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* scan number reading in FLASHDeconvAlgorithm.cpp changed a bit * Adding low resolution cosine. * Now works for low resolution * FLASHDeconvHelperStructure reanmed as FLASHHelperClasses. Also a few changes * implementing Extender. SubDAG implemented. * tag connect and extenstion implemented. node definition and tag start end should be implemented * tag connect and extenstion debugging.. * tag connect and extenstion works with lots of bugs * tag connect and extenstion works for b c ion. y ion does not work yet. * tag connect and extenstion works for b c y z. now start merging part perfect * FLASHExtender bug fixed. But merging should be optimized. In output should be implemented. * FLASHExtender beta version. Need to implement ion type weight, change the iteration, improve start end position finding. works well for no flanking mass tol\ * refactoring for FLASHExtender is almost done.. * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented minor bug fix * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented. Mode 3 done * multi threading implemented! Now only output format is needed * Output needed. Ion type specification needed. * Hit output string ready. formatting is needed * add system librariies * system libraries 2 * one bug in mAb sample. output implemented. FDR for all spectra * FLASHTnT beta verson * FLASHTnT beta verson1 * Revert "system libraries 2" This reverts commit 05e2dc9. * Revert "add system librariies" This reverts commit 9d0d6af. * Works for multiple spectra * support packaging as zip * Explicitely cast int - gives weird compiler error for windows.. * weird * cast to list * use proper conversion * convert to int list * fix last remainder * disable flashtaggeralgorithm tests * Works for multiple spectra1 * only use config? * make cpack filename manually changeable * remove FT * Works for multiple spectra and many bugs about precursor have been fixed * segment fault fixed finally * add error messages * change error to warning * only support windows * explicitely disable parameters (neccessary for vc++ compiler) * fix more msvc compiler related stuff * fix error handling * output format fixed. almost done for complex sample. But now hits have too many modifications * precursor bug fixed * unimod added * FLASHTnT+ done except for the corrected FDR and post processor * FLASHTnT+ done except for the corrected FDR and post processor2 * many bug fixed * tag scoring changed so its n c term masses are considered * diagonal run when start end positions make a diagonal line in spec alignment * diagonal run when start end positions make a diagonal line in spec alignment2 * working on filtration. * Deactivated the tnt+ part. * Deactivated the tnt+ part. debug deactivated * Candidate filtration improved * For tag unfound case, still find fragment masses. Coverage bug fixed. And many minor bug fixes * ProForma for FLASH TnT * use eigen instead of arm-neon * Deactivated simd part and changed the modification start end to be 1 based inclusive. * Deactivated simd part and changed the modification start end to be 1 based inclusive. prefix offset adjusted * ProForma for FlashTnT * Proforma merged * Unmatched tags were removed from TnT output * Tag exclusion bug fixed. * Add support for range modifications in ProForma string parsing and comments are added for clarity * Tag exclusion bug fixed2. * Tag exclusion bug fixed3. * FLASHDeconv testing. * FLASHTnT allow_multi option default true. * FLASHTnT allow_multi option default false. true makes error in FDViewer * Tag exclusion bug fixed4. * Mod mass mismatch fixed. * Fixed modification handling Included functionality for handling ranges in ProForma modifications * Mod mass mismatch fixed - indeed. * Mass match count fixed. * Mass match count fixed2. * Proforma debugging * Final annotation implemented * TnT speed up * Fixed out-of-bounds issue and refactored FLASHTnTFile.cpp * Proforma done * Proforma bug annotation bug scan number bug fixed * fix output for empty mod mass annotations * remove unused parameter * update headers * remove unused parameter in convolution based filter * fixed unsigned requirement for OpenMP for-loops * move hit_size inside omp def * remove hit_size variabe, cast directly in loop * fix python bindings for tagger * adjust python bindings * Proforma bug annotation bug scan number bug fixed. All bug fixed! * cast value again * simplify for loop * further simplification and add missing brackets * adjust tag output * eternal loop in mode 2 has been fixed * eternal loop in mode 2 has been fixed + seg fault in findwithx * fix scan number extraction for merged spectra * return last entry * pushing before reinstall * make warning silent * node definition bug fixed * FDR estimation enhanced * FDR estimation done for profile centroid * Tagger takes ion types into account * fix standard library usage * Many changes to fix bugs in backtracking. Speed up. multiple ion type bug fixed * All fixed except for the strange cut protein case. working on ti * All fixed * All fixed1 * All fixed2 * All fixed3 * A bit polish * A bit polish2 * A bit polish3 * mode 2 pro end range bug fixed * precursor calculation improved * precursor calculation improved2 * precursor calculation improved3 * supress warnign * disable warning * precursor calculation improved4 * precursor calculation improved5 * windows bug fixing * windows bug fixing2 * FLASHDeconv harmonic less strict + file output infinite loop resolved * FLASHTnT proteoform output small bug fixed * FLASHTnT proteoform output small bug fixed2 * use signed integer for loop * FLASHTnT output revised * FLASHTnT output revised2 * FLASHTnT output revised3 * FLASHTnT optimizing * Speed up * Speed up2 * fix output * Speed up3 * Speed up and automatic tolerance adjust * Speed up and automatic tolerance adjust * Speed up and automatic tolerance adjust2 * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution. * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution.2 * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution.3 * Tolerance with gaussian fitting. * Tolerance with gaussian fitting. polished * refactoring FLASHDeconvAlgorithm * fix compiler issue * fix another loop * option description updated. * option description updated2. * option description updated3. * option description updated4. * minor bug fix * fix ini categories * build ci matrix on push to deploy * a few small bugs fixed * fix test spectrum size * add FLASHTnT toolhandler * fix doxygen warnings for deploy * add test run * push on dev * create contrib folder * Move contrib from abibuilder to GitHub (#7482) * add test run * push on dev * create contrib folder * fix spaces * kick folder * get contrib from github * fix jq install * add secret to workflow * remove test file * authors file * consistency * fix source repo * use github cli instead of curl * Readd token * Use correct variable name for token * Fix tar name * fix typo * SpectralDeconvolution_test updated * SpectralDeconvolution_test updated * add test print * disable overlapping peak group removal * comment out second call * second call * first call * both calls * SpectralDeconvolution_test updated2 * disable test for testing * disable second point of failure test for now * SpectralDeconvolution_test debugging * Mac and windows have slight difference but could not catch... should be debugged next tiem * Precursor before and after MS2 are searched. TopPIC 1.7.x version works * Precursor before and after MS2 are searched. TopPIC 1.7.x version works2 * Precursor before and after MS2 are searched. TopPIC 1.7.x version works3 * TopPIC 1.7.x compatibility resolved * remove unused variable declaration * FDR estimation polished. Decoy spectrum implemented * noise decoy weight bug fixed * FDR estimation works for both centroid and profile * FDR estimation works perfectly for centroid. woking on profile * FDR estimation works perfectly for centroid isotope 0 and 1. * FDR estimation works perfectly for centroid isotope 0 and 1. * FDR estimation works perfectly for centroid isotope 0 and 1 2 * FDR estimation works perfectly for centroid isotope 0 and 1 and profile 0 * FDR estimation works perfectly. lets put only centroid results * FDR estimation works perfectly. lets put only centroid results2 * FDR estimation works perfectly. lets put only centroid results3 * FDR estimation works perfectly. lets put only centroid results4 * snr threshold adjusted * Tested with large scale datasets HCD and EThcD * remove unreferenced variable * fix doc * FLASHTnT randomness removed * FDR works again * FDR works + small correction * FDR works + small correction2 * FDR works + small correction3 * FDR works + code poished * FDR works + code poished2 * FDR works + code poished3 * update tests for FLASHDeconvAlgorithm * fix FDAlgo tests * wip * refactoring * refactoring * FDR estimation final version * FDR estimation final version2 * FDR works + small correction4 * FDR estimation final final version * update variable type * remove unreferenced variables * FLASHExtenderAlgorithm polishing * fix doctest * fix test compiler ambiguity * fix tests * fix tests * polishing * disable FLASH*tests * add port to installer deployment * dont report decoys in DeconvMassInfo * Resolve undefined behavior w.r.t. basic_string<unsigned_char> `std::char_traits<unsigned char>` has been undefined behavior since at least C++11 and was recently removed in LLVM/clang. Therefore the latest version of XCode no longer allows: std::basic_string<unsigned char> This means that OpenMS will no longer compile on macOS after recently released system updates are installed. I "fixed" the issue by replacing `std::basic_string` with `std::string` and a cast. Since SQLite is returning a UTF-8 character string, there's a chance that string comparisons will not work the way we expect if wide characters are returned. I still need to verify that the `OSWFile` test is actually checking the section of code changed in this commit. --------- Co-authored-by: KyowonJeong <jeong@informatik.uni-tuebingen.de> Co-authored-by: Tom David Müller <tom.mueller@beachouse.de> Co-authored-by: AyeshaFeroz <102374028+AyeshaFerozAsad@users.noreply.github.com> Co-authored-by: Tom David Müller <57191390+t0mdavid-m@users.noreply.github.com> Co-authored-by: Peter Jones <pjones@devalot.com>
* scan number reading in FLASHDeconvAlgorithm.cpp changed a bit * Adding low resolution cosine. * Now works for low resolution * FLASHDeconvHelperStructure reanmed as FLASHHelperClasses. Also a few changes * implementing Extender. SubDAG implemented. * tag connect and extenstion implemented. node definition and tag start end should be implemented * tag connect and extenstion debugging.. * tag connect and extenstion works with lots of bugs * tag connect and extenstion works for b c ion. y ion does not work yet. * tag connect and extenstion works for b c y z. now start merging part perfect * FLASHExtender bug fixed. But merging should be optimized. In output should be implemented. * FLASHExtender beta version. Need to implement ion type weight, change the iteration, improve start end position finding. works well for no flanking mass tol\ * refactoring for FLASHExtender is almost done.. * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented minor bug fix * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented. Mode 3 done * multi threading implemented! Now only output format is needed * Output needed. Ion type specification needed. * Hit output string ready. formatting is needed * add system librariies * system libraries 2 * one bug in mAb sample. output implemented. FDR for all spectra * FLASHTnT beta verson * FLASHTnT beta verson1 * Revert "system libraries 2" This reverts commit 05e2dc9. * Revert "add system librariies" This reverts commit 9d0d6af. * Works for multiple spectra * support packaging as zip * Explicitely cast int - gives weird compiler error for windows.. * weird * cast to list * use proper conversion * convert to int list * fix last remainder * disable flashtaggeralgorithm tests * Works for multiple spectra1 * only use config? * make cpack filename manually changeable * remove FT * Works for multiple spectra and many bugs about precursor have been fixed * segment fault fixed finally * add error messages * change error to warning * only support windows * explicitely disable parameters (neccessary for vc++ compiler) * fix more msvc compiler related stuff * fix error handling * output format fixed. almost done for complex sample. But now hits have too many modifications * precursor bug fixed * unimod added * FLASHTnT+ done except for the corrected FDR and post processor * FLASHTnT+ done except for the corrected FDR and post processor2 * many bug fixed * tag scoring changed so its n c term masses are considered * diagonal run when start end positions make a diagonal line in spec alignment * diagonal run when start end positions make a diagonal line in spec alignment2 * working on filtration. * Deactivated the tnt+ part. * Deactivated the tnt+ part. debug deactivated * Candidate filtration improved * For tag unfound case, still find fragment masses. Coverage bug fixed. And many minor bug fixes * ProForma for FLASH TnT * use eigen instead of arm-neon * Deactivated simd part and changed the modification start end to be 1 based inclusive. * Deactivated