MsAlign Mass Spec File Reading

[nbollis]

Added support for new MS alignment file types, and updated tests accordingly.

• ClassExtensions.cs: Added ToNullableDouble, and ToNullableInt methods; enhanced documentation for several methods.
• MsAlign.cs, Ms1Align.cs, Ms2Align.cs: Introduced new classes for MS alignment with shared base class MsAlign.
• MsDataFileReader.cs: Updated to support new Ms1Align and Ms2Align file types.
• TestMsAlign.cs: Added comprehensive tests for new MS alignment functionality.
• SupportedFileTypes.cs: Updated file type detection to recognize .msalign files.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 89.97214% with 36 lines in your changes missing coverage. Please review.

Project coverage is 75.68%. Comparing base (983c3b0) to head (1bebec3).

Files with missing lines	Patch %	Lines
mzLib/Readers/MsAlign/MsAlign.cs	88.99%	6 Missing and 30 partials :warning:

Additional details and impacted files

[](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #805 +/- ## ========================================== + Coverage 75.52% 75.68% +0.16% ========================================== Files 202 205 +3 Lines 30945 31303 +358 Branches 3129 3200 +71 ========================================== + Hits 23371 23693 +322 - Misses 7040 7046 +6 - Partials 534 564 +30 ``` | [Files with missing lines](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [mzLib/MzLibUtil/ClassExtensions.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FMzLibUtil%2FClassExtensions.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvTXpMaWJVdGlsL0NsYXNzRXh0ZW5zaW9ucy5jcw==) | `100.00% <100.00%> (ø)` | | | [...sults/ResultFiles/MsDataFileToResultFileAdapter.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FResultFiles%2FMsDataFileToResultFileAdapter.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvUmVzdWx0RmlsZXMvTXNEYXRhRmlsZVRvUmVzdWx0RmlsZUFkYXB0ZXIuY3M=) | `100.00% <100.00%> (ø)` | | | [mzLib/Readers/MsAlign/Ms1Align.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FReaders%2FMsAlign%2FMs1Align.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9Nc0FsaWduL01zMUFsaWduLmNz) | `100.00% <100.00%> (ø)` | | | [mzLib/Readers/MsAlign/Ms2Align.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FReaders%2FMsAlign%2FMs2Align.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9Nc0FsaWduL01zMkFsaWduLmNz) | `100.00% <100.00%> (ø)` | | | [mzLib/Readers/MsDataFileReader.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FReaders%2FMsDataFileReader.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9Nc0RhdGFGaWxlUmVhZGVyLmNz) | `100.00% <100.00%> (ø)` | | | [mzLib/Readers/Util/SupportedFileTypes.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FReaders%2FUtil%2FSupportedFileTypes.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9VdGlsL1N1cHBvcnRlZEZpbGVUeXBlcy5jcw==) | `97.70% <100.00%> (+0.20%)` | :arrow_up: | | [mzLib/Readers/MsAlign/MsAlign.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/805?src=pr&el=tree&filepath=mzLib%2FReaders%2FMsAlign%2FMsAlign.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9Nc0FsaWduL01zQWxpZ24uY3M=) | `88.99% <88.99%> (ø)` | |