Complex Glyphs depicting elements on the inside

[cannin]

If we have another look at the complex in compartments.xml you will find the following glyphs encoded:

<glyph class="complex" id="glyph2"> <bbox x="360" y="150" w="140" h="160" /> </glyph> <glyph class="macromolecule" id="glyph3"> <label text="IGF" /> <bbox x="380" y="171" w="100" h="60" /> </glyph> <glyph class="macromolecule" id="glyph6"> <label text="IGFR" /> <bbox x="380" y="232" w="100" h="60" /> </glyph>

In other words we have glyphs with the same name multiple times in the file! This should not be the case, as this is not allowed by the SBGN specification (the second occurance should have a clone marker). For a human looking at the resulting picture it is clear what is meant: it was intended to depict the insides of the complex. I would argue that this is not how this should be encoded, rather something like the following should be used:

<glyph class="complex" id="glyph2"> <bbox x="360" y="150" w="140" h="160" /> <glyph class="macromolecule" id="glyph3"> <label text="IGF" /> <bbox x="380" y="171" w="100" h="60" /> </glyph> <glyph class="macromolecule" id="glyph6"> <label text="IGFR" /> <bbox x="380" y="232" w="100" h="60" /> </glyph>

</glyph>

Note the containment of the two glyphs inside the compartment glyph!

Reported by: fbergmann

[cannin]

• milestone: --> Milestone 1

Original comment by: amarillion

[cannin]

This has now been implemented, so I'm closing this.

Original comment by: amarillion

[cannin]

• status: open --> closed-fixed

Original comment by: amarillion