Integration of peaks in a given range

[druzinis]

Initial thoughts about the implementation.

A new button Tools would appear to the left of the current Options button. Pressing Tools opens a window with two sections aligned vertically: Peak integration and XIC Overlays.

1) Peak integration One or more fields compose of (a) from value (editable, text), (b) to value (editable, text), *(c) colour selector (only necessary if we have multiple integration fields), and (d)** the result (non-editable text field). Do we need multiple fields?

2) XIC overlays Multiple fields similar to the XIC filtering section in the main window with the addition of a colour selection thing.

[lgatto]

I think your suggestion would do it for multiple XIC overlays. May be we could drop the current XIC plot ion the main window and handle this using the Tools button, as suggested. The user could then extract ion chromatiorams for 1 .. n spectra. The new window would give us the space and flexibility to implement this.

Regarding the integration, I was thinking on something more interactive - a window with a spectrum, like below, and the user would select the area to integrate. .

What you suggest is important to, but this would rather be implemented in the console directly (in MSnbase for example). Here, I think users would rather look for something more interactive, as a validation tool, rather than batch integration.

[druzinis]

Yes, this sounds much better.

• The XIC filter section on the main window left-hand menu can be replaced by a Tools section. It would have two toggle buttons (until we come up with new tools, of course): Zoom (default) and Integrate. Selecting the latter will allow the user to select a range in the spectrum plot which will then be highlighted. Not sure where to display the result for integration, could probably do that in the plot itself (in the same colour as the highlighting, for clarity).
• As opposed to my suggestion above the new button in the upper main window area could be simply called XIC (or Extraction, or something else) and would open a dedicated window for extracting and overlaying multiple chromatograms.

[lgatto]

Sounds good!

[druzinis]

A preliminary version of peak integration is implemented with commit aaf615f887346e483170c18a04471a6061fad8d5.

[druzinis]

Further work on interactive integration: c6d10aef3e40b19124057b4835553d7d9e337181 and 779c550d572f001ba1fa72991487f147e46e2bd9