Refactor of codebase

[jcharkow]

Make codebase more "class based" including abstract class based so that it can be more easily extendable. Also this should allow for a friendlier UI for those working directly with the python package.

Several Classes will add include:

Chromatogram - store np arrays of rt and im as well as meta information (e.g. label)

TransitionGroup - an object contaning both the MS1 and the MS2 chromatograms

• possibly some meta information as well

• getMedian() - returns a median chromatogram object

GenericPeakPicker - abstract class containing functions which all peakPickers should implement

• contains pick() function which requires a transition group and returns a list of PeakFeatures

• Current Classes Inhereting from this include:

  • pyMRMPeakPicker - Justin's python implementation of MRMPeakPicker
  • MRMPeakPicker - Official OpenMS implementation of MRMPeakPicker (from pyopenms)
  • Leon's PeakPicker

PeakFeatures - metainformation about a peak feature including rt apex intensity, left width, right width, area intensity etc. These objects created by all peak pickers

ExternalFileLoader - abstract class containing functions to load chromatogram objects

• loadChromatogram() function which takes a peptide sequence as a string and returns a List of TransitionGroup objects (each run)
• loadFeatures() which takes a peptide and loads the features of that peptide into a list of PeakFeatues

• Classes inhereting from this include: SQMassLoader - inherits from ExternalFileLoader requires osw and list of sqMass files

  MzMLLoader - inherits from ExternalFileLoader requires osw/diann results and mzML file

  timsLoader - inherits from ExternalFileLoader requires osw/diann results and mzML file

Plotter abstract class for plotting chromatograms plotTransitionGroup() requires transition group outputs plot plotPeakFeatures() requires list of peak features and places them on plot

Current Classes Inhereting from this include:
    StaticPlot()
    InteractivePlot()

streamlit functions hopefully should not change too much.

@singjc Please let me know your thoughts

[jcharkow]

Update GenericFileLoader

load(peptide sequence, charge) -> TransitionGroup)

ChromatogramLoader nherit from (SQMassFile, OSWFile) SQMassLoader inherit from (SQMassFile, PQPFile)

ExperimentLoader inherit from ( MZML, OSW) MZMLLoader inherit from ( MzML, tsv file)

charge, rt, im needed in

[singjc]

This has been accomplished with #50 , but was rebased as dev, and old dev was moved to legacy.