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

PairAlign - Dna pairwise alignment module

SYNOPSIS

#To convert between coordinates:

  my $cdna_coord = $pair->genomic2cDNA($gen_coord);
  my $gen_coord  = $pair->cDNA2genomic($cdna_coord);

DESCRIPTION

Contains list of sub alignments making up a dna-dna alignment

Creation:

  my $pair = new Bio::EnsEMBL::FeaturePair(
    -start  => $qstart,
    -end    => $qend,
    -strand => $qstrand,
    -hstart => $hstart,
    -hend   => $hend,
    -hend   => $hstrand,
  );

  my $pairaln = new Bio::EnsEMBL::Analysis::PairAlign;
  $pairaln->addFeaturePair($pair);

Any number of pair alignments can be added to the PairAlign object

eachFeaturePair

 Title   : eachFeaturePair 
 Example : my @pairs = $pair->eachFeaturePair
 Returns : Array of Bio::SeqFeature::FeaturePair
 Args    : none

genomic2cDNA

 Title   : genomic2cDNA
 Usage   : my $cdna_coord = $pair->genomic2cDNA($gen_coord)
 Function: Converts a genomic coordinate to a cdna coordinate
 Returns : int
 Args    : int

cDNA2genomic

 Title   : cDNA2genomic
 Usage   : my $gen_coord = $pair->genomic2cDNA($cdna_coord)
 Function: Converts a cdna coordinate to a genomic coordinate
 Example : 
 Returns : int
 Args    : int

convert_cDNA_feature

 Title   : convert_cDNA_feature
 Usage   : my @newfeatures = $self->convert_cDNA_feature($f);
 Function: Converts a feature on the cDNA into an array of 
           features on the genomic (for features that span across introns);
 Returns : Array of Bio::EnsEMBL::FeaturePair
 Args    : Bio::EnsEMBL::FeaturePair