Sq pk programming

Pika

Change in step 4 options, test for peak height to be less than 0 to be less than user defined value (done in 1.03D)
Warn clearly that changing selected masses is done globally (done in 1.03D)
Add a button in PeakHeights graph to redo pika fits (Keep all user settings from step 4) (done in 1.03D)
Partition Avg ability for v or w mode only runs.
Checkbox for truncating sticks to zero in stacked graphs.

In final peak shape graph add ability to:
- truncate at 3.5 sigma
- trim wings to ensure monotonicity

In final peak width/shape add ability to:
- subtract sq baseline from peak shape algorithm

Prepare for release of O/C Panel at Manchester Users' Meeting
- Coordinate with Allison for code and panel
- Prepare example dataset and tutorial

In the m/z calibration panel, currently the width and accuracy vs m/z graphs don't show a summary of all the runs. E.g. the summary of all the peak widths for all the runs with error bars in the peak shape panel very nicely summarizes this information.
- (Jose) This could be done with a radio button on top of the graph that selects SR/AR (meaning single run / all runs)

We need to add camels, dromedaries, and vw "bug" ions to the lists. We need some notation for these ions, let me suggest vw28, vw23, d28, d32, and c28, c32, with the comment column describing what they are. It is important that those are lowercase letters, so people don't confuse these ions with vanadium (V), tungsten (W), and deuterium (D).

There is a need to consolidate the three sets of m/z lists that exist into a single one. We currently have the list of m/z possibly used in fits,(1) ones actually selected for HR sticks (2) list of m/z used for m/z calibration, and (3) the list of isolated ions. Each list is a subset of the previous one, and we can work with a single big list, and a series of masks to select / deselect the various m/z for the different purposes.

change the field analysis to warn users to check for large CO influence in ab correction; provide a sample pre and post AB correction from Tim to demonstrate

Change saving of the HR sicks matrix from masses that were selected to fit to all known masses.

Mike's pcurser in todo wave names
Changing frag table to reflect info in Allison's paper (in next release, coordinating with Jose for sending email to the users)
Bug found by Mike Q about checking modifications of all frag waves, not just species selected in average mass spec

We need to be able to select some ions to be used in m/z cal and peak shape for V or W only.
Review todo wave name length limitations.
When doing an m/z cal fitting, put runs with bad fits into a separate todo wave.
In the m/z calibration panel, make more clear what the nan pram button does.
From Tim O:During manual (F3) saves, the mass spectral data (e.g. MSOpen_V, MSSOpen_V, etc.) are saved as simple data arrays with the m/z in the rows direction. During autosaving, even if only for one run, these waves are always saved with the m/z in the column (run number in the row dimesion). It turns out that Squirrel can read and process either, just not at the same time. Thus, while he can process the data separately, he cannot ask Squirrel to load and process autosaved data with nonautosaved data interspersed.
Incorporate some peak finding code as per Jesse's request
Deal with Fast runs truncatings
Update squirrel web site

Change frag table of sulfate according to suggestion from Ann
- Current frag_sulphate -> frag_sulphate_old
- New frag_sulphate doesn't depend on frag_SO3 and frag_H2SO4 (Ann will wori up this new table)
- Frag_SO3 and H2SO4 are kept in Squirrel for reference and if someone wants to put them back to use, but not used by default