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SynBioDex / libSBOLj

Java Library for Synthetic Biology Open Language (SBOL)
Apache License 2.0
38 stars 24 forks source link

Add a flatten SBOL function #202

Open cjmyers opened 9 years ago

cjmyers commented 9 years ago

Add a function that flattens out hierarchy in an SBOL file. This should eliminate all Modules and Components in a design.

mgaldzic commented 9 years ago

is this in reference to the syntax hierarchy or actually remove information?

On Thu, Oct 8, 2015 at 3:28 PM cjmyers notifications@github.com wrote:

Add a function that flattens out hierarchy in an SBOL file. This should eliminate all Modules and Components in a design.

— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/202.

cjmyers commented 9 years ago

This would be used to just remove hierarchy. Think of it like inlining of function calls. It is useful, for example, when you want to check global consistency of a design. It might also make global optimization easier.

On Oct 8, 2015, at 4:34 PM, Michal Galdzicki notifications@github.com wrote:

is this in reference to the syntax hierarchy or actually remove information?

On Thu, Oct 8, 2015 at 3:28 PM cjmyers notifications@github.com wrote:

Add a function that flattens out hierarchy in an SBOL file. This should eliminate all Modules and Components in a design.

— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/202.

— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/202#issuecomment-146706603.

cjmyers commented 9 years ago

Must give good error messages when flattening fails.

cjmyers commented 8 years ago

flatten in ModuleDefinition is prototyped but not complete. For example, it has no implementation for merge refinementType.