simd part and changed the modification start end to be 1 based inclusive. prefix offset adjusted * ProForma for FlashTnT * Proforma merged * Unmatched tags were removed from TnT output * Tag exclusion bug fixed. * Add support for range modifications in ProForma string parsing and comments are added for clarity * Tag exclusion bug fixed2. * Tag exclusion bug fixed3. * FLASHDeconv testing. * FLASHTnT allow_multi option default true. * FLASHTnT allow_multi option default false. true makes error in FDViewer * Tag exclusion bug fixed4. * Mod mass mismatch fixed. * Fixed modification handling Included functionality for handling ranges in ProForma modifications * Mod mass mismatch fixed - indeed. * Mass match count fixed. * Mass match count fixed2. * Proforma debugging * Final annotation implemented * TnT speed up * Fixed out-of-bounds issue and refactored FLASHTnTFile.cpp * Proforma done * Proforma bug annotation bug scan number bug fixed * fix output for empty mod mass annotations * remove unused parameter * update headers * remove unused parameter in convolution based filter * fixed unsigned requirement for OpenMP for-loops * move hit_size inside omp def * remove hit_size variabe, cast directly in loop * fix python bindings for tagger * adjust python bindings * Proforma bug annotation bug scan number bug fixed. All bug fixed! * cast value again * simplify for loop * further simplification and add missing brackets * adjust tag output * eternal loop in mode 2 has been fixed * eternal loop in mode 2 has been fixed + seg fault in findwithx * fix scan number extraction for merged spectra * return last entry * pushing before reinstall * make warning silent * node definition bug fixed * FDR estimation enhanced * FDR estimation done for profile centroid * Tagger takes ion types into account * fix standard library usage * Many changes to fix bugs in backtracking. Speed up. multiple ion type bug fixed * All fixed except for the strange cut protein case. working on ti * All fixed * All fixed1 * All fixed2 * All fixed3 * A bit polish * A bit polish2 * A bit polish3 * mode 2 pro end range bug fixed * precursor calculation improved * precursor calculation improved2 * precursor calculation improved3 * supress warnign * disable warning * precursor calculation improved4 * precursor calculation improved5 * windows bug fixing * windows bug fixing2 * FLASHDeconv harmonic less strict + file output infinite loop resolved * FLASHTnT proteoform output small bug fixed * FLASHTnT proteoform output small bug fixed2 * use signed integer for loop * FLASHTnT output revised * FLASHTnT output revised2 * FLASHTnT output revised3 * FLASHTnT optimizing * Speed up * Speed up2 * fix output * Speed up3 * Speed up and automatic tolerance adjust * Speed up and automatic tolerance adjust * Speed up and automatic tolerance adjust2 * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution. * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution.2 * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution.3 * Tolerance with gaussian fitting. * Tolerance with gaussian fitting. polished * refactoring FLASHDeconvAlgorithm * fix compiler issue * fix another loop * option description updated. * option description updated2. * option description updated3. * option description updated4. * minor bug fix * fix ini categories * build ci matrix on push to deploy * a few small bugs fixed * fix test spectrum size * add FLASHTnT toolhandler * fix doxygen warnings for deploy * add test run * push on dev * create contrib folder * Move contrib from abibuilder to GitHub (#7482) * add test run * push on dev * create contrib folder * fix spaces * kick folder * get contrib from github * fix jq install * add secret to workflow * remove test file * authors file * consistency * fix source repo * use github cli instead of curl * Readd token * Use correct variable name for token * Fix tar name * fix typo * SpectralDeconvolution_test updated * SpectralDeconvolution_test updated * add test print * disable overlapping peak group removal * comment out second call * second call * first call * both calls * SpectralDeconvolution_test updated2 * disable test for testing * disable second point of failure test for now * SpectralDeconvolution_test debugging * Mac and windows have slight difference but could not catch... should be debugged next tiem * Precursor before and after MS2 are searched. TopPIC 1.7.x version works * Precursor before and after MS2 are searched. TopPIC 1.7.x version works2 * Precursor before and after MS2 are searched. TopPIC 1.7.x version works3 * TopPIC 1.7.x compatibility resolved * remove unused variable declaration * FDR estimation polished. Decoy spectrum implemented * noise decoy weight bug fixed * FDR estimation works for both centroid and profile * FDR estimation works perfectly for centroid. woking on profile * FDR estimation works perfectly for centroid isotope 0 and 1. * FDR estimation works perfectly for centroid isotope 0 and 1. * FDR estimation works perfectly for centroid isotope 0 and 1 2 * FDR estimation works perfectly for centroid isotope 0 and 1 and profile 0 * FDR estimation works perfectly. lets put only centroid results * FDR estimation works perfectly. lets put only centroid results2 * FDR estimation works perfectly. lets put only centroid results3 * FDR estimation works perfectly. lets put only centroid results4 * snr threshold adjusted * Tested with large scale datasets HCD and EThcD * remove unreferenced variable * fix doc * FLASHTnT randomness removed * FDR works again * FDR works + small correction * FDR works + small correction2 * FDR works + small correction3 * FDR works + code poished * FDR works + code poished2 * FDR works + code poished3 * update tests for FLASHDeconvAlgorithm * fix FDAlgo tests * wip * refactoring * refactoring * FDR estimation final version * FDR estimation final version2 * FDR works + small correction4 * FDR estimation final final version * update variable type * remove unreferenced variables * FLASHExtenderAlgorithm polishing * fix doctest * fix test compiler ambiguity * fix tests * fix tests * polishing * disable FLASH*tests * add port to installer deployment * dont report decoys in DeconvMassInfo * Resolve undefined behavior w.r.t. basic_string<unsigned_char> `std::char_traits<unsigned char>` has been undefined behavior since at least C++11 and was recently removed in LLVM/clang. Therefore the latest version of XCode no longer allows: std::basic_string<unsigned char> This means that OpenMS will no longer compile on macOS after recently released system updates are installed. I "fixed" the issue by replacing `std::basic_string` with `std::string` and a cast. Since SQLite is returning a UTF-8 character string, there's a chance that string comparisons will not work the way we expect if wide characters are returned. I still need to verify that the `OSWFile` test is actually checking the section of code changed in this commit. --------- Co-authored-by: KyowonJeong <jeong@informatik.uni-tuebingen.de> Co-authored-by: Tom David Müller <tom.mueller@beachouse.de> Co-authored-by: AyeshaFeroz <102374028+AyeshaFerozAsad@users.noreply.github.com> Co-authored-by: Tom David Müller <57191390+t0mdavid-m@users.noreply.github.com> Co-authored-by: Peter Jones <pjones@devalot.com>
* scan number reading in FLASHDeconvAlgorithm.cpp changed a bit * Adding low resolution cosine. * Now works for low resolution * FLASHDeconvHelperStructure reanmed as FLASHHelperClasses. Also a few changes * implementing Extender. SubDAG implemented. * tag connect and extenstion implemented. node definition and tag start end should be implemented * tag connect and extenstion debugging.. * tag connect and extenstion works with lots of bugs * tag connect and extenstion works for b c ion. y ion does not work yet. * tag connect and extenstion works for b c y z. now start merging part perfect * FLASHExtender bug fixed. But merging should be optimized. In output should be implemented. * FLASHExtender beta version. Need to implement ion type weight, change the iteration, improve start end position finding. works well for no flanking mass tol\ * refactoring for FLASHExtender is almost done.. * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented minor bug fix * Tag edge visiting is now not redundant. Bug in path finding for different modification count fixed. Only output needs to be implemented. Mode 3 done * multi threading implemented! Now only output format is needed * Output needed. Ion type specification needed. * Hit output string ready. formatting is needed * add system librariies * system libraries 2 * one bug in mAb sample. output implemented. FDR for all spectra * FLASHTnT beta verson * FLASHTnT beta verson1 * Revert "system libraries 2" This reverts commit 05e2dc9. * Revert "add system librariies" This reverts commit 9d0d6af. * Works for multiple spectra * support packaging as