Adding clonebio command to simply enable a user to copy and re-name a biochemistry object
Added addCompartmentFromHash() function
Expanded biochemistry creation to include ModelSEED proton and compartments, still unsure if should fix uuid for proton?
Updated addCompoundFromHash for special case of recognizing protons
Updated interpretation of optional arguments to accomodate for empty strings being fed in from tabulated data
Updated loadEquation() to accomodate for a wider range of ways in which equations can be formatted in a table
simple change to expand use of reaction compartment listed in table
Updated addrxntable.pm and addcpdtable.pm to account for various possible inconsitencies in user input files and to allow for different column separators
Merge branch 'master' into Compound_Reaction_Loading
Updated comment
Fixed bugs in using matchbyname option, added option for adding aliases to namespace used to merge, and expanded to allow for the use of a separate column in the files for namespace merging
minor change in variable name
Update to consolidatebio to enforce consolidation of compounds, which is not used in mergebio
Updated use of searchnames to enfore unique searchnames and use of consolidate option to enforce single match between databases
Merge branch 'master' into Compound_Reaction_Loading
minor bug fix
Added function for including reactions that are elementally balanced and fixed a couple of bugs
Adding options to ignore or include protons/water when balancing reactions
Correcting charge of proton
Adding/Fixing functions for detecting protons and water and rejecting elementally unbalanced reactions