Glycogenius

Bugs fixed:
- Fixed GG Draw module not drawing multiple glycans when you filter out a different glycan between adding to the plot;
- Improved scrolling experience on Group Selection window for Metaboanalyst (Save Results window), Custom Monosaccharides window and GG Draw glycan selection window;
- Fixed a bug that would freeze GG when saving results containing MS2 data;
- Corrected a bug where Custom Monosaccharides would fail on library building;
- Fixed a bug where GG would fail to launch on Python versions < 3.12 due to incorrect quotation marks nesting in formatted strings on File Editor module;
- Allows to select the adduct by selecting a peak in it, when holding CTRL for multiple selection;
- Removed "Single-Letter Code" from custom monosaccharides window. Now it's determined internally;
- Improved logic of permethylated monosaccharides. It's not perfect, but should work for most cases.

Known issues:
- Permethylated glycans fragments annotation will miss some fragments. A solution is being worked on to improve the annotation.

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- Added option to input custom monosaccharides;
- Added an option to fill as much missing values as possible with AUC of peaks that match the expected retention time, even if their scores are below thresholds;
- QC distribution window starts by default arranged by m/z values;
- Peptide backbone is now an option at the reducing end tag dropdown menu;
- Option to lock zoom in the chromatogram/electropherogram and spectra viewer;
- Changed numerical entries into spinboxes;
- Added option to trim the chromatographic/electropherographic run in File Editor;
- Fixed and improved the behavior when selecting multiple glycans to plot;
- Minor bug fixes and optimizations.

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Implemented latest version of GG backend, which includes:
- Replaced zero-values for missing values in Metaboanalyst table;
- Fixed freeze when running MS2 analysis on data files without MS2;
- Fixed bug regarding fragments library building in negative mode.

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- Updated GG backend version to 1.2.9, which includes minor improvements to feature detection and filtering.

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- Updated GG backend to 1.2.8, which includes a fix for negative mode library building and alkylates cysteines of peptides used as reducing end.

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Tentative publication version.

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- GG Draw now only creates cartoons of selected glycans, reducing initial loading time.

Other minor adjustments:
- Logo improved;
- Readme file adjustments;
- Instructions Manual now included.

The executable may be automatically blocked by Windows SmartScreen. This is default behavior from executable files built with PyInstaller and downloaded from the internet and in this case is a false alarm. Click on more info and "Run it anyway".

If you find any issue, feel free to report it on this repository's Issues section.