Update use of autoadd option to allow for whether a reaction is rejected, or a compound is automatically added, when a compound is missing
Merge branch 'master' of https://github.com/ModelSEED/ModelSEED into Compound_Reaction_Loading
Fixed bug in utilities::translateArrayOptions()
Debugging leaving out protons in equationCode
Debugged use of multiple namespaces when checking fo duplicate compounds, and added checkForProton() function
Debugging use of biochemistry objects in merging and consolidating, including use of multiple namespaces
Merge branch 'master' into Compound_Reaction_Loading
Updating use of name aliasSet, expanding to use searchname aliasSet, and debugging mergebio command
minor bug with searchname aliases
Merge branch 'master' into Compound_Reaction_Loading
Fixing MS::Reaction::calculateAtomsFromFormula() to handle multi-component formulas separated by periods
Updating Reaction.pm to handle proton reagents instead of defaultProtons() when balancing a reaction
Adding new command that balances all reactions and saves the same biochemistry object
Expanded balancing of reactions to properly consider protons in transporter and debugged. Runs fine without error.
Merge branch 'master' of https://github.com/ModelSEED/ModelSEED
Merge branch 'master' of https://github.com/ModelSEED/ModelSEED
Merge branch 'master' of https://github.com/ModelSEED/ModelSEED