now with spectral averaging

Read one based precursor scan number from mzml (#664)

* correct Within calculation

* update unit tests

* this is the spot

* readPrecursorScanNumber

* return reported scan and precursor scan numbers when reading mzml

* unit test exception check for no scan number in mzml

* no real change

* delete empty line

Co-authored-by: MICHAEL SHORTREED <[email protected]>
Co-authored-by: Lei Lu <[email protected]>

Spectrum Averaging and Kullback-Liebler Added

Spectral Averaging Incorporation (#651)

* Added Spectral averaging extensions to mzlib
tested a few classes including Spectra Outputting

* Tested Spectral Averaging Extensions

* Fixed broken tests

* Added additional Test Coverage

* Adjusted code coverage to not look at the tests

* Dealt with some possible null reference warnings and renamed tests to fit convention

* One more potential null error

* Changed Dynamic MzML test to wait for the writing to finish and not repeat a test case

* Implemented Hash Code for MzSpectrum to resolve error and Alex's comment

* Removed Json as it was not utilized and unnecessary, adjusted the exceptions being thrown to be MzLib Exceptions

* Changed a few more exceptions to MzLib Exceptions

* Adjusted configuration manager

Period Tolerant Filename Without Extension and Compression

• correct Within calculation

• update unit tests

• add period tolerant get filename utility

• now handles compressed files skipping the compressed file extension

Nuget Package Updates

The following nuget packages were updated in this release:
MathNet.Numerics" Version="5.0.0
NetSerializer" Version="4.1.2
Easy.Common" Version="4.3.0
NUnit3TestAdapter" Version="4.3.0-alpha-net7.4
SharpLearning.Optimization" Version="0.28.0

Also, a small bug fix is included that renames product ions so that they don't contain integers in the name.

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 <[email protected]>
Co-authored-by: Anthony <[email protected]>

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 <[email protected]>