Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Utils::Converter::bio_ens_hsp Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::Converter::bio_ens_hsp:

List of all members.


Class Summary

Definition at line 7 of file bio_ens_hsp.pm.

Available Methods

protected _bio_ens_seqFeature_converter ()
protected _convert_single ()
protected _convert_single_to_alignFeature ()
protected _convert_single_to_featurePair ()
protected _convert_single_to_proteinFeature ()
protected _guess_module ()
protected _initialize ()
protected _load_module ()
protected _rearrange ()
public L analysis ()
public analysis_dbID ()
public analysis_logic_name ()
public contig ()
public contig_dbID ()
public contig_name ()
public An convert ()
public L dbadaptor ()
public ensembl_db ()
public new ()
public slice_chr_start_end ()
public L slice_dbID ()
public stack_trace ()
public stack_trace_dump ()
public throw ()
public translation_id ()
public verbose ()
public warn ()

Method Documentation

protected Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::_bio_ens_seqFeature_converter ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::_convert_single ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Utils::Converter.

protected Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::_convert_single_to_alignFeature ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::_convert_single_to_featurePair ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::_convert_single_to_proteinFeature ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::Utils::Converter::bio_ens::_guess_module ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Utils::Converter.

protected Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::_initialize ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Utils::Converter::bio_ens.

protected Bio::EnsEMBL::Utils::Converter::_load_module ( ) [inherited]
  
  This method is copied from Bio::Root::Root
 
Code:
click to view
protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
Deprecated:
 
Code:
click to view
public L Bio::EnsEMBL::Utils::Converter::bio_ens::analysis ( ) [inherited]
  Title   : analysis
  Usage   : $self->analysis
  Function: get and set for analysis
  Return  : Bio::EnsEMBL::Analysis
  Args    : Bio::EnsEMBL::Analysis
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::analysis_dbID ( ) [inherited]
  Title   : analysis_dbID
  Usage   : 
  Function: 
  Return  :
  Args    :
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::analysis_logic_name ( ) [inherited]
  Title   : analysis_logic_name
  Usage   : 
  Function: 
  Return  :
  Args    :
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::contig ( ) [inherited]
  Title   : contig
  Usage   : $self->contig
  Function: get and set for contig
  Return  : 
  Args    :
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene.

public Bio::EnsEMBL::Utils::Converter::bio_ens::contig_dbID ( ) [inherited]
  Title   : contig_dbID
  Usage   : $self->contig_dbID
  Function: get and set for contig_dbID
  Return  : 
  Args    :
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::contig_name ( ) [inherited]
  Title   : contig_name
  Usage   : $self->contig_name
  Function: get and set for contig_name
  Return  : 
  Args    :    
 
Code:
click to view
public An Bio::EnsEMBL::Utils::Converter::convert ( ) [inherited]
    
    Title   : convert
    Usage   : my $array_ref = $converter->convert(\@input);
    Function: does the actual conversion
    Returns : an array ref of converted objects
    Args    : an array ref of converting objects
 
Code:
click to view
public L Bio::EnsEMBL::Utils::Converter::bio_ens::dbadaptor ( ) [inherited]
  Title   : dbadaptor
  Usage   : $self->dbadaptor
  Function: get and set for dbadaptor
  Return  : Bio::EnsEMBL::DBSQL::DBAdaptor
  Args    : Bio::EnsEMBL::DBSQL::DBAdaptor
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::ensembl_db ( ) [inherited]
  Title   : ensembl_db
  Usage   : 
  Function: 
  Return  :
  Args    :
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::new ( ) [inherited]
Please see Bio::EnsEMBL::Utils::Converter::new
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::Utils::Converter.

public Bio::EnsEMBL::Utils::Converter::bio_ens::slice_chr_start_end ( ) [inherited]
  Title   : slice_chr_start_end
  Usage   : my $slice = $self->slice_chr_start_end($chr, $start, $end);
  Function: get and set for slice_chr_start_end
  Return  : 
  Args    :    
 
Code:
click to view
public L Bio::EnsEMBL::Utils::Converter::bio_ens::slice_dbID ( ) [inherited]
  Title   : slice
  Usage   : $self->slice
  Function: get and set for slice
  Return  : Bio::EnsEMBL::Slice
  Args    : Bio::EnsEMBL::Slice   
 
Code:
click to view
public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
Deprecated:
 
Code:
click to view
public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
Deprecated:
 
Code:
click to view
public Bio::EnsEMBL::Root::throw ( ) [inherited]
Deprecated:
 
Code:
click to view
public Bio::EnsEMBL::Utils::Converter::bio_ens::translation_id ( ) [inherited]

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Root::verbose ( ) [inherited]
Deprecated:
 
Code:
click to view
public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
Code:
click to view

The documentation for this class was generated from the following file: