Nicklas Nordborg wrote: > Steve Taylor wrote: > >>Hi, >> >>I am thinking of writing a plugin that reformats a tiling array >>biossay set to GFF >>(http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml) and WIG >>format (http://genome.ucsc.edu/goldenPath/help/wiggle.html). It seems >>the best way would be to build an Export plugin. I have a had a look >>at the the example plugins and it makes sense so far but I have some >> questions. Any help or pointers to relevant docs or example/existing >>code would great! > > > http://base.thep.lu.se/wiki/DeveloperInformation is the main entry point > for (plug-in and core) developer documentation. > > >>1) For each reporter there is an chromosome start and stop (imported >>as part of the annotations for the reporter) and I will need to use >>this to construct the file. How can I access reporter information >>from a plugin? > > > If you have the BASE internal ID use: > ReporterData reporter = Reporter.getById() > > or if you have the external ID: > ReporterData reporter = Reporter.getByExternalId() > > If you do this for a lot of reporters you should use a > ReporterBatcher.getByExternalId() instead since it can reuse a single > prepared statement instead of creating a new one each time as > Reporter.getByExternalId() does. > > > >>2) Is it possible to set a custom Type (i.e non BASE) >>of the exported file so it can be filtered e.g. GFF or WIG under the >>'Files and directories' section ? > > > It is currently not possible to create more file types. > > > 3) With an exported file is there a > >>method to add comments to the 'description' property? Can the text in >>these comments be hyperlinked? > > > File.setDescription(). Parts of the text that looks like a link or email > address will automatically be linked, for example: > > For more more info see: http://base.thep.lu.se > > > >>4) Is it possible to add a custom >>'Action' in 'Files and directories' so that the output could exported >>directly to another database or uploaded to a genome browser? > > > You will have to modify the JSP page for that. >
Thanks. One thing I am not quite clear on is can the result of an Analysis plugin be a single file or set of files? Or does it always have to be a bioassay set? If the latter is true I do you think the best place is to modify BioAssaySetExporter? Thanks again, Steve ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
