source: tags/ms_r16q2/HELP_SOURCE/oldhelp/namesadmin.hlp

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UP      arb.hlp
UP      glossary.hlp

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# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE           NAME_SERVER ADMIN

OCCURRENCE      ARB_NT/Tools/Name server admin

SECTION         General warning

                        Most of the functions here will destroy or at least affect the consistency
                        of the species IDs (shortnames) for all users of the affected names.dat.

                        Please only use these functions if you really know what you are doing.
                        Otherwise ask your local ARB guru.

DESCRIPTION     Delete old names file

                       After using the nameserver for a while, the names database
                       may contain several entries which are used nowhere.

                       This happens e.g. if you've changed accession numbers during
                       your data curation or if you had species in one of your database
                       which you don't store anymore.

                       To get rid of these unused IDs click 'Delete old names file'.
                       Your names database will be deleted and all IDs will be regenerated.

                Edit names file

                       The names database is a simple text file, which may be modified
                       with a texteditor.

                       Use this feature with care!

                Remove ARB_XXXX entries

                       ARB automatically generates accession numbers if they are missing.
                       e.g if you import plain sequence data.

                       Use this to get rid of all nameserver entries using ARB_xxx accession
                       numbers.

                After using any of the above functions

                        you should consider to synchronize IDs (see LINK{sp_rename.hlp}) in
                        all your arb-databases.

                Additional species ID field

                       If you have good reasons, why you have to keep several species
                       with identical accession numbers in your databases, you'll normally
                       get problems with the ARB nameserver, because it handles these species
                       as "identical" and gives them IDs like 'HalHalob.2', 'HalHalob.3' etc.
                       to mark them as duplicates.

                       Here you can specify an additional DB-species-field, which will be used
                       for species identification in addition to 'acc' (accession number).

                       This setting is database-specific - so you have to set it for each database
                       where it's needed. 

                       For each field you use, a separate name server will be generated.
                       That means:

                       - You have to add a new entry into arb_tcp.dat (except for field 'start'
                         where a predefined entry exists)

                       - Names between database using different additional fields (or no add.
                         field) are NOT compatible. To merge such databases, change this setting
                         such that both databases use equal additional fields and synchronize species IDs.
                         Otherwise you'll most likely merge the data of non-equal species, which will
                         corrupt your data!

NOTES           If you comment out the default ARB_NAME_SERVER entry in arb_tcp.dat, renaming
                with empty 'Additional species ID field' will lead to an error. Use this to
                avoid creating databases that use the standard name server with no additional field.

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known