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Bio::EnsEMBL::IdMapping::TinyGene Class Reference
Inheritance diagram for Bio::EnsEMBL::IdMapping::TinyGene:

List of all members.


Class Summary

Synopsis

 # fetch a gene from the db and create a lightweight gene object from it
  my $gene = $gene_adaptor-\>fetch_by_stable_id('ENSG000345437');
  my $lightweight_gene = Bio::EnsEMBL::IdMapping::TinyGene-\>new_fast( [
      $gene-\>dbID,                   $gene-\>stable_id,
      $gene-\>version,                $gene-\>created_date,
      $gene-\>modified_date,          $gene-\>start,
      $gene-\>end,                    $gene-\>strand,
      $gene-\>slice-\>seq_region_name, $gene-\>biotype,
      $gene-\>status,                 $gene-\>analysis-\>logic_name,
      ( $gene-\>is_known ? 1 : 0 ),
  ] );

Description

This is a lightweight gene object for the stable Id mapping. See the
documentation in TinyFeature for general considerations about its
design.
 

Definition at line 29 of file TinyGene.pm.

Available Methods

public void add_Transcript ()
public String biotype ()
public String created_date ()
public Int end ()
public Arrayref get_all_Transcripts ()
public Int id ()
public Boolean is_known ()
public Int length ()
public String logic_name ()
public String modified_date ()
public
Bio::EnsEMBL::IdMapping::TinyFeature 
new_fast ()
public String seq_region_name ()
public String stable_id ()
public Int start ()
public status ()
public Int strand ()
public String to_string ()
public Int version ()

Method Documentation

public void Bio::EnsEMBL::IdMapping::TinyGene::add_Transcript ( )
  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyTranscript $tr - the transcript to
                add
  Example     : $tiny_gene->add_Transcript($tiny_transcript);
  Description : Adds a transcript to a gene.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public String Bio::EnsEMBL::IdMapping::TinyGene::biotype ( )
  Arg[1]      : (optional) String - the gene's biotype
  Description : Getter/setter for the gene's biotype.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public String Bio::EnsEMBL::IdMapping::TinyFeature::created_date ( ) [inherited]
  Arg[1]      : (optional) String - the feature's stable Id creation date
  Description : Getter/setter for the feature's stable Id creation date.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
 
Code:
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public Int Bio::EnsEMBL::IdMapping::TinyGene::end ( )
  Arg[1]      : (optional) Int - the gene's end coordinate
  Description : Getter/setter for the gene's end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public Arrayref Bio::EnsEMBL::IdMapping::TinyGene::get_all_Transcripts ( )
  Example     : foreach my $tr (@{ $tiny_gene->get_all_Transcripts }) {
                  # do something with transcript
                }
  Description : Returns all transcripts attached to that gene.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyTranscript objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public Int Bio::EnsEMBL::IdMapping::TinyFeature::id ( ) [inherited]
  Arg[1]      : (optional) Int - the feature's internal Id ("dbID")
  Description : Getter/setter for the feature's internal Id.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
 
Code:
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public Boolean Bio::EnsEMBL::IdMapping::TinyGene::is_known ( )
  Arg[1]      : (optional) Boolean - the gene's "known" status
  Description : Getter/setter for the gene's "known" status.
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public Int Bio::EnsEMBL::IdMapping::TinyGene::length ( )
  Description : Returns the gene length (distance between start and end).
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public String Bio::EnsEMBL::IdMapping::TinyGene::logic_name ( )
  Arg[1]      : (optional) String - the gene's analysis' logic_name
  Description : Getter/setter for the gene's analysis' logic_name.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public String Bio::EnsEMBL::IdMapping::TinyFeature::modified_date ( ) [inherited]
  Arg[1]      : (optional) String - the feature's stable Id modification date
  Description : Getter/setter for the feature's stable Id modification date.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
 
Code:
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public Bio::EnsEMBL::IdMapping::TinyFeature Bio::EnsEMBL::IdMapping::TinyFeature::new_fast ( ) [inherited]
  Arg[1]      : Arrayref $array_ref - the arrayref to bless into the new object 
  Description : Constructor.
  Return type : Bio::EnsEMBL::IdMapping::TinyFeature implementing class
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
 
Code:
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public String Bio::EnsEMBL::IdMapping::TinyGene::seq_region_name ( )
  Arg[1]      : (optional) String - seq_region name
  Description : Getter/setter for the seq_region name of the slice the gene is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public String Bio::EnsEMBL::IdMapping::TinyFeature::stable_id ( ) [inherited]
  Arg[1]      : (optional) String - the feature's stable Id
  Description : Getter/setter for the feature's stable Id.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
 
Code:
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public Int Bio::EnsEMBL::IdMapping::TinyGene::start ( )
  Arg[1]      : (optional) Int - the gene's start coordinate
  Description : Getter/setter for the gene's start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public Bio::EnsEMBL::IdMapping::TinyGene::status ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::IdMapping::TinyGene::strand ( )
  Arg[1]      : (optional) Int - the gene's strand
  Description : Getter/setter for the gene's strand.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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  Arg[1]      : (optional) String - the gene's status
  Description : Getter/setter for the gene's status.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 

/**

public String Bio::EnsEMBL::IdMapping::TinyFeature::to_string ( ) [inherited]
  Example     : print LOG "Created ", $f->to_string, "\\n";
  Description : Prints a string representation of the feature for debug
                purposes.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public Int Bio::EnsEMBL::IdMapping::TinyFeature::version ( ) [inherited]
  Arg[1]      : (optional) Int - the feature's stable Id version
  Description : Getter/setter for the feature's stable Id version.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
 
Code:
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The documentation for this class was generated from the following file: