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

List of all members.


Class Summary

Description

 

Description

A subclass of Member which extends it to allow it to be aligned with other AlignedMember objects.
General enough to allow for global, local, pair-wise and multiple alignments.
At the moment used primarily in NestedSet Tree data-structure, but there are plans to extend its usage.
 

Definition at line 15 of file AlignedMember.pm.

Available Methods

protected _compose_sequence_exon_bounded ()
public adaptor ()
public String alignment_string ()
public String alignment_string_bounded ()
public Bio::Seq bioseq ()
public String cdna_alignment_string ()
public chr_end ()
public chr_name ()
public chr_start ()
public Boolean chr_strand ()
public Int cigar_end ()
public String cigar_line ()
public Int cigar_start ()
public
Bio::EnsEMBL::Compara::AlignedMember 
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 Int method_link_species_set_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 Int perc_cov ()
public Int perc_id ()
public Int perc_pos ()
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 ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member::adaptor ( ) [inherited]
  Arg [1]    : string $adaptor (optional)
               corresponding to a perl module
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public String Bio::EnsEMBL::Compara::AlignedMember::alignment_string ( )
  Arg [1]     : (optional) bool $exon_cased
  Example     : my $alignment_string = $object->alignment_string();
  Example     : my $alignment_string = $object->alignment_string(1);
  Description : Returns the aligned sequence for this object. For sequences
                split in exons, the $exon_cased flag permits to request
                that each exon is represented in alternative upper and lower
                case.
                For local alignments, when the alignment does not cover the
                whole protein, only the part of the sequence in the alignemnt
                is returned. Currently only global alignments are provided.
                Therefore the alignment_string always returns the whole aligned
                sequence.
  Returntype  : string
  Exceptions  : throws if the cigar_line is not defined for this object.
  Caller      : general
  Status      : Stable
 
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public String Bio::EnsEMBL::Compara::AlignedMember::alignment_string_bounded ( )
  Arg [1]     : none
  Example     : my $alignment_string_bounded = $object->alignment_string_bounded();
  Description : Returns the aligned sequence for this object with padding characters
                representing the introns.
  Returntype  : string
  Exceptions  : throws if the cigar_line is not defined for this object or if the
                cigar_start or cigar_end are defined.
  Caller      : general
  Status      : Stable
 
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public Bio::Seq Bio::EnsEMBL::Compara::Member::bioseq ( ) [inherited]
  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 String Bio::EnsEMBL::Compara::AlignedMember::cdna_alignment_string ( )
  Arg [1]    : none
  Example    : my $cdna_alignment = $aligned_member->cdna_alignment_string();
  Description: Converts the peptide alignment string to a cdna alignment
               string.  This only works for EnsEMBL peptides whose cdna can
               be retrieved from the attached core databse.
               If the cdna cannot be retrieved undef is returned and a
               warning is thrown.
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::chr_end ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::chr_name ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::chr_start ( ) [inherited]
 
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public Boolean Bio::EnsEMBL::Compara::Member::chr_strand ( ) [inherited]
  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 Int Bio::EnsEMBL::Compara::AlignedMember::cigar_end ( )
  Arg [1]     : (optional) $cigar_end
  Example     : $object->cigar_end($cigar_end);
  Example     : $cigar_end = $object->cigar_end();
  Description : Getter/setter for the cigar_end attribute. For non-global
                alignments, this represent the ending point of the local
                alignment.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using global alignments and the
                cigar_end is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public String Bio::EnsEMBL::Compara::AlignedMember::cigar_line ( )
  Arg [1]     : (optional) $cigar_line
  Example     : $object->cigar_line($cigar_line);
  Example     : $cigar_line = $object->cigar_line();
  Description : Getter/setter for the cigar_line attribute. The cigar line
                represents the modifications that are required to go from
                the original sequence to the aligned sequence. In particular,
                it shows the location of the gaps in the sequence. The cigar
                line is built with a series of numbers and characters where
                the number represents the number of positions in the mode
                defined by the next charcater. When the number is 1, it can be
                omitted. For example, the cigar line '23MD4M' means that there
                are 23 matches or mismatches, then 1 deletion (gap) and then
                another 4 matches or mismatches. The aligned sequence is
                obtained by inserting 1 gap at the right location.
  Returntype  : string
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::cigar_start ( )
  Arg [1]     : (optional) $cigar_start
  Example     : $object->cigar_start($cigar_start);
  Example     : $cigar_start = $object->cigar_start();
  Description : Getter/setter for the cigar_start attribute. For non-global
                alignments, this represent the starting point of the local
                alignment.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using global alignments and the
                cigar_start is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::AlignedMember Bio::EnsEMBL::Compara::AlignedMember::copy ( )
  Arg [1]     : none
  Example     : $copy = $aligned_member->copy();
  Description : Creates a new AlignedMember object from an existing one
  Returntype  : Bio::EnsEMBL::Compara::AlignedMember
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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Reimplemented from Bio::EnsEMBL::Compara::Member.

Reimplemented in Bio::EnsEMBL::Compara::GeneTreeMember.

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

Undocumented method

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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::gene_member ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::genome_db_id ( ) [inherited]
 
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public Array Bio::EnsEMBL::Compara::Member::get_all_peptide_Members ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Compara::Member::get_Gene ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  Arg [1]    : int $member_id (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::method_link_species_set_id ( )
  Arg [1]     : (optional) $method_link_species_set_id
  Example     : $object->method_link_species_set_id($method_link_species_set_id);
  Example     : $method_link_species_set_id = $object->method_link_species_set_id();
  Description : Getter/setter for the method_link_species_set_id attribute. Please,
                refer to the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet module
                for more information on the method_link_species_set_id.
  Returntype  : int
  Exceptions  : Returns 0 if the method_link_species_set_id is not defined.
  Caller      : general
  Status      : Stable
 
public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::new ( ) [inherited]
    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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 Int Bio::EnsEMBL::Compara::AlignedMember::perc_cov ( )
  Arg [1]     : (optional) $perc_cov
  Example     : $object->perc_cov($perc_cov);
  Example     : $perc_cov = $object->perc_cov();
  Description : Getter/setter for the perc_cov attribute. For non-global
                alignments, this represent the coverage of the alignment in
                percentage of the total length of the sequence.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using global alignments (the whole
                sequence is always included) and the perc_cov is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::perc_id ( )
  Arg [1]     : (optional) $perc_id
  Example     : $object->perc_id($perc_id);
  Example     : $perc_id = $object->perc_id();
  Description : Getter/setter for the perc_id attribute. This is generally
                used for pairwise relationships. The percentage identity
                reprensents the number of positions that are identical in
                the alignment in both sequences.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using multiple alignments and the
                perc_id is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::perc_pos ( )
  Arg [1]     : (optional) $perc_pos
  Example     : $object->perc_pos($perc_pos);
  Example     : $perc_pos = $object->perc_pos();
  Description : Getter/setter for the perc_pos attribute. This is generally
                used for pairwise relationships. The percentage positivity
                reprensents the number of positions that are positive in
                the alignment in both sequences. Currently, this is calculated
                for protein sequences using the BLOSUM62 scoring matrix.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using multiple alignments and the
                perc_cov is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public void Bio::EnsEMBL::Compara::Member::print_member ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member::sequence_exon_bounded ( ) [inherited]

Undocumented method

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public String Bio::EnsEMBL::Compara::Member::sequence_exon_cased ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::stable_id ( ) [inherited]
  Arg [1]    : string $stable_id (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::Member::taxon ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::taxon_id ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::transcript ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member::translation ( ) [inherited]

Undocumented method

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