Revert Determination of Intensity Pairs for Spectrum Similarity

What's Changed

• Revert intensity pairs pr765 by @trishorts in #784

Full Changelog: 1.0.548...1.0.549

1.0.548 - Bug Fixes and QoL Improvements

What's Changed

• Handled edge case with digestion product having a null parent by @nbollis in #763
• Test fixed mod gptmd mod competition during digestion by @trishorts in #764
• Update dotnet.yml by @Alexander-Sol in #767
• Improved intensity pairs trying to make spectrum library comparisons faster by @trishorts in #765
• Fragger Result reading by @nbollis in #770
• Update dotnet.yml by @Alexander-Sol in #778
• Allow SSRCalc to be called from just base sequence without constructing PeptideWithSetModifications by @nbollis in #773
• Allow multiple custom fragmentations by @nbollis in #780
• FlashLFQ now enables selection of peptides to be quantified by @Alexander-Sol in #779

Full Changelog: 1.0.547...1.0.548

1.0.547 - Nucleotides, bug fixes, and refactoring

What's Changed

• Nucleotide, Rnase, Digestion Params Clone Method, and Interface Modificaiton by @nbollis in #757
• Add leucine to chymo cleavage motif by @trishorts in #759
• Changed Deconvoluter to have a static call by @nbollis in #760
• Mbr refactor by @Alexander-Sol in #758
• Edited the MatchedFramgentIon Equals method by @Alexander-Sol in #751

Full Changelog: 1.0.546...1.0.547

Minor Tweak to Digestion Parameters

What's Changed

• Changed behavior of masked members in Digestionparams by @nbollis in #756
  Enables toml reading and writing in MetaMorpheus

Full Changelog: 1.0.545...1.0.546

1.0.545 fix bugs in flashLFQ output

What's Changed

• Eliminate extra tab from chromatographic peak by @trishorts in #749
• Create CODE_OF_CONDUCT.md by @trishorts in #741
• Create CONTRIBUTING.md by @trishorts in #742

Full Changelog: 1.0.544...1.0.545

Update classes and class arrangment to accommodate both peptides and oligos

What's Changed

• Eliminate extra tab from chromatographic peak by @trishorts in #747
• Rearranging classes to fit within the Transcriptomics Structure by @nbollis in #743

Full Changelog: 1.0.543...1.0.544

Spectrum Match from Tsv for peptide and oligo

What's Changed

• PsmFromTsv Reader that also will work for RNA by @trishorts in #737

Full Changelog: 1.0.542...1.0.543

1.0.542

What's Changed

• Encyclopedia formated peptide full sequence including mass shift in brackets by @trishorts in #726
• EncyclopeDIA amodified peptides format mass shift by @trishorts in #730
• Disabled Development Tests from Running Automatically by @nbollis in #731
• Raw file connection not closing by @elaboy in #709
• Above Averaging Algorithm Rework and Crash Fix by @nbollis in #739
• Allowed reading of scan descriptions from Raw Files by @nbollis in #736
• Toppic search result reading by @nbollis in #735

Full Changelog: 1.0.541...1.0.542

Support for reading outside data and bug fixes

Added support for Bruker data #702
Fixed chemical formula bug
Update to uniprot ptmlist.txt loader
Fixed xml.gz compression bug so we load complete xml
Improved comments in FlashLFQ
Added support for FlashDecon and TopFD file parsing
New method to check valid amino acid sequence to help with reading data from outside programs
Improved ability of FlashLFQ to handle unusual characters in file input
Added support for negative deconvolution

Updates to Readers

Reader Refactor

mzLib 1.0.539 is not backwards compatible. The IO.MzmlMethods class has been moved to Readers.MzmlMethods, but all functionality has been maintained. Updating to mzLib 1.0.539 will require using directives to be changed to reflect the new namespace.

MsDataFile is now an abstract type defining methods to read data from files, both statically and dynamically.
Previously supported data types (.raw, .mzml. .mgf) are still supported with previous syntax, but can also now be constructed with the unified syntax below:

MsDataFile file = MsDataFileReader.ReadDataFile("msFilePath.raw");
MsDataFile file = MsDataFileReader.ReadDataFile("msFilePath.mzML");
MsDataFile file = MsDataFileReader.ReadDataFile("msFilePath.mgf");

To receive the data from the MsDataFile object, the following methods are available:

• GetMsDataScans() -> an array of all scans
• GetAllScansList() -> a list of all scans
• GetMs1Scans() -> a list of all Ms1 scans
• GetOneBasedScan(int scanNumber) -> get a scan from the file based upon its scan number
• GetMsScansInTimeRange(startTime, endTime) -> gets all scans within retention time range
• GetClosestOneBasedScanNumber(retentionTime) -> gets scan number of scan closest to retentionTime

To receive data dynamically (without loading the whole file), each MsdataFile class has the following methods available:

• InitiateDynamicConnection() -> initiates the dynamic connection
• GetOneBasedScanFromDynamicConnection(scanNumber) -> gets a single scan from the dynamic connection based upon its scan number
• CloseDynamicConnection() -> disposes of the dynamic connection

To add a new supported data type:

1. Create a new class for the data type, inherit from MsDataScan, and implement all of the required methods.
2. Add a case to the switch method in the MsDataFileReader class for the new data type

Other Changes

• There was a bug wherein adding two chemical formulas with negative isotopes gave the wrong answer. The example was deamidation (H-1N-1O) plus deamidation. The expected answer is H-2N-2O2 but the original gave O2. Added by @trishorts in #697
• Deconvolution Testing Environment was added by @nbollis in #690. This environment is not included in release versions of mzLib
• Added option to quantify ambiguous peptides in FlashLFQ by @Alexander-Sol in #700
• Averaging Updates by @nbollis in #683

Full Changelog: 1.0.538...1.0.539