Index

A

actions() (kdvs.core.env.ExecutionEnvironment method) ActionSpec (class in kdvs.core.action) addAction() (kdvs.core.env.ExecutionEnvironment method) addAttrs() (kdvs.core.log.Logger method) addCallable() (kdvs.core.env.ExecutionEnvironment method) ADDED (kdvs.fw.Job.JobStatus attribute) addGroup() (kdvs.fw.Job.JobGroupManager method) addJob() (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) (kdvs.fw.Job.JobContainer method) (kdvs.fw.impl.job.SimpleJob.SimpleJobContainer method)

addJobIDToGroup() (kdvs.fw.Job.JobGroupManager method) addVar() (kdvs.core.env.ExecutionEnvironment method) App (class in kdvs.fw.App) appEpilog() (kdvs.fw.App.App method) (kdvs.fw.impl.app.CmdLineApp.CmdLineApp method) AppProfile (class in kdvs.fw.App) appProlog() (kdvs.fw.App.App method) (kdvs.fw.impl.app.CmdLineApp.CmdLineApp method) as_tuple() (kdvs.core.action.ActionSpec method)

B

BDMap (class in kdvs.fw.Map) build() (kdvs.fw.Categorizer.Orderer method) (kdvs.fw.Map.GeneIDMap method) (kdvs.fw.Map.PKCGeneMap method) (kdvs.fw.Map.PKCIDMap method) (kdvs.fw.SubsetHierarchy.SubsetHierarchy method) (kdvs.fw.impl.data.Null.NullOrderer method) (kdvs.fw.impl.data.PKDrivenData.PKDrivenDBSubsetHierarchy method) (kdvs.fw.impl.data.SubsetSize.SubsetSizeOrderer method) (kdvs.fw.impl.map.GeneID.GPL.GeneIDMapGPL method) (kdvs.fw.impl.map.GeneID.HGNC_GPL.GeneIDMapHGNCGPL method) (kdvs.fw.impl.map.PKCID.GPL.PKCIDMapGOGPL method) (kdvs.tests.t.fw.SubsetHierarchy.MockSubsetHierarchy1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.MockPKCIDMap method) buildDerivedMap() (kdvs.fw.Map.ChainMap static method) buildGeneIDMap() (in module kdvs.bin.experiment)

buildPKCIDMap() (in module kdvs.bin.experiment) buildPKDrivenDataSubsets() (in module kdvs.bin.experiment) buildSubsetHierarchy() (in module kdvs.bin.experiment)

C

calculateConfusionMatrix() (in module kdvs.fw.Stat) calculateMCC() (in module kdvs.fw.Stat) categories() (kdvs.fw.Categorizer.Categorizer method) categorize() (kdvs.fw.Categorizer.Categorizer method) Categorizer (class in kdvs.fw.Categorizer) categorizeSubset() (kdvs.fw.impl.data.PKDrivenData.PKDrivenDataManager static method) ChainMap (class in kdvs.fw.Map) check_min_numpy_version() (in module kdvs.tests.utils) checkTableExistence() (kdvs.core.provider.DBProvider method) (kdvs.core.provider.SQLite3DBProvider method) className() (in module kdvs.core.util) clear() (kdvs.contrib.ordereddict.OrderedDict method) (kdvs.fw.DBShelve.DBShelve method) (kdvs.fw.Job.JobContainer method) (kdvs.fw.Job.JobGroupManager method) (kdvs.fw.Map.BDMap method) clearActions() (kdvs.core.env.ExecutionEnvironment method) clearMiscData() (kdvs.fw.Job.JobContainer method) close() (kdvs.core.db.DBManager method) (kdvs.core.log.NullHandler method) (kdvs.fw.DBResult.DBResult method) (kdvs.fw.DBShelve.DBShelve method) (kdvs.fw.DSV.DSV method) (kdvs.fw.Job.JobContainer method) (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) (kdvs.fw.impl.job.SimpleJob.SimpleJobContainer method) (kdvs.fw.impl.job.SimpleJob.SimpleJobExecutor method) CmdLineApp (class in kdvs.fw.impl.app.CmdLineApp)

CommentSkipper() (in module kdvs.core.util) Configurable (class in kdvs.core.util) configure() (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) (kdvs.fw.PK.PKCManager method) (kdvs.fw.Stat.Plot method) (kdvs.fw.impl.stat.L1L2.L1L2ErrorBoxplotMuGraph method) (kdvs.fw.impl.stat.L1L2.L1L2KfoldErrorsGraph method) (kdvs.fw.impl.stat.Plot.MatplotlibPlot method) connect() (kdvs.core.provider.DBProvider method) (kdvs.core.provider.SQLite3DBProvider method) Constant (class in kdvs.core.util) copy() (kdvs.contrib.counter.Counter method) (kdvs.contrib.ordereddict.OrderedDict method) correctHGNCApprovedSymbols() (in module kdvs.fw.impl.annotation.HGNC) correlated_dataset() (in module kdvs.contrib.dataset_generation) count_lines() (in module kdvs.tests.utils) Counter (class in kdvs.contrib.counter) countRows() (kdvs.fw.DBTable.DBTable method) create() (kdvs.fw.DBTable.DBTable method) (kdvs.fw.Stat.Plot method) (kdvs.fw.impl.stat.L1L2.L1L2ErrorBoxplotMuGraph method) (kdvs.fw.impl.stat.L1L2.L1L2KfoldErrorsGraph method) (kdvs.fw.impl.stat.Plot.MatplotlibPlot method) CREATED (kdvs.fw.Job.JobStatus attribute) createJob() (kdvs.fw.impl.stat.L1L2.L1L2_L1L2 method) (kdvs.fw.Stat.Technique method) (kdvs.fw.impl.stat.L1L2.L1L2_OLS method) (kdvs.fw.impl.stat.L1L2.L1L2_RLS method) createLocation() (kdvs.fw.StorageManager.StorageManager method)

D

DataSet (class in kdvs.fw.DataSet) DBManager (class in kdvs.core.db) DBProvider (class in kdvs.core.provider) DBResult (class in kdvs.fw.DBResult) DBShelve (class in kdvs.fw.DBShelve) DBSHELVE_TMPL (in module kdvs.fw.DBShelve) DBTable (class in kdvs.fw.DBTable) DBTemplate (class in kdvs.fw.DBTable) dbtemplate_keys (in module kdvs.fw.DBTable) DEFAULT_CALLARGS_LISTING_THR (in module kdvs.fw.Job) DEFAULT_CLASSIFICATION_RESULTS (in module kdvs.fw.Stat) DEFAULT_ENVOP_PARAMETERS (in module kdvs.fw.EnvOp) DEFAULT_GLOBAL_PARAMETERS (in module kdvs.fw.Stat)

DEFAULT_REPORTER_PARAMETERS (in module kdvs.fw.Report) DEFAULT_RESULTS (in module kdvs.fw.Stat) DEFAULT_SELECTION_RESULTS (in module kdvs.fw.Stat) delVar() (kdvs.core.env.ExecutionEnvironment method) deriveMap() (kdvs.fw.Map.ChainMap static method) deserializeObj() (in module kdvs.core.util) deuniquifyCategory() (kdvs.fw.Categorizer.Categorizer static method) DSV (class in kdvs.fw.DSV) DSV_DEFAULT_ID_COLUMN (in module kdvs.fw.DSV) dump() (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) (kdvs.fw.PK.PKCManager method) dumpBwdMap() (kdvs.fw.Map.BDMap method) dumpFwdMap() (kdvs.fw.Map.BDMap method)

E

elements() (kdvs.contrib.counter.Counter method) EM2ANNOTATION_TMPL (in module kdvs.fw.Annotation) emit() (kdvs.core.log.NullHandler method) emptyCall() (in module kdvs.core.util) emptyGenerator() (in module kdvs.core.util) EnvOp (class in kdvs.fw.EnvOp) Error

evaluateDefaultCfg() (in module kdvs.core.config) evaluateUserCfg() (in module kdvs.core.config) execute() (kdvs.core.env.ExecutionEnvironment method) (kdvs.core.env.LoggedExecutionEnvironment method) (kdvs.fw.Job.Job method) executeSubsetOperations() (in module kdvs.bin.experiment) EXECUTING (kdvs.fw.Job.JobStatus attribute) ExecutionEnvironment (class in kdvs.core.env)

F

fileProvider() (in module kdvs.core.provider) finalize() (kdvs.fw.Report.Reporter method) findGroupByJobID() (kdvs.fw.Job.JobGroupManager method) FINISHED (kdvs.fw.Job.JobStatus attribute) flush() (kdvs.core.log.NullHandler method)

fpBzip2File (class in kdvs.core.provider) fpGzipFile (class in kdvs.core.provider) fromkeys() (kdvs.contrib.counter.Counter class method) (kdvs.contrib.ordereddict.OrderedDict class method) fromTemplate() (kdvs.fw.DBTable.DBTable static method)

G

GeneIDMap (class in kdvs.fw.Map) GeneIDMapGPL (class in kdvs.fw.impl.map.GeneID.GPL) GeneIDMapHGNCGPL (class in kdvs.fw.impl.map.GeneID.HGNC_GPL) generateHGNCPreviousSymbols() (in module kdvs.fw.impl.annotation.HGNC) generateHGNCSynonyms() (in module kdvs.fw.impl.annotation.HGNC) get() (kdvs.fw.DBResult.DBResult method) (kdvs.fw.DBTable.DBTable method) get_em2annotation() (in module kdvs.fw.Annotation) getAdditionalData() (kdvs.fw.Report.Reporter method) getAll() (kdvs.fw.DBResult.DBResult method) (kdvs.fw.DBTable.DBTable method) getAncestors() (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) getArray() (kdvs.fw.DBTable.DBTable method) getBwdMap() (kdvs.fw.Map.BDMap method) getCommentSkipper() (kdvs.fw.DSV.DSV method) getConnectionFunc() (kdvs.core.provider.DBProvider method) (kdvs.core.provider.SQLite3DBProvider method) getDB() (kdvs.core.db.DBManager method) getDBloc() (kdvs.core.db.DBManager method) getDefaultCfgFilePath() (in module kdvs.core.config) getDefaultDataRootPath() (in module kdvs.core.config) getDescendants() (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) getEngine() (kdvs.core.provider.DBProvider method) (kdvs.core.provider.SQLite3DBProvider method) getFileNameComponent() (in module kdvs.core.util) getFwdMap() (kdvs.fw.Map.BDMap method) getGODataPath() (in module kdvs.core.config) getGroupJobsIDs() (kdvs.fw.Job.JobGroupManager method) getGroups() (kdvs.fw.Job.JobGroupManager method) getHandle() (kdvs.fw.DSV.DSV static method) getIDs() (kdvs.fw.DBTable.DBTable method) getJob() (kdvs.fw.Job.JobContainer method) getJobCount() (kdvs.fw.Job.JobContainer method) getJobIDForKey() (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) getJobInputKey() (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) getJobOutputKey() (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) getJobResult() (kdvs.fw.Job.JobContainer method) getJobResults() (kdvs.fw.impl.job.SimpleJob.SimpleJobExecutor method)

getJobStatus() (kdvs.fw.Job.JobContainer method) getLabels() (kdvs.fw.Stat.Labels method) getLocation() (kdvs.fw.StorageManager.StorageManager method) getMap() (kdvs.fw.Map.BDMap method) (kdvs.fw.Map.ChainMap method) getMapForDomain() (kdvs.fw.impl.map.PKCID.GPL.PKCIDMapGOGPL method) getMiscData() (kdvs.fw.Job.JobContainer method) getOperationalError() (kdvs.core.provider.DBProvider method) (kdvs.core.provider.SQLite3DBProvider method) getPKC() (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) (kdvs.fw.PK.PKCManager method) getReports() (kdvs.fw.Report.Reporter method) getRootLocation() (kdvs.fw.StorageManager.StorageManager method) getRootLocationID() (kdvs.fw.StorageManager.StorageManager method) getSamples() (kdvs.fw.Stat.Labels method) getSerializableContent() (in module kdvs.core.util) getSubset() (kdvs.fw.impl.data.PKDrivenData.PKDrivenDataManager method) (kdvs.fw.impl.data.PKDrivenData.PKDrivenDBDataManager method) getSynonyms() (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) getTextColumnType() (kdvs.core.provider.DBProvider method) (kdvs.core.provider.SQLite3DBProvider method) getThreshold() (kdvs.fw.impl.data.SubsetSize.SubsetSizeCategorizer method) getVisDataPath() (in module kdvs.core.config) global_parameters (kdvs.fw.impl.report.L1L2.L1L2_PKC_Reporter attribute) (kdvs.fw.impl.report.L1L2.L1L2_PKC_UTL_Reporter attribute) (kdvs.fw.impl.report.L1L2.L1L2_VarCount_Reporter attribute) (kdvs.fw.impl.report.L1L2.L1L2_VarFreq_Reporter attribute) GO_BP_DS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_CC_DS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_DEF_RECOGNIZED_RELATIONS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_DOMAINS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_DS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_EVIDENCE_CODES (in module kdvs.fw.impl.pk.go.GeneOntology) GO_id2num() (in module kdvs.fw.impl.pk.go.GeneOntology) GO_INV_EVIDENCE_CODES (in module kdvs.fw.impl.pk.go.GeneOntology) GO_MF_DS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_num2id() (in module kdvs.fw.impl.pk.go.GeneOntology) GO_OBOXML_ROOT_TAG (in module kdvs.fw.impl.pk.go.GeneOntology) GO_ROOT_TERMS (in module kdvs.fw.impl.pk.go.GeneOntology) GO_UNKNOWN_EV_CODE (in module kdvs.fw.impl.pk.go.GeneOntology) GOManager (class in kdvs.fw.impl.pk.go.GeneOntology) GOTERM2EM_TMPL (in module kdvs.fw.impl.map.PKCID.GPL)

H

hasJobs() (kdvs.fw.Job.JobContainer method) HGNC_APPROVED_SYMBOL_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_EGENE_ID_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_ENSEMBL_ID_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_FIELD_EMPTY (in module kdvs.fw.impl.annotation.HGNC) HGNC_FIELDS_SEP (in module kdvs.fw.impl.annotation.HGNC) HGNC_LOCUS_TYPE_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_PREVIOUS_SYMBOLS_COL (in module kdvs.fw.impl.annotation.HGNC)

HGNC_REFSEQ_ID_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_STATUS_APPROVED (in module kdvs.fw.impl.annotation.HGNC) HGNC_STATUS_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_STATUS_WITHDRAWN (in module kdvs.fw.impl.annotation.HGNC) HGNC_SYNONYMS_COL (in module kdvs.fw.impl.annotation.HGNC) HGNC_WITHDRAWN_GS_PART (in module kdvs.fw.impl.annotation.HGNC) HGNCPREVIOUS_TMPL (in module kdvs.fw.impl.annotation.HGNC) HGNCSYNONYMS_TMPL (in module kdvs.fw.impl.annotation.HGNC)

I

importComponent() (in module kdvs.core.util) initialize() (kdvs.fw.impl.report.L1L2.L1L2_PKC_Reporter method) (kdvs.fw.Report.Reporter method) (kdvs.fw.impl.report.L1L2.L1L2_PKC_UTL_Reporter method) (kdvs.fw.impl.report.L1L2.L1L2_VarCount_Reporter method) (kdvs.fw.impl.report.L1L2.L1L2_VarFreq_Reporter method) InnerSelector (class in kdvs.fw.impl.stat.PKCSelector) InnerSelector_ClassificationErrorThreshold_AllVars (class in kdvs.fw.impl.stat.PKCSelector) InnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq (class in kdvs.fw.impl.stat.PKCSelector) isConfigured() (kdvs.fw.PK.PKCManager method) isCreated() (kdvs.fw.DBTable.DBTable method) isDirWritable() (in module kdvs.core.util) isEmpty() (kdvs.fw.DBTable.DBTable method)

isGOID() (in module kdvs.fw.impl.pk.go.GeneOntology) isIntegralNumber() (in module kdvs.core.util) isListOrTuple() (in module kdvs.core.util) isTuple() (in module kdvs.core.util) items() (kdvs.contrib.ordereddict.OrderedDict method) iteritems() (kdvs.contrib.ordereddict.OrderedDict method) iterkeys() (kdvs.contrib.ordereddict.OrderedDict method) itervalues() (kdvs.contrib.ordereddict.OrderedDict method)

J

Job (class in kdvs.fw.Job) JobContainer (class in kdvs.fw.Job) JOBERROR (in module kdvs.fw.Job)

JobGroupManager (class in kdvs.fw.Job) JobStatus (class in kdvs.fw.Job)

