Access to static fields in cytoscape core

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Thomas Pfau

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Jul 20, 2016, 3:32:29 AM7/20/16
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Hi,

I was wondering, whether it would be possible to make static fields in
internal cytoscape classes accessible via the API.
The reason I ask this, is that currently, when trying to build code that
uses some "implementation detail" from internal classes (like the name
given to a column when parsing sbml files with the default parser), it
is impossible to do so in a way that is not using local strings.
However, this makes an app dependent on the actual implementation of the
code used by cytoscape, which might simply change. Or one has to have
loads of "selection" dialogs, which is terribly annoying to the end user.
So, from a design point, would it make sense to have static field
classes in the API, that simply provide these types of objects?
In the sbml example: Having an SBMLFields class with all the static
final field declarations from the SBMLNetworkViewReader class?

Best,

Thomas

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Matthias König

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Jul 20, 2016, 4:00:19 AM7/20/16
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+1
I also want to access the SBMLReader fields (mainly to provide the identical column names than the core reader).

People writing apps using networks read from core network parsers should be able to get the column names which are created.
I.e. there should be a static class for all the core readers which is exported by the reader app.
Not only SBML, but also biopax, graphml, ...
This will allow to easily write apps on top of standard file formats.

Matthias König

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Jul 20, 2016, 5:54:45 AM7/20/16
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I opened an issue
http://code.cytoscape.org/redmine/issues/3638
I would be willing to contribute this if there is a core developer mentoring me

Matthias
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