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iVis-at-Bilkent / sbgnviz.js

A web based visualization tool for process description maps in SBGN
http://www.cs.bilkent.edu.tr/~ivis/SBGNViz_sample_app/
GNU Lesser General Public License v3.0
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Changes for cytoscape.js 3.2.16 upgrade #200

Closed metincansiper closed 6 years ago

metincansiper commented 6 years ago

Made changes for cytoscape.js upgrade, so should be merged together with the related PR in ivis fork of Cytoscape.js. Also used 'barrel' and 'bottomroundrectangle' shapes of cytoscape as the base shapes of 'compartment' and 'nucleic acid feature' respectively. However, old draw function of nucleic acid feature is still remaining with a different name since it is needed for drawing clone markers of macromolecule and nucleic acid feature shapes. Needed it because 'bottomroundrectangle' shape did not work well for clonemarker. It was giving the following result:

screen shot 2018-08-30 at 4 57 04 pm

Also considered using 'cutrectangle' as the base shape of complexes but it did not render as expected when the shape dimensions are very small. The most visible case was the "BA Complex" node since the sizes of complex unit of information there is small. You can see the this fiddle to see how it looks for small sizes. You can play with width and height parameters in js code to render the shape in different sizes.

metincansiper commented 6 years ago

I created this issue in cytoscape.js related to cutrectangle rendering problem for small dimensions.