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update #18
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update #18
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* Implement SILAC in digestion by allowing modification of the residue dictionary * ZR Review * Change order in SILAC protein constructor to prevent ambiguous calls when strings are null * Fix null issue for fixed/variable, because GetModifiedPeptides no longer uses ProteinDigestion * Rob Review * Add chemical formula to silac label * add parameterless silac label for toml reading * remove useless variable to get appveyor to try again * Code coverage issue? * remove my constructor in a vain attempt to pass appveyor * Try not to cry. Cry a lot. * Update ptm unit test (Why do we even have that unit test)
* Implement SILAC in digestion by allowing modification of the residue dictionary * ZR Review * Change order in SILAC protein constructor to prevent ambiguous calls when strings are null * Fix null issue for fixed/variable, because GetModifiedPeptides no longer uses ProteinDigestion * Rob Review * Add chemical formula to silac label * add parameterless silac label for toml reading * remove useless variable to get appveyor to try again * Code coverage issue? * remove my constructor in a vain attempt to pass appveyor * Try not to cry. Cry a lot. * Update ptm unit test (Why do we even have that unit test) * Add protein accession constructor when giving a new sequence * Update method call for protein accession
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss * adjusted window normalization such that spectrum TIC is maintained. Xcorr no longer uses 50max
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss * adjusted window normalization such that spectrum TIC is maintained. Xcorr no longer uses 50max * change xcorr range to scan range not observed min and max mzs
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss * adjusted window normalization such that spectrum TIC is maintained. Xcorr no longer uses 50max * change xcorr range to scan range not observed min and max mzs * hand NaN intensities in xcorr. removed rand spectrum generation in unit test
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss * adjusted window normalization such that spectrum TIC is maintained. Xcorr no longer uses 50max * change xcorr range to scan range not observed min and max mzs * hand NaN intensities in xcorr. removed rand spectrum generation in unit test * added unit test to keep most intense peaks after filtering * re-adding sort after merge deleted it * codacy
* Implement SILAC in digestion by allowing modification of the residue dictionary * ZR Review * Change order in SILAC protein constructor to prevent ambiguous calls when strings are null * Fix null issue for fixed/variable, because GetModifiedPeptides no longer uses ProteinDigestion * Rob Review * Add chemical formula to silac label * add parameterless silac label for toml reading * remove useless variable to get appveyor to try again * Code coverage issue? * remove my constructor in a vain attempt to pass appveyor * Try not to cry. Cry a lot. * Update ptm unit test (Why do we even have that unit test) * Add protein accession constructor when giving a new sequence * Update method call for protein accession * Fix FlashLfq bug that removed peptides if they had more than one id and no identified envelopes * Allow multiple SILAC labels per replicate. Allow searching for only labeled proteins * Remove debug code * Add comma * code coverage * Moar code coverage
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss * adjusted window normalization such that spectrum TIC is maintained. Xcorr no longer uses 50max * change xcorr range to scan range not observed min and max mzs * hand NaN intensities in xcorr. removed rand spectrum generation in unit test * added unit test to keep most intense peaks after filtering * re-adding sort after merge deleted it * codacy * fix xcorr add xcorr unit test * fixed unit tests * delete unnecessary lines * remove commented code
* trim zero intensity peaks from xcorr array * make mass bin in xcorr more changealbe * Changed window count to window width * minus parsimony stuff * merge upstream/master * remove nothing test * nothing changed * fiddled with mod count to get appveyor to pass * change == to equals * small unit tests * boomerang windows back * unit tests to cover multipurpose filtering * making zach happy * fix oversize window width error * set peak normaliztion to bool and intensity to 100 * code maid * normalization max = 1 * Acccccccccccorsss * adjusted window normalization such that spectrum TIC is maintained. Xcorr no longer uses 50max * change xcorr range to scan range not observed min and max mzs * hand NaN intensities in xcorr. removed rand spectrum generation in unit test * added unit test to keep most intense peaks after filtering * re-adding sort after merge deleted it * codacy * fix xcorr add xcorr unit test * fixed unit tests * delete unnecessary lines * remove commented code * bug check and change normalization to 50 * one liner
* Add isoform database and start test * Fixed Isoform Database reading error for fasta and xml * remove debugging code * remove comments * Codacy fixes and file copy always * more codacy edits * codacy * clean up code
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