Dear Anne. On Tue Jun 12 16:12:04 2012, Ménard Anne wrote: > I create an account on http://issues.jalview.org with the username : menard. I've added you to the list of users that are allowed to push to the jalview git repository. You should be able to check out the code with a command like:
git clone https://[email protected]/git/jalview.git You should then create your own branch to work in off the development branch git checkout develop git branch -b <your own branch name> you'll be able to make this branch public by doing this: git push --all Check that you can see your branch by looking at the public repository : http://source.jalview.org/gitweb/?p=jalview.git;a=heads > Not having succeeded in having access to the git sources, I used > google summer of code 2011 sources code but there was only the > sources and not the utils , lib, examples etc .. please take a look at the latest code in the develop branch. I've done some work to integrate the GSOC 2011 code into the core of Jalview. >> jalview.datamodel.NCList<IntervalContainer> implements List >> { >> /** >> * find all intervals on (if start_inclusive is set), and before or >> after start >> */ >> public List<IntervalContainer> find(long start, boolean >> start_inclusive, boolean before_or_after); >> >> /** >> * find all intervals on or between start and end (according to >> start_inclusive and end_inclusive) >> */ >> public List<IntervalContainer> find(long start, boolean >> start_inclusive, long end, boolean end_inclusive); >> } > > In fact I thought it would import a library (not available under java > so use JPython). Also, I thought it would take longer to encode. I don't quite understand what you said here. Are you suggesting that you import a library ? If you can find a native Java implementation that is licensed in a way compatible with the GPL, then that would be fine, but I don't think a JPython libary would be efficient for this. >>> simply a list of pairs that must be searched through each time. > > I did not understand what that means but it might be a problem with English. What i mean is that currently, Jalview stores base pairs like: Pairs: ((..))..((.(..))) Jalview datamodel: (1,6),(2,5),(9,17),(10,16),(12,15) So to find all pairs involving base 10, Jalview would need to check the whole list. A nested containment list would mean the search would only be made on base pairs involved in the region of base 10. > > For tonight, I'll look at the file: > jalview.datamodel.AlignmentAnnotation and write the algorithm and data > structure of containment nescent list as Yann Ponty advise me . OK. > Can I disturb you again tomorrow if I have more questions? Sure. > I think we should await the return of Yann to talk on skype. OK. I'll wait until tomorrow to talk. Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
