Dear all, Thank you for you response .
I can't connect to the server with the following command: git clone https://[email protected]/git/jalview.git When I enter the password.I get the following error: fatal: https://[email protected]/git/jalview.git/info/refs download error - server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none However the password is correct, then it is the same as that used on issues.jalview. >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. I summarize to check if I understand. I) I enter an id in Jalview eg RF00360 Jalview will pick on rfam: http://rfam.sanger.ac.uk/family/my_id for this example : http://rfam.sanger.ac.uk/family/RF00360 II) Then I go to Rfam. I have access to all necessary information: sequences, secondary structure prediction, alignments .. but I can only download the alignment in Stockholm format. So, I think that the file is "downloaded" in cache memory and it formats it to get the alignment pretty visible under jalview. III) I don't see how one obtains the secondary structure. From a Rfam file or recalculates from the sequence? What are the references for the sequence alignment ? For the sequence consensus, It's ok . Then I suppose that VARNA help to transform "((.))" into a visible sequence interactions . It is in this last part that I work, I have to improve "((" so that it can have different noncanonical interactions : Hoogsteen and Sugar. Currently , is that correct ? and where can I find the informations mentioned above . Sincerely, Anne . 2012/6/13, Jim Procter <[email protected]>: > 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
