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Bio::EnsEMBL::Compara::GenomicAlignGroup Class Reference

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::GenomicAlignGroup;
  
  my $genomic_align_group = new Bio::EnsEMBL::Compara::GenomicAlignGroup (
          -adaptor =\> $genomic_align_group_adaptor,
          -genomic_align_array =\> [$genomic_align1, $genomic_align2...]
      );

SET VALUES
  $genomic_align_group-\>adaptor($gen_ali_group_adaptor);
  $genomic_align_group-\>dbID(12);
  $genomic_align_group-\>genomic_align_array([$genomic_align1, $genomic_align2]);

GET VALUES
  my $genomic_align_group_adaptor = $genomic_align_group-\>adaptor();
  my $dbID = $genomic_align_group-\>dbID();
  my $genomic_aligns = $genomic_align_group-\>genomic_align_array();

Description

The GenomicAlignGroup object defines groups of alignments.
 

Definition at line 33 of file GenomicAlignGroup.pm.

Available Methods

public
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor 
adaptor ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
add_GenomicAlign ()
public String aligned_sequence ()
public
Bio::EnsEMBL::Compara::GenomicAlignGroup 
copy ()
public Int dbID ()
public
Bio::EnsEMBL::Compara::DnaFrag 
dnafrag ()
public Int dnafrag_end ()
public Int dnafrag_start ()
public Int dnafrag_strand ()
public
Bio::EnsEMBL::Compara::GenomeDB 
genome_db ()
public Array genomic_align_array ()
public Array get_all_GenomicAligns ()
public
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroup 
new ()
public new_fast ()

Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor Bio::EnsEMBL::Compara::GenomicAlignGroup::adaptor ( )
  Arg [1]    : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor $adaptor
  Example    : my $gen_ali_grp_adaptor = $genomic_align_block->adaptor();
  Example    : $genomic_align_block->adaptor($gen_ali_grp_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor object
  Exceptions : thrown if $adaptor is not a
               Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor object
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignGroup::add_GenomicAlign ( )
  Arg [1]    : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Example    : $genomic_align_block->add_GenomicAlign($genomic_align);
  Description: adds another Bio::EnsEMBL::Compara::GenomicAlign object to the set of
               Bio::EnsEMBL::Compara::GenomicAlign objects in the attribute
               genomic_align_array.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : thrown if wrong argument
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::Compara::GenomicAlignGroup::aligned_sequence ( )
  Arg [1]     : -none-
  Example     : $aligned_sequence = $object->aligned_sequence();
  Description : Get the aligned sequence for this group. When the group
                contains one single sequence, returns its aligned sequence.
                For composite segments, returns the combined aligned seq.
  Returntype  : string
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::GenomicAlignGroup::copy ( )
  Arg         : none
  Example     : my $new_gag = $gag->copy()
  Description : Create a copy of this Bio::EnsEMBL::Compara::GenomicAlignGroup
                object
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignGroup::dbID ( )
  Arg [1]    : integer $dbID
  Example    : my $dbID = $genomic_align_group->dbID();
  Example    : $genomic_align_group->dbID(12);
  Description: Getter/Setter for the attribute dbID
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DnaFrag Bio::EnsEMBL::Compara::GenomicAlignGroup::dnafrag ( )
  Arg [1]     : -none-
  Example     : $dnafrag = $object->dnafrag();
  Description : Get the dnafrag object from the underlying GenomicAlign objects
  Returntype  : Bio::EnsEMBL::Compara::DnaFrag
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignGroup::dnafrag_end ( )
  Arg [1]     : -none-
  Example     : $dnafrag_end = $object->dnafrag_end();
  Description : Get the dnafrag_end value from the underlying GenomicAlign objects
  Returntype  : int
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignGroup::dnafrag_start ( )
  Arg [1]     : -none-
  Example     : $dnafrag_start = $object->dnafrag_start();
  Description : Get the dnafrag_start value from the underlying GenomicAlign objects
  Returntype  : int
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignGroup::dnafrag_strand ( )
  Arg [1]     : -none-
  Example     : $dnafrag_strand = $object->dnafrag_strand();
  Description : Get the dnafrag_strand value from the underlying GenomicAlign objects
  Returntype  : int
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Bio::EnsEMBL::Compara::GenomeDB Bio::EnsEMBL::Compara::GenomicAlignGroup::genome_db ( )
  Arg [1]     : -none-
  Example     : $genome_db = $object->genome_db();
  Description : Get the genome_db object from the underlying GenomicAlign objects
  Returntype  : Bio::EnsEMBL::Compara::GenomeDB
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Array Bio::EnsEMBL::Compara::GenomicAlignGroup::genomic_align_array ( )
  Arg [1]    : array reference containing Bio::EnsEMBL::Compara::GenomicAlign objects
  Example    : $genomic_aligns = $genomic_align_group->genomic_align_array();
               $genomic_align_group->genomic_align_array([$genomic_align1, $genomic_align2]);
  Description: get/set for attribute genomic_align_array
  Returntype : array reference containing Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Array Bio::EnsEMBL::Compara::GenomicAlignGroup::get_all_GenomicAligns ( )
  Arg [1]    : none
  Example    : $genomic_aligns = $genomic_align_block->get_all_GenomicAligns();
  Description: returns the set of Bio::EnsEMBL::Compara::GenomicAlign objects in
               the attribute genomic_align_array.
  Returntype : array reference containing Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroup Bio::EnsEMBL::Compara::GenomicAlignGroup::new ( )
  Arg [-DBID] : (opt.) int $dbID (the database internal ID for this object)
  Arg [-ADAPTOR]
              : (opt.) Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor $adaptor
                (the adaptor for connecting to the database)
  Arg [-GENOMIC_ALIGN_ARRAY]
              : (opt.) array_ref $genomic_aligns (a reference to the array of
                Bio::EnsEMBL::Compara::GenomicAlign objects corresponding to this
                Bio::EnsEMBL::Compara::GenomicAlignGroup object)
  Example    : my $genomic_align_group =
                   new Bio::EnsEMBL::Compara::GenomicAlignGroup(
                       -adaptor => $genomic_align_group_adaptor,
                       -genomic_align_array => [$genomic_align1, $genomic_align2...]
                   );
  Description: Creates a new GenomicAligngroup object
  Returntype : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroup
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignGroup::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     :
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: