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Bio::EnsEMBL::Compara::Production::DnaFragChunk Class Reference

List of all members.


Class Summary

Synopsis

Description

 

Definition at line 16 of file DnaFragChunk.pm.

Available Methods

public adaptor ()
public Bio::Seq bioseq ()
public cache_sequence ()
public dbID ()
public String display_id ()
public dnafrag ()
public dnafrag_id ()
public dump_chunks_to_fasta_file ()
public dump_to_fasta_file ()
public Bio::Seq fetch_masked_sequence ()
public length ()
public masking_options ()
public masking_tag_name ()
public method_link_species_set_id ()
public new ()
public seq_end ()
public seq_start ()
public sequence ()
public sequence_id ()
public Bio::EnsEMBL::Slice slice ()

Method Documentation

public Bio::EnsEMBL::Compara::Production::DnaFragChunk::adaptor ( )

Undocumented method

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public Bio::Seq Bio::EnsEMBL::Compara::Production::DnaFragChunk::bioseq ( )
  Description: returns sequence of this chunk as a Bio::Seq object
               will fetch from core if not previously cached in compara
  Args       : none
  Example    : my $bioseq = $chunk->bioseq;
  Returntype : Bio::Seq object
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::cache_sequence ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::dbID ( )

Undocumented method

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public String Bio::EnsEMBL::Compara::Production::DnaFragChunk::display_id ( )
  Args       : none
  Example    : my $id = $chunk->display_id;
  Description: returns string describing this chunk which can be used
               as display_id of a Bio::Seq object or in a fasta file.
               Uses dnafrag information in addition to start and end.  
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::dnafrag ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::dnafrag_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::dump_chunks_to_fasta_file ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::dump_to_fasta_file ( )

Undocumented method

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public Bio::Seq Bio::EnsEMBL::Compara::Production::DnaFragChunk::fetch_masked_sequence ( )
  Description: Meta method which uses the slice associated with this chunk
               and from the external core database associated with the slice
               it extracts the masked DNA sequence.
               Returns as Bio::Seq object.  does not cache sequence internally
  Arg [1]    : (int or string) masked status of the sequence [optional]
                0 or ''     = unmasked (default)
                1 or 'hard' = masked
                2 or 'soft' = soft-masked
  Arg[2]     : (ref to hash) hash of masking options [optional]
  Example    : $bioseq = $chunk->get_sequence(1);
  Returntype : Bio::Seq or undef if a problem
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::length ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::masking_options ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::masking_tag_name ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::method_link_species_set_id ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::DnaFragChunk::new ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::seq_end ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::seq_start ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::sequence ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::DnaFragChunk::sequence_id ( )

Undocumented method

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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::Production::DnaFragChunk::slice ( )
  Arg        : none
  Example    : $slice = $chunk->slice;
  Description: Meta method which uses the dnafrag of this chunk to get the genomeDB
               to connect to corresponding core database, and then to uses the core
               SliceAdaptor to get a slice associated with the dnafrag type and name and
               the this chunks start,end.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : none
  Caller     : general, self->fetch_masked_sequence()
 
Code:
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The documentation for this class was generated from the following file: