T-Coffee color scheme

oops - forgot to send this to the dev list…

> Hi Jim,
> What do you mean for ID coloring? Could you provide a practical example?
You have one yourself. In the t-coffee output, there is a 'per sequence' 
colour that shades the sequence ID according to the overall reliability 
- these are shown in the top half of the html output, above the 
alignment rows.

The scores are useful because someone can easily pick out and eliminate 
poor homologs in the alignment, since they have a significantly lower 
average reliability. There are other ways that this facility might be 
implemented - since the scores could also be useful to sort the 
alignment, but jalview currently has no score based shading scheme for 
sequence IDs, and my suggestion may be the easiest way to do it.

> I will update as well the documentation.
great !
> About the other steps, before I would commit a stable version of what I've done, so you can provide some feedback on that.
good idea.
> Can I commit in the "master" branch, from where I've download the source ?
no. The 'master' branch is for the latest stable version of Jalview. I 
merge releases onto this branch.

I've been pondering about how best to do this. The best thing would be 
for you create a new branch on the jalview.git repository for your 
patches. I can then check that branch out and take a look.

In eclipse, you do this via the Push .. dialog. Assuming you've given 
your branch a unique name (ideally including the Jalview issue number - 
JAL-1065) then you can add it to the list of local and remote branches 
that should be pushed to.

However, once you do that, you will need to modify the pull mode for 
your branch so it doesn't rebase from the remote/develop branch anymore, 
otherwise your local commits might get out of sync with their public 
In the current version of EGit, the only way you seem to be able to do 
this is via the Git repository browser. Switch to that perspective, 
select your local jalview repository, and pick the 'Repository 
properties' tab. Then click on the edit button (a little window with a 
pencil) and delete the property <your local branch name>.merge

[ sorry if my detailed instructions seem patronising - I don't regularly 
use EGit after having run into problems with earlier versions, so I'm 
being extra careful ! ].

>   I more thing, how do you report error messages in Jalview? do you a particular method? syso.println ?
Depends on the error and also where it occurs. The basic philosophy is 
to throw 'Error' objects for implementation problems, throw exceptions 
which get dumped to System.err if there are unexpected errors due to 
input, and try to give an informative message to the user.

For alignment input files, there is a standard method for raising 
dialogs for the user, but there isn't anything yet for importing 
annotation files (something for my TODO list), so for the moment, send 
errors to System.err and I'll take a look and see if there's a better way.



Subject: Re: T-Coffee color scheme
Date: Sat, 07 Apr 2012 10:52:47 +0100
From: Jim Procter jprocter@compbio.dundee.ac.uk
To: Paolo Di Tommaso Paolo.DiTommaso@crg.eu