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.
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?
*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