Hi Anne. On Thu Jun 21 12:57:25 2012, Ménard Anne wrote: > I forgot to send to Yann. > I put the link from the website created : > https://sites.google.com/site/jalview2012/ > It is empty for the moment . I originally thought you would use the NESCent wiki. Will you still use the wiki - or will you blog your progress at this site, instead ?
> > I begin to look the "first case" that is say modified : > jalview.gui.AssociatePdbFileWithSeq class in order to add the > annotations in the sequence . > Next, I look for show the data in the frame Jalview and not in the > console . > and Finally , I would recover the same information but when the user > provides a pdb file (with the help of Annote3D) great plan! > I have not fallen too far behind for Tori for the integration of > tertiary annotations? > I would not prevent the advance. Do not worry about this. You are on schedule at the moment. > All right, I can see all the elements in the console.On Varna , the > sequence and the annotations are stored in an ArrayList named results > but I did not understand where the results were stored for RfamFile > and StockolmFile because the method parse () returns void. > In stockolmFile , the data is stored in a or several Hashtable(s) but > How is it sent to be displayed on the screen? Jalview uses a variant* on the 'Builder' design pattern (http://www.vincehuston.org/dp/builder.html) to instanstiate an alignment from a data source. The actual datasource is specified via a FileParse object (handles low level IO error handling, multi-pass and multi-part streams), and the abstract architecture for the alignment data provider is specified by jalview.io.AlignFile. With a few exceptions, concrete file formats are implemented by classes extending from AlignFile (mostly). [ * - it is a builder pattern, but only just ;) ] Please look at jalview.io.AppletFormatAdapter.readFile class to see how Jalview builds an annotated jalview.datamodel.Alignment object from these classes. (and please ignore the embarrassing code duplication between jalview.io.AppletFormatAdapter.readFile and jalview.io.AppletFormatAdapter.readFromFile - these methods, should be merged so the same logic is used in both methods). Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
