Refactor OmicsContainer and OmicsDataMap classes to allow multi-sample preprocessing

[vvvieira]

This paper describes a very straightforward framework for gene/reaction-level omics integration. The current wrappers are only good for generic pipelines where the sample is already preprocessed before calling reconstruction methods.

To this end, OmicsContainer and IntegrationStrategy classes should be changed to accommodate the following parameters described in the paper:

• Thresholding at the gene vs reaction level
• Threshold based on a global value vs local-values for each gene/reaction across multiple samples (e.g. median, quantiles)
• Which functions replace AND/OR operators

[vvvieira]

Addressed partially on #7 .