Hi lauren, thanks for the updates!
Just a quick update so you know where I am, and some notes I have
-I changed the covariation color scheme to be initialized more similar
to the AnnotationGradientScheme and is now called "By RNA helices" in
the menu. I'm a bit worried that there are some bugs in there, but
I'm going to check for them after I finish writing the documentation.
I commented out the covariation scheme code in GAlignFrame,
AlignFrame, and PopupMenu. I kept it in since I'll probably add a
covariance color scheme similar to Rfam's in the future, but I'm
actually considering adding this as an option in a popup menu similiar
to the one that comes up for the "By Annotation" option.
We can talk about that. It might need a little storyboarding to work out what you need to have in the dialog box before you start coding it up.
-Changed the default coloring for the RNA helices color scheme to be
purine/pyrimidine so the sequence logo shows up-jalview.utils.ColourUtil class has been checked into the repository
-Fixed the Group Colour menu bug - I forgot a "setText" for the
purine/pyrimidine scheme in PopupMenu.
easily done! good work.
I cleaned up the code and wrote the help files. I've committed these
changes if you'd like to take a look. Instead of "RNA support" I put
"Nucleic Acid Support" although I haven't decided if this is better or
not.
I think 'nucleic acid support' is better - the documentation would get even more complex if we distinguish dna and rna too much !
One comment about the documentation - try to add in useful links to external resources where necessary - e.g. the WUSS notation, which will not be familiar to many Jalview users (the help viewer is a basic web browser, and most pages will display ok (if a little oddly) if they don't rely on Javascript). You could even embed a sample stockholm file to demonstrate the WUSS notation in action.
I'm going to write a summary of what I did and what is left
tomorrow and put it in the docs folder. Then I'll make a diff. It
looks like I won't be able to submit the diff until August 30, so we
don't have to stress about submitting this right now. I'll also be
finishing the nescent requirements tomorrow.
great!
I wanted to change the RNA helices colouring to be the same in the
annotation panel, but I couldn't figure out how to update the panel
after the "By RNA helices" coloring option was selected. I added a
"RNA helix" option to defining a type of secondary structure in the
annotation panel. I didn't get to spend much time fixing the
annotation diaplay for the WUSS notation -- I'd like to fix this
before you put my code into a new release, but unless you think this
is a quick fix, I won't try to fix it tomorrow.
We can talk briefly about this today if you want. I'm not sure if its a quick fix or not, so we can take a look at it together.
Do you think the "By RNA helices" coloring should only be available if
a Stockholm file was loaded?
I think it should only be available if there is rna secondary structure annotation on the alignment.. so there's an alignmentAnnotation object with a valid secondary structure pairs list that can be used to intialise it.
I'll try to be on at our usual meeting time tomorrow if you'd like to
discuss anything. Otherwise, do you want to meet Tuesday morning my
time?
Lets try and briefly meet Monday morning, just to check over the questions above. If we can keep it short, then I expect we'll probably need to meet again on Tuesday just to clear up any final issues you have before the pencils down date.
Jim.
···
On 15/08/2010 02:44, Lauren Lui wrote:
On 16/08/2010 09:11, Lauren Lui wrote:
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
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