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Bio::EnsEMBL::Compara::Member Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Member:

List of all members.


Class Summary

Definition at line 9 of file Member.pm.

Available Methods

protected _compose_sequence_exon_bounded ()
public adaptor ()
public Bio::Seq bioseq ()
public chr_end ()
public chr_name ()
public chr_start ()
public Boolean chr_strand ()
public copy ()
public dbID ()
public String description ()
public display_label ()
public gene ()
public
Bio::EnsEMBL::Compara::Member 
gene_member ()
public Int gene_member_id ()
public genome_db ()
public genome_db_id ()
public Array get_all_peptide_Members ()
public
Bio::EnsEMBL::Compara::Member 
get_canonical_peptide_Member ()
public
Bio::EnsEMBL::Compara::Member 
get_canonical_transcript_Member ()
public get_exon_bounded_sequence ()
public Bio::EnsEMBL::Gene get_Gene ()
public Bio::EnsEMBL::Transcript get_Transcript ()
public Bio::EnsEMBL::Gene get_Translation ()
public member_id ()
public
Bio::EnsEMBL::Compara::Member 
new ()
public new_fast ()
public
Bio::Ensembl::Compara::Member 
new_from_gene ()
public
Bio::Ensembl::Compara::Member 
new_from_transcript ()
public void print_member ()
public Int seq_length ()
public String sequence ()
public sequence_cds ()
public sequence_exon_bounded ()
public String sequence_exon_cased ()
public Int sequence_id ()
public source_name ()
public stable_id ()
public taxon ()
public taxon_id ()
public transcript ()
public translation ()
public version ()

Method Documentation

protected Bio::EnsEMBL::Compara::Member::_compose_sequence_exon_bounded ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Member::adaptor ( )
  Arg [1]    : string $adaptor (optional)
               corresponding to a perl module
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Bio::Seq Bio::EnsEMBL::Compara::Member::bioseq ( )
  Args       : none
  Example    : my $primaryseq = $member->primaryseq;
  Description: returns sequence this member as a Bio::Seq object
  Returntype : Bio::Seq object
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::chr_end ( )
 
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public Bio::EnsEMBL::Compara::Member::chr_name ( )
 
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public Bio::EnsEMBL::Compara::Member::chr_start ( )
 
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public Boolean Bio::EnsEMBL::Compara::Member::chr_strand ( )
  Arg [1]    : integer
  Description: Returns the strand of the member.  Defined strands are 1 or -1.
               0 is undefined strand.
  Returntype : 1,0,-1
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::copy ( )
  Arg [1]    : object $parent_object (optional)
  Example    :
  Description: copies the object, optionally by topping up a given structure (to support multiple inheritance)
  Returntype :
  Exceptions :
  Caller     :
 
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Reimplemented in Bio::EnsEMBL::Compara::AlignedMember, and Bio::EnsEMBL::Compara::GeneTreeMember.

public Bio::EnsEMBL::Compara::Member::dbID ( )
  Arg [1]    : int $dbID (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public String Bio::EnsEMBL::Compara::Member::description ( )
  Arg [1]    : string $description (optional)
  Example    :
  Description:
  Returntype : string
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::Member::display_label ( )
  Arg [1]    : string $display_label (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::Member::gene ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::gene_member ( )
  Arg[1]     : Bio::EnsEMBL::Compara::Member $geneMember (optional)
  Example    : my $gene_member = $member->gene_member;
  Description: returns gene member object for this protein member
  Returntype : Bio::EnsEMBL::Compara::Member object
  Exceptions : if arg[0] is not a Bio::EnsEMBL::Compara::Member object
  Caller     : MemberAdaptor(set), general
 
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public Int Bio::EnsEMBL::Compara::Member::gene_member_id ( )
  Arg [1]    : int $gene_member_id
  Example    : my $gene_member_id = $member->gene_member_id;
  Description: Gene_member_id of this protein member
  Returntype : int
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::genome_db ( )
 
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public Bio::EnsEMBL::Compara::Member::genome_db_id ( )
 
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public Array Bio::EnsEMBL::Compara::Member::get_all_peptide_Members ( )
  Args       : none
  Example    : $pepMembers = $gene_member->get_all_peptide_Members
  Description: return listref of all peptide members of this gene_member
  Returntype : array ref of Bio::EnsEMBL::Compara::Member 
  Exceptions : throw if not an ENSEMBLGENE
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::get_canonical_peptide_Member ( )
  Args       : none
  Example    : $canonicalPepMember = $member->get_canonical_peptide_Member
  Description: if member is an "ENSEMBLGENE" it will return the canonical peptide member
               if member is an 'ENSEMBLPEP' it will get its gene member and have it
               return the canonical peptide (which could be the same as the starting member)
  Returntype : Bio::EnsEMBL::Compara::Member or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::get_canonical_transcript_Member ( )
  Args       : none
  Example    : $canonical_trans_member = $member->get_canonical_transcript_Member
  Description: if member is an "ENSEMBLGENE" it will return the canonical transcript member
               if member is an 'ENSEMBLTRANS' it will get its gene member and have it
               return the canonical transcript (which could be the same as the starting member).
               Note: This method is intended for ncRNA genes only. To access the canonical
               transcript for a protein-coding gene, please refer to the
               get_canonical_peptide_Member method
  Returntype : Bio::EnsEMBL::Compara::Member or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::get_exon_bounded_sequence ( )

