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Bio::EnsEMBL::SNP Class Reference

List of all members.


Class Summary

Synopsis

    $snp = new Bio::EnsEMBL::SNP(
      -start   =\> 10,
      -end     =\> 10,
      -strand  =\> 1,
      -source  =\> 'The SNP Consortium',
      -score   =\> 99,                     # new meaning
      -status  =\> 'suspected',            # new
      -alleles =\> 't|c'                   # new
    );

   # add it to an annotated sequence

  $annseq-\>add_SeqFeature($feat);

Description

This class was written because the EnsEMBL::ExternalData::Variation
object is way too slow.  There was simply too much chaining to bioperl
methods many, many layers deep.  This object behaves like a Variation
but has a much faster constructor, and faster accessors for the relevant
methods needed by the web.
 

Definition at line 32 of file SNP.pm.

Available Methods

public dbID ()
public String display_name ()
public end ()
public new_fast ()
public position ()
public score ()
public source ()
public source_tag ()
public source_version ()
public start ()

Method Documentation

public Bio::EnsEMBL::SNP::dbID ( )

Undocumented method

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public String Bio::EnsEMBL::SNP::display_name ( )
  Arg [1]    : none
  Example    : print $snp->display_name();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  For snps this is the
               returns the same thing as the id method.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
 
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public Bio::EnsEMBL::SNP::end ( )

Undocumented method

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public Bio::EnsEMBL::SNP::new_fast ( )

Undocumented method

Code:
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public Bio::EnsEMBL::SNP::position ( )

Undocumented method

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public Bio::EnsEMBL::SNP::score ( )

Undocumented method

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public Bio::EnsEMBL::SNP::source ( )

Undocumented method

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public Bio::EnsEMBL::SNP::source_tag ( )

Undocumented method

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public Bio::EnsEMBL::SNP::source_version ( )

Undocumented method

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public Bio::EnsEMBL::SNP::start ( )

Undocumented method

Code:
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The documentation for this class was generated from the following file: