org.embl.ebi.escience.scuflworkers.biomart
Class BiomartProcessor

java.lang.Object
  org.embl.ebi.escience.scufl.Processor
      org.embl.ebi.escience.scuflworkers.biomart.BiomartProcessor

All Implemented Interfaces:

java.io.Serializable, IProcessor, HTMLSummarisableProcessor

public class BiomartProcessor
extends Processor
implements HTMLSummarisableProcessor

Author:

Tom Oinn, David Withers, Stuart Owen

See Also:

Serialized Form

Field Summary

Fields inherited from interface org.embl.ebi.escience.scufl.IProcessor

ENACTOR

Constructor Summary

BiomartProcessor(ScuflModel model, java.lang.String processorName, org.biomart.martservice.MartQuery query)

Method Summary

java.lang.String	getHTMLSummary(java.util.List<HTMLSummarisableProcessor> processors, java.util.Map<java.lang.String,Processor> names) Generates the html tables for a list of processors, creating a table grouped by resource host.
java.util.Properties	getProperties() Return a properties object containing the processor specific properties for this processor type instance.
org.biomart.martservice.MartQuery	getQuery()
org.jdom.Element	getQueryElement(org.jdom.Namespace namespace)
int	htmlTablePlacement() int indicating the placement for this type of processor in the order of tables displayed

Methods inherited from class org.embl.ebi.escience.scufl.Processor

addAlternate, addAnnotationTemplate, addBreakpoint, addPort, defaultAnnotationTemplates, fireModelEvent, getAlternatesArray, getAlternatesList, getAnnotationTemplates, getBackoff, getBoundInputPorts, getBoundOutputPorts, getCritical, getDefaultWorkers, getDescription, getInputPorts, getIterationStrategy, getLogLevel, getMaximumWorkers, getModel, getName, getOutputPorts, getPorts, getRealLogLevel, getResourceHost, getRetries, getRetryDelay, getTimeout, getWorkers, hasBreakpoint, isBoring, isOffline, locatePort, locatePort, removeAlternate, removeAnnotationTemplate, removePort, rmvBreakpoint, setBackoff, setBoring, setCritical, setDescription, setIterationStrategy, setLogLevel, setName, setOffline, setOnline, setRetries, setRetryDelay, setTimeout, setWorkers, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BiomartProcessor

public BiomartProcessor(ScuflModel model,
                        java.lang.String processorName,
                        org.biomart.martservice.MartQuery query)
                 throws ProcessorCreationException,
                        DuplicateProcessorNameException

Parameters:

model -

name -

Throws:

ProcessorCreationException

DuplicateProcessorNameException

Method Detail

getProperties

public java.util.Properties getProperties()

Description copied from class: Processor

Return a properties object containing the processor specific properties for this processor type instance. This is used by the user interface code to display additional properties for each processor and should be implemented by the subclasses to display useful information.

Specified by:

getProperties in interface IProcessor

Specified by:

getProperties in class Processor

Returns:

a Properties instance containing all processor-specific properties, or optinally null if there are none

getQuery

public org.biomart.martservice.MartQuery getQuery()

getQueryElement

public org.jdom.Element getQueryElement(org.jdom.Namespace namespace)

getHTMLSummary

public java.lang.String getHTMLSummary(java.util.List<HTMLSummarisableProcessor> processors,
                                       java.util.Map<java.lang.String,Processor> names)

Description copied from interface: HTMLSummarisableProcessor

Generates the html tables for a list of processors, creating a table grouped by resource host.

Specified by:

getHTMLSummary in interface HTMLSummarisableProcessor

Returns:

htmlTablePlacement

public int htmlTablePlacement()

Description copied from interface: HTMLSummarisableProcessor

int indicating the placement for this type of processor in the order of tables displayed

Specified by:

htmlTablePlacement in interface HTMLSummarisableProcessor

Returns: