Added methods get_all_sorted_GenomicAligns, original_sequence and cigar_line and some simple tests
Removed debug print statement
Set the species_order for PECAN alignments
Need to check if the tree has been restricted when trying to assign the reference_genomic_align when calling fetch_by_GenomicAlignBlock
Added sort_children function. Decided not to overwrite the inherited sorted_children function
Set the reference_genomic_align_node when creating a Bio::EnsEMBL::Compara::GenomicAlignTree object
Merge branch 'master' of https://github.com/Ensembl/ensembl-compara