++ed by:
1 non-PAUSE user
Author image Jason E. Stewart

Changes for version 2.6.0

  • 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

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

Modules

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

Provides

in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm
in ControlledVocab/ControlledVocab.pm