ammonia and water loss product fragment ions given fragmentation mode and terminus

Provides a method to return the types of water and ammonia loss product ions given a fragmentation mode and a fragmentation terminus. this allows the identification of these ions in a search separate from the primary ions.

Target Decoy Pairing and New Scrambled Decoy

The two big changes in this release are:
1.) We added target decoy pairing to peptideWithSetMods. Now, we create a decoy from a target directly and store a hash with the target pwsm and the decoy pwsm that links the two. This will allow for new methods of peptide FDR control described by Noble.
2.) There is a new scrambled decoy method. Here, the decoy is created by rearranging amino acids of the target while preserving the protease motif. Mods are moved with their respective amino acids. Before acceptance, we try to achieve a minimum homology difference. If, after 10 tries the homology difference is not achieved, nothing is done.

1.0.531

Fixing uniprot queries (#640)

* fixed queries

* Returned line to original

new spectrum similarity measures

added kullbeck-leibler algorithm
added searle spectral similarity
added spectral entropy
added new protease proalanase
fixed uniprot proteome download bug

Ignore Empty Scans Reading mzML No Error Reporting

Ignore empty mzml scans during read (#628)

* correct Within calculation

* update unit tests

* this is the spot

* return null if bad scan

* unit test for skipping scan with missing spectrum

* updated unit test

* test update and comments

* remove unread scans

Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
Co-authored-by: Anthony <anthony.cesnik@gmail.com>

biomarker to truncation

[WIP] Top down biomarker (#627)

* correct Within calculation

* update unit tests

* first correct top-down biomarker test

* remove unused test code

* quotable protease

* unquotable

* add full length proteoform proteolysis products for biomarker search with  unit tests

* new strategy for adding proteolysis products

* more complete biomarker addition

* works for protein.xml databases

* add unit test biomarkers with xml database

* clean up

* more clean up

* fix unit test

* adjust biomarker generation for three initiator methionine behaviors (cleave, retain, variable)

* make sure decoy biomarkers for standard xml proteolysis products are generated

* deal appropriately w/ n-terminal methionine cleavage

* last litle unit test tweaks

* delete unused code

* add biomarkers during protein database load

* greater clarity for biomarker proteolysis product entries

* change digest for top-down biomarker search to resolve issues in MM

* bro. shouldn't have been that hard

* cleanup

* add unit test

* don't need to cover unit tests with unit tests

* increase unit test coverage of protein.cs

* codemaid

* biomarkers on protein with no methionine

* unit test booster

* ACs comments

* more summary statemsn

* deleted mzlib.sln scarry

* delete empty line

* c-terminal products w/ and w/o methionine

* delete remaining initiator meth behavior dependances

* remove reference to meth behavior in biomarker test functions

* fix effected unit tests

* fix more unit tests

* Biomarkers changed to Truncations

* Biomarker to truncation

* added method summaries

* MsDataScan tests to boost coverage

* more MsDataScan tests

* more MsDataFile tests

* delete unused comment

* deleting the last vestiges of the term biomarker

Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>

Update to .NET 6.0

.NET 6.0 (#615)

* net6.0

* merge upstream and update workflows

* use nuget pack not dotnet pack

* name

* setup nuget separately

* change release name back

* readme

* image before releases

* replace webclient with httpclient

* use multiline

* use line concatenation for a couple places

* no slash

* use &&

* break up steps more

* fix xml writer errors and such

* more fixes

* fix httpclient

* code cleanup

* add back comments

Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>

proteoform truncation products

Top down biomarker III (#626)

* correct Within calculation

* update unit tests

* first correct top-down biomarker test

* remove unused test code

* quotable protease

* unquotable

* add full length proteoform proteolysis products for biomarker search with  unit tests

* new strategy for adding proteolysis products

* more complete biomarker addition

* works for protein.xml databases

* add unit test biomarkers with xml database

* clean up

* more clean up

* fix unit test

* adjust biomarker generation for three initiator methionine behaviors (cleave, retain, variable)

* make sure decoy biomarkers for standard xml proteolysis products are generated

* deal appropriately w/ n-terminal methionine cleavage

* last litle unit test tweaks

* delete unused code

* add biomarkers during protein database load

* greater clarity for biomarker proteolysis product entries

* change digest for top-down biomarker search to resolve issues in MM

* bro. shouldn't have been that hard

* cleanup

* add unit test

* don't need to cover unit tests with unit tests

* increase unit test coverage of protein.cs

* codemaid

* biomarkers on protein with no methionine

* unit test booster

* ACs comments

* more summary statemsn

* deleted mzlib.sln scarry

* delete empty line

* c-terminal products w/ and w/o methionine

* delete remaining initiator meth behavior dependances

* remove reference to meth behavior in biomarker test functions

* fix effected unit tests

* fix more unit tests

* Biomarkers changed to Truncations

* Biomarker to truncation

* added method summaries

* MsDataScan tests to boost coverage

* more MsDataScan tests

* more MsDataFile tests

* delete unused comment

Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>

proteoform truncation and biomarker products

Top down biomarker (#621)

* correct Within calculation

* update unit tests

* first correct top-down biomarker test

* remove unused test code

* quotable protease

* unquotable

* add full length proteoform proteolysis products for biomarker search with  unit tests

* new strategy for adding proteolysis products

* more complete biomarker addition

* works for protein.xml databases

* add unit test biomarkers with xml database

* clean up

* more clean up

* fix unit test

* adjust biomarker generation for three initiator methionine behaviors (cleave, retain, variable)

* make sure decoy biomarkers for standard xml proteolysis products are generated

* deal appropriately w/ n-terminal methionine cleavage

* last litle unit test tweaks

* delete unused code

* add biomarkers during protein database load

* greater clarity for biomarker proteolysis product entries

* change digest for top-down biomarker search to resolve issues in MM

* bro. shouldn't have been that hard

* cleanup

* add unit test

* don't need to cover unit tests with unit tests

* increase unit test coverage of protein.cs

* codemaid

* biomarkers on protein with no methionine

* unit test booster

* ACs comments

* more summary statemsn

* deleted mzlib.sln scarry

Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>

proteoform bifurcation among other things

1.0.524

Use multiline commands in build-test actions to get proper exit codes…