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Introduction

Database names can have from one to 16 letters and must not include a full stop or spaces. The database itself consists of two files; a file of records and an index file. If the database is called `FRED' then version 0 of the database comprises the pair of files named `FRED.0' and `FRED.0.aux', the latter of these being the index file. The version is the character after the full stop in these filenames. Versions are not limited to numbers alone, but can only be one character.

When a database is in use a `BUSY' file is created. For the `FRED' database this will be named `FRED.0.BUSY'. The file is used as a safeguard against two people editing the same database simultaneously. In the event of a program or system crash this busy file will be left on the disk, even though the database is not being used. In this case remove the busy file (after checking that it really isn't in use) using the unix rm command before opening the database. Eg "rm FRED.0.BUSY"

The earlier assembly program, Bap, used a different database format consisting of five files. Gap cannot access these old databases directly. We provide a convert program (named appropriately enough convert) to create gap format databases from either bap or dap databases. See section Converting Old Databases.

The gap database is robustly designed. Killing the program whilst updating the database should never yield and inconsistent state. A "roll-back" mechanism is utilised to undo any partially written updates and revert to the last consistent database. Hence quitting abnormally may result in the loss of some data. Always quit using the Exit command within the File menu.

However it is advised that copies of the database still be made regularly to safeguard against any software bugs or system disk corruptions (hopefully both will be unlikely).


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This page is maintained by James Bonfield. Last generated on 29 April 1996.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_14.html