LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::ProjectionSegment - part of the list that is returned from project function calls

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().

METHODS

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

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

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