zip * Explicitely cast int - gives weird compiler error for windows.. * weird * cast to list * use proper conversion * convert to int list * fix last remainder * disable flashtaggeralgorithm tests * Works for multiple spectra1 * only use config? * make cpack filename manually changeable * remove FT * Works for multiple spectra and many bugs about precursor have been fixed * segment fault fixed finally * add error messages * change error to warning * only support windows * explicitely disable parameters (neccessary for vc++ compiler) * fix more msvc compiler related stuff * fix error handling * output format fixed. almost done for complex sample. But now hits have too many modifications * precursor bug fixed * unimod added * FLASHTnT+ done except for the corrected FDR and post processor * FLASHTnT+ done except for the corrected FDR and post processor2 * many bug fixed * tag scoring changed so its n c term masses are considered * diagonal run when start end positions make a diagonal line in spec alignment * diagonal run when start end positions make a diagonal line in spec alignment2 * working on filtration. * Deactivated the tnt+ part. * Deactivated the tnt+ part. debug deactivated * Candidate filtration improved * For tag unfound case, still find fragment masses. Coverage bug fixed. And many minor bug fixes * ProForma for FLASH TnT * use eigen instead of arm-neon * Deactivated simd part and changed the modification start end to be 1 based inclusive. * Deactivated simd part and changed the modification start end to be 1 based inclusive. prefix offset adjusted * ProForma for FlashTnT * Proforma merged * Unmatched tags were removed from TnT output * Tag exclusion bug fixed. * Add support for range modifications in ProForma string parsing and comments are added for clarity * Tag exclusion bug fixed2. * Tag exclusion bug fixed3. * FLASHDeconv testing. * FLASHTnT allow_multi option default true. * FLASHTnT allow_multi option default false. true makes error in FDViewer * Tag exclusion bug fixed4. * Mod mass mismatch fixed. * Fixed modification handling Included functionality for handling ranges in ProForma modifications * Mod mass mismatch fixed - indeed. * Mass match count fixed. * Mass match count fixed2. * Proforma debugging * Final annotation implemented * TnT speed up * Fixed out-of-bounds issue and refactored FLASHTnTFile.cpp * Proforma done * Proforma bug annotation bug scan number bug fixed * fix output for empty mod mass annotations * remove unused parameter * update headers * remove unused parameter in convolution based filter * fixed unsigned requirement for OpenMP for-loops * move hit_size inside omp def * remove hit_size variabe, cast directly in loop * fix python bindings for tagger * adjust python bindings * Proforma bug annotation bug scan number bug fixed. All bug fixed! * cast value again * simplify for loop * further simplification and add missing brackets * adjust tag output * eternal loop in mode 2 has been fixed * eternal loop in mode 2 has been fixed + seg fault in findwithx * fix scan number extraction for merged spectra * return last entry * pushing before reinstall * make warning silent * node definition bug fixed * FDR estimation enhanced * FDR estimation done for profile centroid * Tagger takes ion types into account * fix standard library usage * Many changes to fix bugs in backtracking. Speed up. multiple ion type bug fixed * All fixed except for the strange cut protein case. working on ti * All fixed * All fixed1 * All fixed2 * All fixed3 * A bit polish * A bit polish2 * A bit polish3 * mode 2 pro end range bug fixed * precursor calculation improved * precursor calculation improved2 * precursor calculation improved3 * supress warnign * disable warning * precursor calculation improved4 * precursor calculation improved5 * windows bug fixing * windows bug fixing2 * FLASHDeconv harmonic less strict + file output infinite loop resolved * FLASHTnT proteoform output small bug fixed * FLASHTnT proteoform output small bug fixed2 * use signed integer for loop * FLASHTnT output revised * FLASHTnT output revised2 * FLASHTnT output revised3 * FLASHTnT optimizing * Speed up * Speed up2 * fix output * Speed up3 * Speed up and automatic tolerance adjust * Speed up and automatic tolerance adjust * Speed up and automatic tolerance adjust2 * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution. * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution.2 * Speed up and