Eclipse resources investigation

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Involved users:Ola
Bioclipse version:N/A
Last updated:2009-10-10

This is to investigate how eclipse Resource framework can be used in Bioclipse.

Roadmap for testCNF

Available from SVN path: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/trunk/bioclipse2/testing/testCNF

Resources

The workspace contains a collection of resources. From the user's perspective, there are three different types of resources: projects, folders, and files. A project is a collection of any number of files and folders. It is a container for organizing other resources that relate to a specific area. Files and folders are just like files and directories in the file system. A folder contains other folders or files. A file contains an arbitrary sequence of bytes. Its content is not interpreted by the platform. Source:

It is also possible to extend resources to be e.g. databases or external connections (like SVN). This will have to be investigated further but seems very powerful. An article about this is available on: http://aashishpatil.blogspot.com/2006/07/displaying-non-resource-content-using.html with example code at: https://bugs.eclipse.org/bugs/attachment.cgi?id=46334

Projects

If we decide to go for Projects (as Eclipse does) it means you always have to create a new project in order to start working with biocliopse. This is IMO a bit confusing, but adds a lot of power as we can create SpectrumProject, MolecularDynamics projects etc. We should probably have a general Project (like eclipse has) that manages just files (like Bioclipse1 navigator).

I am beginning to like the idea of Projects in Bioclipse, and actually we got many questions asking "how do we import files into Bioclipse" which is how people generally are used to work with similar programs. The General Project is a standard project contributed by Eclipse Resources plugin and can be used out of the box.

Navigator

Objective: Investigate the Eclipse Common Navigator Framework (CNF) to build our navigator.

This seems to be just what we are looking for. A navigator that can dynamically create child nodes for linking with open editor.

Cnf.jpg

Think of the screenshot but replaced with info directly from e.g. a molecule/spectra with desired components (structure, sequence, etc). You can link this content with any open editor as well. Kind of an advanced, extensible BioResourceNavigator. Really like the idea. With filters, users can easily decide what he wants to display, and allows us to make different versions with different appearance. The big issue is here to keep things simple as to not overwhelm the user. We'll have to discuss this in detail further on.


Articles:

I will write up an RCP app that uses CNF for testing purposes as a base for Bioclipse2.

Categories:Eclipse