If you have a .acedbrc in your home directory then this is read. If this does not exist then $ACEDB/wspec/acedbrc is tried. If none of these exist then the internal default values are used. $ACEDB/wspec/acedbrc should be set up by the database administrators to set up the default preferences for the users. On saving the database the preferences for the user are saved to .acedbrc in their home directory. If database administrators copy there ~/.acedbrc to $ACEDB/wspec/acedbrc then they will not have to bother knowing anything about the format for this file. The preferences menu will in time contain more and more information as it can deal with boolean,int,float and colours.

The worm peptide management has now been automated. For the new code to be used several files will have to be altered. Failure to change the files will result in the running of the old code and hence other projects should not be affected.

i) database.wrm need to add the line

PEPMANAGE subclass format start end

e.g PEPMANAGE Wormpep WP:%05d 1000 5000

Where Wormpep is the subclass, WP:%05d is the format etc So the first Worm Peptide created would be WP:01000 and the last would be WP05000.

ii) subclasses.wrm

need to add the subclass

Class Wormpep

Hidden

Is_a_subclass_of Protein

Filter Wormpep

iii) models.wrm Wormpep needs to be added to the Sequence (if not already done). Checksum is also added to the Protein and length.(")

The new code will only run if the above file changes are made.

Operation.

---------

Upon fixing a temp gene the database.wrm is checked to see if PEPMANAGE is set. If it is, then subclass etc are read in. Next the sequence is checked to make sure that the Wormpep tag is set (We only want to use the new code on certain sequences specified by the wormpep tag). Finally all the Proteins in the subclass "class" are then checked against the gene to see if they are the same. If they are identical then the gene is saved with the identical Protein as the correspondiing protein, else a new protein is created (using the format to create a new name) and the temp gene is saved with the new protein as the corresponding protein.

spread->sortColonne = 1 ; /* default */ without this missing initialisation, very long tables were not cut in pices resulting in malloc failures, say on a table with 300.000 lines this also had very adverse effects on the aceserver preventing slicing in clients

THis has become visible in the server when i added a correct handling of tables which are not in their natural column order, those ofcourse must be accumulated in full before exportation this may actually crash the server we could have a line that says, over 100.00 lines, col 1 must be col 1 but i hate these hard limits

?ManyPep Protein ?Protein

also for the display to work options.wrm should have the following line

_VManyPep -V -D PEPMAP