Namespaces

• cli_db
  • propel
    • map
    • om
• cli_import
• LoggedPDO
• None
• PHP
• webservices
  • cart
  • combisearch
  • details
    • annotations
      • feature
  • graphs
    • barplot
    • genome
  • listing
  • queue

Classes

• cli_db\AbstractTable
• cli_db\Acquisition
• cli_db\Analysis
• cli_db\Assay
• cli_db\Biomaterial
• cli_db\Contact
• cli_db\Feature
• cli_db\Organism
• cli_db\propel\Acquisition
• cli_db\propel\AcquisitionPeer
• cli_db\propel\AcquisitionQuery
• cli_db\propel\Analysis
• cli_db\propel\AnalysisPeer
• cli_db\propel\AnalysisQuery
• cli_db\propel\Assay
• cli_db\propel\AssayBiomaterial
• cli_db\propel\AssayBiomaterialPeer
• cli_db\propel\AssayBiomaterialQuery
• cli_db\propel\AssayPeer
• cli_db\propel\AssayQuery
• cli_db\propel\Biomaterial
• cli_db\propel\BiomaterialPeer
• cli_db\propel\Biomaterialprop
• cli_db\propel\BiomaterialpropPeer
• cli_db\propel\BiomaterialpropQuery
• cli_db\propel\BiomaterialQuery
• cli_db\propel\BiomaterialRelationship
• cli_db\propel\BiomaterialRelationshipPeer
• cli_db\propel\BiomaterialRelationshipQuery
• cli_db\propel\Contact
• cli_db\propel\ContactPeer
• cli_db\propel\ContactQuery
• cli_db\propel\Cv
• cli_db\propel\CvPeer
• cli_db\propel\CvQuery
• cli_db\propel\Cvterm
• cli_db\propel\CvtermPeer
• cli_db\propel\CvtermQuery
• cli_db\propel\Db
• cli_db\propel\DbPeer
• cli_db\propel\DbQuery
• cli_db\propel\Dbxref
• cli_db\propel\DbxrefPeer
• cli_db\propel\DbxrefQuery
• cli_db\propel\Feature
• cli_db\propel\FeatureCvterm
• cli_db\propel\FeatureCvtermDbxref
• cli_db\propel\FeatureCvtermDbxrefPeer
• cli_db\propel\FeatureCvtermDbxrefQuery
• cli_db\propel\FeatureCvtermPeer
• cli_db\propel\FeatureCvtermprop
• cli_db\propel\FeatureCvtermpropPeer
• cli_db\propel\FeatureCvtermpropQuery
• cli_db\propel\FeatureCvtermPub
• cli_db\propel\FeatureCvtermPubPeer
• cli_db\propel\FeatureCvtermPubQuery
• cli_db\propel\FeatureCvtermQuery
• cli_db\propel\FeatureDbxref
• cli_db\propel\FeatureDbxrefPeer
• cli_db\propel\FeatureDbxrefQuery
• cli_db\propel\FeaturePeer
• cli_db\propel\FeaturePub
• cli_db\propel\FeaturePubPeer
• cli_db\propel\FeaturePubQuery
• cli_db\propel\FeatureQuery
• cli_db\propel\FeatureSynonym
• cli_db\propel\FeatureSynonymPeer
• cli_db\propel\FeatureSynonymQuery
• cli_db\propel\map\AcquisitionTableMap
• cli_db\propel\map\AnalysisTableMap
• cli_db\propel\map\AssayBiomaterialTableMap
• cli_db\propel\map\AssayTableMap
• cli_db\propel\map\BiomaterialpropTableMap
• cli_db\propel\map\BiomaterialRelationshipTableMap
• cli_db\propel\map\BiomaterialTableMap
• cli_db\propel\map\ContactTableMap
• cli_db\propel\map\CvTableMap
• cli_db\propel\map\CvtermTableMap
• cli_db\propel\map\DbTableMap
• cli_db\propel\map\DbxrefTableMap
• cli_db\propel\map\FeatureCvtermDbxrefTableMap
• cli_db\propel\map\FeatureCvtermpropTableMap
• cli_db\propel\map\FeatureCvtermPubTableMap
• cli_db\propel\map\FeatureCvtermTableMap
• cli_db\propel\map\FeatureDbxrefTableMap
• cli_db\propel\map\FeaturePubTableMap
• cli_db\propel\map\FeatureSynonymTableMap
• cli_db\propel\map\FeatureTableMap
• cli_db\propel\map\OrganismTableMap
• cli_db\propel\map\ProtocolTableMap
• cli_db\propel\map\PubauthorTableMap
• cli_db\propel\map\PubDbxrefTableMap
• cli_db\propel\map\PubpropTableMap
• cli_db\propel\map\PubRelationshipTableMap
• cli_db\propel\map\PubTableMap
• cli_db\propel\map\QuantificationTableMap
• cli_db\propel\map\SynonymTableMap
• cli_db\propel\om\BaseAcquisition
• cli_db\propel\om\BaseAcquisitionPeer
• cli_db\propel\om\BaseAcquisitionQuery
• cli_db\propel\om\BaseAnalysis
• cli_db\propel\om\BaseAnalysisPeer
• cli_db\propel\om\BaseAnalysisQuery
• cli_db\propel\om\BaseAssay
• cli_db\propel\om\BaseAssayBiomaterial
• cli_db\propel\om\BaseAssayBiomaterialPeer
• cli_db\propel\om\BaseAssayBiomaterialQuery
• cli_db\propel\om\BaseAssayPeer
• cli_db\propel\om\BaseAssayQuery
• cli_db\propel\om\BaseBiomaterial
• cli_db\propel\om\BaseBiomaterialPeer
• cli_db\propel\om\BaseBiomaterialprop
• cli_db\propel\om\BaseBiomaterialpropPeer
• cli_db\propel\om\BaseBiomaterialpropQuery
• cli_db\propel\om\BaseBiomaterialQuery
• cli_db\propel\om\BaseBiomaterialRelationship
• cli_db\propel\om\BaseBiomaterialRelationshipPeer
• cli_db\propel\om\BaseBiomaterialRelationshipQuery
• cli_db\propel\om\BaseContact
• cli_db\propel\om\BaseContactPeer
• cli_db\propel\om\BaseContactQuery
• cli_db\propel\om\BaseCv
• cli_db\propel\om\BaseCvPeer
• cli_db\propel\om\BaseCvQuery
• cli_db\propel\om\BaseCvterm
• cli_db\propel\om\BaseCvtermPeer
• cli_db\propel\om\BaseCvtermQuery
• cli_db\propel\om\BaseDb
• cli_db\propel\om\BaseDbPeer
• cli_db\propel\om\BaseDbQuery
• cli_db\propel\om\BaseDbxref
• cli_db\propel\om\BaseDbxrefPeer
• cli_db\propel\om\BaseDbxrefQuery
• cli_db\propel\om\BaseFeature
• cli_db\propel\om\BaseFeatureCvterm
• cli_db\propel\om\BaseFeatureCvtermDbxref
• cli_db\propel\om\BaseFeatureCvtermDbxrefPeer
• cli_db\propel\om\BaseFeatureCvtermDbxrefQuery
• cli_db\propel\om\BaseFeatureCvtermPeer
• cli_db\propel\om\BaseFeatureCvtermprop
• cli_db\propel\om\BaseFeatureCvtermpropPeer
• cli_db\propel\om\BaseFeatureCvtermpropQuery
• cli_db\propel\om\BaseFeatureCvtermPub
• cli_db\propel\om\BaseFeatureCvtermPubPeer
• cli_db\propel\om\BaseFeatureCvtermPubQuery
• cli_db\propel\om\BaseFeatureCvtermQuery
• cli_db\propel\om\BaseFeatureDbxref
• cli_db\propel\om\BaseFeatureDbxrefPeer
• cli_db\propel\om\BaseFeatureDbxrefQuery
• cli_db\propel\om\BaseFeaturePeer
• cli_db\propel\om\BaseFeaturePub
• cli_db\propel\om\BaseFeaturePubPeer
• cli_db\propel\om\BaseFeaturePubQuery
• cli_db\propel\om\BaseFeatureQuery
• cli_db\propel\om\BaseFeatureSynonym
• cli_db\propel\om\BaseFeatureSynonymPeer
• cli_db\propel\om\BaseFeatureSynonymQuery
• cli_db\propel\om\BaseOrganism
• cli_db\propel\om\BaseOrganismPeer
• cli_db\propel\om\BaseOrganismQuery
• cli_db\propel\om\BaseProtocol
• cli_db\propel\om\BaseProtocolPeer
• cli_db\propel\om\BaseProtocolQuery
• cli_db\propel\om\BasePub
• cli_db\propel\om\BasePubauthor
• cli_db\propel\om\BasePubauthorPeer
• cli_db\propel\om\BasePubauthorQuery
• cli_db\propel\om\BasePubDbxref
• cli_db\propel\om\BasePubDbxrefPeer
• cli_db\propel\om\BasePubDbxrefQuery
• cli_db\propel\om\BasePubPeer
• cli_db\propel\om\BasePubprop
• cli_db\propel\om\BasePubpropPeer
• cli_db\propel\om\BasePubpropQuery
• cli_db\propel\om\BasePubQuery
• cli_db\propel\om\BasePubRelationship
• cli_db\propel\om\BasePubRelationshipPeer
• cli_db\propel\om\BasePubRelationshipQuery
• cli_db\propel\om\BaseQuantification
• cli_db\propel\om\BaseQuantificationPeer
• cli_db\propel\om\BaseQuantificationQuery
• cli_db\propel\om\BaseSynonym
• cli_db\propel\om\BaseSynonymPeer
• cli_db\propel\om\BaseSynonymQuery
• cli_db\propel\Organism
• cli_db\propel\OrganismPeer
• cli_db\propel\OrganismQuery
• cli_db\propel\Protocol
• cli_db\propel\ProtocolPeer
• cli_db\propel\ProtocolQuery
• cli_db\propel\Pub
• cli_db\propel\Pubauthor
• cli_db\propel\PubauthorPeer
• cli_db\propel\PubauthorQuery
• cli_db\propel\PubDbxref
• cli_db\propel\PubDbxrefPeer
• cli_db\propel\PubDbxrefQuery
• cli_db\propel\PubPeer
• cli_db\propel\Pubprop
• cli_db\propel\PubpropPeer
• cli_db\propel\PubpropQuery
• cli_db\propel\PubQuery
• cli_db\propel\PubRelationship
• cli_db\propel\PubRelationshipPeer
• cli_db\propel\PubRelationshipQuery
• cli_db\propel\Quantification
• cli_db\propel\QuantificationPeer
• cli_db\propel\QuantificationQuery
• cli_db\propel\Synonym
• cli_db\propel\SynonymPeer
• cli_db\propel\SynonymQuery
• cli_db\Protocol
• cli_db\Publication
• cli_db\Quantification
• cli_import\AbstractImporter
• cli_import\Importer_Annotations_Dbxref
• cli_import\Importer_Annotations_Description
• cli_import\Importer_Annotations_EC
• cli_import\Importer_Annotations_GO
• cli_import\Importer_Annotations_Interpro
• cli_import\Importer_Annotations_MapMan
• cli_import\Importer_Annotations_Repeatmasker
• cli_import\Importer_Differential_Expressions
• cli_import\Importer_Expressions
• cli_import\Importer_Sequence_Ids
• cli_import\Importer_Sequences_FASTA
• Console_CommandLine_Action_ExtendedHelp
• LightOpenID
• Log_firebugJSON
• LoggedPDO\PDO
• LoggedPDO\PDOStatement
• PDO
• PDOStatement
• WebService
• webservices\cart\Sync
• webservices\combisearch\Hasgo
• webservices\combisearch\Hasgo_or_children
• webservices\details\annotations\feature\Dbxref
• webservices\details\annotations\feature\Interpro_predpeps
• webservices\details\annotations\feature\Mapman
• webservices\details\annotations\feature\Pub
• webservices\details\annotations\feature\Repeatmasker
• webservices\details\annotations\feature\Synonym
• webservices\details\Features
• webservices\details\Isoform
• webservices\details\Statistical_information
• webservices\details\Unigene
• webservices\graphs\barplot\Quantifications
• webservices\graphs\genome\Isoform
• webservices\listing\Differential_expressions
• webservices\listing\Filters
• webservices\listing\Filters_diffexp
• webservices\listing\Isoforms
• webservices\listing\Multisearch
• webservices\listing\Organism_release
• webservices\listing\Searchbox
• webservices\queue\Job_program_databases
• webservices\queue\Job_results
• webservices\queue\Job_start

Interfaces

• CLI_Command
• cli_db\Table
• cli_import\Importer
• Traversable

Exceptions

• ErrorException
• Exception

Functions

• acquire_database
• cli_error_handler
• connect_queue_db
• create_job
• display_feature
• display_feature_by_id
• display_isoform_by_id
• display_unigene_by_id
• download
• execute_command
• execute_job
• execute_query_dir
• get_db_connection
• get_job_results
• get_program_databases
• myErrorHandler
• pdo_connect
• report_results_cleanup
• requestVal
• smarty_function_call_webservice
• smarty_function_dbxreflink
• smarty_function_interprolink
• smarty_function_publink
• smarty_modifier_clean_id
• split_fasta
• unzip

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