DAVIDWebService(...)
stub
:email
:show()
: summary()
: initialize(email="",
..., url)
:setEmail(mail)
: getEmail()
: getStub
:
is.connected()
: connect()
: getIdTypes()
: getAllAnnotationCategoryNames()
: getDefaultCategoryNames()
: getGeneListNames()
:
getBackgroundListNames()
: getListName(listType=c("Gene", "Background"),
position=1L)
:getSpecieNames()
:
getCurrentGeneListPosition()
: getCurrentBackgroundListPosition()
: getCurrentSpeciesPosition()
: setCurrentGeneListPosition(position)
:
setCurrentBackgroundPosition(position)
:
setCurrentSpecies(species)
: setAnnotationCategories(categories)
:
addList(inputIds, idType,
listName, listType=c("Gene", "Background"))
: getGeneCategoriesReport()
: getAnnotationSummary()
:
getGeneListReportFile(fileName)
:
getGeneListReport()
: getFunctionalAnnotationChartFile(fileName,
threshold=0.1, count=2L)
: getFunctionalAnnotationChart(...)
:getClusterReportFile(fileName, type=c("Term",
"Gene"), overlap=4L, initialSeed=4L, finalSeed=4L,
linkage=0.5, kappa=35L)
:getClusterReport(type=c("Term", "Gene"),
...)
: getFunctionalAnnotationTableFile(fileName)
:
getFunctionalAnnotationTable()
:
DAVIDWebService
class is implemented as a
reference class, to manage a single instance connection
to DAVIS's server by means of web services using a
registered e-mail. For user registration, go to
http://david.abcc.ncifcrf.gov/webservice/register.html.
The implementation uses Java Remote Method Implementation
(RMI) to connect the client and server side of DAVID. The
main functionalities include: addList
,
addList
, connect
,
connect
,
getAllAnnotationCategoryNames
,
getAllAnnotationCategoryNames
,
getAnnotationSummary
,
getAnnotationSummary
,
getBackgroundListNames
,
getBackgroundListNames
,
getClusterReport
,
getClusterReport
,
getClusterReportFile
,
getClusterReportFile
,
getCurrentBackgroundListPosition
,
getCurrentBackgroundListPosition
,
getCurrentGeneListPosition
,
getCurrentGeneListPosition
,
getCurrentSpeciesPosition
,
getCurrentSpeciesPosition
,
getDefaultCategoryNames
,
getDefaultCategoryNames
,
getEmail
, getEmail
,
getFunctionalAnnotationChart
,
getFunctionalAnnotationChart
,
getFunctionalAnnotationChartFile
,
getFunctionalAnnotationChartFile
,
getFunctionalAnnotationTable
,
getFunctionalAnnotationTable
,
getFunctionalAnnotationTableFile
,
getFunctionalAnnotationTableFile
,
getGeneCategoriesReport
,
getGeneCategoriesReport
,
getGeneListNames
,
getGeneListNames
,
getGeneListReport
,
getGeneListReport
,
getGeneListReportFile
,
getGeneListReportFile
,
getIdTypes
, getIdTypes
,
getListName
, getListName
,
getSpecieNames
,
getSpecieNames
, getStub
,
getStub
, is.connected
,
is.connected
,
setAnnotationCategories
,
setAnnotationCategories
,
setCurrentBackgroundPosition
,
setCurrentBackgroundPosition(position)
,
setCurrentGeneListPosition
,
setCurrentGeneListPosition
,
setCurrentSpecies
,
setCurrentSpecies
, setEmail
,
setEmail
,
setEmail,DAVIDWebService-method
,
summary
, summary
,
summary
, summary