K

kdvs.__init__ (module) kdvs.bin (module) kdvs.bin.experiment (module) kdvs.contrib (module) kdvs.contrib.counter (module) kdvs.contrib.dataset_generation (module) kdvs.contrib.ordereddict (module) kdvs.core (module) kdvs.core._version (module) kdvs.core.action (module) kdvs.core.config (module) kdvs.core.db (module) kdvs.core.dep (module) kdvs.core.env (module) kdvs.core.error (module) kdvs.core.log (module) kdvs.core.provider (module) kdvs.core.util (module) kdvs.fw (module) kdvs.fw.Annotation (module) kdvs.fw.App (module) kdvs.fw.Categorizer (module) kdvs.fw.DataSet (module) kdvs.fw.DBResult (module) kdvs.fw.DBShelve (module) kdvs.fw.DBTable (module) kdvs.fw.DSV (module) kdvs.fw.EnvOp (module) kdvs.fw.impl (module) kdvs.fw.impl.annotation (module) kdvs.fw.impl.annotation.HGNC (module) kdvs.fw.impl.app.CmdLineApp (module) kdvs.fw.impl.app.Profile (module) kdvs.fw.impl.data (module) kdvs.fw.impl.data.Null (module) kdvs.fw.impl.data.PKDrivenData (module) kdvs.fw.impl.data.SubsetSize (module) kdvs.fw.impl.envop (module) kdvs.fw.impl.envop.L1L2 (module) kdvs.fw.impl.job (module) kdvs.fw.impl.job.PPlusJob (module) kdvs.fw.impl.job.SimpleJob (module) kdvs.fw.impl.map (module) kdvs.fw.impl.map.GeneID (module) kdvs.fw.impl.map.GeneID.GPL (module) kdvs.fw.impl.map.GeneID.HGNC_GPL (module) kdvs.fw.impl.map.PKCID (module) kdvs.fw.impl.map.PKCID.GPL (module) kdvs.fw.impl.pk (module) kdvs.fw.impl.pk.go (module) kdvs.fw.impl.pk.go.GeneOntology (module) kdvs.fw.impl.report (module) kdvs.fw.impl.report.L1L2 (module) kdvs.fw.impl.stat (module) kdvs.fw.impl.stat.L1L2 (module) kdvs.fw.impl.stat.PKCSelector (module) kdvs.fw.impl.stat.Plot (module) kdvs.fw.Job (module) kdvs.fw.Map (module)

kdvs.fw.PK (module) kdvs.fw.Report (module) kdvs.fw.Stat (module) kdvs.fw.StorageManager (module) kdvs.fw.SubsetHierarchy (module) kdvs.tests (module) kdvs.tests.f (module) kdvs.tests.f.t1 (module) kdvs.tests.runTests (module) kdvs.tests.s (module) kdvs.tests.s.t1 (module) kdvs.tests.t (module) kdvs.tests.t.core (module) kdvs.tests.t.fw.Annotation (module) kdvs.tests.t.fw.App (module) kdvs.tests.t.fw.Categorizer (module) kdvs.tests.t.fw.DataSet (module) kdvs.tests.t.fw.DBResult (module) kdvs.tests.t.fw.DBShelve (module) kdvs.tests.t.fw.DBTable (module) kdvs.tests.t.fw.DSV (module) kdvs.tests.t.fw.EnvOp (module) kdvs.tests.t.fw.impl.annotation.HGNC (module) kdvs.tests.t.fw.impl.app.CmdLineApp (module) kdvs.tests.t.fw.impl.data.Null (module) kdvs.tests.t.fw.impl.data.PKDrivenData (module) kdvs.tests.t.fw.impl.data.SubsetSize (module) kdvs.tests.t.fw.impl.envop.L1L2 (module) kdvs.tests.t.fw.impl.job.PPlusJob (module) kdvs.tests.t.fw.impl.job.SimpleJob (module) kdvs.tests.t.fw.impl.map.GeneID.GPL (module) kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL (module) kdvs.tests.t.fw.impl.map.PKCID.GPL (module) kdvs.tests.t.fw.impl.pk.go.GeneOntology (module) kdvs.tests.t.fw.impl.report.L1L2 (module) kdvs.tests.t.fw.impl.stat.L1L2 (module) kdvs.tests.t.fw.impl.stat.PKCSelector (module) kdvs.tests.t.fw.impl.stat.Plot (module) kdvs.tests.t.fw.Job (module) kdvs.tests.t.fw.Map (module) kdvs.tests.t.fw.PK (module) kdvs.tests.t.fw.Report (module) kdvs.tests.t.fw.Stat (module) kdvs.tests.t.fw.StorageManager (module) kdvs.tests.t.fw.SubsetHierarchy (module) kdvs.tests.utils (module) kdvs.tools (module) kdvs.tools.pplus_job_verifier (module) kdvs.tools.predictions_extractor (module) kdvs.tools.v1vs2 (module) kdvs.tools.v1vs2.countvars (module) kdvs.tools.v1vs2.err_stats (module) kdvs.tools.v1vs2.freqvars_l1l2 (module) kdvs.tools.v1vs2.freqvars_ols (module) kdvs.tools.v1vs2.subsets (module) kdvs.tools.v1vs2.utl (module) keyIsMissing() (kdvs.fw.Map.BDMap method) keys() (kdvs.contrib.ordereddict.OrderedDict method) (kdvs.core.util.Configurable method) (kdvs.fw.DBShelve.DBShelve method) (kdvs.fw.PK.PriorKnowledgeConcept method) (kdvs.fw.Stat.Results method)

L

L1L2_L1L2 (class in kdvs.fw.impl.stat.L1L2) l1l2_l1l2_job_wrapper() (in module kdvs.fw.impl.stat.L1L2) L1L2_OLS (class in kdvs.fw.impl.stat.L1L2) l1l2_ols_job_wrapper() (in module kdvs.fw.impl.stat.L1L2) L1L2_PKC_Reporter (class in kdvs.fw.impl.report.L1L2) L1L2_PKC_UTL_Reporter (class in kdvs.fw.impl.report.L1L2) L1L2_RLS (class in kdvs.fw.impl.stat.L1L2) l1l2_rls_job_wrapper() (in module kdvs.fw.impl.stat.L1L2) L1L2_UniformExtSplitProvider (class in kdvs.fw.impl.envop.L1L2) L1L2_VarCount_Reporter (class in kdvs.fw.impl.report.L1L2) L1L2_VarFreq_Reporter (class in kdvs.fw.impl.report.L1L2)

L1L2ErrorBoxplotMuGraph (class in kdvs.fw.impl.stat.L1L2) L1L2KfoldErrorsGraph (class in kdvs.fw.impl.stat.L1L2) Labels (class in kdvs.fw.Stat) ListBDMap (class in kdvs.fw.Map) load() (kdvs.fw.DBTable.DBTable method) (kdvs.fw.PK.PKCManager method) (kdvs.fw.impl.pk.go.GeneOntology.GOManager method) loadAll() (kdvs.fw.DSV.DSV method) loadStaticData() (in module kdvs.bin.experiment) loadUserData() (in module kdvs.bin.experiment) LoggedExecutionEnvironment (class in kdvs.core.env) Logger (class in kdvs.core.log)

M

MA_GO_Experiment_App (class in kdvs.bin.experiment) MA_GO_PROFILE (in module kdvs.fw.impl.app.Profile) main() (in module kdvs.bin.experiment) (in module kdvs.contrib.dataset_generation) (in module kdvs.tests.runTests) (in module kdvs.tools.pplus_job_verifier) (in module kdvs.tools.predictions_extractor) (in module kdvs.tools.v1vs2.countvars) (in module kdvs.tools.v1vs2.err_stats) (in module kdvs.tools.v1vs2.freqvars_l1l2) (in module kdvs.tools.v1vs2.freqvars_ols) (in module kdvs.tools.v1vs2.subsets) (in module kdvs.tools.v1vs2.utl) MATPLOTLIB_GRAPH_BACKEND_PDF (in module kdvs.fw.impl.stat.Plot) MATPLOTLIB_GRAPH_BACKEND_PNG (in module kdvs.fw.impl.stat.Plot) MatplotlibPlot (class in kdvs.fw.impl.stat.Plot) mergeCfg() (in module kdvs.core.config)

Mock_em2annotation (class in kdvs.tests.t.fw.impl.report.L1L2) MockDataset (class in kdvs.tests.t.fw.impl.data.SubsetSize) MockL1L2_OLS (class in kdvs.tests.t.fw.impl.stat.L1L2) MockPKCIDMap (class in kdvs.tests.t.fw.impl.data.PKDrivenData) MockSubsetHierarchy1 (class in kdvs.tests.t.fw.SubsetHierarchy) most_common() (kdvs.contrib.counter.Counter method) MULTIFIELD_SEP (in module kdvs.fw.Annotation)

N

next() (kdvs.core.util.NPGenFromTxtWrapper method) nostderr() (in module kdvs.tests.utils) nostdout() (in module kdvs.tests.utils) NOTCATEGORIZED (in module kdvs.fw.Categorizer) NOTMAPPED (in module kdvs.fw.Map) NOTPRESENT (in module kdvs.fw.Stat) NOTPRODUCED (in module kdvs.fw.Job)

