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Clean apps

Ludovic Cottret requested to merge cleanApps into develop

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
Edited by Ludovic Cottret

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