Undocumented method

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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Compara::Member::get_Gene ( )
  Args       : none
  Example    : $gene = $member->get_Gene
  Description: if member is an 'ENSEMBLGENE' returns Bio::EnsEMBL::Gene object
               by connecting to ensembl genome core database
               REQUIRES properly setup Registry conf file or
               manually setting genome_db->db_adaptor for each genome.
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Compara::Member::get_Transcript ( )
  Args       : none
  Example    : $transcript = $member->get_Transcript
  Description: if member is an 'ENSEMBLPEP' returns Bio::EnsEMBL::Transcript object
               by connecting to ensembl genome core database
               REQUIRES properly setup Registry conf file or
               manually setting genome_db->db_adaptor for each genome.
  Returntype : Bio::EnsEMBL::Transcript or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Compara::Member::get_Translation ( )
  Args       : none
  Example    : $translation = $member->get_Translation
  Description: if member is an 'ENSEMBLPEP' returns Bio::EnsEMBL::Translation object
               by connecting to ensembl genome core database
               REQUIRES properly setup Registry conf file or
               manually setting genome_db->db_adaptor for each genome.
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::member_id ( )
  Arg [1]    : int $member_id (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::new ( )
    Arg [-DBID] : (opt) 
        : int $dbID (the database internal ID for this object)
    Arg [-ADAPTOR] 
        : Bio::EnsEMBL::Compara::DBSQL::Member $adaptor
                (the adaptor for connecting to the database)
    Arg [-DESCRIPTION] (opt) 
         : string $description
    Arg [-SOURCE_NAME] (opt) 
         : string $source_name 
         (e.g., "ENSEMBLGENE", "ENSEMBLPEP", "Uniprot/SWISSPROT", "Uniprot/SPTREMBL")
    Arg [-TAXON_ID] (opt)
         : int $taxon_id
         (NCBI taxonomy id for the member)
    Arg [-GENOME_DB_ID] (opt)
        : int $genome_db_id
        (the $genome_db->dbID for a species in the database)
    Arg [-SEQUENCE_ID] (opt)
        : int $sequence_id
        (the $sequence_id for the sequence table in the database)
    Example :
	my $member = new Bio::EnsEMBL::Compara::Member;
       Description: Creates a new Member object
       Returntype : Bio::EnsEMBL::Compara::Member
       Exceptions : none
       Caller     : general
       Status     : Stable
 
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public Bio::EnsEMBL::Compara::Member::new_fast ( )
  Arg [1]    : hash reference $hashref
  Example    : none
  Description: This is an ultra fast constructor which requires knowledge of
               the objects internals to be used.
  Returntype :
  Exceptions : none
  Caller     :
 
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public Bio::Ensembl::Compara::Member Bio::EnsEMBL::Compara::Member::new_from_gene ( )
  Args       : Requires both an Bio::Ensembl:Gene object and a
             : Bio::Ensembl:Compara:GenomeDB object
  Example    : $member = Bio::EnsEMBL::Compara::Member->new_from_gene(
                -gene   => $gene,
                -genome_db => $genome_db);
  Description: contructor method which takes an Ensembl::Gene object
               and Compara:GenomeDB object and creates a new Member object
               translating from the Gene object
  Returntype : Bio::Ensembl::Compara::Member
  Exceptions :
  Caller     :
 
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public Bio::Ensembl::Compara::Member Bio::EnsEMBL::Compara::Member::new_from_transcript ( )
  Arg[1]     : Bio::Ensembl:Transcript object
  Arg[2]     : Bio::Ensembl:Compara:GenomeDB object
  Arg[3]     : string where value='translate' causes transcript object to translate
               to a peptide
  Example    : $member = Bio::EnsEMBL::Compara::Member->new_from_transcript(
                  $transcript, $genome_db,
                -translate);
  Description: contructor method which takes an Ensembl::Gene object
               and Compara:GenomeDB object and creates a new Member object
               translating from the Gene object
  Returntype : Bio::Ensembl::Compara::Member
  Exceptions :
  Caller     :
 
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public void Bio::EnsEMBL::Compara::Member::print_member ( )
  Arg[1]     : string $postfix
  Example    : $member->print_member("BRH");
  Description: used for debugging, prints out key descriptive elements
               of member
  Returntype : none
  Exceptions : none
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::Member::seq_length ( )
  Example    : my $seq_length = $member->seq_length;
  Description: get the sequence length of this member
  Returntype : int
  Exceptions : none
  Caller     : general
 
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public String Bio::EnsEMBL::Compara::Member::sequence ( )
  Arg [1]    : string $sequence
  Example    : my $seq = $member->sequence;
  Description: Get/set the sequence string of this member
               Will lazy load by sequence_id if needed and able
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::sequence_cds ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Member::sequence_exon_bounded ( )

Undocumented method

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public String Bio::EnsEMBL::Compara::Member::sequence_exon_cased ( )
  Args       : none
  Example    : my $sequence_exon_cased = $member->sequence_exon_cased;
  Description: Get/set the sequence string of this peptide member with
               alternating upper and lower case corresponding to the translateable exons.
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::Member::sequence_id ( )
  Arg [1]    : int $sequence_id
  Example    : my $sequence_id = $member->sequence_id;
  Description: Extracts the sequence_id of this member
  Returntype : int
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::source_name ( )
 
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public Bio::EnsEMBL::Compara::Member::stable_id ( )
  Arg [1]    : string $stable_id (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::Member::taxon ( )
 
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public Bio::EnsEMBL::Compara::Member::taxon_id ( )
 
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public Bio::EnsEMBL::Compara::Member::transcript ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Member::translation ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Member::version ( )
  Arg [1]    :
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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The documentation for this class was generated from the following file: