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

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::MethodLinkSpeciesSet;
  my $method_link_species_set = new Bio::EnsEMBL::Compara::MethodLinkSpeciesSet(
                       -adaptor =\> $method_link_species_set_adaptor,
                       -method_link_type =\> "MULTIZ",
                       -species_set =\> [$gdb1, $gdb2, $gdb3],
                       -max_alignment_length =\> 10000,
                   );

SET VALUES
  $method_link_species_set-\>dbID(12);
  $method_link_species_set-\>adaptor($meth_lnk_spcs_adaptor);
  $method_link_species_set-\>method_link_id(23);
  $method_link_species_set-\>method_link_type("MULTIZ");
  $method_link_species_set-\>species_set([$gdb1, $gdb2, $gdb3]);
  $method_link_species_set-\>max_alignment_length(10000);

GET VALUES
  my $dbID = $method_link_species_set-\>dbID();
  my $meth_lnk_spcs_adaptor = $method_link_species_set-\>adaptor();
  my $meth_lnk_id = $method_link_species_set-\>method_link_id();
  my $meth_lnk_type = $method_link_species_set-\>method_link_type();
  my $meth_lnk_species_set = $method_link_species_set-\>species_set();
  my $max_alignment_length = $method_link_species_set-\>max_alignment_length();

Definition at line 35 of file MethodLinkSpeciesSet.pm.

Available Methods

protected void _load_tags ()
public
Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor 
adaptor ()
public Boolean add_tag ()
public void AUTOLOAD ()
public Int dbID ()
public delete_tag ()
public Array get_all_tags ()
public ArrayRef get_all_values_for_tag ()
public Array get_common_classification ()
public Scalar get_tagvalue ()
public Hashref get_tagvalue_hash ()
public Scalar get_value_for_tag ()
public Boolean has_tag ()
public Int max_alignment_length ()
public String method_link_class ()
public Int method_link_id ()
public String method_link_type ()
public String name ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
new ()
public new_fast ()
public String source ()
public Listref species_set ()
public Int species_set_id ()
public store_tag ()
public String url ()

Method Documentation

protected void Bio::EnsEMBL::Compara::Taggable::_load_tags ( ) [inherited]
  Description: loads all the tags (from the database) if possible.
               Otherwise, an empty hash is created
  Example    : $ns_node->_load_tags();
  Returntype : none
  Exceptions : none
  Caller     : internal
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::adaptor ( )
  Arg [1]    : (opt.) Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor
  Example    : my $meth_lnk_spcs_adaptor = $method_link_species_set->adaptor();
  Example    : $method_link_species_set->adaptor($meth_lnk_spcs_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor
  Exceptions : none
  Caller     : general
 
Code:
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public Boolean Bio::EnsEMBL::Compara::Taggable::add_tag ( ) [inherited]
  Description: adds metadata tags to a node.  Both tag and value are added
               as metdata with the added ability to retreive the value given
               the tag (like a perl hash). In case of one to many relation i.e.
               one tag and different values associated with it, the values are
               returned in a array reference.
  Arg [1]    : <string> tag
  Arg [2]    : <string> value
  Arg [3]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $ns_node->add_tag('scientific name', 'Mammalia');
               $ns_node->add_tag('lost_taxon_id', 9593, 1);
  Returntype : Boolean indicating if the tag could be added
  Exceptions : none
  Caller     : general
 
Code:
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public void Bio::EnsEMBL::Compara::Taggable::AUTOLOAD ( ) [inherited]
  Description: matches the get_value_for_XXX calls to get_value_for_tag('XXX') and other calls
  Returntype : none
  Exceptions : none
  Caller     : system
 
