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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.
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
GenericPeakPicker - abstract class containing functions which all peakPickers should implement
- contains pick() function which requires a transition group and returns a list of PeakFeatures
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
Plotter abstract class for plotting chromatograms
plotTransitionGroup() requires transition group outputs plot
plotPeakFeatures() requires list of peak features and places them on plot
streamlit functions hopefully should not change too much.
@singjc Please let me know your thoughts
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