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. /Nicklas ------------------------------------------------------------------------- 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
