Package ubic.gemma.web.controller.genome.gene

Class GeneController

java.lang.Object

ubic.gemma.web.controller.BaseController

ubic.gemma.web.controller.genome.gene.GeneController

@Controller
@RequestMapping({"/gene","/g"})
public class GeneController
extends BaseController

Author:

daq2101, pavlidis, joseph

Field Summary

Fields inherited from class ubic.gemma.web.controller.BaseController

log

Constructor Summary

Constructors

Constructor	Description
GeneController()

Method Summary

Modifier and Type	Method	Description
Collection<ubic.gemma.model.common.description.AnnotationValueObject>	findGOTerms(Long geneId)
String	getGeneABALink(Long geneId)
Collection<ubic.gemma.model.genome.gene.GeneProductValueObject>	getProducts(Long geneId)
ModelAndView	handleRequestInternal(javax.servlet.http.HttpServletRequest request)
Collection<ubic.gemma.core.image.aba.Image>	loadAllenBrainImages(Long geneId)	AJAX NOTE: this method updates the value object passed in
ubic.gemma.model.genome.gene.GeneValueObject	loadGeneDetails(Long geneId)
Collection<ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject<? extends ubic.gemma.model.association.phenotype.PhenotypeAssociation>>	loadGeneEvidence(Long taxonId, boolean showOnlyEditable, Collection<Long> databaseIds, Long geneId, String[] phenotypeValueUris)	AJAX used to show gene info in the phenotype tab FIXME Why is the taxonId a parameter, since we have the gene ID?
ubic.gemma.model.genome.gene.GeneValueObject	loadGenePhenotypes(Long geneId)
ModelAndView	show(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)

Methods inherited from class ubic.gemma.web.controller.BaseController

addMessage, getMessageUtil, getText, getText, saveMessage, saveMessage, sendConfirmationEmail, setMailEngine, setMessageSource, setMessageUtil

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneController

public GeneController()

Method Detail

findGOTerms

public Collection<ubic.gemma.model.common.description.AnnotationValueObject> findGOTerms(Long geneId)

getProducts

public Collection<ubic.gemma.model.genome.gene.GeneProductValueObject> getProducts(Long geneId)

loadAllenBrainImages

public Collection<ubic.gemma.core.image.aba.Image> loadAllenBrainImages(Long geneId)

AJAX NOTE: this method updates the value object passed in

loadGeneDetails

public ubic.gemma.model.genome.gene.GeneValueObject loadGeneDetails(Long geneId)

getGeneABALink

public String getGeneABALink(Long geneId)

loadGeneEvidence

public Collection<ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject<? extends ubic.gemma.model.association.phenotype.PhenotypeAssociation>> loadGeneEvidence(Long taxonId,
                                                                                                                                                                                  boolean showOnlyEditable,
                                                                                                                                                                                  Collection<Long> databaseIds,
                                                                                                                                                                                  Long geneId,
                                                                                                                                                                                  String[] phenotypeValueUris)

AJAX used to show gene info in the phenotype tab FIXME Why is the taxonId a parameter, since we have the gene ID?

loadGenePhenotypes

public ubic.gemma.model.genome.gene.GeneValueObject loadGenePhenotypes(Long geneId)

show

@RequestMapping(value={"/showGene.html","/"},
                method=GET)
public ModelAndView show(javax.servlet.http.HttpServletRequest request,
                         javax.servlet.http.HttpServletResponse response)

handleRequestInternal

@RequestMapping("/downloadGeneList.html")
public ModelAndView handleRequestInternal(javax.servlet.http.HttpServletRequest request)