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Updating SageAdapter with new functionality + compatibility with new …
…Sage versions (OpenMS#7577) * First Attempt to cluster, data reading already works * Clustering test * Clustering with KDE works now, access to masses in unimod.obo implemented * CLustering functional, defect pushing mod-mass up during KDE still a probem * Clustering (with workaround), mapping, and reading to idXML completed * Output as a .tsv file complete, sorting based on charge implemented * Added some bug checks to help debug streamlit app * Added multiple masses being written to output * Removed print-bloat * Annotation meta values are now saved, FDR filtering implemented * Added annotation feature * Edited annotation notation * Fixed naming of output-table for PTMs * Added wide-window option, improved annotation * Updated variable modification specification to be compatible with sage v0.15.0 * Re-added some filtering, tweaked backend, wide window mode available now * Removed smoothing to speed up code, removed some old print statements * Cleaned up code a bit, preparing for PR * Removed unnecessary functions * Refactored code to be compliant with OpenMS coding conventions * Also updated minor changes in percolator to be form-compliant * Update AUTHORS * Update CHANGELOG * Changed matching back-end, removed white-space changes to other files * Added better handling for combinations of mods + speed-up through binary search * Changed ini, some code * Changed to ModificationsDB * THIRDPARTY submodule updated * Updated submodule to latest master * Refactored code and made mapping less buggy, changed two thresholds * Removed old ini file and fixed whitespac issues * Removed commented out code block * Added isotope check to mapping * Changed description of smoothing option * add doc * todo * Added parameter to check for Sage * Refactored and rewrote core parts, clarified names * Added parameter description to Percolator, updated ini * Updated ini file, updated .idXML test file, fixed weird segfault bug in percolator * Removed unnecessary files * Removed last unecessary table * Update src/openms/source/FORMAT/PercolatorInfile.cpp Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de> * Formatting fixes * Fixed build issue on Windows, fixed .idXML test-file * Changed cmake file for tests --------- Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
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Submodule THIRDPARTY
updated
5 files
+ − | Linux/64bit/Sage/sage | |
+ − | MacOS/64bit/Sage/sage | |
+ − | MacOS/aarch64/Sage/sage | |
+13 −1 | Windows/64bit/Sage/README.md | |
+ − | Windows/64bit/Sage/sage.exe |
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