This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated .
  1. 27 Aug, 2010 10 commits
  2. 26 Aug, 2010 11 commits
  3. 25 Aug, 2010 7 commits
  4. 24 Aug, 2010 4 commits
  5. 23 Aug, 2010 5 commits
    • Andreas Kusalananda Kähäri's avatar
    • Andreas Kusalananda Kähäri's avatar
      Add method equals(): · eb84e13d
      Andreas Kusalananda Kähäri authored
        Arg [1]       : Bio::EnsEMBL::Gene gene
        Example       : if ($geneA->equals($geneB)) { ... }
        Description   : Compares two genes 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 genes are *not* equal.
                        2. If the biotypes differ, then the genes are *not*
                           equal.
                        3. If both genes have stable IDs: if these are the
                           same, the genes are equal, otherwise not.
                        4. If both genes have the same number of transcripts
                           and if these are (when compared pair-wise sorted by
                           start-position and length) the same, then they are
                           equal, otherwise not.
      
        Return type   : Boolean (0, 1)
      
        Exceptions    : Thrown if a non-gene is passed as the argument.
      eb84e13d
    • Andreas Kusalananda Kähäri's avatar
      Add equals() method: · 1a3cc1b6
      Andreas Kusalananda Kähäri authored
        Arg [1]       : Bio::EnsEMBL::Transcript transcript
        Example       : if ($transcriptA->equals($transcriptB)) { ... }
        Description   : Compares two transcripts 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 transcripts are *not* equal.
                        2. If the biotypes differ, then the transcripts are
                           *not* equal.
                        3. If both transcripts have stable IDs: if these are
                           the same, the transcripts are equal, otherwise not.
                        4. If both transcripts have the same number of exons
                           and if these are (when compared pair-wise sorted by
                           start-position and length) the same, then they are
                           equal, otherwise not.
      
        Return type   : Boolean (0, 1)
      
        Exceptions    : Thrown if a non-transcript is passed as the argument.
      1a3cc1b6
    • 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
    • Andreas Kusalananda Kähäri's avatar
      New method for features: equals() · 3848b396
      Andreas Kusalananda Kähäri authored
      Arg [1]       : Bio::EnsEMBL::Feature object
      Example       : if ($featureA->equals($featureB)) { ... }
      Description   : Compares two features using various criteria.  The
                      test for eqality goes through the following list and
                      terminates at the first true match:
      
                     1. If the two features are the same object, they are
                        equal.
      
                     2. If they are of different types (e.g., transcript and
                        gene), they are *not* equal.
      
                     3. If they both have dbIDs: if these are equal, then they
                        are equal otherwise not.
      
                     4. If they have slices and analysis objects: if analysis
                        dbIDs are the same and the seq_region_id are the same,
                        along with seq_region_start and seq_region_end, then
                        they are equal, otherwise not.
      
                     If none of the above is able to determine equality,
                     undef is returned.
      
      Return type : tri-Boolean (0, 1, undef = "unknown")
      
      Exceptions  : Thrown if a non-feature is passed as the argument.
      3848b396
  6. 20 Aug, 2010 3 commits