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
Edited by Ludovic Cottret