The Options menu allows selection of the Consensus algorithm and the genetic code to use, and adjustment of various parameters used throughout gap4. It also provides a way of setting more trivial things such as fonts and colours.
Most of these options have "OK Permanent" buttons in addition to the normal "OK" button. The "OK Permanent" button will save the current settings to the `.gaprc' file in the user's home directory.
In general users will not need to be aware of this method as the most important configuration options are all available from within the graphical user interface. However there are many additional configurable parameters which may be referred to throughout the manual. These too are stored in the `.gaprc' files.
When gap4 starts up it will first load the complete set of configurations from the `$STADENROOT/tables/gaprc' file. Next it loads `.gaprc' from the user's home directory, and finally `.gaprc' from the user's current project directory. This means that the setting stored in the `.gaprc' file in the user's project directory will have priority over those found in the home directory, which, in turn, have priority of those found in the Staden Package installation directories.
Note that searching for the `.gaprc' files only applies when starting gap4 and not when opening new or different databases. Hence if the user changes directory to their project directory and starts gap4, then gap4 will read the `.gaprc' file found in that directory. If the user starts up gap4 from another directory and then uses the filebrowser to open a database, the `.gaprc' file in the project directory will not be read.
The format of commands in the `.gaprc' file are:
"#" followed by anything is a comment.
"set_def VARIABLE value" sets the parameter "VARIABLE" to the value "value". Note that value must be enclosed in double quotes if it contains spaces.
"set_defx temp VARIABLE value" sets a parameter in a temporary list named "temp". This has no effect unless it is then used within a set_def command. In this case we use "$temp" as the "value" parameter of a set_def command.
An example follows:
set_def FIJ.MAXMIS.VALUE 30.00 set_def TEMPLATE.PRIMER_REVERSE_COLOUR "green" set_def CONTIG_EDITOR.DISAGREE_MODE 2 set_def CONTIG_EDITOR.DISAGREE_CASE 0 set_def CONTIG_EDITOR.MAX_HEIGHT 25
Note that some adjustments will effect more than just gap4. For example, the colours of traces are stored in the `.tk_utilsrc' file, and this file is used by both gap4 and trev. For colour blind users it can be useful to change these particular settings. For example the following is a `.tk_utilsrc' file to change the colours for the trace displays.
set_def TRACE.COLOUR_A white set_def TRACE.COLOUR_C blue set_def TRACE.COLOUR_G black set_def TRACE.COLOUR_T "#ff8000" set_def TRACE.LINE_WIDTH 2