[ensembl-dev] Removal of deprecated methods in the Compara API

[Matthieu Muffato]

Dear developers,

Over the past two years, we have intensively worked on the gene side of 
the Compara API. Among other things, we have unified the API to access 
protein and ncRNA trees.
This lead to the deprecation of various methods and objects since 
several releases (a year and a half, in some cases), and the time has 
now come to drop support for those.

As a result, the following objects will be removed in e73:
  - ProteinTreeAdaptor
  - NCTreeAdaptor
  - Subset
  - SubsetAdaptor
Several methods of the following objects will be removed as well:
  - MethodLinkSpeciesSet
  - GeneTreeNode

Regarding gene trees, the GeneTree object / adaptor is now the preferred 
way of accessing gene trees. The GeneTree object has been introduced as 
a "header" for the gene trees (previously, the API could only deal with 
nodes, and a tree was actually a root node). As of e73, the former 
ProteinTree and NCTree objects / adaptors will be removed. Several 
methods from the GeneTreeNode adaptor (which was a base class for 
ProteinTreeAdaptor and NCTreeAdaptor) will be removed as well. They all 
have an equivalent in the GeneTree adaptor / object

With the release 73, we'll also drop support for several methods of the 
MethodLinkSpeciesSet object, in order to consolidate the object model 
around the SpeciesSet and Method objects.

Finally, we'll remove the Subset object / adaptor as they were used only 
for production purposes, and we have replaced them with appropriate 
methods of the Member object / adaptor.

Speaking of the Member object, you may have seen that we have introduced 
two new objects in release 71. GeneMember is an object that maps to 
genes; SeqMember represents a gene product, such as a ncRNA or a protein 
(and bears a sequence).
That leads to the deprecation of several methods that were previously 
ambiguous (getting the sequence of a gene, getting the peptide products 
of a peptide, etc). The final move will happen in e75.


Please let us know if you have any questions

Best,
Matthieu