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update #18

Merged
merged 15 commits into from
Apr 8, 2019
Merged

update #18

merged 15 commits into from
Apr 8, 2019

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zrolfs
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@zrolfs zrolfs commented Apr 8, 2019

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zrolfs and others added 15 commits February 22, 2019 10:13
* 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
@zrolfs zrolfs merged commit 9755638 into zrolfs:master Apr 8, 2019
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4 participants