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Bio::EnsEMBL::Compara::Production::DnaFragChunkSet Class Reference

List of all members.


Class Summary

Synopsis

Description

An object to hold a set or group of DnaFragChunk objects.  Used in production to reduce
overhead of feeding sequences into alignment programs like blastz and exonerate.
 

Definition at line 19 of file DnaFragChunkSet.pm.

Available Methods

public adaptor ()
public add_dnafrag_chunk_id ()
public add_DnaFragChunk ()
public Int count ()
public dbID ()
public String description ()
public Reference dnafrag_chunk_ids ()
public String dump_loc ()
public Reference get_all_DnaFragChunks ()
public new ()
public Int total_basepairs ()

Method Documentation

public Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::adaptor ( )
 Title   : adaptor
 Usage   :
 Function: getter/setter of the adaptor for this object
 Example :
 Returns :
 Args    :
 
Code:
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public Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::add_dnafrag_chunk_id ( )
  Arg [1]    : $chunk_id
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::add_DnaFragChunk ( )

Undocumented method

Code:
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public Int Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::count ( )
  Example    : $count = $chunkSet->count;
  Description: returns count of DnaFragChunks in this set
  Returntype : int
  Exceptions :
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::dbID ( )
  Arg [1]    : int $dbID (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
Code:
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public String Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::description ( )
  Arg [1]    : string $description (optional)
  Example    :
  Description:
  Returntype : string
  Exceptions :
  Caller     :
 
Code:
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public Reference Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::dnafrag_chunk_ids ( )
  Example    : @chunk_ids = @{$chunkSet->dnafrag_chunk_ids};
  Description:
  Returntype : reference to array of dnafrag_chunk_id
  Exceptions :
  Caller     :
 
Code:
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public String Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::dump_loc ( )
  Arg [1]    : string $dump_loc (optional)
  Example    :
  Description:
  Returntype : string
  Exceptions :
  Caller     :
 
Code:
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public Reference Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::get_all_DnaFragChunks ( )
  Example    : @chunks = @{$chunkSet->get_all_DnaFragChunks};
  Description: returns array reference to all the DnaFragChunk objects in this set
               will lazy load the set if it was not previously loaded
  Returntype : reference to array of Bio::EnsEMBL::Compara::Production::DnaFragChunk objects
  Exceptions :
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::new ( )

Undocumented method

Code:
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public Int Bio::EnsEMBL::Compara::Production::DnaFragChunkSet::total_basepairs ( )
  Example    : $size = $chunkSet->total_basepairs;
  Description: returns summed length of all DnaFragChunks in this set
  Returntype : int
  Exceptions :
  Caller     :
 
Code:
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The documentation for this class was generated from the following file: