uk.ac.ebi.microarray.zooma.utils
Class Configurator

java.lang.Object
  uk.ac.ebi.microarray.zooma.utils.Configurator

public class Configurator
extends java.lang.Object

A simple class used for conveniently loading ZOOMA configurations. Classes that depend on config files for ranking sources and ontologies to generate mappings can use this class to read in the standard set of config files.

Author:

Tony Burdett

Field Summary

protected static java.lang.String	ontologiesResource The name of the resource containing the default ontology ranking configuration
static java.lang.String	ontologiesSuffix The resource name suffix for ontology config files
protected static java.lang.String	rejectedOntologiesResource The name of the resource containing the default rejected ontology configuration
static java.lang.String	rejectedOntologiesSuffix The resource name suffix for config files listing the ontologies to reject outright
protected static java.lang.String	sourcesResource The name of the resource containing the default source ranking configuration
static java.lang.String	sourcesSuffix The resource name suffix for source config files

Constructor Summary

Configurator()

Method Summary

protected org.slf4j.Logger	getLog()
java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>>	getOntologiesConfig()
java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>>	getRejectedOntologiesConfig()
java.util.List<Source>	getSourcesConfig()
void	loadConfiguration()
java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>>	readOntologiesConfig(java.io.InputStream ontologiesInputStream)
java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>>	readRejectedOntologiesConfig(java.io.InputStream rejectedOntologiesInputStream)
java.util.List<Source>	readSourcesConfig(java.io.InputStream sourcesInputStream)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sourcesSuffix

public static final java.lang.String sourcesSuffix

The resource name suffix for source config files

See Also:

Constant Field Values

ontologiesSuffix

public static final java.lang.String ontologiesSuffix

The resource name suffix for ontology config files

See Also:

Constant Field Values

rejectedOntologiesSuffix

public static final java.lang.String rejectedOntologiesSuffix

The resource name suffix for config files listing the ontologies to reject outright

See Also:

Constant Field Values

sourcesResource

protected static java.lang.String sourcesResource

The name of the resource containing the default source ranking configuration

ontologiesResource

protected static java.lang.String ontologiesResource

The name of the resource containing the default ontology ranking configuration

rejectedOntologiesResource

protected static java.lang.String rejectedOntologiesResource

The name of the resource containing the default rejected ontology configuration

Constructor Detail

Configurator

public Configurator()

Method Detail

getLog

protected org.slf4j.Logger getLog()

loadConfiguration

public void loadConfiguration()

readSourcesConfig

public java.util.List<Source> readSourcesConfig(java.io.InputStream sourcesInputStream)

readOntologiesConfig

public java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>> readOntologiesConfig(java.io.InputStream ontologiesInputStream)

readRejectedOntologiesConfig

public java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>> readRejectedOntologiesConfig(java.io.InputStream rejectedOntologiesInputStream)

getSourcesConfig

public java.util.List<Source> getSourcesConfig()

getOntologiesConfig

public java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>> getOntologiesConfig()

getRejectedOntologiesConfig

public java.util.LinkedHashMap<java.lang.String,java.util.List<java.lang.String>> getRejectedOntologiesConfig()