change to subroutine transcript_display+xref_sources so that it now return the list to use and also a hash of those to ignore if they match the regular expression given

Don't project if a GO term with the same accession, but IEA evidence code, exists, as this will lead to duplicates when the projected term has its evidence code changed to IEA after projection

fetch_all_by_external_name() in GeneAdaptor.pm, TranscriptAdaptor.pm,
and in TranslationAdaptor.pm.

This will limit the returned genes, transcripts, or translations, to
those that originates from the named external database.

This also means adding the optional argument to
list_gene_ids_by_extids(), list_transcript_ids_by_extids(),
list_translation_ids_by_extids(), and to _type_by_external_id() in
DBEntryAdaptor.pm.

The matching is done on 'db_name' in the 'external_db' table with LIKE
and an appended '%' to the given $external_db_name.

ficex Go to use ALL tax ids for a particular species (anonpholese fix but useful if more species get strains)

Also keep help text below 80 chars/line.

Added ability to project (apparent)one2many orthologs as well. Multiple targets are labeled "1 of 2", "2 of 2" etc

new code to work out the cmp seq regions that have multuple assemblys. This is now stored in the seq_region_attrib table

    Allow aliases to also be specified in the 'default' section, but
    require that there must also be a 'species' setting in the same
    section.  Aliases will never be installed if there is no 'speices'
    setting in the current section.  The 'species' section may be
    inherited from the 'default' section.

    Example:

    [default]
    host    = db.example.com
    user    = anonymous
    species = Human
    alias   = H_Sapiens
    alias   = Homo_Sapiens
    alias   = Me

    [my_core_db]
    group   = core
    dbname  = homo_sapiens_core_45_36g

    [my_estgene_db]
    group   = estgene
    dbname  = homo_sapiens_estgene_29_35b

  - allow mismatches
  - fixes to cope with changes to ConversionSupport->sort_chromosomes()
  - allow most scripts (with the exception of load_alternative_assembly.pl) to
    use source and target dbs on different hosts
  - various other improvements

Reimplemented the dump_interpro method so that it dumps any xrefs, object_xrefs and go_xrefs that may be dependent on the interpro xrefs

Added ens-research:3309

The Registry will try to load the specified file (specified by argument
to the method load_all(), in the envrionment variable ENSEMBL_REGISTRY,
or the file '~/.ensembl_init', as before) as an ini-file.  If this fails
due to the file having the wrong format, the code reverts to the old
behaviour of using require() on the same file.

This is an example of a simple ini-file.  There is no check to see
that e.g. 'dbname' is actually present or to avoid calling the adaptor
initialization routines with unnecessary parameters (we trust the user
to get this right).  The correct adaptor is chosen by peeking at the
'group' setting.


; Simple Ensembl config file example

; The 'default' section is special and its settings will be implicit for
; all other sections in this file but may be overridden by individual           ; sections.  There should be no 'alias' settings in the 'default'
; section.

[default]
user    = anonymous
host    = ensembldb.ensembl.org
group   = Core

[the_human_db]
species = Human
dbname  = homo_sapiens_core_45_36g
alias   = mary
alias   = john

[the_mouse_db]
species = Mouse
dbname  = mus_musculus_core_45_36f
alias   = minnie
alias   = mickey

; Configuration ends here