NOTSELECTED (in module kdvs.fw.Stat) NPGenFromTxtWrapper (class in kdvs.core.util) NULL_PROFILE (in module kdvs.fw.impl.app.Profile) NullCategorizer (class in kdvs.fw.impl.data.Null) NullHandler (class in kdvs.core.log) NullOrderer (class in kdvs.fw.impl.data.Null)

O

obtainDatasetFromSymbol() (kdvs.fw.impl.data.PKDrivenData.PKDrivenDBSubsetHierarchy method) (kdvs.fw.SubsetHierarchy.SubsetHierarchy method) (kdvs.tests.t.fw.SubsetHierarchy.MockSubsetHierarchy1 method) obtainLabels() (in module kdvs.bin.experiment) openReport() (kdvs.fw.Report.Reporter method) order() (kdvs.fw.Categorizer.Orderer method) (kdvs.fw.impl.data.Null.NullOrderer method) (kdvs.fw.impl.data.SubsetSize.SubsetSizeOrderer method)

OrderedDict (class in kdvs.contrib.ordereddict) Orderer (class in kdvs.fw.Categorizer) OuterSelector (class in kdvs.fw.impl.stat.PKCSelector) OuterSelector_ClassificationErrorThreshold (class in kdvs.fw.impl.stat.PKCSelector)

P

pairwise() (in module kdvs.core.util) Parametrizable (class in kdvs.core.util) perform() (kdvs.fw.EnvOp.EnvOp method) (kdvs.fw.Stat.Selector method) (kdvs.fw.impl.envop.L1L2.L1L2_UniformExtSplitProvider method) (kdvs.fw.impl.stat.PKCSelector.InnerSelector method) (kdvs.fw.impl.stat.PKCSelector.InnerSelector_ClassificationErrorThreshold_AllVars method) (kdvs.fw.impl.stat.PKCSelector.InnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq method) (kdvs.fw.impl.stat.PKCSelector.OuterSelector method) (kdvs.fw.impl.stat.PKCSelector.OuterSelector_ClassificationErrorThreshold method) performSelections() (in module kdvs.bin.experiment) PKC2EM_TMPL (in module kdvs.fw.Annotation) PKC_DETAIL_ELEMENTS (in module kdvs.fw.PK) PKCGeneMap (class in kdvs.fw.Map) PKCIDMap (class in kdvs.fw.Map) PKCIDMapGOGPL (class in kdvs.fw.impl.map.PKCID.GPL) PKCManager (class in kdvs.fw.PK) PKDrivenDataManager (class in kdvs.fw.impl.data.PKDrivenData) PKDrivenDBDataManager (class in kdvs.fw.impl.data.PKDrivenData) PKDrivenDBSubsetHierarchy (class in kdvs.fw.impl.data.PKDrivenData) Plot (class in kdvs.fw.Stat) plot() (kdvs.fw.impl.stat.L1L2.L1L2ErrorBoxplotMuGraph method) (kdvs.fw.Stat.Plot method) (kdvs.fw.impl.stat.L1L2.L1L2KfoldErrorsGraph method) (kdvs.fw.impl.stat.Plot.MatplotlibPlot method) pop() (kdvs.contrib.ordereddict.OrderedDict method)

popitem() (kdvs.contrib.ordereddict.OrderedDict method) postActionCallback() (kdvs.core.env.ExecutionEnvironment method) (kdvs.core.env.LoggedExecutionEnvironment method) postClose() (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) (kdvs.fw.Job.JobContainer method) (kdvs.fw.impl.job.SimpleJob.SimpleJobContainer method) postprocessStaticData() (in module kdvs.bin.experiment) postprocessSubsetOperations() (in module kdvs.bin.experiment) PPlusJobContainer (class in kdvs.fw.impl.job.PPlusJob) pprintObj() (in module kdvs.core.util) prepare() (kdvs.bin.experiment.MA_GO_Experiment_App method) (kdvs.fw.App.App method) prepareEnv() (kdvs.fw.App.App method) (kdvs.fw.impl.app.CmdLineApp.CmdLineApp method) prepareReports() (in module kdvs.bin.experiment) PriorKnowledgeConcept (class in kdvs.fw.PK) produce() (kdvs.fw.impl.report.L1L2.L1L2_PKC_Reporter method) (kdvs.fw.Report.Reporter method) (kdvs.fw.impl.report.L1L2.L1L2_VarCount_Reporter method) (kdvs.fw.impl.report.L1L2.L1L2_VarFreq_Reporter method) produceForHierarchy() (kdvs.fw.impl.report.L1L2.L1L2_PKC_UTL_Reporter method) (kdvs.fw.Report.Reporter method) produceResults() (kdvs.fw.impl.stat.L1L2.L1L2_L1L2 method) (kdvs.fw.Stat.Technique method) (kdvs.fw.impl.stat.L1L2.L1L2_OLS method) (kdvs.fw.impl.stat.L1L2.L1L2_RLS method) Python Enhancement Proposals PEP 249, [1]

Q

quote() (in module kdvs.core.util)

R

readline() (kdvs.core.util.NPGenFromTxtWrapper method) recache() (kdvs.fw.DataSet.DataSet method) RECOGNIZED_FILE_PROVIDERS (in module kdvs.core.provider) remGroup() (kdvs.fw.Job.JobGroupManager method) removeJob() (kdvs.fw.Job.JobContainer method) removeLocation() (kdvs.fw.StorageManager.StorageManager method) Reporter (class in kdvs.fw.Report) resolve_unittest() (in module kdvs.tests) resolveIndexes() (in module kdvs.core.util) resolveProfileComponents() (in module kdvs.bin.experiment) resolveStaticDataFiles() (in module kdvs.bin.experiment)

Results (class in kdvs.fw.Stat) RESULTS_PLOTS_ID_KEY (in module kdvs.fw.Stat) RESULTS_RUNTIME_KEY (in module kdvs.fw.Stat) RESULTS_SUBSET_ID_KEY (in module kdvs.fw.Stat) revIndices() (in module kdvs.core.util) ROOT_IMPORT_PATH (in module kdvs.__init__) RotatingFileLogger (class in kdvs.core.log) ROW_SIZE_GREATER (kdvs.fw.impl.data.SubsetSize.SubsetSizeCategorizer attribute) ROW_SIZE_LESSER (kdvs.fw.impl.data.SubsetSize.SubsetSizeCategorizer attribute) run() (kdvs.fw.App.App method) (kdvs.fw.impl.job.SimpleJob.SimpleJobExecutor method)