Code:
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public Int Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::dbID ( )
  Arg [1]    : (opt.) integer dbID
  Example    : my $dbID = $method_link_species_set->dbID();
  Example    : $method_link_species_set->dbID(12);
  Description: Getter/Setter for the dbID of this object in the database
  Returntype : integer dbID
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::Taggable::delete_tag ( ) [inherited]
  Description: removes a tag from the metadata. If the value is provided, it tries
               to delete only it (if present). Otherwise, it just clears the tag,
               whatever value it was containing
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <string> value
  Example    : $ns_node->remove_tag('scientific name', 'Mammalia');
               $ns_node->remove_tag('lost_taxon_id', 9593);
  Returntype : 0 if the tag couldn't be removed,
               1 if it is only in the PERL object,
               2 if it is also stored in the database
  Exceptions : none
  Caller     : general
 
Code:
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public Array Bio::EnsEMBL::Compara::Taggable::get_all_tags ( ) [inherited]
  Description: returns an array of all the available tags
  Example    : $ns_node->get_all_tags();
  Returntype : Array
  Exceptions : none
  Caller     : general
 
Code:
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public ArrayRef Bio::EnsEMBL::Compara::Taggable::get_all_values_for_tag ( ) [inherited]
  Description: returns all the values of the tag, or $default (undef
               if not provided) if the tag doesn't exist. In case of
               a single value, it is wrapped with an array
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : ArrayRef
  Exceptions : none
  Caller     : general
 
Code:
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public Array Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::get_common_classification ( )
  Arg [1]    : -none-
  Example    : my $common_classification = $method_link_species_set->
                   get_common_classification();
  Description: This method fetches the taxonimic classifications for all the
               species included in this
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object and
               returns the common part of them.
  Returntype : array of strings
  Exceptions : 
  Caller     : general
 
Code:
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public Scalar Bio::EnsEMBL::Compara::Taggable::get_tagvalue ( ) [inherited]
  Description: returns the value(s) of the tag, or $default (undef
               if not provided) if the tag doesn't exist.
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : Scalar or ArrayRef
  Exceptions : none
  Caller     : general
 
Code:
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public Hashref Bio::EnsEMBL::Compara::Taggable::get_tagvalue_hash ( ) [inherited]
  Description: returns the underlying hash that contains all
               the tags
  Example    : $ns_node->get_tagvalue_hash();
  Returntype : Hashref
  Exceptions : none
  Caller     : general
 
Code:
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public Scalar Bio::EnsEMBL::Compara::Taggable::get_value_for_tag ( ) [inherited]
  Description: returns the value of the tag, or $default (undef
               if not provided) if the tag doesn't exist. In case
               of multiple values, the first one is returned.
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : Scalar
  Exceptions : none
  Caller     : general
 
Code:
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public Boolean Bio::EnsEMBL::Compara::Taggable::has_tag ( ) [inherited]
  Description: indicates whether the tag exists in the metadata
  Arg [1]    : <string> tag
  Example    : $ns_node->has_tag('scientific name');
  Returntype : Boolean
  Exceptions : none
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::max_alignment_length ( )
 
  Arg [1]    : (opt.) int $max_alignment_length
  Example    : my $max_alignment_length = $method_link_species_set->
                   max_alignment_length();
  Example    : $method_link_species_set->max_alignment_length(1000);
  Description: get/set for attribute max_alignment_length
  Returntype : integer
  Exceptions : 
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::method_link_class ( )
 
  Arg [1]    : (opt.) string method_link_class
  Example    : my $meth_lnk_class = $method_link_species_set->method_link_class();
  Example    : $method_link_species_set->method_link_class("GenomicAlignBlock.multiple_alignment");
  Description: get/set for attribute method_link_class
  Returntype : string
  Exceptions : none
  Caller     : general
 
public Int Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::method_link_id ( )
 
  Arg [1]    : (opt.) integer method_link_id
  Example    : my $meth_lnk_id = $method_link_species_set->method_link_id();
  Example    : $method_link_species_set->method_link_id(23);
  Description: get/set for attribute method_link_id
  Returntype : integer
  Exceptions : none
  Caller     : general
 
public String Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::method_link_type ( )
 
