Before any database accessing can take place the gap4 database must be opened.
This is done using the open_db
call. This returns an io handle
which should be passed to all other functions accessing the database.
open_db
-name database_name
?-version version?
?-create boolean?
?-access access_mode?
This opens a database named database_name. The actual files used will be
database_name.version. The routine is used for both creating a new
database and opening an existing database. The value returned is the io handle
of the opened database. More than one database may be opened at one time.
- -name database_name
-
Specifies the database name. The name is the start component of the two
filenames used for storing the database and so is the section up to, but not
including, the full stop. This is not an optional argument.
- -version version
-
This optional parameter specifies the database version. The version is
the single character after the full stop in the UNIX database filenames. It is
expected to be a single character. The default value (as used for newly
created databases) is "0".
- -create boolean
-
Whether to open an existing database (-create 0) or a new database (-create
1). The default here is 0; to open an existing database.
- -access access_mode
-
The access_mode specifies whether the database is to be opened in
read-only mode or read-write mode. Valid arguments are "r", "READONLY", "rw"
and "WRITE". If a database is opened in "rw" or "WRITE" mode a BUSY file will
be created. If the BUSY file already exists then the database is opened in
read-only mode instead. Either way, the
read_only
Tcl variable is set
to 0 for read-write and 1 for read-only mode.
close_db
-io io_handle
This closes a previously opened database. Returns nothing, but produces a Tcl
error for failure.
- -io io
-
Specifies which database to close. The io is the io handle returned from a
previous
open_db
call. Attempting to close databases that have not been
opened will lead to undefined results.
copy_db
-io io_handle
-version version
?-collect boolean?
This command copies a currently open database to a new version number. The
currently opened database is not modified. After copying the current open
database referred to by io_handle is still the original database.
- -io io
-
Specifies which database to copy. The io is the io handle returned from a
previous
open_db
call. Attempting to copy databases that have not been
opened will lead to undefined results.
- -version version
-
This parameter specifies the database version to create to place the copy in.
- -collect boolean
-
This optional parameter specifies whether to perform garbage collection when
copying the file. A value of 0 means no garbage collection; which is simply to
do a raw byte-by-byte copy of the two database files. A non zero value will
read and write each reading, contig, (etc) in turn to the new database, thus
resolving any database fragmentation. The default value is "0".
This page is maintained by
staden-package.
Last generated on 1 March 2001.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/scripting_49.html