S

SELECTED (in module kdvs.fw.Stat) SELECTIONERROR (in module kdvs.fw.Stat) Selector (class in kdvs.fw.Stat) serializeObj() (in module kdvs.core.util) serializeTxt() (in module kdvs.core.util) SetBDMap (class in kdvs.fw.Map) setdefault() (kdvs.contrib.ordereddict.OrderedDict method) setUp() (kdvs.tests.t.core.TestCommentSkipper method) (kdvs.tests.t.core.TestConfig method) (kdvs.tests.t.core.TestConfigurable1 method) (kdvs.tests.t.core.TestDBManager method) (kdvs.tests.t.core.TestEnv method) (kdvs.tests.t.core.TestLog method) (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.core.TestProvider method) (kdvs.tests.t.fw.App.TestAppProfile1 method) (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) (kdvs.tests.t.fw.DBResult.TestDBResult1 method) (kdvs.tests.t.fw.DBShelve.TestDTShelve1 method) (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.DBTable.TestDBTable1 method) (kdvs.tests.t.fw.DBTable.TestDBTable2 method) (kdvs.tests.t.fw.DBTable.TestDBTable3 method) (kdvs.tests.t.fw.DBTable.TestDBTable4 method) (kdvs.tests.t.fw.DBTable.TestDBTable5 method) (kdvs.tests.t.fw.DBTable.TestDBTable6 method) (kdvs.tests.t.fw.DBTable.TestDBTable7 method) (kdvs.tests.t.fw.DBTable.TestDBTable8 method) (kdvs.tests.t.fw.DBTable.TestDBTable9 method) (kdvs.tests.t.fw.DBTable.TestDBTemplate1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DSV.TestDSV2 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.DataSet.TestDataSet2 method) (kdvs.tests.t.fw.EnvOp.TestEnvOp1 method) (kdvs.tests.t.fw.Job.TestJob1 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) (kdvs.tests.t.fw.Map.TestChainMap1 method) (kdvs.tests.t.fw.Map.TestChainMap2 method) (kdvs.tests.t.fw.Map.TestGeneIDMap1 method) (kdvs.tests.t.fw.Map.TestListBDMap1 method) (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestPKCGeneMap1 method) (kdvs.tests.t.fw.Map.TestPKCIDMap1 method) (kdvs.tests.t.fw.Map.TestSetBDMap1 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) (kdvs.tests.t.fw.PK.TestPKC1 method) (kdvs.tests.t.fw.Report.TestReporter1 method) (kdvs.tests.t.fw.Report.TestReporter2 method) (kdvs.tests.t.fw.Stat.TestLabels1 method) (kdvs.tests.t.fw.Stat.TestResults1 method) (kdvs.tests.t.fw.Stat.TestStatUtils1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager2 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager3 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.annotation.HGNC.TestHGNC1 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBSubsetHierarchy1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeCategorizer1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) (kdvs.tests.t.fw.impl.envop.L1L2.TestL1L2_UniformExtSplitProvider1 method) (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) (kdvs.tests.t.fw.impl.map.GeneID.GPL.TestGeneIDMapGPL1 method) (kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL.TestGeneIDMapHGNCGPL1 method) (kdvs.tests.t.fw.impl.map.PKCID.GPL.TestPKCIDMapGOGPL1 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager3 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) (kdvs.tests.t.fw.impl.report.L1L2.TestL1L2_VarCount_Reporter1 method) (kdvs.tests.t.fw.impl.report.L1L2.TestL1L2_VarFreq_Reporter1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_L1L2_1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS2 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_RLS_1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_AllVars1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestOuterSelector_ClassificationErrorThreshold1 method) (kdvs.tests.t.fw.impl.stat.Plot.TestMatplotlibPlot1 method) SimpleJobContainer (class in kdvs.fw.impl.job.SimpleJob) SimpleJobExecutor (class in kdvs.fw.impl.job.SimpleJob) specific_parameters (kdvs.fw.impl.report.L1L2.L1L2_PKC_Reporter attribute) (kdvs.fw.impl.report.L1L2.L1L2_PKC_UTL_Reporter attribute) (kdvs.fw.impl.report.L1L2.L1L2_VarCount_Reporter attribute) (kdvs.fw.impl.report.L1L2.L1L2_VarFreq_Reporter attribute) SQLite3DBProvider (class in kdvs.core.provider) start() (kdvs.fw.impl.job.PPlusJob.PPlusJobContainer method) (kdvs.fw.Job.JobContainer method) (kdvs.fw.impl.job.SimpleJob.SimpleJobContainer method)

statuses (kdvs.fw.Job.JobStatus attribute) stdAttrs() (kdvs.core.log.Logger method) StorageManager (class in kdvs.fw.StorageManager) storeCompleteResults() (in module kdvs.bin.experiment) StreamLogger (class in kdvs.core.log) SUBLOCATION_SEPARATOR (in module kdvs.fw.StorageManager) submitSubsetOperations() (in module kdvs.bin.experiment) SubsetHierarchy (class in kdvs.fw.SubsetHierarchy) SubsetSizeCategorizer (class in kdvs.fw.impl.data.SubsetSize) SubsetSizeOrderer (class in kdvs.fw.impl.data.SubsetSize) SYSTEM_NAME_LC (in module kdvs.__init__) SYSTEM_NAME_UC (in module kdvs.__init__) SYSTEM_ROOT_PATH (in module kdvs.__init__)

