prevent SINA from updating PTSERVER / allow use of ':' as reference source

[westram]

Situation:

SINA mixes two concepts which are separated in ARB:

• detection of reference
• alignment of reference

Both are forced into the same database, and that database hast to exist as saved file.

ARB handles these concepts separated, i.e.

• the database used to build the PTSERVER may differ from
• the database providing the references alignment.

In ARB the latter may be provided from the current working database (e.g. when using fast aligner).

Unwanted behavior:

• if the reference database is newer than the selected PTSERVER, SINA performs an update of the selected PTSERVER.
• cannot use reference alignment from the current working database.
• instead SINA uses the saved state, causing probably wrong, out-dated alignment (if current database differs from saved reference in alignment). This would not happen, if SILVA would read references from current working database.

Required fixes (SINA):

• remove requirement to access the reference database as file (allow :, i.e. database running in arb)
• do not auto-update ptserver if called from arb (add an CLI option to prevent that behavior)

The detection shall be performed based on the PTSERVER. The alignment of the references should be taken from the reference database.

Refer to ​http://help.arb-home.de/sina_main.html#OPTIONS for details on current behavior.