Standard Masala Plugins

Description

The Standard Masala Plugins library version 1.0 contains discrete cost function network (CFN) and continuous real-valued local (RVL) optimizers. It also contains a framework for defining scoring functions, file interpreters, and selectors.

Authors

• Vikram K. Mulligan, Ph.D., Research Scientist, Center for Computational Biology, Flatiron Institute (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).
• Tristan Zaborniak, Ph.D. Candidate, Department of Computer Science, University of Victoria (tzabo.nosp@m.rnia.nosp@m.k@fla.nosp@m.tiro.nosp@m.ninst.nosp@m.itut.nosp@m.e.org).
• Noora Azadvari, Ph.D. Candidate, Department of Bioengineering, University of Oregon (eazad.nosp@m.var@.nosp@m.uoreg.nosp@m.on.e.nosp@m.du).
• Qiyao Zhu, Ph.D., Flatiron Research Fellow, Center for Computational Biology, Flatiron Institute (qzhu@.nosp@m.flat.nosp@m.ironi.nosp@m.nsti.nosp@m.tute..nosp@m.org).
• S.M. Bargeen A. Turzo, Ph.D., Flatiron Research Fellow, Center for Computational Biology, Flatiron Institute (bturz.nosp@m.o@fl.nosp@m.atiro.nosp@m.nins.nosp@m.titut.nosp@m.e.or.nosp@m.g).
• P. Douglas Renfrew, Ph.D., Research Scientist, Center for Computatinoal Biology, Flatiron Institute (pdren.nosp@m.frew.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Library organization

This library is divided into hand-written sub-libraries and auto-generated API sub-libraries. All sub-libraries are in appropriately named sub-directories of the src/ directory; all namespaces start with standard_masala_plugins, and then follow the directory structure. The namespaces of the hand-written sub-libraries are:

• standard_masala_plugins::file_interpreters
• standard_masala_plugins::optimizers
• standard_masala_plugins::registration
• standard_masala_plugins::scoring
• standard_masala_plugins::selectors

The corresponding auto-generated libraries are in the following namespaces:

• standard_masala_plugins::file_interpreters_api
• standard_masala_plugins::optimizers_api
• standard_masala_plugins::registration_api
• standard_masala_plugins::scoring_api
• standard_masala_plugins::selectors_api

Using this library as a conventional library linked at compilation time

If you choose the link this library at compilation time, it is only safe to directly call functions or instantiate classes in the auto-generated API namespaces. These have stable APIs that will be preserved in future versions of the Standard Masala Plugins library, or deprecated in a manner that provides ample warning. Handwritten libraries are not part of the API, and can change without warning.

Using this library as a dynamically-linked library only provided at runtime

As an alternative, you may choose only to link the Masala Core library. In that case, you can use the masala::base::managers::plugin_module::MasalaPluginLibraryManager to load the Standard Masala Plugins at runtime, which will trigger registration of all plugin modules in this library that have API definitions with the masala::base::managers::plugin_module::MasalaPluginModuleManager, which your code may interrogate to obtain Masala plugins. The interface for plugin modules may be accessed through the masala::base::api::MasalaObjectAPIDefinition for each plugin module.