T

T1 (class in kdvs.tests.f.t1) (class in kdvs.tests.s.t1) tearDown() (kdvs.tests.t.core.TestDBManager method) (kdvs.tests.t.core.TestEnv method) (kdvs.tests.t.core.TestLog method) (kdvs.tests.t.fw.DBResult.TestDBResult1 method) (kdvs.tests.t.fw.DBShelve.TestDTShelve1 method) (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.DBTable.TestDBTable1 method) (kdvs.tests.t.fw.DBTable.TestDBTable2 method) (kdvs.tests.t.fw.DBTable.TestDBTable3 method) (kdvs.tests.t.fw.DBTable.TestDBTable4 method) (kdvs.tests.t.fw.DBTable.TestDBTable5 method) (kdvs.tests.t.fw.DBTable.TestDBTable6 method) (kdvs.tests.t.fw.DBTable.TestDBTable7 method) (kdvs.tests.t.fw.DBTable.TestDBTable8 method) (kdvs.tests.t.fw.DBTable.TestDBTable9 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DSV.TestDSV2 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.DataSet.TestDataSet2 method) (kdvs.tests.t.fw.Map.TestChainMap1 method) (kdvs.tests.t.fw.Map.TestChainMap2 method) (kdvs.tests.t.fw.Map.TestGeneIDMap1 method) (kdvs.tests.t.fw.Map.TestListBDMap1 method) (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestPKCGeneMap1 method) (kdvs.tests.t.fw.Map.TestPKCIDMap1 method) (kdvs.tests.t.fw.Map.TestSetBDMap1 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) (kdvs.tests.t.fw.Report.TestReporter2 method) (kdvs.tests.t.fw.Stat.TestLabels1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager2 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager3 method) (kdvs.tests.t.fw.impl.annotation.HGNC.TestHGNC1 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBSubsetHierarchy1 method) (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.impl.map.GeneID.GPL.TestGeneIDMapGPL1 method) (kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL.TestGeneIDMapHGNCGPL1 method) (kdvs.tests.t.fw.impl.map.PKCID.GPL.TestPKCIDMapGOGPL1 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager3 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) (kdvs.tests.t.fw.impl.report.L1L2.TestL1L2_VarCount_Reporter1 method) (kdvs.tests.t.fw.impl.report.L1L2.TestL1L2_VarFreq_Reporter1 method) Technique (class in kdvs.fw.Stat) test_1() (kdvs.tests.f.t1.T1 method) (kdvs.tests.s.t1.T1 method) test_2() (kdvs.tests.f.t1.T1 method) (kdvs.tests.s.t1.T1 method) test_ActionSpec1() (kdvs.tests.t.core.TestAction method) test_ActionSpec2() (kdvs.tests.t.core.TestAction method) test_ActionSpec3() (kdvs.tests.t.core.TestAction method) test_ActionSpec4() (kdvs.tests.t.core.TestAction method) test_addGroup1() (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) test_addJob1() (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_addJob2() (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_addJob3() (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) test_addJob4() (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) test_addJobIDToGroup1() (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) test_build1() (kdvs.tests.t.fw.Categorizer.TestOrderer1 method) (kdvs.tests.t.fw.Map.TestGeneIDMap1 method) (kdvs.tests.t.fw.Map.TestPKCGeneMap1 method) (kdvs.tests.t.fw.Map.TestPKCIDMap1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy1 method) (kdvs.tests.t.fw.impl.data.Null.TestNullOrderer1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) (kdvs.tests.t.fw.impl.map.GeneID.GPL.TestGeneIDMapGPL1 method) (kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL.TestGeneIDMapHGNCGPL1 method) (kdvs.tests.t.fw.impl.map.PKCID.GPL.TestPKCIDMapGOGPL1 method) test_build2() (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) test_buildDerivedMap1() (kdvs.tests.t.fw.Map.TestChainMap2 method) test_buildDerivedMap2() (kdvs.tests.t.fw.Map.TestChainMap2 method) test_calculateConfusionMatrix1() (kdvs.tests.t.fw.Stat.TestStatUtils1 method) test_calculateConfusionMatrix2() (kdvs.tests.t.fw.Stat.TestStatUtils1 method) test_calculateConfusionMatrix3() (kdvs.tests.t.fw.Stat.TestStatUtils1 method) test_calculateMCC1() (kdvs.tests.t.fw.Stat.TestStatUtils1 method) test_categories1() (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) test_categorize1() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeCategorizer1 method) test_categorize2() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeCategorizer1 method) test_categorize3() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeCategorizer1 method) test_categorize4() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeCategorizer1 method) test_categorize5() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) test_categorizeSubset1() (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) test_categorizeSubset2() (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) test_className() (kdvs.tests.t.core.TestClassName method) test_clear1() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) test_close1() (kdvs.tests.t.fw.DSV.TestDSV2 method) test_CommentSkipper1() (kdvs.tests.t.core.TestCommentSkipper method) test_CondExecEnv1() (kdvs.tests.t.core.TestEnv method) test_CondExecEnv2() (kdvs.tests.t.core.TestEnv method) test_Config1() (kdvs.tests.t.core.TestConfig method) test_Config2() (kdvs.tests.t.core.TestConfig method) test_Config3() (kdvs.tests.t.core.TestConfig method) test_configure1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager1 method) (kdvs.tests.t.fw.impl.stat.Plot.TestMatplotlibPlot1 method) test_configure2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager1 method) (kdvs.tests.t.fw.impl.stat.Plot.TestMatplotlibPlot1 method) test_contains1() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) test_correctHGNCApprovedSymbols1() (kdvs.tests.t.fw.impl.annotation.HGNC.TestHGNC1 method) test_createJob1() (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_L1L2_1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS2 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_RLS_1 method) test_createJob2() (kdvs.tests.t.fw.Stat.TestTechnique1 method) test_createJob3() (kdvs.tests.t.fw.Stat.TestTechnique1 method) test_createJob4() (kdvs.tests.t.fw.Stat.TestTechnique1 method) test_createLocation1() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager2 method) test_createLocation2() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager2 method) test_createLocation3() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager2 method) TEST_DATA_ROOT (in module kdvs.tests) test_DBManager0() (kdvs.tests.t.core.TestDBManager method) test_DBManager1() (kdvs.tests.t.core.TestDBManager method) test_DBManager2() (kdvs.tests.t.core.TestDBManager method) test_DBManager3() (kdvs.tests.t.core.TestDBManager method) test_DBManager4() (kdvs.tests.t.core.TestDBManager method) test_DBManager5() (kdvs.tests.t.core.TestDBManager method) test_DBManager6() (kdvs.tests.t.core.TestDBManager method) test_del1() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) test_deriveMap1() (kdvs.tests.t.fw.Map.TestChainMap2 method) test_deriveMap2() (kdvs.tests.t.fw.Map.TestChainMap2 method) test_deuniquifyCategory1() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) test_dir_writable() (in module kdvs.tests.utils) test_em2annotation1() (kdvs.tests.t.fw.impl.map.GeneID.GPL.TestGeneIDMapGPL1 method) (kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL.TestGeneIDMapHGNCGPL1 method) test_emptyGenerator() (kdvs.tests.t.core.TestEmptyGenerator method) test_ExecEnv1() (kdvs.tests.t.core.TestEnv method) test_ExecEnv2() (kdvs.tests.t.core.TestEnv method) test_ExecEnv3() (kdvs.tests.t.core.TestEnv method) test_ExecEnv4() (kdvs.tests.t.core.TestEnv method) test_execute1() (kdvs.tests.t.fw.Job.TestJob1 method) test_FileProvider1() (kdvs.tests.t.core.TestProvider method) test_finalize1() (kdvs.tests.t.fw.Report.TestReporter1 method) test_findGroupByJobID1() (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) test_generateHGNCPreviousSymbols1() (kdvs.tests.t.fw.impl.annotation.HGNC.TestHGNC1 method) test_generateHGNCSynonyms1() (kdvs.tests.t.fw.impl.annotation.HGNC.TestHGNC1 method) test_get1() (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) test_getAncestors1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) test_getAncestors2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) test_getDescendants1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) test_getDescendants2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) test_getJob1() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_getJob2() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_getJobResults1() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_getJobStatus1() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_getLabels1() (kdvs.tests.t.fw.Stat.TestLabels1 method) test_getLabels2() (kdvs.tests.t.fw.Stat.TestLabels1 method) test_getLabels3() (kdvs.tests.t.fw.Stat.TestLabels1 method) test_getLabels4() (kdvs.tests.t.fw.Stat.TestLabels1 method) test_getPKC1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) test_getPKC2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) test_getSamples1() (kdvs.tests.t.fw.Stat.TestLabels1 method) test_getSamples2() (kdvs.tests.t.fw.Stat.TestLabels1 method) test_getset1() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.Map.TestChainMap2 method) test_getset2() (kdvs.tests.t.fw.Map.TestChainMap2 method) test_getSubset1() (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDataManager1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) test_getSubset2() (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) test_getSubset3() (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) test_getSubset4() (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) test_getSynonyms() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager4 method) test_hasJobs1() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_hasJobs2() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_hierarchy1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager3 