New XIC Calculation and Reprocessing Button

- The new XIC calculation occurs when no XIC peak is found (sometimes
due to heavy deuteration). We walk our spectrum to find the correct
mass/z in order to build a good XIC (will be changed). This is currently
done at gaps of 4 * 1 / z for a maximum of 20 / z steps (which should
usually be  5 steps).

- Reprocessing button now under the property viewer. Reprocessing is
done using that button rather than "per-action" events. Still need to
link the manual chosing of MS peaks into deuteration calculation.

- (Minor) Adjusted the D - H mass difference to be 1.006277

- (Minor) Allow 2 decimal places to be displayed instead of all for the
RT property in the peptide viewer.
Re-processing changes.

Checkboxes allow a user to manually make changes to the list of peaks
chosen by automatically. The choice to go back to automatic is
available.

Modified redundant MSpeak picking for the same XIC information. If the
XIC information changes, new MS peaks will the chosen, otherwise use
cache.

Reprocessing button moved on the interface.

Removed attribute: FirstPeakInCalculation, because it is redundant with
the new manual MS peak picking.

Working on fixing the focus issue on propertygrid. Issue: If the user
does not press enter or move focus, the interface does not actually pass
on the new value of the respective field.
Bound actual peaks in calculation with manual MS peak picking

- Fixed a bug where manually chosing MS peaks would not work before a
reprocess.

- ActualPeaksInCalculation is now also bound to the manual peak chosing.
Decreasing the number will remove peaks from the manual peaks chosen.
Increasing the number will chose new peaks automatically, while still
keeping the previous selection intact.

- Added some documentation.
Unit test updates.

Deuteration calculations still need to be properly tested.
XIC Generator options updated

Added the options for XIC generation (and xic selection):
- FirstXicWithValidPeak: if we do not have a monoisotopic peak, we
search for  the first peak that can generate an XIC at  the correct RT
- XicWithMostInteseValidPeak: search at mz increments for the best XIC
possible (most intense XIC peak within the correct RT). This option is
more thorough, but requires more processing time.
Testing required for this feature.

- Minor adjustments to the decimal places displayed in tables (as
discussed in meeting: 2 for RT, 6 for MZ, 0 for intensity).
Peaks outside the valid MS rang are not shown by default

- Peaks outside the given MS range are nto shown by default in the MS
peak table. A user can see them by enabling the "Show hidden peaks"
checkbox on the table header. The checkbox is global for any selection.

- Fix to the XicWithMostIntenseValidPeak. Redundant XIC finding
eliminated. We now use caching to hold on to the important XICs.
Additionally, if no XIC is found by the end of the search, we show the
XIC of the monoisotopic MZ, instad of no XIC at all.
Temporarily disabled deutdist

Other minor bug fixes.
Redesigned Interface. Added fragment ion viewer for MSMS projects

- Re-partitioned the default interface for better visibility of graphs.
Added a separate view for fragment ions for MS/MS experiments. By
default, this view is enabled, and will appear for normal experiments
too... but that can be changed.

- Minor bug fixes (crashes).
Minor interface fixes
Enabled default "run as admin" mode. Fixes closing crash when trying to save layout.xml

- Temporary addition of the fragment spectrum viewer and associated
table. This will be moved into a different project type when we inclue
mascot.
New experiment type ready to use Mascot files.

- Set up the wizard to handle a Mascot result file for MS/MS
experiments. The details on how to interpret the mascot data are still
not implemented.
Added Mascot file reading functionality from old Hydra.

The wizard now supports adding a Mascot file during creating of a
project. The Mascot file will be read and processed, however the data is
not currently used. The application will report if it finds any matches
between the peptides found by mascot and the peptides in the csv.
Included the MGF file reader for loading MS/MS data

Ported the old MGF file from Hydra. Needs testing.
Automatic fragment selection based on an MGF file.

A user may load an MGF file into MassSpecStudio as part of the
MascotMSMSHydra experiment type. The software analyses the MGF files to
find all the interesting ion fragments, thus the user can go directly
into the processing stage.
Added properties for loading files using MGF reader.

Other small interface changes.
Changed UI for handling both MS and MS/MS manual validation as different views in the same project
Integrating normal MS data in MS/MS runs

Temporary solution. There is a better way of structuring things.
MS/MS fragment data now properly displayed on UI

MS/MS fragment data now shows up in the fragment viewer. Fixes some
interface bugs, removed reprocessing call when selecting different
fragment ions. Fixed "re-execute" for MSMS Fragment Analyzer.

Bugs:
- Subclass ValidationWrapper for fragmentions and peptides individually.
- 1 MS/MS Unit test should fail. We will handle this later.
Re-indent commit test

Testing VS 2008 auto-indent vs. old code indent.
Indentation Changes

Finally everything is indented in a consistent manner.