sbgn / libsbgn

Libraries for the Systems Biology Graphical Notation (SBGN); Java and C++
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Bug in compartments.xml or how to do associations #16

Closed cannin closed 8 years ago

cannin commented 14 years ago

The example in compartments.xml is wrong .... here the associations is encoded as:

<glyph class="association" id="pn1"> <bbox x="280" y="270" w="20" h="20" /> <port x="280" y="280" id="pn1.1" /> <port x="300" y="280" id="pn1.2" /> </glyph>

instead the port definitions need to be on the glyphs ... and the association should be encoded as arc.

Reported by: fbergmann

cannin commented 14 years ago

Actually ... sorry for the false alarm ... the above is consistent with the approach for processes ... the actual problem is that:

<arc class="production"> <source x="300" y="280" ref="pn1.2" /> <target x="0" y="0" ref="glyph2" /> </arc> <arc class="consumption"> <source x="0" y="0" ref="glyph4" /> <target x="280" y="280" ref="pn1.1" /> </arc> <arc class="consumption"> <source x="0" y="0" ref="glyph5" /> <target x="280" y="280" ref="pn1.1" /> </arc>

have their source / target coordinates for the glyphs set to 0, 0

Original comment by: fbergmann

cannin commented 14 years ago

I updated the source / target coordinates.

Original comment by: tobicz

cannin commented 14 years ago

Great, thanks. I guess the bug can be closed, right? Or is there a remaining issue?

Original comment by: nobody

cannin commented 13 years ago

Original comment by: amarillion

cannin commented 13 years ago

Ok, I think this can be closed. Please don't hesitate to re-open if there is any remaining issue.

Original comment by: amarillion