method) test_hierarchy2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager3 method) test_hierarchy3() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager3 method) test_id2num1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGeneOntology1 method) test_init0() (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS1 method) test_init1() (kdvs.tests.t.core.TestConfigurable1 method) (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.fw.App.TestAppProfile1 method) (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) (kdvs.tests.t.fw.Categorizer.TestOrderer1 method) (kdvs.tests.t.fw.DBShelve.TestDTShelve1 method) (kdvs.tests.t.fw.DBTable.TestDBTemplate1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.EnvOp.TestEnvOp1 method) (kdvs.tests.t.fw.Job.TestJob1 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) (kdvs.tests.t.fw.Map.TestChainMap1 method) (kdvs.tests.t.fw.Map.TestGeneIDMap1 method) (kdvs.tests.t.fw.Map.TestListBDMap1 method) (kdvs.tests.t.fw.Map.TestPKCGeneMap1 method) (kdvs.tests.t.fw.Map.TestPKCIDMap1 method) (kdvs.tests.t.fw.Map.TestSetBDMap1 method) (kdvs.tests.t.fw.PK.TestPKC1 method) (kdvs.tests.t.fw.PK.TestPKCManager1 method) (kdvs.tests.t.fw.Report.TestReporter1 method) (kdvs.tests.t.fw.Stat.TestLabels1 method) (kdvs.tests.t.fw.Stat.TestResults1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.data.Null.TestNullCategorizer1 method) (kdvs.tests.t.fw.impl.data.Null.TestNullOrderer1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBDataManager1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBSubsetHierarchy1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDataManager1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeCategorizer1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) (kdvs.tests.t.fw.impl.envop.L1L2.TestL1L2_UniformExtSplitProvider1 method) (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) (kdvs.tests.t.fw.impl.map.GeneID.GPL.TestGeneIDMapGPL1 method) (kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL.TestGeneIDMapHGNCGPL1 method) (kdvs.tests.t.fw.impl.map.PKCID.GPL.TestPKCIDMapGOGPL1 method) (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_AllVars1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestOuterSelector_ClassificationErrorThreshold1 method) (kdvs.tests.t.fw.impl.stat.Plot.TestMatplotlibPlot1 method) test_init10() (kdvs.tests.t.fw.DSV.TestDSV1 method) test_init11() (kdvs.tests.t.fw.DSV.TestDSV1 method) test_init12() (kdvs.tests.t.fw.DSV.TestDSV1 method) test_init13() (kdvs.tests.t.fw.DSV.TestDSV1 method) test_init2() (kdvs.tests.t.core.TestConfigurable1 method) (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.fw.App.TestAppProfile1 method) (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) (kdvs.tests.t.fw.DBTable.TestDBTemplate1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.EnvOp.TestEnvOp1 method) (kdvs.tests.t.fw.Job.TestJob1 method) (kdvs.tests.t.fw.Map.TestChainMap1 method) (kdvs.tests.t.fw.Map.TestListBDMap1 method) (kdvs.tests.t.fw.Map.TestSetBDMap1 method) (kdvs.tests.t.fw.PK.TestPKC1 method) (kdvs.tests.t.fw.Report.TestReporter1 method) (kdvs.tests.t.fw.Stat.TestLabels1 method) (kdvs.tests.t.fw.Stat.TestResults1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.data.Null.TestNullCategorizer1 method) (kdvs.tests.t.fw.impl.data.PKDrivenData.TestPKDrivenDBSubsetHierarchy1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) (kdvs.tests.t.fw.impl.envop.L1L2.TestL1L2_UniformExtSplitProvider1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS1 method) test_init3() (kdvs.tests.t.core.TestConfigurable1 method) (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.fw.App.TestAppProfile1 method) (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) (kdvs.tests.t.fw.DBTable.TestDBTemplate1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.Stat.TestResults1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.data.Null.TestNullCategorizer1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS1 method) test_init4() (kdvs.tests.t.core.TestConfigurable1 method) (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.fw.App.TestAppProfile1 method) (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) (kdvs.tests.t.fw.DBTable.TestDBTemplate1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.Stat.TestResults1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.StorageManager.TestFSStorageManager1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) test_init5() (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.fw.Categorizer.TestCategorizer1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) test_init6() (kdvs.tests.t.core.TestParametrizable1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) test_init7() (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) test_init8() (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy2 method) test_init9() (kdvs.tests.t.fw.DataSet.TestDataSet1 method) (kdvs.tests.t.fw.DSV.TestDSV1 method) test_initialize1() (kdvs.tests.t.fw.Report.TestReporter1 method) TEST_INVARIANTS (in module kdvs.tests) test_isGOID1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGeneOntology1 method) test_IsIntegralNumber() (kdvs.tests.t.core.TestIsIntegralNumber method) test_IsListOrTuple() (kdvs.tests.t.core.TestIsListOrTuple method) test_IsTuple() (kdvs.tests.t.core.TestIsTuple method) test_keys1() (kdvs.tests.t.fw.PK.TestPKC1 method) test_L1L2_VarCount_Reporter_1() (kdvs.tests.t.fw.impl.report.L1L2.TestL1L2_VarCount_Reporter1 method) test_L1L2_VarFreq_Reporter_1() (kdvs.tests.t.fw.impl.report.L1L2.TestL1L2_VarFreq_Reporter1 method) test_load1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) (kdvs.tests.t.fw.PK.TestPKCManager1 method) test_load2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) test_load3() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGOManager2 method) test_loadall1() (kdvs.tests.t.fw.DSV.TestDSV2 method) test_loadall2() (kdvs.tests.t.fw.DSV.TestDSV2 method) test_loadall3() (kdvs.tests.t.fw.DSV.TestDSV2 method) test_loadall4() (kdvs.tests.t.fw.DSV.TestDSV2 method) test_LoggedExecEnv1() (kdvs.tests.t.core.TestEnv method) test_LoggedExecEnv2() (kdvs.tests.t.core.TestEnv method) test_LoggedExecEnv3() (kdvs.tests.t.core.TestEnv method) test_miscData1() (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_negative() (kdvs.tests.t.core.TestDep method) test_NullLogger() (kdvs.tests.t.core.TestLog method) test_num2id1() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGeneOntology1 method) test_num2id2() (kdvs.tests.t.fw.impl.pk.go.GeneOntology.TestGeneOntology1 method) test_obtainDatasetFromSymbol1() (kdvs.tests.t.fw.SubsetHierarchy.TestSubsetHierarchy1 method) test_openReport1() (kdvs.tests.t.fw.Report.TestReporter2 method) test_openReport2() (kdvs.tests.t.fw.Report.TestReporter2 method) test_order1() (kdvs.tests.t.fw.Categorizer.TestOrderer1 method) (kdvs.tests.t.fw.impl.data.Null.TestNullOrderer1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) test_order2() (kdvs.tests.t.fw.Categorizer.TestOrderer1 method) (kdvs.tests.t.fw.impl.data.SubsetSize.TestSubsetSizeOrderer1 method) test_perform1() (kdvs.tests.t.fw.EnvOp.TestEnvOp1 method) (kdvs.tests.t.fw.impl.envop.L1L2.TestL1L2_UniformExtSplitProvider1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_AllVars1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestOuterSelector_ClassificationErrorThreshold1 method) test_perform2() (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_AllVars1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) (kdvs.tests.t.fw.impl.stat.PKCSelector.TestOuterSelector_ClassificationErrorThreshold1 method) test_perform3() (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) test_perform4() (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) test_perform5() (kdvs.tests.t.fw.impl.stat.PKCSelector.TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 method) test_plot1() (kdvs.tests.t.fw.impl.stat.Plot.TestMatplotlibPlot1 method) test_plot2() (kdvs.tests.t.fw.impl.stat.Plot.TestMatplotlibPlot1 method) test_positive() (kdvs.tests.t.core.TestDep method) test_postActionCb1() (kdvs.tests.t.core.TestEnv method) test_postActionCb2() (kdvs.tests.t.core.TestEnv method) test_postClose1() (kdvs.tests.t.fw.impl.job.PPlusJob.TestPPlusJobContainer1 method) (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_produceResults1() (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_L1L2_1 method) (kdvs.tests.t.fw.Stat.TestTechnique1 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS2 method) (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_RLS_1 method) test_produceResults2() (kdvs.tests.t.fw.impl.stat.L1L2.TestL1L2_OLS2 method) test_recache1() (kdvs.tests.t.fw.DataSet.TestDataSet2 method) test_recache2() (kdvs.tests.t.fw.DataSet.TestDataSet2 method) test_recache3() (kdvs.tests.t.fw.DataSet.TestDataSet2 method) test_remGroup1() (kdvs.tests.t.fw.Job.TestJobGroupManager1 method) test_removeJob1() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_removeJob2() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_removeJob3() (kdvs.tests.t.fw.Job.TestJobContainer1 method) test_removeLocation1() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager3 method) test_removeLocation2() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager3 method) test_removeLocation3() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager3 method) test_removeLocation4() (kdvs.tests.t.fw.StorageManager.TestFSStorageManager3 method) test_RFLogger1() (kdvs.tests.t.core.TestLog method) test_RFLogger2() (kdvs.tests.t.core.TestLog method) test_rowscols1() (kdvs.tests.t.fw.DataSet.TestDataSet1 method)

