Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Compara::BaseGenomicAlignSet Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::BaseGenomicAlignSet:

List of all members.


Class Summary

Definition at line 6 of file BaseGenomicAlignSet.pm.

Available Methods

public Int end ()
public void get_original_strand ()
public Bio::EnsEMBL::Slice reference_slice ()
public Int reference_slice_end ()
public Int reference_slice_start ()
public Int reference_slice_strand ()
public
Bio::EnsEMBL::Compara::GenomicAlignBlock 
restrict_between_reference_positions ()
public Bio::EnsEMBL::Slice slice ()
public Int start ()
public Int strand ()

Method Documentation

public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::end ( )
  Arg [1]    : (optional) integer $end
  Example    : my $end = $genomic_align_block->end;
  Example    : $genomic_align_block->end(1283);
  Description: get/set for attribute reference_slice_end. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
 
Code:
click to view
public void Bio::EnsEMBL::Compara::BaseGenomicAlignSet::get_original_strand ( )
  Args       : none
  Example    : if (!$genomic_align_block->get_original_strand()) {
                 # original GenomicAlignBlock has been reverse-complemented
               }
  Description: getter for the _orignal_strand attribute
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice ( )
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : my $reference_slice = $genomic_align_block->reference_slice;
  Example    : $genomic_align_block->reference_slice($slice);
  Description: Alias for slice method. TO BE

Deprecated:
Returntype : Bio::EnsEMBL::Slice object Exceptions : Caller : general Status : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_end ( )
  Arg [1]    : integer $reference_slice_end
  Example    : my $reference_slice_end = $genomic_align_block->reference_slice_end;
  Example    : $genomic_align_block->reference_slice_end(1283);
  Description: get/set for attribute reference_slice_end. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_start ( )
  Arg [1]    : integer $reference_slice_start
  Example    : my $reference_slice_start = $genomic_align_block->reference_slice_start;
  Example    : $genomic_align_block->reference_slice_start(1035);
  Description: get/set for attribute reference_slice_start. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_strand ( )
  Arg [1]    : integer $reference_slice_strand
  Example    : my $reference_slice_strand = $genomic_align_block->reference_slice_strand;
  Example    : $genomic_align_block->reference_slice_strand(-1);
  Description: get/set for attribute reference_slice_strand. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Compara::GenomicAlignBlock Bio::EnsEMBL::Compara::BaseGenomicAlignSet::restrict_between_reference_positions ( )
  Arg[1]     : [optional] int $start, refers to the reference_dnafrag
  Arg[2]     : [optional] int $end, refers to the reference_dnafrag
  Arg[3]     : [optional] Bio::EnsEMBL::Compara::GenomicAlign $reference_GenomicAlign
  Arg[4]     : [optional] boolean $skip_empty_GenomicAligns
  Example    : none
  Description: restrict this GenomicAlignBlock. It returns a new object unless no
               restriction is needed. In that case, it returns the original unchanged
               object
               It might be the case that the restricted region coincide with a gap
               in one or several GenomicAligns. By default these GenomicAligns are
               returned with a dnafrag_end equals to its dnafrag_start + 1. For instance,
               a GenomicAlign with dnafrag_start = 12345 and dnafrag_end = 12344
               correspond to a block which goes on this region from before 12345 to
               after 12344, ie just between 12344 and 12345. You can choose to remove
               these empty GenomicAligns by setting $skip_empty_GenomicAligns to any
               true value.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object in scalar context. In
               list context, returns the previous object and the start and end
               positions of the restriction in alignment coordinates (from 1 to
               alignment_length)
  Exceptions : return undef if reference positions lie outside of the alignment
  Caller     : general
  Status     : At risk
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Compara::GenomicAlignTree.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::BaseGenomicAlignSet::slice ( )
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : my $slice = $genomic_align_block->slice;
  Example    : $genomic_align_block->slice($slice);
  Description: get/set for attribute slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : 
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::start ( )
  Arg [1]    : (optional) integer $start
  Example    : my $start = $genomic_align_block->start;
  Example    : $genomic_align_block->start(1035);
  Description: get/set for attribute reference_slice_start. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::strand ( )
  Arg [1]    : integer $strand
  Example    : my $strand = $genomic_align_block->strand;
  Example    : $genomic_align_block->strand(-1);
  Description: get/set for attribute strand. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view

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