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  1. 15 Jul, 2013 1 commit
    • Alessandro Vullo's avatar
      Storable gets a new_fast implementation which transfers to all its descendants. · 29b0c52f
      Alessandro Vullo authored
      This means that CoordSystem, DensityType, Map::Marker, Map::Ditag, Map::Qtl,
      MiscSet, OntologyTerm and SeqRegionSynonym have now a fast constructor available.
      
      Accordingly, new_fast is removed from Analysis, Feature, DataFile, DBEntry, RepeatConsensus,
      Translation and UnmappedObject together with the import of weaken and isweak from
      Scalar::Util.
      29b0c52f
  2. 03 Apr, 2013 1 commit
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  15. 06 Oct, 2010 2 commits
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  20. 23 Aug, 2010 1 commit
    • Andreas Kusalananda Kähäri's avatar
      Add equals() method: · 4ccc1a4e
      Andreas Kusalananda Kähäri authored
        Arg [1]       : Bio::EnsEMBL::Exon exon
        Example       : if ($exonA->equals($exonB)) { ... }
        Description   : Compares two exons for equality.
                        The test for eqality goes through the following list
                        and terminates at the first true match:
      
                        1. If Bio::EnsEMBL::Feature::equals() returns false,
                           then the exons are *not* equal.
                        2. If both exons have stable IDs: if these are the
                           same, the exons are equal, otherwise not.
                        3. If the exons have the same start, end, strand, and
                           phase, then they are equal, otherwise not.
      
        Return type   : Boolean (0, 1)
      
        Exceptions    : Thrown if a non-transcript is passed as the argument.
      4ccc1a4e
  21. 16 Aug, 2010 1 commit
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  24. 06 Jul, 2010 1 commit
    • Andreas Kusalananda Kähäri's avatar
      New method load() for Exon, Gene, Transcript, and Translation. · a2456cf1
      Andreas Kusalananda Kähäri authored
      =head2 load
      
        Arg [1]       : Boolean $load_xrefs
                        Load (or don't load) xrefs.  Default is to load xrefs.
        Example       : $translation->load();
        Description   : The Ensembl API makes extensive use of
                        lazy-loading.  Under some circumstances (e.g.,
                        when copying genes between databases), all data of
                        an object needs to be fully loaded.  This method
                        loads the parts of the object that are usually
                        lazy-loaded.
        Returns       : Nothing.
      
      =cut
      a2456cf1
  25. 06 May, 2010 1 commit
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  36. 03 Apr, 2007 2 commits
    • Andreas Kusalananda Kähäri's avatar
      Fixed POD. · 5f89f8df
      Andreas Kusalananda Kähäri authored
      Fixed comment.
      5f89f8df
    • Andreas Kusalananda Kähäri's avatar
      Added new methods: · 6520767f
      Andreas Kusalananda Kähäri authored
          $exon->cdna_start($transcript);
              # Returns the start position of the exon in cDNA coordinates.
      
          $exon->cdna_end($transcript);
              # Returns the end position of the exon in cDNA coordinates.
      
      
          $exon->cdna_coding_start($transcript);
              # Returns the start position of the coding region of the exon
              # in cDNA coordinates.  Returns undef if the whole exon is
              # non-coding.
      
          $exon->cdna_coding_end($transcript);
              # Returns the end position of the coding region of the exon
              # in cDNA coordinates.  Returns undef if the whole exon is
              # non-coding.
      
      
          $exon->coding_region_start($transcript);
              # Returns the start position of the coding region of the exon in
              # genomic coordinates on the forward strand.  Returns undef if
              # the whole exon is non-coding.
      
          $exon->coding_region_end($transcript);
              # Returns the end position of the coding region of the exon in
              # genomic coordinates on the forward strand.  Returns undef if
              # the whole exon is non-coding.
      
      
      Since an exon may be part of one or more transcripts, the relevant
      transcript must be given as argument ot these methods.
      6520767f
  37. 12 Mar, 2007 1 commit