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  • Michele Clamp's avatar
    Moved core code to FeatureAdaptor and AnalysisAdaptor · 4167cfe7
    Michele Clamp authored
    tests will not work as I havent' changed the dumps yet.
    
    Changed the way genscans are stored and retrieved
    
    Clone
     - removed Feature_Obj and Gene_Obj use statements
    
    Exon
     - inherits from Bio::EnsEMBL::SeqFeature to use the extra gubbins
     - added temporary_id as for Transcript and Gene
    
    SeqFeature
     - debug
    
    Transcript
     - debug
    
    Translation
     - added temporary_id
    
    ContigI
     - removed string checking - takes *far too long for big contigs
    
    FeatureAdaptor
     - debug on inserts
    
    RawContig
     - removed Feature_Obj and Gene_Obj use statements - changed to AnalysisAdaptor and FeatureAdaptor
     - changed analysis to analysisprocess in several methods
     - removed Feature_Obj - changed to AnalysisAdaptor
     - changed the way genscans are fetched.
    
    Utils
     - added fset2transcript_3frame method
    
    StaticContig
     - changed analysis to analysisprocess
     - gets analysis by AnalysisAdaptor and not Feature_Obj
     - gets genscans differently
    4167cfe7