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TODO.rst

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Ideas For Things To Do

  • plot all 1d traces in same axes, each 2d gets its own axes (but x-axis is linked?)

  • allow scaling/stacking of 1d traces

  • remove "extras", "graph style" options from graph menu

  • axes labels? (e.g. R.T. (min), etc)

  • make all columns display in tables properly

  • save AIA/CDF, mzML & mzXML

  • RAW file support - look at linking to unfinnigan? (https://code.google.com/p/unfinnigan/)

  • Bruker file formats

  • Waters file formats

  • Chemstation A fraction collection

  • Chemstation B+ FIA

  • MSMS support - Agilent MSMS Peak file format - Bruker MSMS spectra

  • work on spectral display

  • compound libraries

  • inner product/neutral loss chromatograms

  • Agilent .REG scraping - method parameters

  • autoalign chromatograms

  • baseline detection

  • smarter peak editing? - peak groups - adjustable peaks (little selectors on each end of "baseline") - allow user-selected peaks to be re-interpreted &

    coelution spots to be found

  • spectra from Agilent MS SIM method (e.g. CM1292) have a "0" mz that may be erroneous and should be removed?

  • fix color scaling as more chromatograms added: hard to keep track

  • put retention time on extracted spectra

  • buttons for spectral navigation?

  • xcms interface

  • MSMS support - tune MSMS file format performance (rewrites in C?) - spectral range display (as average) for Agilent MSMS - MSMS points on graph / MSMS data display

  • Method Database - allow calibration curves to be saved for compounds - method editor? - setting to allow run info to be loaded from method DB

  • remote database support

  • have multiple plots and allow user to choose which plot each trace goes on? - have datafile return units associated with trace types to allow for multiple y axes

  • allow fake datafiles to be generated and added to the library for chromatography models

  • display x axes in seconds (or hours or scans) (http://stackoverflow.com/questions/9451395/customize-x-axis-in-matplotlib)

  • help manual / tutorials

  • package example data with aston (for tests / quality control)

  • write unit tests

  • MWD import: check changes in "peak width", e.g. sampling rate (0x212 or 0x214?)

  • package size on Macs

  • setup/disttools? need better versioning

  • use hashes of data instead of filenames to match data to database entries - but how to handle duplicate files?

  • refactor code to remove references to "ions"; should be mz or wavelength?

  • 2D display of multiple chromatograms at once (i.e. "color bars" of TICs of multiple files vertically stacked)

  • make TimeSeries either have a string descriptor for ions or an array of numbers

  • TraceFiles should be able to match filenames using regex