Options in Wfccm2

Instead of forcing the load and save dialogs, we could have import/export options with buttons or a menu. Are we going to only use the flat file storage or are there any plans for using the Windows Regisitry?

• General
  • Data
    • type - MicroArray or MassSpec
    • normalized - DataExplorer or WaveletPreprocessing
  • Methods - default statistical methods to run
  • Autoload
    • info set - if selected, auto load *_info.txt from the current directory.
    • logged data - if selected, auto load *_log10.txt or *_log2.txt from the current directory.
    • grouping specification - *_groups.txt
    • topN and cutoff - *_models.txt
  • Cross-Validation
    • enabled
    • k - set the K-fold.
  • Outfile
    • autosave scores - if selected, auto save scores as *_scores.txt at the current directory.
    • Individual Training output - if selected, produce a individual folder of training output.
    • Individual Testing output - if selected, produce a individual folder of testing output.
    • filtered training data - if selected, produce a individual folder of filtered training data.
    • filtered testing data - if selected, produce a individual folder of filtered testing data.

• Visualization
  • summary charts
    • location - chose "in the distance output folder" or "in a universal images folder".
    • resolution - set output size.
  • Cluster
    • resolution - set output size or point pixel size.

• Future
  • ROC curve output
  • quality control
  • Colors - more control over group colors used in cluster and ballgraph

Issues

Static Save and Load

Currently, the Save and Load methods have to be rewritten everytime the OptionData members are changed. This also forces the saved file to have a very specific order without anything missing. Instead, I think we should investigate a way to dynamically get and set members/properties so that an incomplete, randomly ordered options file will load. Save and Load would not have to be changed, keeping them from getting longer and longer.

Dictionary

We could use a dictionary to save the options, but this removes the type safety without creating an enum of all options. It would definitely make the calls to get/set options longer.