Closed d2fong closed 7 years ago
For example, I notice that simple chemicals can be 60x60, 40x40, 36x40 width/height depending on the sbgnml file.
@IgorRodchenkov is there any reason for this? I assume that some backend java library is computing these width/height values and then spitting them into the sbgnml?
@IgorRodchenkov Here is an example:
<glyph id="http___www.reactome.org_biopax_48887SmallMolecule18http___www.reactome.org_biopax_48887BiochemicalReaction2195LEFT_TO_RIGHT" class="simple chemical" compartmentRef="nucleoplasm">
<label text="ATP" />
<bbox y="399.78652908166936" x="600.8036470146063" w="36" h="40" />
<clone />
</glyph>
It's github.com/BioPAX/Paxtools sbgn-converter module. You can create an issue there about this, mention @ozgunbabur, @metin... @istemi.. etc folks
On Feb 22, 2017, at 3:37 PM, Dylan notifications@github.com wrote:
@IgorRodchenkov Here is an example:
<glyph id="http___www.reactome.org_biopax_48887SmallMolecule18http___www.reactome.org_biopax_48887BiochemicalReaction2195LEFT_TO_RIGHT" class="simple chemical" compartmentRef="nucleoplasm"> <label text="ATP" /> <bbox y="399.78652908166936" x="600.8036470146063" w="36" h="40" /> <clone /> </glyph>
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I agree the inconsistency in node dimensions should be fixed. @ozgunbabur why do you think this is happening (if it's really coming from paxtools)?
it's perhaps coming from a paxtools dependency, such as Chilay...
On Feb 22, 2017, at 3:37 PM, Dylan notifications@github.com wrote:
@IgorRodchenkov Here is an example:
<glyph id="http___www.reactome.org_biopax_48887SmallMolecule18http___www.reactome.org_biopax_48887BiochemicalReaction2195LEFT_TO_RIGHT" class="simple chemical" compartmentRef="nucleoplasm"> <label text="ATP" /> <bbox y="399.78652908166936" x="600.8036470146063" w="36" h="40" /> <clone /> </glyph>
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no chilay takes dimensions as input, doesn't assign dimensions @IgorRodchenkov
Well, Paxtools sbgn-converter (biopax to sbgn-ml) uses chilay-sbgn, etc., does layout and stores coordinates in the sbgn-ml data, which then initially used by our sbgnviz related js tools... May I'm wrong in that these coordinates is a different matter from what this issue is about...
On Feb 23, 2017, at 6:36 AM, ugurdogrusoz notifications@github.com wrote:
no chilay takes dimensions as input, doesn't assign dimensions @IgorRodchenkov
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Paxtools has, e.g., these:
https://github.com/BioPAX/Paxtools/blob/master/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java#L333 https://github.com/BioPAX/Paxtools/blob/master/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/SBGNLayoutManager.java#L40
Pathway Commons (PC2 web service, cPath2 software) calls L3ToSBGNPDConverter, and the default setting is that it called SBGNLayoutManager to aply cose layout... The result SBGN-ML file the then served and, you know, used by our javascript apps and libraries, such as SBGNViz.
Please, hey sbgn-converter developers, review and fix if required (including in chilay-sbgn and libsbgn, and deploy those properly to Central Maven or OSSRH at least...) This is important for Pathway Commons and SBGN projects, no?
On Thu, Feb 23, 2017 at 7:13 AM, Igor R rodche@gmail.com wrote:
Well, Paxtools sbgn-converter (biopax to sbgn-ml) uses chilay-sbgn, etc., does layout and stores coordinates in the sbgn-ml data, which then initially used by our sbgnviz related js tools... May I'm wrong in that these coordinates is a different matter from what this issue is about...
On Feb 23, 2017, at 6:36 AM, ugurdogrusoz notifications@github.com wrote:
no chilay takes dimensions as input, doesn't assign dimensions @IgorRodchenkov https://github.com/IgorRodchenkov
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When tinkering/refactoring the stylesheet. I noticed that the size of sbgn nodes are not consistent. A simple chemical in one graph is not the same size as a simple chemical in another.
It is possible that there could be some scheme that can approximate good looking graphs in the general case using the min-width/height properties.