automatic tolerance adjust3 - Poisson works perfectly to approx. ppm error distribution.3 * Tolerance with gaussian fitting. * Tolerance with gaussian fitting. polished * refactoring FLASHDeconvAlgorithm * fix compiler issue * fix another loop * option description updated. * option description updated2. * option description updated3. * option description updated4. * minor bug fix * fix ini categories * build ci matrix on push to deploy * a few small bugs fixed * fix test spectrum size * add FLASHTnT toolhandler * fix doxygen warnings for deploy * add test run * push on dev * create contrib folder * Move contrib from abibuilder to GitHub (#7482) * add test run * push on dev * create contrib folder * fix spaces * kick folder * get contrib from github * fix jq install * add secret to workflow * remove test file * authors file * consistency * fix source repo * use github cli instead of curl * Readd token * Use correct variable name for token * Fix tar name * fix typo * SpectralDeconvolution_test updated * SpectralDeconvolution_test updated * add test print * disable overlapping peak group removal * comment out second call * second call * first call * both calls * SpectralDeconvolution_test updated2 * disable test for testing * disable second point of failure test for now * SpectralDeconvolution_test debugging * Mac and windows have slight difference but could not catch... should be debugged next tiem * Precursor before and after MS2 are searched. TopPIC 1.7.x version works * Precursor before and after MS2 are searched. TopPIC 1.7.x version works2 * Precursor before and after MS2 are searched. TopPIC 1.7.x version works3 * TopPIC 1.7.x compatibility resolved * remove unused variable declaration * FDR estimation polished. Decoy spectrum implemented * noise decoy weight bug fixed * FDR estimation works for both centroid and profile * FDR estimation works perfectly for centroid. woking on profile * FDR estimation works perfectly for centroid isotope 0 and 1. * FDR estimation works perfectly for centroid isotope 0 and 1. * FDR estimation works perfectly for centroid isotope 0 and 1 2 * FDR estimation works perfectly for centroid isotope 0 and 1 and profile 0 * FDR estimation works perfectly. lets put only centroid results * FDR estimation works perfectly. lets put only centroid results2 * FDR estimation works perfectly. lets put only centroid results3 * FDR estimation works perfectly. lets put only centroid results4 * snr threshold adjusted * Tested with large scale datasets HCD and EThcD * remove unreferenced variable * fix doc * FLASHTnT randomness removed * FDR works again * FDR works + small correction * FDR works + small correction2 * FDR works + small correction3 * FDR works + code poished * FDR works + code poished2 * FDR works + code poished3 * update tests for FLASHDeconvAlgorithm * fix FDAlgo tests * wip * refactoring * refactoring * FDR estimation final version * FDR estimation final version2 * FDR works + small correction4 * FDR estimation final final version * update variable type * remove unreferenced variables * FLASHExtenderAlgorithm polishing * fix doctest * fix test compiler ambiguity * fix tests * fix tests * polishing * disable FLASH*tests * add port to installer deployment * dont report decoys in DeconvMassInfo * Resolve undefined behavior w.r.t. basic_string<unsigned_char> `std::char_traits<unsigned char>` has been undefined behavior since at least C++11 and was recently removed in LLVM/clang. Therefore the latest version of XCode no longer allows: std::basic_string<unsigned char> This means that OpenMS will no longer compile on macOS after recently released system updates are installed. I "fixed" the issue by replacing `std::basic_string` with `std::string` and a cast. Since SQLite is returning a UTF-8 character string, there's a chance that string comparisons will not work the way we expect if wide characters are returned. I still need to verify that the `OSWFile` test is actually checking the section of code changed in this commit. --------- Co-authored-by: KyowonJeong <jeong@informatik.uni-tuebingen.de> Co-authored-by: Tom David Müller <tom.mueller@beachouse.de> Co-authored-by: AyeshaFeroz <102374028+AyeshaFerozAsad@users.noreply.github.com> Co-authored-by: Tom David Müller <57191390+t0mdavid-m@users.noreply.github.com> Co-authored-by: Peter Jones <pjones@devalot.com>
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Merges current develop into flash branch.