePair

inTestMode() - Static method in class org.bridgedb.utils.ConfigReader

L

LOCAL_FILE_NAME - Static variable in class org.bridgedb.utils.ConfigReader

LOG_PROPERTIES_FILE - Static variable in class org.bridgedb.utils.ConfigReader

loggerSetup - Static variable in class org.bridgedb.utils.ConfigReader

logToConsole() - Static method in class org.bridgedb.utils.ConfigReader

O

org.bridgedb.pairs - package org.bridgedb.pairs

org.bridgedb.utils - package org.bridgedb.utils

P

println(String) - Static method in class org.bridgedb.utils.Reporter

Messages that should always goto the System out stream.

R

Reporter - Class in org.bridgedb.utils

Util functions that allows messages to be output.

Reporter() - Constructor for class org.bridgedb.utils.Reporter

S

SyscodeBasedCodeMapper - Class in org.bridgedb.pairs

Basic code mapper which always uses xref.id and DataSource.systemCode

SyscodeBasedCodeMapper() - Constructor for class org.bridgedb.pairs.SyscodeBasedCodeMapper

T

toIdSysCodePair(Xref) - Method in interface org.bridgedb.pairs.CodeMapper

Creates an IdSysCodePair based on a xref.

toIdSysCodePair(Xref) - Method in class org.bridgedb.pairs.SyscodeBasedCodeMapper

toString() - Method in class org.bridgedb.pairs.IdSysCodePair

toXref(IdSysCodePair) - Method in interface org.bridgedb.pairs.CodeMapper

Creates a xref based on an IdSysCodePair Changes the ref.id and dataSource.systemCode if required.

toXref(IdSysCodePair) - Method in class org.bridgedb.pairs.SyscodeBasedCodeMapper

U

useTest - Static variable in class org.bridgedb.utils.ConfigReader

useTest() - Static method in class org.bridgedb.utils.ConfigReader

W

warn(String) - Static method in class org.bridgedb.utils.Reporter

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