Hi, I would like to extend some methods in the Base1PluginExecuter for another purpose. I'm trying to create a more general version of the plug-in that is allowed to run on both 1- and 2-channel data.
So if possible. I would want to have the following methods/classes changed to 'protected': getPluginDirectory getExecDirectory importFiles importData StreamHandler copy deleteDir I think that's all but there could still be something missing. Personnaly I would prefer all methods/variables in Base1PluginExecuter being made protected or public. But maybe there are good reasons for keeping some things private. Best Regards, Adam Ameur PhD Student The Linnaeus Centre for Bioinformatics Uppsala University Sweden On Aug 28, 2007, at 1:41 PM, vegard nygaard wrote: > > Hi. > >> >> I add this as a ticket. Can you specify the methods that you need >> acces to. >> >> /Johan >> > > I tried using the "protected" modifier Kjell proposed. And for that > worked > except for ListMap Which I think is a so called inner class of > Base1PluginExecuter. It had to be public. > > I changed in modifier from private to "protected" for these > methods/variables: > > Base1PluginExecuter.java > usedColumnsParameter > usedFieldsParameter > getPluginDirectory > geneAveragesParameter > jobParametersParameter > serialFormatParameter > getJobParametersFromXML > ListMap had to be public, protected was not enough. > > BioAssaySetExporter.java > getBaseFileQIMap > exportBaseFileSectionHead > exportBaseFileSectionAssays > getBaseFileSpotSectionCount > exportBaseFileSectionSpots > > > I think this was sufficient for me now, but I am not sure. I > propose that > methods/variables in classes that might be extended should use the > protected > or public modifier. But there might be other downsides with that > approach > that I don't see. > > Best Regards > Vegard Nygaard > Software Engineer > Department of Tumor Biology (Montebello) > Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo > Bioinformatics user support (NMC) > Phone 0047 22935590 > > > > >> >> 17 aug 2007 kl. 16.18 skrev vegard nygaard: >> >>> >>> >>> I want to export more than standard information in the base-file >>> sent to my >>> plug-in. That is more "sections" describing the samples, hybs, >>> arrays and >>> their relationships. My first plan was to extend >>> BioAssaySetExporter and >>> Base1PluginExecuter, and then override the methods where the >>> information is >>> written to file (stdin.txt) adding my extra stuff. This approach >>> failed when >>> I encountered lots of private methods in Base1PluginExecuter and >>> BioAssaySetExporter, making them less useful for extension since I >>> have to >>> override all the private parts I need even if I don't need to alter >>> them. >>> Why are those methods private and not public? Is there a better way >>> to solve >>> my problem? >>> >>> A more cumbersome approach is to copy both files (and others if >>> needed), >>> rename them, do my modifications and it will work. This is what I >>> have done >>> for years with BASE1, giving me an extra cut and paste job each >>> time base1 >>> was updated and I had to re-update my custom files. I hope BASE2 >>> can do this >>> in a more neat way. >>> >>> Best Regards >>> >>> Vegard Nygaard >>> Software Engineer >>> Department of Tumor Biology (Montebello) >>> Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo >>> Bioinformatics user support (NMC) >>> Phone 0047 22935590 >>> >>> >>> >>> -------------------------------------------------------------------- >>> -- >>> --- >>> This SF.net email is sponsored by: Splunk Inc. >>> Still grepping through log files to find problems? 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