Package ubic.gemma.web.services
Class GeneCoexpressionEndpoint
- java.lang.Object
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- org.springframework.xml.transform.TransformerObjectSupport
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- org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint
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- ubic.gemma.web.services.AbstractGemmaEndpoint
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- ubic.gemma.web.services.GeneCoexpressionEndpoint
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- 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
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Field Summary
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Fields inherited from class ubic.gemma.web.services.AbstractGemmaEndpoint
DELIMITER, manualAuthenticationService, NAMESPACE_URI, REQUEST, RESPONSE
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Constructor Summary
Constructors Constructor Description GeneCoexpressionEndpoint()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected ElementinvokeInternal(Element requestElement, Document document)Reads the givenrequestElement, and sends a the response back.voidsetGeneCoexpressionSearchService(GeneCoexpressionSearchService geneCoexpressionSearchService)voidsetGeneCoexpressionService(GeneCoexpressionSearchService geneCoexpressionService)voidsetGeneService(GeneService geneS)voidsetTaxonService(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
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Methods inherited from class org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint
createDocumentBuilder, createDocumentBuilderFactory, getDocumentElement, invoke, setAlwaysTransform, setExpandEntityReferences, setNamespaceAware, setValidating
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Method Detail
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setGeneCoexpressionSearchService
public void setGeneCoexpressionSearchService(GeneCoexpressionSearchService geneCoexpressionSearchService)
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setGeneCoexpressionService
public void setGeneCoexpressionService(GeneCoexpressionSearchService geneCoexpressionService)
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setGeneService
public void setGeneService(GeneService geneS)
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setTaxonService
public void setTaxonService(TaxonService taxonService)
Sets the "business service" to delegate to.
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invokeInternal
protected Element invokeInternal(Element requestElement, Document document)
Reads the givenrequestElement, and sends a the response back.- Specified by:
invokeInternalin classorg.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint- Parameters:
requestElement- the contents of the SOAP message as DOM elementsdocument- a DOM document to be used for constructingNodes- Returns:
- the response element
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