Bio::Das::ProServer::SourceAdaptor::simpledb - Builds simple DAS features from a database


Bio-Das-ProServer documentation  | view source Contained in the Bio-Das-ProServer distribution.

Index


NAME

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Bio::Das::ProServer::SourceAdaptor::simpledb - Builds simple DAS features from a database

VERSION

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$LastChangedRevision: 524 $

SYNOPSIS

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  Build simple segment:start:stop features from a basic database table structure:

  segmentid,featureid,start,end,type,note,link

DESCRIPTION

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SUBROUTINES/METHODS

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capabilities

build_features - Return an array of features based on a query given in the config file

  my @aFeatures = $oSourceAdaptor->build_features({
                                                   segment => $sSegmentId,
                                                   start   => $iSegmentStart, # Optional
                                                   end     => $iSegmentEnd,   # Optional
                                                   dsn     => $sDSN,          # if used as part of a hydra
                                                  });
=head1 DIAGNOSTICS

CONFIGURATION AND ENVIRONMENT

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  [mysource]
  adaptor   = simpledb
  transport = dbi
  dbhost    = mysql.example.com
  dbport    = 3308
  dbname    = proserver
  dbuser    = proserverro
  dbpass    = topsecret
  dbtable   = mytable

  Or for SourceHydra use:
  [mysimplehydra]
  adaptor   = simpledb           # SourceAdaptor to clone
  hydra     = dbi                # Hydra implementation to use
  transport = dbi
  basename  = hydra              # dbi: basename for db tables containing servable data
  dbname    = proserver
  dbhost    = mysql.example.com
  dbuser    = proserverro
  dbpass    = topscret

DEPENDENCIES

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 Bio::Das::ProServer::SourceAdaptor

INCOMPATIBILITIES

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BUGS AND LIMITATIONS

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AUTHOR

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$Author: Roger M Pettett$

LICENSE AND COPYRIGHT

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Bio-Das-ProServer documentation  | view source Contained in the Bio-Das-ProServer distribution.