Update to goals

Jalview Developers
1

Hi Jim,

Below is a list of goals that I need to add to the wiki. Right now I’m converting the RALEE code for parsing the secondary structure line into Java. I’m also thinking about getting the coloring scheme for pyrimidine/purine done this weekend. It doesn’t look to hard. It doesn’t need the information from the secondary structure line and I can get used to how the coloring schemes are implemented in Jalview. If you have time to meet on Sunday, please let me know.

Cheers,

Lauren

Secondary structure line parsing
*Add recognition that secondary structure annotation line pertains directly to RNA or proteins
*Parse secondary structure annotation line with pairing of positions to ease color scheme goals.
—Add new Annotation class
*Some stockholm files from RFAM are not being read. Need to fix StockholmFile.java
*check that secondary structure line and sequence are the same length. Does Jalview already do this?
*convert all WUSS symbols to something simple, like how Jalview already does for protein secondary structure (simple helices and sheets)
*Need to figure out how to detect pseudoknots

Color Schemes/User Interface
*Add support for error checking when a user adds a base pair annotation. Make sure same number of column groups are selected
*How will colors cycle for different numbers of stems?

Later goals
*change all bracket types to () for VARNA, it doesn’t like other bracket types. Probably this can be done during the above goals easily.
*Add goal for later in the summer to add changes to the applet gui in addition to the main gui

2

Hi lauren. Meeting on sunday is fine. I assume we'll skype at the usual time.

Below is a list of goals that I need to add to the wiki. Right now I'm converting the RALEE code for parsing the secondary structure line into Java.

ok. that's a great start.

I'm also thinking about getting the coloring scheme for pyrimidine/purine done this weekend. It doesn't look to hard. It doesn't need the information from the secondary structure line and I can get used to how the coloring schemes are implemented in Jalview.

good idea. It shouldn't take you too long! Remember that the standard colourschemes are all documented in the html pages under doc/html.Secondary structure line parsing

*Add recognition that secondary structure annotation line pertains directly to RNA or proteins

We should talk about how you'll do this on Sunday.

*Parse secondary structure annotation line with pairing of positions to ease color scheme goals.
---Add new Annotation class
*Some stockholm files from RFAM are not being read. Need to fix StockholmFile.java

You should probably try to do a bulk test for this. If you can, try downloading the whole of RFAM, and make a script to loop through and import all the alignments (I actually have a groovy script to do this test - we can discuss it during the week).

*check that secondary structure line and sequence are the same length. Does Jalview already do this?

For annotation associated with a sequence, Jalview does check. However, there are no checks for alignment associated annotation.

*convert all WUSS symbols to something simple, like how Jalview already does for protein secondary structure (simple helices and sheets)

Again, we should talk about this on Sunday.

*Need to figure out how to detect pseudoknots

Color Schemes/User Interface
*Add support for error checking when a user adds a base pair annotation. Make sure same number of column groups are selected
*How will colors cycle for different numbers of stems?

Later goals
*change all bracket types to () for VARNA, it doesn't like other bracket types. Probably this can be done during the above goals easily.

this relates to the WUSS translation too, so we can discuss on Sunday - however, basically, you should think of it like this :

{stockholm + WUSS} -> stockholm parser -> { Jalview internal RNA secondary structure rep }
this happens when you import the file.

The translation for opening in VARNA:
{ Jalview internal RNA secondary structure rep } <-> jalview.gui.VARNA <-> { Secondary structure line + pair annotation info + sequence for VARNA }

*Add goal for later in the summer to add changes to the applet gui in addition to the main gui

ok. That all looks good, I'll take a look at the wiki page before we meet on Sunday.

Jim

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On 05/06/2010 10:29, Lauren Lui wrote:

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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
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