Bio::EnsEMBL::ProjectionSegment Class Reference

Public Member Functions
public Int	from_start ()
public Int	from_end ()
public Bio::EnsEMBL::Slice	to_Slice ()

Detailed Description

Synopsis

$slice =
  $sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
 
my $projection = $slice->project("clone");
 
foreach my $projection_segment (@$projection) {
  print( "  from_start ", $projection_segment->from_start(), "\n" );
  print( "  from_end   ", $projection_segment->from_end(),   "\n" );
  print( "  to_Slice   ",
    $projection_segment->to_Slice()->name(), "\n" );
}

Description

The ProjectionSegment is a helper object to make the arrays returned by
project more accessible. Instead of writing $segment->[0], $segment->[1]
or $segment->[2] its possible to use the more descriptive notation of
$segment->from_start(), $segement->from_end(), $segment->to_Slice().

Definition at line 27 of file ProjectionSegment.pm.

Member Function Documentation

from_end()

public Int Bio::EnsEMBL::ProjectionSegment::from_end

(

)

  Args       : none
  Example    :

$coord_in_feature_end = $segment->from_end()

  Description: Second element in projects returned segment lists
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

from_start()

public Int Bio::EnsEMBL::ProjectionSegment::from_start

(

)

  Args       : none
  Example    :

$coord_in_fetaure_start = $segment->from_start()

  Description: First element in projects returned segment lists
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

to_Slice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::ProjectionSegment::to_Slice

(

)

  Args       : none
  Example    :

$target_slice = $segment->to_Slice()

  Description: Third element in projects returned segment lists
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/ProjectionSegment.pm