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

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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