Changing rank and negative handling parameters to the model level

[flemingjf]

Recreating results requires knowledge of how to handle negative data and how to rank results. While the TxpResult class contains txpResultParams which contains those values, compatibility with the GUI can become confusing. When reading in GUI files with txpImportGUI, there is no way to default the parameters to that of the GUI. Furthermore, when sharing models, unless the result S4 object is shared alongside the model, the results might not be recreated accurately. With the use of csv files often for sharing results, this can be problematic. Thus, these parameters are being implemented as slots in TxpModel, and the use of them in txpCalculateScores is being deprecated.