update #18
Merged
update #18
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.