test_run1() (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) test_run2() (kdvs.tests.t.fw.impl.app.CmdLineApp.TestCmdLineApp1 method) (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) test_run3() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) test_run4() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) test_run5() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobExecutor1 method) test_set1() (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) test_set2() (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) test_set3() (kdvs.tests.t.fw.Map.TestListBDMap2 method) (kdvs.tests.t.fw.Map.TestSetBDMap2 method) test_SQLite3DBProvider1() (kdvs.tests.t.core.TestProvider method) test_start1() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_start2() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_start3() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_start4() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_start5() (kdvs.tests.t.fw.impl.job.SimpleJob.TestSimpleJobContainer1 method) test_StreamLogger1() (kdvs.tests.t.core.TestLog method) test_StreamLogger2() (kdvs.tests.t.core.TestLog method) test_uniquifyCategory1() (kdvs.tests.t.fw.Categorizer.TestCategorizer2 method) test_update1() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.Map.TestChainMap2 method) test_update2() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) (kdvs.tests.t.fw.Map.TestChainMap2 method) test_view1() (kdvs.tests.t.fw.DBShelve.TestDTShelve2 method) TEST_WRITE_ROOT (in module kdvs.tests) TestAction (class in kdvs.tests.t.core) TestAppProfile1 (class in kdvs.tests.t.fw.App) TestCategorizer1 (class in kdvs.tests.t.fw.Categorizer) TestCategorizer2 (class in kdvs.tests.t.fw.Categorizer) TestChainMap1 (class in kdvs.tests.t.fw.Map) TestChainMap2 (class in kdvs.tests.t.fw.Map) TestClassName (class in kdvs.tests.t.core) TestCmdLineApp1 (class in kdvs.tests.t.fw.impl.app.CmdLineApp) TestCommentSkipper (class in kdvs.tests.t.core) TestConfig (class in kdvs.tests.t.core) TestConfigurable1 (class in kdvs.tests.t.core) TestDataSet1 (class in kdvs.tests.t.fw.DataSet) TestDataSet2 (class in kdvs.tests.t.fw.DataSet) TestDBManager (class in kdvs.tests.t.core) testDBR_get1() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get2() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get3() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get4() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get5() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get6() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get7() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) testDBR_get8() (kdvs.tests.t.fw.DBResult.TestDBResult1 method) TestDBResult1 (class in kdvs.tests.t.fw.DBResult) testDBT_count1() (kdvs.tests.t.fw.DBTable.TestDBTable3 method) testDBT_count2() (kdvs.tests.t.fw.DBTable.TestDBTable3 method) testDBT_create1() (kdvs.tests.t.fw.DBTable.TestDBTable2 method) testDBT_create2() (kdvs.tests.t.fw.DBTable.TestDBTable2 method) testDBT_create3() (kdvs.tests.t.fw.DBTable.TestDBTable2 method) testDBT_create4() (kdvs.tests.t.fw.DBTable.TestDBTable2 method) testDBT_create5() (kdvs.tests.t.fw.DBTable.TestDBTable2 method) testDBT_create6() (kdvs.tests.t.fw.DBTable.TestDBTable2 method) testDBT_fromTemplate1() (kdvs.tests.t.fw.DBTable.TestDBTable9 method) testDBT_fromTemplate2() (kdvs.tests.t.fw.DBTable.TestDBTable9 method) testDBT_get1() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get10() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get2() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get3() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get4() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get5() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get6() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get7() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get8() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_get9() (kdvs.tests.t.fw.DBTable.TestDBTable4 method) testDBT_getAll1() (kdvs.tests.t.fw.DBTable.TestDBTable7 method) testDBT_getAll2() (kdvs.tests.t.fw.DBTable.TestDBTable7 method) testDBT_getAll3() (kdvs.tests.t.fw.DBTable.TestDBTable7 method) testDBT_getAll4() (kdvs.tests.t.fw.DBTable.TestDBTable7 method) testDBT_getArray1() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray10() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray11() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray2() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray3() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray4() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray5() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray6() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray7() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray8() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getArray9() (kdvs.tests.t.fw.DBTable.TestDBTable8 method) testDBT_getIDs1() (kdvs.tests.t.fw.DBTable.TestDBTable6 method) testDBT_getIDs2() (kdvs.tests.t.fw.DBTable.TestDBTable6 method) testDBT_getIDs3() (kdvs.tests.t.fw.DBTable.TestDBTable6 method) testDBT_init1() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init2() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init3() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init4() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init5() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init6() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init7() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_init8() (kdvs.tests.t.fw.DBTable.TestDBTable1 method) testDBT_isEmpty1() (kdvs.tests.t.fw.DBTable.TestDBTable5 method) testDBT_isEmpty2() (kdvs.tests.t.fw.DBTable.TestDBTable5 method) testDBT_load1() (kdvs.tests.t.fw.DBTable.TestDBTable3 method) testDBT_load2() (kdvs.tests.t.fw.DBTable.TestDBTable3 method) testDBT_load3() (kdvs.tests.t.fw.DBTable.TestDBTable3 method) testDBT_load4() (kdvs.tests.t.fw.DBTable.TestDBTable3 method) TestDBTable1 (class in kdvs.tests.t.fw.DBTable) TestDBTable2 (class in kdvs.tests.t.fw.DBTable) TestDBTable3 (class in kdvs.tests.t.fw.DBTable) TestDBTable4 (class in kdvs.tests.t.fw.DBTable) TestDBTable5 (class in kdvs.tests.t.fw.DBTable) TestDBTable6 (class in kdvs.tests.t.fw.DBTable) TestDBTable7 (class in kdvs.tests.t.fw.DBTable) TestDBTable8 (class in kdvs.tests.t.fw.DBTable) TestDBTable9 (class in kdvs.tests.t.fw.DBTable) TestDBTemplate1 (class in kdvs.tests.t.fw.DBTable) TestDep (class in kdvs.tests.t.core) TestDSV1 (class in kdvs.tests.t.fw.DSV) TestDSV2 (class in kdvs.tests.t.fw.DSV) TestDTShelve1 (class in kdvs.tests.t.fw.DBShelve) TestDTShelve2 (class in kdvs.tests.t.fw.DBShelve) TestEmptyGenerator (class in kdvs.tests.t.core) TestEnv (class in kdvs.tests.t.core) TestEnvOp1 (class in kdvs.tests.t.fw.EnvOp) TestError TestFSStorageManager1 (class in kdvs.tests.t.fw.StorageManager) TestFSStorageManager2 (class in kdvs.tests.t.fw.StorageManager) TestFSStorageManager3 (class in kdvs.tests.t.fw.StorageManager) TestGeneIDMap1 (class in kdvs.tests.t.fw.Map) TestGeneIDMapGPL1 (class in kdvs.tests.t.fw.impl.map.GeneID.GPL) TestGeneIDMapHGNCGPL1 (class in kdvs.tests.t.fw.impl.map.GeneID.HGNC_GPL) TestGeneOntology1 (class in kdvs.tests.t.fw.impl.pk.go.GeneOntology) TestGOManager1 (class in kdvs.tests.t.fw.impl.pk.go.GeneOntology) TestGOManager2 (class in kdvs.tests.t.fw.impl.pk.go.GeneOntology) TestGOManager3 (class in kdvs.tests.t.fw.impl.pk.go.GeneOntology) TestGOManager4 (class in kdvs.tests.t.fw.impl.pk.go.GeneOntology) TestHGNC1 (class in kdvs.tests.t.fw.impl.annotation.HGNC) TestInnerSelector_ClassificationErrorThreshold_AllVars1 (class in kdvs.tests.t.fw.impl.stat.PKCSelector) TestInnerSelector_ClassificationErrorThreshold_L1L2_VarsFreq1 (class in kdvs.tests.t.fw.impl.stat.PKCSelector) TestIsIntegralNumber (class in kdvs.tests.t.core) TestIsListOrTuple (class in kdvs.tests.t.core) TestIsTuple (class in kdvs.tests.t.core) TestJob1 (class in kdvs.tests.t.fw.Job) TestJobContainer1 (class in kdvs.tests.t.fw.Job) TestJobGroupManager1 (class in kdvs.tests.t.fw.Job) TestL1L2_L1L2_1 (class in kdvs.tests.t.fw.impl.stat.L1L2) TestL1L2_OLS1 (class in kdvs.tests.t.fw.impl.stat.L1L2) TestL1L2_OLS2 (class in kdvs.tests.t.fw.impl.stat.L1L2) TestL1L2_RLS_1 (class in kdvs.tests.t.fw.impl.stat.L1L2) TestL1L2_UniformExtSplitProvider1 (class in kdvs.tests.t.fw.impl.envop.L1L2) TestL1L2_VarCount_Reporter1 (class in kdvs.tests.t.fw.impl.report.L1L2) TestL1L2_VarFreq_Reporter1 (class in kdvs.tests.t.fw.impl.report.L1L2) TestLabels1 (class in kdvs.tests.t.fw.Stat) TestListBDMap1 (class in kdvs.tests.t.fw.Map) TestListBDMap2 (class in kdvs.tests.t.fw.Map) TestLog (class in kdvs.tests.t.core) TestMatplotlibPlot1 (class in kdvs.tests.t.fw.impl.stat.Plot) TestNullCategorizer1 (class in kdvs.tests.t.fw.impl.data.Null) TestNullOrderer1 (class in kdvs.tests.t.fw.impl.data.Null) TestOrderer1 (class in kdvs.tests.t.fw.Categorizer) TestOuterSelector_ClassificationErrorThreshold1 (class in kdvs.tests.t.fw.impl.stat.PKCSelector) TestParametrizable1 (class in kdvs.tests.t.core) TestPKC1 (class in kdvs.tests.t.fw.PK) TestPKCGeneMap1 (class in kdvs.tests.t.fw.Map) TestPKCIDMap1 (class in kdvs.tests.t.fw.Map) TestPKCIDMapGOGPL1 (class in kdvs.tests.t.fw.impl.map.PKCID.GPL) TestPKCManager1 (class in kdvs.tests.t.fw.PK) TestPKDrivenDataManager1 (class in kdvs.tests.t.fw.impl.data.PKDrivenData) TestPKDrivenDBDataManager1 (class in kdvs.tests.t.fw.impl.data.PKDrivenData) TestPKDrivenDBSubsetHierarchy1 (class in kdvs.tests.t.fw.impl.data.PKDrivenData) TestPPlusJobContainer1 (class in kdvs.tests.t.fw.impl.job.PPlusJob) TestProvider (class in kdvs.tests.t.core) TestReporter1 (class in kdvs.tests.t.fw.Report) TestReporter2 (class in kdvs.tests.t.fw.Report) TestResults1 (class in kdvs.tests.t.fw.Stat) testRFLogger3() (kdvs.tests.t.core.TestLog method) TestSetBDMap1 (class in kdvs.tests.t.fw.Map) TestSetBDMap2 (class in kdvs.tests.t.fw.Map) TestSimpleJobContainer1 (class in kdvs.tests.t.fw.impl.job.SimpleJob) TestSimpleJobExecutor1 (class in kdvs.tests.t.fw.impl.job.SimpleJob) TestStatUtils1 (class in kdvs.tests.t.fw.Stat) TestSubsetHierarchy1 (class in kdvs.tests.t.fw.SubsetHierarchy) TestSubsetHierarchy2 (class in kdvs.tests.t.fw.SubsetHierarchy) TestSubsetSizeCategorizer1 (class in kdvs.tests.t.fw.impl.data.SubsetSize) TestSubsetSizeOrderer1 (class in kdvs.tests.t.fw.impl.data.SubsetSize) TestTechnique1 (class in kdvs.tests.t.fw.Stat)

U

UC (in module kdvs.fw.Categorizer) uesp_parameters (kdvs.fw.impl.envop.L1L2.L1L2_UniformExtSplitProvider attribute) uniquifyCategory() (kdvs.fw.Categorizer.Categorizer method)

update() (kdvs.contrib.counter.Counter method) (kdvs.contrib.ordereddict.OrderedDict method) (kdvs.fw.DBShelve.DBShelve method) (kdvs.fw.Map.ChainMap method) updateVars() (kdvs.core.env.ExecutionEnvironment method)

V

values() (kdvs.contrib.ordereddict.OrderedDict method) (kdvs.fw.DBShelve.DBShelve method) var() (kdvs.core.env.ExecutionEnvironment method) varkeys() (kdvs.core.env.ExecutionEnvironment method)

verifyDepModule() (in module kdvs.core.dep) version (in module kdvs.core._version) (kdvs.fw.impl.envop.L1L2.L1L2_UniformExtSplitProvider attribute) (kdvs.tests.t.fw.impl.stat.L1L2.MockL1L2_OLS attribute) view() (kdvs.fw.DBShelve.DBShelve method)

W

Warn	writeObj() (in module kdvs.core.util)