Andy. You need to download the latest development version of Jalview to get my changes. This is available from
http://WWW.Jalview.org/versions.html
J. B. Procter Jalview/enfin Barton group
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-----Original Message-----
From: Andy Lai <andycw.lai@utoronto.ca>
To: Jalview Development List <jalview-dev@jalview.org>
Sent: Tue, 05 Jul 2011 23:05
Subject: Re: [Jalview-dev] allowing Jalview windows to be created by other Java programs
Thanks fo the reply.
ok - so in reality, what you want is to provide an interface that allows the user to select from a database of alignments, and load them into the Jalview desktop, which is no problem. Do you want the user to be able to save annotation or edits back to the database as well ?
No. I don’t think that functionality is needed
hmm. I think you have not configured your netbeans project correctly. Jalview’s build script uses a classes directory to compile and assemble all the resources, then - assuming you execute the makedist or makefulldist targets, it assembles all the necessary Jars in the ‘dist’ directory. The build/classes folder sounds like something that netbeans created - so you need to tweak the netbeans project configuration to ensure the build directory is the same as the one that Jalview’s build.xml script is using.
Having said the above - It turns out that doing it is a real pain in NetBeans - and in fact, the easiest way was to add in a custom netbeans build script to ensure the ‘buildindices’ target in jalview’s build.xml is called with NetBean’s build/classes folder as the class output folder (see http://issues.jalview.org/browse/JAL-848 for the commit history). Now, you should be able to open the latest copy of the jalview development source (either from the web site, or pulling from the git repository) as a properly configured project in NetBeans.
I downloaded the latest development source (2.6.1.) and it appears to give me the same results (I assume it includes the fixed build.xml from ticket JAL-848). Since my knowledge of ANT scripts is quite limited, it’d help if you can tell me what is expected in the dist folder and in the jar file.
I assume the dist folder should contain the lib folder and the jar. The jar, in turn, should contain resources and the properties file. So far, I don’t see any of this when I clean + build. You are right, though, that build/classes is a default NetBeans thing.
I am not very sure what else I can configure in NetBeans anyway… I did change the first line of build.xml from
to
.
Point taken - and I think it should be possible to set up any IDE to work with the Jalview source, since we all have our own preferred IDE. However, be warned - UI building tools like the one in NetBeans will probably fail to work correctly with many of Jalview’s classes, since a fair amount of Jalview’s UI is dynamic (ie certain menus and dialogs are created on the fly, rather than as static layouts).
Jim.
Yes, that’s fine. The part that uses NetBean’s UI builder is quite independent of JalView.
Andy