update #18
Merged
update #18
Commits on Feb 22, 2019
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Parameterless constructor for SilacLabel so tomls can read it. (#455)
* 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)
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Allow accession modification of proteins for SILAC in constructor (#457)
* 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
Commits on Mar 12, 2019
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change window count to window width in filtering (#458)
* 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
Commits on Mar 14, 2019
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multipurpose spectrum filtering (#459)
* 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
Commits on Mar 15, 2019
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fix a little error in allowed window range for filtering (#460)
* 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
Commits on Mar 18, 2019
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change window peak normaliztion to bool (#462)
* 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
Commits on Mar 19, 2019
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changed multi window normaliztion to maintain spectrum tic (#463)
* 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
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* 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
Commits on Mar 20, 2019
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deal with NaN peaks in xcorr (#465)
* 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
Commits on Mar 21, 2019
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unit test to keep most intense peaks after filtering (#467)
* 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
Commits on Mar 25, 2019
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Allow Multiple Silac Mods Per Replicate (#461)
* 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
Commits on Mar 27, 2019
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* 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
Commits on Mar 28, 2019
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* 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
Commits on Apr 2, 2019
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Fix Isoform reading bug for FASTA and XML (#471)
* 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
Commits on Apr 3, 2019
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