Special Note Types

Several types of note have special meanings. These include the OPEN, CLOS and RAWD note types.

OPEN

CLOS

Notes of type OPEN and CLOS should contain pure Tcl code. If they exist, they will be executed when the database is opened (OPEN) and closed (CLOS). Take great care in creating and editing a note with these types! The purpose is to allow configuration options to be attached to a database, and hence allow for different gap4 configurations to be used when a UNIX directory contains more than one database. In general use of the `.gaprc' file (see section Options Menu) is probably safer. If there is a problem with a database containing a malformed OPEN or CLOS note, it may be opened using gap4 -no_exec_notes. This will prevent gap4 from executing the OPEN and CLOS notes and so allow them to be fixed using the Note Editor.

RAWD

This note specifies an alternative to the RAWDATA environment variable and should be set to be the full directory name for the location of the trace files for the database. If both the environment variable and the note are exist then the note will take priority. This automatic use of this note can be disabled be using the -no_rawdata_note command line option to gap4.

INFO

When created on a reading or a contig, this note may be displayed in the contig editor "information line" (see section The Editor Information Line) when the user moves the mouse over the editor sequence name list.

It is possible to create your own types by editing the `$STADENROOT/tables/NOTEDB' file. The format is fairly self explainatory, and is very similar to the `GTAGDB' file. Each note type should consist of the long name followed by a colon and id=4_letter_short_name, optionally followed by dt="any default text for this note". Lines may be split at colons by adding a backslash to the end of the line. See the standard `NOTEDB' file for examples.