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Bio::EnsEMBL::Compara::AlignSlice::Exon Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::AlignSlice::Exon:

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::AlignSlice::Exon;
  
  my $exon = new Bio::EnsEMBL::Compara::AlignSlice::Exon(
      );

SET VALUES

GET VALUES

Definition at line 21 of file Exon.pm.

Available Methods

protected _deprecated_transform ()
protected String _get_aligned_sequence_from_original_sequence_and_cigar_line ()
protected _get_stable_entry_info ()
protected
Bio::EnsEMBL::Mapper::Coordinate 
_merge_ajoining_coords ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public add_sub_SeqFeature ()
public void add_supporting_features ()
public Bio::EnsEMBL::Exon adjust_start_end ()
public Bio::EnsEMBL::Analysis analysis ()
public append_Exon ()
public Int cdna_coding_end ()
public Int cdna_coding_start ()
public Int cdna_end ()
public Int cdna_start ()
public String cigar_line ()
public Int coding_region_end ()
public Int coding_region_start ()
public contig ()
public String coord_system_name ()
public
Bio::EnsEMBL::Compara::AlignSlice::Exon 
copy ()
public created ()
public String created_date ()
public Int dbID ()
public String display_id ()
public Int end ()
public Int end_phase ()
public Boolean equals ()
public Bio::EnsEMBL::Exon exon ()
public Bio::EnsEMBL::Slice feature_Slice ()
public void find_supporting_evidence ()
public flush_sub_SeqFeature ()
public flush_supporting_features ()
public Int frame ()
public get_aligned_end ()
public get_aligned_start ()
public Reference get_all_alt_locations ()
public get_all_DAS_Features ()
public Listreference get_all_supporting_features ()
public Bio::EnsEMBL::Gene get_nearest_Gene ()
public List get_overlapping_Genes ()
public String hashkey ()
public id ()
public Int is_constitutive ()
public Int is_current ()
public Boolean is_stored ()
public Int length ()
public Nothing load ()
public
Bio::EnsEMBL::Compara::AlignSlice::Exon 
map_Exon_on_Slice ()
public modified ()
public String modified_date ()
public void move ()
public
Bio::EnsEMBL::Compara::AlignSlice::Exon 
new ()
public Bio::EnsEMBL::Feature new_fast ()
public Int original_rank ()
public Boolean overlaps ()
public Bio::Seq peptide ()
public Int phase ()
public prepend_Exon ()
public List project ()
public List project_to_slice ()
public Bio::Seq seq ()
public Int seq_region_end ()
public Unsigned seq_region_length ()
public String seq_region_name ()
public Int seq_region_start ()
public Boolean seq_region_strand ()
public String seqname ()
public Bio::EnsEMBL::Slice slice ()
public String species ()
public String stable_id ()
public Int start ()
public Int strand ()
public sub_SeqFeature ()
public Hashref summary_as_hash ()
public temporary_id ()
public Bio::EnsEMBL::Gene transfer ()
public Bio::EnsEMBL::Exon transform ()
public type ()
public String version ()

Method Documentation

protected String Bio::EnsEMBL::Compara::AlignSlice::Exon::_get_aligned_sequence_from_original_sequence_and_cigar_line ( )
  Arg [1]    : string $original_sequence
  Arg [1]    : string $cigar_line
  Example    : $aligned_sequence = _get_aligned_sequence_from_original_sequence_and_cigar_line(
                   "CGTAACTGATGTTA", "3MD8M2D3M")
  Description: get gapped sequence from original one and cigar line
  Returntype : string $aligned_sequence
  Exceptions : thrown if cigar_line does not match sequence length
  Caller     : methodname
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon::append_Exon ( )
  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :
 
Code:
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public String Bio::EnsEMBL::Compara::AlignSlice::Exon::cigar_line ( )
  Arg[1]     : (optional) string $cigar_line
  Example    : $align_exon->cigar_line($cigar_line);
  Example    : $cigar_line = $align_exon->cigar_line();
  Description: Get/set the attribute cigar_line.
  Returntype : string
  Exceptions : none
  Caller     : object->methodname
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::copy ( )
  Arg[1]     : none
  Example    : my $new_align_slice = $old_align_slice->copy()
  Description: Creates a new Bio::EnsEMBL::AlignSlice::Exon object which
               is an exact copy of the calling object
  Returntype : Bio::EnsEMBL::Compara::AlignSlice::Exon object
  Exceptions : 
  Caller     : $obeject->methodname
 
Code:
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public Bio::EnsEMBL::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::exon ( )
  Arg[1]     : (optional) Bio::EnsEMBL::Exon $original_exon
  Example    : $align_exon->exon($original_exon);
  Example    : $start = $align_exon->start();
  Description: Get/set the attribute start. This method is overloaded in order to
               return the starting postion on the AlignSlice instead of the
               original one. Original starting position may be retrieved using
               the SUPER::start() method or the orginal_start() method
  Returntype : Bio::EnsEMBL::Exon object
  Exceptions :
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon::get_aligned_end ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon::get_aligned_start ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::map_Exon_on_Slice ( )
  Arg[1]     : Bio::EnsEMBL::Mapper $from_mapper
  Arg[2]     : Bio::EnsEMBL::Mapper $to_mapper
  Example    : $align_exon->map_Exon_on_Slice($from_mapper, $to_mapper);
  Description: This function takes the original exon and maps it on the slice
               using the mappers.
  Returntype : Bio::EnsEMBL::Compara::AlignSlice::Exon object
  Exceptions : returns undef if not enough information is provided
  Exceptions : returns undef if no piece of the original exon can be mapped.
  Caller     : new
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::new ( )
  Arg[1]     : a reference to a hash where keys can be:
                 -exon
                 -adaptor
                 -reference_slice
  Example    : my $align_slice =
                   new Bio::EnsEMBL::Compara::AlignSlice(
                       -exon => $original_exon
                       -reference_slice => $reference_slice,
                   );
  Description: Creates a new Bio::EnsEMBL::AlignSlice::Exon object
  Returntype : Bio::EnsEMBL::Compara::AlignSlice::Exon object
  Exceptions : return an object with no start, end nor strand if the
               exon cannot be mapped on the reference Slice.
 
Code:
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Reimplemented from Bio::EnsEMBL::Exon.

public Int Bio::EnsEMBL::Compara::AlignSlice::Exon::original_rank ( )
  Arg[1]     : (optional) integer $original_rank
  Example    : $align_exon->original_rank(5);
  Example    : $original_rank = $align_exon->original_rank();
  Description: Get/set the attribute original_rank. The orignal_rank
               is the position of the orginal Exon in the original
               Transcript
  Returntype : integer
  Exceptions :
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Exon::prepend_Exon ( )
  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :
 
Code:
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public Bio::Seq Bio::EnsEMBL::Compara::AlignSlice::Exon::seq ( )
  Arg [1]    : none
  Example    : my $seq_str = $exon->seq->seq;
  Description: Retrieves the dna sequence of this Exon.
               Returned in a Bio::Seq object.  Note that the sequence may
               include UTRs (or even be entirely UTR).
  Returntype : Bio::Seq or undef
  Exceptions : warning if argument passed,
               warning if exon does not have attatched slice
               warning if exon strand is not defined (or 0)
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Exon.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::AlignSlice::Exon::slice ( )
  Arg[1]     : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : $align_exon->slice($reference_slice);
  Example    : $reference_slice = $align_exon->slice();
  Description: Get/set the attribute slice. This method is overloaded in order
               to map original coordinates onto the reference Slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions :
 
Code:
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Reimplemented from Bio::EnsEMBL::Exon.


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/AlignSlice/Exon.pm