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Bio-Genex-2.6.0
River stage zero No dependents
1 ++

Changes for version 2.6.0 - 2001-02-06

  • XMLUtils.pm: Added the beginings of a real XML API, defining db2xml() and all2xml() for some classes Now defines Bio::Genex::GeneXML and ::GeneXML::USF helper classes Fixed pretty_print() to preserve whitespace
  • DBUtils.pm: now has many more assert_* methods new helper method: fetch_db_ids_for_species() that does a join accross the USF, and ExternalDatabase tables
  • Genex.pm: now has timestamp() helper method, so that all DB timestamps can be formatted identically
  • GenexAdmin.pm: Class interface to new table. This enables a DB history mechanism to record changes to the DB installation
  • get_objects() fixed for all classes
  • db2xml.pl: fixed a BlastHits bug added pretty_print() again Fixed caching of control bundles, so that the <misc_list> is specific to each download
  • cv-insert.pl: now records info into GenexAdmin now uses --name option to identify *who* made the changes uses --dbname to specify what DB to use
  • status.pl: New CGI script that shows all version information pertinent to the server installation.

Documentation

Bio::Genex::AL_Spots
Methods for processing data from the GeneX DB table: AL_Spots
Bio::Genex::AM_FactorValues
Methods for processing data from the GeneX DB linking table: AM_FactorValues
Bio::Genex::AM_Spots
Methods for processing data from the GeneX DB table: AM_Spots
Bio::Genex::AM_SuspectSpots
Methods for processing data from the GeneX DB linking table: AM_SuspectSpots
Bio::Genex::ArrayLayout
Methods for processing data from the GeneX DB table: ArrayLayout
Bio::Genex::ArrayMeasurement
Methods for processing data from the GeneX DB table: ArrayMeasurement
Bio::Genex::BlastHits
Methods for processing data from the GeneX DB table: BlastHits
Bio::Genex::CSF_ExternalDBLink
Methods for processing data from the GeneX DB linking table: CSF_ExternalDBLink
Bio::Genex::CanonicalSequenceFeature
Methods for processing data from the GeneX DB table: CanonicalSequenceFeature
Bio::Genex::Chromosome
Methods for processing data from the GeneX DB table: Chromosome
Bio::Genex::Citation
Methods for processing data from the GeneX DB table: Citation
Bio::Genex::CitationLink
Methods for processing data from the GeneX DB linking table: CitationLink
Bio::Genex::Contact
Methods for processing data from the GeneX DB table: Contact
Bio::Genex::ControlledVocab
Methods for processing data from the GeneX DB table: ControlledVocab
DBUtils
a module for useful Database utilities
Bio::Genex::ExperimentFactors
Methods for processing data from the GeneX DB table: ExperimentFactors
Bio::Genex::ExperimentSet
Methods for processing data from the GeneX DB table: ExperimentSet
Bio::Genex::ExternalDatabase
Methods for processing data from the GeneX DB table: ExternalDatabase
Genex
Perl extension for processing data from a GeneX DB
Bio::Genex::GroupLink
Methods for processing data from the GeneX DB linking table: GroupLink
Bio::Genex::GroupSec
Methods for processing data from the GeneX DB table: GroupSec
HTMLUtils
a module for useful HTML utilities for Genex DBs
Bio::Genex::HotSpots
Methods for processing data from the GeneX DB linking table: HotSpots
Bio::Genex::Protocol
Methods for processing data from the GeneX DB table: Protocol
Bio::Genex::RelatedCSF
Methods for processing data from the GeneX DB linking table: RelatedCSF
Bio::Genex::Sample
Methods for processing data from the GeneX DB table: Sample
Bio::Genex::SampleProtocols
Methods for processing data from the GeneX DB linking table: SampleProtocols
Bio::Genex::Scanner
Methods for processing data from the GeneX DB table: Scanner
Bio::Genex::Software
Methods for processing data from the GeneX DB table: Software
Bio::Genex::Species
Methods for processing data from the GeneX DB table: Species
Bio::Genex::SpotLink
Methods for processing data from the GeneX DB linking table: SpotLink
Bio::Genex::Spotter
Methods for processing data from the GeneX DB table: Spotter
Bio::Genex::TL_FactorValues
Methods for processing data from the GeneX DB linking table: TL_FactorValues
Bio::Genex::TreatmentLevel
Methods for processing data from the GeneX DB table: TreatmentLevel
Bio::Genex::Treatment_AMs
Methods for processing data from the GeneX DB linking table: Treatment_AMs
Bio::Genex::USF_ExternalDBLink
Methods for processing data from the GeneX DB linking table: USF_ExternalDBLink
Bio::Genex::UserCanonicalLink
Methods for processing data from the GeneX DB linking table: UserCanonicalLink
Bio::Genex::UserSec
Methods for processing data from the GeneX DB table: UserSec
Bio::Genex::UserSequenceFeature
Methods for processing data from the GeneX DB table: UserSequenceFeature
XMLUtils
a module for useful XML utilities for Genex DBs
control-bundle.pl:
curation-tool-login.pl:
db2xml.pl:

Modules

Bio::Genex::AL_Spots
Methods for processing data from the GeneX DB table: AL_Spots
Bio::Genex::AM_FactorValues
Methods for processing data from the GeneX DB linking table: AM_FactorValues
Bio::Genex::AM_Spots
Methods for processing data from the GeneX DB table: AM_Spots
Bio::Genex::AM_SuspectSpots
Methods for processing data from the GeneX DB linking table: AM_SuspectSpots
Bio::Genex::ArrayLayout
Methods for processing data from the GeneX DB table: ArrayLayout
Bio::Genex::ArrayMeasurement
Methods for processing data from the GeneX DB table: ArrayMeasurement
Bio::Genex::BlastHits
Methods for processing data from the GeneX DB table: BlastHits
Bio::Genex::Chromosome
Methods for processing data from the GeneX DB table: Chromosome
Bio::Genex::Citation
Methods for processing data from the GeneX DB table: Citation
Bio::Genex::Contact
Methods for processing data from the GeneX DB table: Contact
Bio::Genex::ControlledVocab
Methods for processing data from the GeneX DB table: ControlledVocab
Bio::Genex::ExperimentFactors
Methods for processing data from the GeneX DB table: ExperimentFactors
Bio::Genex::ExperimentSet
Methods for processing data from the GeneX DB table: ExperimentSet
Bio::Genex::ExternalDatabase
Methods for processing data from the GeneX DB table: ExternalDatabase
Bio::Genex::Fkey
Perl extension for representing Database Foreign Keys
Bio::Genex::GenexAdmin
Methods for processing data from the GeneX DB table: GenexAdmin
Bio::Genex::GroupLink
Methods for processing data from the GeneX DB linking table: GroupLink
Bio::Genex::GroupSec
Methods for processing data from the GeneX DB table: GroupSec
Bio::Genex::HotSpots
Methods for processing data from the GeneX DB linking table: HotSpots
Bio::Genex::Protocol
Methods for processing data from the GeneX DB table: Protocol
Bio::Genex::Sample
Methods for processing data from the GeneX DB table: Sample
Bio::Genex::SampleProtocols
Methods for processing data from the GeneX DB linking table: SampleProtocols
Bio::Genex::Scanner
Methods for processing data from the GeneX DB table: Scanner
Bio::Genex::Software
Methods for processing data from the GeneX DB table: Software
Bio::Genex::Species
Methods for processing data from the GeneX DB table: Species
Bio::Genex::SpotLink
Methods for processing data from the GeneX DB linking table: SpotLink
Bio::Genex::Spotter
Methods for processing data from the GeneX DB table: Spotter
Bio::Genex::TL_FactorValues
Methods for processing data from the GeneX DB linking table: TL_FactorValues
Bio::Genex::TreatmentLevel
Methods for processing data from the GeneX DB table: TreatmentLevel
Bio::Genex::Treatment_AMs
Methods for processing data from the GeneX DB linking table: Treatment_AMs
Bio::Genex::USF_ExternalDBLink
Methods for processing data from the GeneX DB linking table: USF_ExternalDBLink
Bio::Genex::UserSec
Methods for processing data from the GeneX DB table: UserSec
Bio::Genex::UserSequenceFeature
Methods for processing data from the GeneX DB table: UserSequenceFeature

Provides

Bio::Genex::ALS_SpotType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AL_Coating
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AL_DefaultSpotConcUnits
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AL_IdentifierCode
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AL_Medium
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AL_TechnologyType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AM_EquationType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AM_SpotMeasurementUnits
in ControlledVocab/ControlledVocab.pm
Bio::Genex::AM_Type
in ControlledVocab/ControlledVocab.pm
Bio::Genex::ContactType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::EF_MajorCategory
in ControlledVocab/ControlledVocab.pm
Bio::Genex::EF_MinorCategory
in ControlledVocab/ControlledVocab.pm
Bio::Genex::ES_QuantitySeriesType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::ES_TreatmentType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::HS_ThresholdType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::PRT_Type
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SCN_ModelDescription
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_AgeUnits
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_DevelopmentStageName
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_DevelopmentStageUnits
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_GeneticStatus
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_OrganType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_OrganismIntactness
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_PrimaryCellType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_SexMatingType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SMP_TissueType
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SPC_CellStructure
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SPC_GeneralClassification
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SPT_ModelDescription
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SW_Name
in ControlledVocab/ControlledVocab.pm
Bio::Genex::SW_Type
in ControlledVocab/ControlledVocab.pm
Bio::Genex::USF_Type
in ControlledVocab/ControlledVocab.pm

Examples

Other files