Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Class Reference

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
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

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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

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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

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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

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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

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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
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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet::new_fast | ( | ) |
Undocumented method

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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

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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

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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

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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

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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

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The documentation for this class was generated from the following file:
- Bio/EnsEMBL/Compara/MethodLinkSpeciesSet.pm