Package ubic.gemma.web.services

Class GeneCoexpressionEndpoint

java.lang.Object

org.springframework.xml.transform.TransformerObjectSupport

org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint

ubic.gemma.web.services.AbstractGemmaEndpoint

ubic.gemma.web.services.GeneCoexpressionEndpoint

All Implemented Interfaces:

org.springframework.ws.server.endpoint.PayloadEndpoint

public class GeneCoexpressionEndpoint
extends AbstractGemmaEndpoint

Allows access to the gene co-expression analysis. Given 1) a collection of gene ids, 2) a taxon id, 3) a stringency, 4) an expression experiment set id, and 5) a boolean for whether to return results that are within the query set only. The Expression Experiment Set ID (4) can be found by using the ExpressionExperimentSetIDEndpoint, which will return all the expression experiment set ids for all taxons and their corresponding description. The stringency is the minimum number of times we found a particular relationship. Returns a list consisting of 7 columns: 1) the query Gene, 2) the query gene ID, 3) the found Gene, 4) the found gene ID, 5) the support ( the number of times that coexpression was found ), 6) Sign(+/-; denotes whether the correlation between the coexpression pair is positive or negative), and 7)the experiment ids that this co-expression was found in (since there should be more than 1 experiment this list will be returned as a space delimited string of EE Ids.)

Author:

gavin, klc

Field Summary

Fields inherited from class ubic.gemma.web.services.AbstractGemmaEndpoint

DELIMITER, manualAuthenticationService, NAMESPACE_URI, REQUEST, RESPONSE

Fields inherited from class org.springframework.xml.transform.TransformerObjectSupport

logger

Constructor Summary

Constructors

Constructor	Description
GeneCoexpressionEndpoint()

Method Summary

Modifier and Type	Method	Description
protected Element	invokeInternal(Element requestElement, Document document)	Reads the given requestElement, and sends a the response back.
void	setGeneCoexpressionSearchService(ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService geneCoexpressionSearchService)
void	setGeneCoexpressionService(ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService geneCoexpressionService)
void	setGeneService(ubic.gemma.persistence.service.genome.gene.GeneService geneS)
void	setTaxonService(ubic.gemma.persistence.service.genome.taxon.TaxonService taxonService)	Sets the "business service" to delegate to.

Methods inherited from class ubic.gemma.web.services.AbstractGemmaEndpoint

authenticate, buildBadResponse, buildWrapper, encode, getArrayValues, getLastSingleNodeValue, getNodeValue, getOptionalNodeValue, getSingleNodeValue, readReport, readReport, readReport, setLocalName, setManualAuthenticationService, writeReport

Methods inherited from class org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint

createDocumentBuilder, createDocumentBuilderFactory, getDocumentElement, invoke, setAlwaysTransform, setExpandEntityReferences, setNamespaceAware, setValidating

Methods inherited from class org.springframework.xml.transform.TransformerObjectSupport

createTransformer, getTransformerFactory, newTransformerFactory, setTransformerFactoryClass, transform

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneCoexpressionEndpoint

public GeneCoexpressionEndpoint()

Method Detail

setGeneCoexpressionSearchService

public void setGeneCoexpressionSearchService(ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService geneCoexpressionSearchService)

setGeneCoexpressionService

public void setGeneCoexpressionService(ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService geneCoexpressionService)

setGeneService

public void setGeneService(ubic.gemma.persistence.service.genome.gene.GeneService geneS)

setTaxonService

public void setTaxonService(ubic.gemma.persistence.service.genome.taxon.TaxonService taxonService)

Sets the "business service" to delegate to.

invokeInternal

protected Element invokeInternal(Element requestElement,
                                 Document document)

Reads the given requestElement, and sends a the response back.

Specified by:

invokeInternal in class org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint

Parameters:

requestElement - the contents of the SOAP message as DOM elements

document - a DOM document to be used for constructing Nodes

Returns:

the response element