[EMBOSS] AbiView color change suggested

[Bassi, Sebastian]

Hi,

As I note in the previous mail, I've been working in a GUI for ABIVIEW.
I found a little problem the the output of abiview. The colors choosen for the bases are not the standard that ABI uses. We have 2 ABIs machines: 310 and 3100, in both of them the default color code is:
A=GREEN
C=BLUE
T=RED
G=BLACK (or yellow using black background).
I also have the book "Bioinformatics Sequence and Genome Analysis" by David Mount (*) and there is an ABI output sample at page 21, where the color code I stated above is used.
Sequence from a third party sequencer team gave us an eletrogram with those color also.
But the abiview output are in different color.
Here is the color code for abiview:
A=GREEN
C=RED
T=BLACK
G=BLUE
For me this is not a problem, since I work with the text file, but people on the wetlab are used to the ABI original color codes.
As their request, I modified the source code of ABIVIEW to reflect color code. Here is the relevant line:
 return ((B)=='C'?RED:(B)=='A'?GREEN:(B)=='G'?BLUE:(B)=='T'?BLACK:YELLOW);
this was changed to:
 return ((B)=='T'?RED:(B)=='A'?GREEN:(B)=='C'?BLUE:(B)=='G'?BLACK:YELLOW);

The question/request are:
1- Could this change make into the main tree?
2- Another option would be to include a command line option to change the colors. If the color are somehow related with the dye used, color could change from run to run. So a parameter to change it would be nice.
3- There should be an option for a "silence" mode, I mean, no output to stdout (just write the files), this would help on scritping. Now the program is sending to stdout the names of the files is generates (at least is doing this when is writing pngs files).

Sebastian Bassi.
Advanta Seeds. Balcarce Research Station.