Clean apps

The goal is to check the met4j-toolbox apps, especially :

• names of the apps
• documentation
• names of the parameters to be consistent between apps

Let's apply these rules :

• Starting the name of an app by Sbml is useless since almost all apps take SBML as input.
• The name must be concise and meaningful
• Sbml in the name of an app must be written in camel case, not SBML
• The short description must be as concise as possible
• The parameter for the main input must be -i
• The parameter for the main output must be -o
• System.err must only be used for errors not logs
• When two formats of output are possible (ex: GML or TSV), indicate Txt

To make consistent the behaviour of the apps, some utils methods will be created:

• readSbml
• writeSbml
• getMetabolitesFromFile

Apps to check:

• attributes/DecomposeSBML.java
• attributes/ExtractPathways.java
• attributes/ExtractSbmlAnnot.java
• attributes/GetGenesFromReactions.java
• attributes/GetReactantsFromReactions.java
• attributes/SbmlSetChargesFromFile.java
• attributes/SbmlSetEcsFromFile.java
• attributes/SbmlSetFormulasFromFile.java
• attributes/SbmlSetGprsFromFile.java
• attributes/SbmlSetIdsFromFile.java
• attributes/SbmlSetNamesFromFile.java
• attributes/SbmlSetPathwaysFromFile.java
• attributes/SbmlSetRefsFromFile.java
• attributes/SbmlToMetaboliteTable.java
• bigg/GetModelProteome.java
• convert/FbcToNotes.java
• convert/Kegg2Sbml.java
• convert/Sbml2Graph.java
• convert/Sbml2Tab.java
• convert/SBMLwizard.java
• convert/Tab2Sbml.java
• mapping/NameMatcher.java
• mapping/ORApathwayEnrichment.java
• networkAnalysis/BipartiteDistanceMatrix.java
• networkAnalysis/CarbonSkeletonNet.java
• networkAnalysis/ChemSimilarityWeighting.java
• networkAnalysis/ChokePoint.java
• networkAnalysis/CompoundNet.java
• networkAnalysis/DegreeWeighting.java
• networkAnalysis/DistanceMatrix.java
• networkAnalysis/ExtractSubBipNetwork.java
• networkAnalysis/ExtractSubNetwork.java
• networkAnalysis/ExtractSubReactionNetwork.java
• networkAnalysis/LoadPoint.java
• networkAnalysis/MetaboRank.java
• networkAnalysis/NetworkSummary.java
• networkAnalysis/PathwayNet.java
• networkAnalysis/PrecursorNetwork.java
• networkAnalysis/ReactionDistanceMatrix.java
• networkAnalysis/ScopeNetwork.java
• networkAnalysis/SeedsAndTargets.java
• networkAnalysis/SideCompoundsScan.java
• networkAnalysis/TopologicalPathwayAnalysis.java
• reconstruction/CreateMetaNetwork.java
• reconstruction/SbmlCheckBalance.java