Glycogenius-gui

- Fixed Library Building;
- Added option to batch calibrate files in GG File Editor;
- Improved antenna generation on GG Draw;
- Other minor fixes.

If GlycoGenius gets stuck, use the -console version and open an issue for the error you find, describing what led to it.

- Small fix to safeguard system;
- Two new major features:
- GG File Editor:
- Allows you to calibrate MzXML and MzML files within GlycoGenius, using standard calibrants, specific m/z or glycans from your loaded library;
- Includes visualization of found peaks;
- Makes a report in PDF after calibration is done;
- More features planned for File Editor;
- GG Draw:
- A module that's able to draw glycans for using in publication quality pictures within GG;
- When you enable, it checks if the glycans found in sample already have a picture ready to be used, otherwise generates them on the go and saves within Assets folder for later usage;
- Will take a while the first time it is activated;
- It will pick a random structure compatible with the composition and display on the chromatogram/electropherogram, pointing to the "good" peaks for the given composition;
- You can double click a drawing to change the structure for a given glycan or remove it;
- You can drag the drawings around to better fit the chromatogram/electropherogram;
- You can edit the scale of the drawings using a slider;
- Currently only able to draw non-Xylosylated N-glycans and O-glycans;
- More options will be made available in the future.

If GlycoGenius gets stuck, use the -console version and open an issue for the error you find, describing what led to it.

Includes all changes from previous release plus a small fix to metaboanalyst groups window.

If GlycoGenius gets stuck, use the -console version and open an issue for the error you find, describing what led to it.

- Completely restructured the .gg and .ggl files structure:
- This allows for much more efficient memory management during analysis (approximately 1/30th of memory required when compared to former GG versions);
- Now .gg file should load much faster after selecting it on the Select File menu and pressing OK;
- A lot of other minor optimizations on this side.
- Restructured the layout of the main window, mainly on the backend, bringing several benefits:
- Now the left-side panel containing the glycans' list can be stretched by clicking and dragging between it and the plots;
- Also the chromatogram plot and spectra plot can be stretched by clicking and dragging between the two plots;
- Now MS2 is integrated into the main window, in a separate tab on the spectra plot;
- Improved the distribution of elements such as the coordinates legend, retention time text on top of spectra plot, precursor information, etc.
- Completely remade the 2D plot window:
- Now loads much faster and is fully interactable;
- Up to three 2D plots available: one combining MS1 and MS2, with crosses marking precursors and connecting it to its respective MS2 spectrum, one only for MS1 and another one for MS2 with the precursors marked with crosses;
- Added a ruler function that can be used to measure the distance between pixels on either axes (time fraction or m/z).
- Added a lot of new tooltips to better explain the functions of buttons, entry fields and other elements of the GUI;
- Added a placeholder text to the glycan list filter field to make it easier to find it;
- Added option to filter the glycans' list by glycans whose MS2 spectra were analyzed by typing 'ms2' in the filter field;
- Metaboanalyst groups window should not stretch now with long file names and instead they will be shortened and the full name can be checked by hovering over the names;
- New features:
- New scaling options for the spectra plot, allowing to scale the plot by square root (sqrt), log or linearly;
- Now rulers can be drawn in the spectra plot to allow measuring the distance between peaks. Detailed information on how to use are available on the buttons upon hovering over them.
- A lot of minor improvements/fixes:
- Tooltips close to the right edge of the screen will now be displayed on the left side;
- Improved QC distribution plots and now the labels won't be under the interface elements;
- Plot graph window is now arranged by intensity and the plotting area has been fixed so that labels are not displayed behind the interface elements;
- Hovering tooltips on the plot graph window and on the QC distributions now display on the left side of the mouse cursor when close to the right edge of the plot;
- The values of m/z displayed on the spectra plot will no longer be displayed over the axes;
- A lot of code cleanup.

Known regression:
- Now chromatograms alignment might take longer than before, which should impact mainly the first time the "Compare Samples" button is clicked.

If GlycoGenius gets stuck, use the -console version and open an issue for the error you find, describing what led to it.

- Same isotopic peak will not get picked twice when tolerance is set too broad;
- Reduced memory usage during analysis by up to 10 times;
- Multithreaded the library generation algorithm, now should be significantly faster for large libraries;
- Small fix to better deal with corrupted MzML/MzXML files;
- Added a message on spectraviewer when you have a .gg file loaded but not the corresponding sample spectra file.

If GlycoGenius gets stuck, use the -console version and report the error you find, as well as what led to it.

- Generates .gg file after MS1 is done if MS2 is set to be performed and MS1 tracings have taken over 2 hours to complete, to avoid loss of data in case of crashes or lack of memory to finish the whole run;
- Options for forcing O-Glycans and GAGs compositions with proper restrictions to reduce search space efficiently;
- Reworked internal standard system, now supports chemical formula, glycans formula or mass, which then has its chemical formula derived from it, and now internal standard is properly deconvoluted and deisotopized, improving its quality;
- Added option to filter out glycans not found in at least a certain number of samples;
- Added percentage of glycans that are fucosylated, sialylated or both; Custom file name can now be set for .ggl and .gg file when generating library or starting an analysis;
- A lot of fixes.

If GlycoGenius gets stuck, use the -console version and report the error you find, as well as what led to it.