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 <[email protected]>