Second attempt... This version creates a Bio::EnsEMBL::Translation object with a start and an end position within the limits of the Bio::EnsEMBL::Compara::AlignSlice::Slice object if possible. When the translation cannot be mapped because if maps outside of the Bio::EnsEMBL::Compara::AlignSlice object, a fake Bio::EnsEMBL::Translation is created and the coding_region_start and coding_region_end of the corresponding Bio::EnsEMBL::Transcript are set to a negative value (always outside of the Bio::EnsEMBL::Compara::AlignSlice::Slice object )
Second attempt... This version creates a Bio::EnsEMBL::Translation object with a start and an end position within the limits of the Bio::EnsEMBL::Compara::AlignSlice::Slice object if possible. When the translation cannot be mapped because if maps outside of the Bio::EnsEMBL::Compara::AlignSlice object, a fake Bio::EnsEMBL::Translation is created and the coding_region_start and coding_region_end of the corresponding Bio::EnsEMBL::Transcript are set to a negative value (always outside of the Bio::EnsEMBL::Compara::AlignSlice::Slice object )

This new algorithm deals properly with Bio::EnsEMBL::Compara::AlignSlice::Exon objects resulting of the fusion of the same Bio::EnsEMBL::Exon object (this may happen during the mapping).

kumarsaurabh20/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,etapanari/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,danstaines/ensembl-compara,etapanari/ensembl-compara,ckongEbi/ensembl-compara,danstaines/ensembl-compara,dbolser-ebi/ensembl-compara,kumarsaurabh20/ensembl-compara,etapanari/ensembl-compara,ckongEbi/ensembl-compara,dbolser-ebi/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,etapanari/ensembl-compara,ckongEbi/ensembl-compara,Ensembl/ensembl-compara