  Arg [1]    : (opt.) string method_link_type
  Example    : my $meth_lnk_type = $method_link_species_set->method_link_type();
  Example    : $method_link_species_set->method_link_type("BLASTZ_NET");
  Description: get/set for attribute method_link_type
  Returntype : string
  Exceptions : none
  Caller     : general
 
public String Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::name ( )
  Arg [1]    : (opt.) string $name
  Example    : my $name = $method_link_species_set->name();
  Example    : $method_link_species_set->name("families");
  Description: get/set for attribute name
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::new ( )
  Arg [-DBID] : (opt.) int $dbID (the database internal ID for this object)
  Arg [-ADAPTOR]
              : (opt.) Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor $adaptor
                (the adaptor for connecting to the database)
  Arg [-METHOD_LINK_ID]
              : (opt.) int $method_link_id (the database internal ID for the method_link)
  Arg [-METHOD_LINK_TYPE]
              : (opt.) string $method_link_type (the name of the method_link)
  Arg [-METHOD_LINK_CLASS]
              : (opt.) string $method_link_class (the class of the method_link)
  Arg [-SPECIES_SET_ID]
              : (opt.) int $species_set_id (the database internal ID for the species_set)
  Arg [-SPECIES_SET]
              : (opt.) arrayref $genome_dbs (a reference to an array of
                Bio::EnsEMBL::Compara::GenomeDB objects)
  Arg [-NAME]
              : (opt.) string $name (the name for this method_link_species_set)
  Arg [-SOURCE]
              : (opt.) string $source (the source of these data)
  Arg [-URL]
              : (opt.) string $url (the original url of these data)
  Arg [-MAX_ALGINMENT_LENGTH]
              : (opt.) int $max_alignment_length (the length of the largest alignment
                for this MethodLinkSpeciesSet (only used for genomic alignments)
  Example     : my $method_link_species_set =
                   new Bio::EnsEMBL::Compara::MethodLinkSpeciesSet(
                       -adaptor => $method_link_species_set_adaptor,
                       -method_link_type => "MULTIZ",
                       -species_set => [$gdb1, $gdb2, $gdb3],
                       -max_alignment_length => 10000,
                   );
  Description : Creates a new MethodLinkSpeciesSet object
  Returntype  : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions  : none
  Caller      : general
 
Code:
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public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::new_fast ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::source ( )
  Arg [1]    : (opt.) string $name
  Example    : my $name = $method_link_species_set->source();
  Example    : $method_link_species_set->source("ensembl");
  Description: get/set for attribute source. The source refers to who
               generated the data in a first instance (ensembl, ucsc...)
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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public Listref Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::species_set ( )
 
  Arg [1]    : (opt.) listref of Bio::EnsEMBL::Compara::GenomeDB objects
  Example    : my $meth_lnk_species_set = $method_link_species_set->species_set();
  Example    : $method_link_species_set->species_set([$gdb1, $gdb2, $gdb3]);
  Description: get/set for attribute species_set
  Returntype : listref of Bio::EnsEMBL::Compara::GenomeDB objects
  Exceptions : Thrown if any argument is not a Bio::EnsEMBL::Compara::GenomeDB
               object or a GenomeDB entry appears several times
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::species_set_id ( )
  Arg [1]    : (opt.) integer species_set_id
  Example    : my $species_set_id = $method_link_species_set->species_set_id();
  Example    : $method_link_species_set->species_set_id(23);
  Description: get/set for attribute species_set_id
  Returntype : integer
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::Taggable::store_tag ( ) [inherited]
  Description: calls add_tag and then stores the tag in the database. Has the
               exact same arguments as add_tag
  Arg [1]    : <string> tag
  Arg [2]    : <string> value
  Arg [3]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $ns_node->store_tag('scientific name', 'Mammalia');
               $ns_node->store_tag('lost_taxon_id', 9593, 1);
  Returntype : 0 if the tag couldn't be stored,
               1 if it is only in the PERL object,
               2 if it is also stored in the database
  Exceptions : none
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::url ( )
  Arg [1]    : (opt.) string $url
  Example    : my $name = $method_link_species_set->source();
  Example    : $method_link_species_set->url("http://hgdownload.cse.ucsc.edu/goldenPath/monDom1/vsHg17/");
  Description: get/set for attribute url. Defines where the data come from if they
               have been imported
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: