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smith-chem-wisc / mzLib

Library for mass spectrometry projects
GNU Lesser General Public License v3.0
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Transcriptomics Digestion and Fragmentation #801

Closed nbollis closed 1 week ago

nbollis commented 1 month ago

Implemented the derived calasses of the Omics abstracts and interfaces for RNA

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 92.78261% with 83 lines in your changes missing coverage. Please review.

Project coverage is 76.48%. Comparing base (983c3b0) to head (04f7e67). Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
...zLib/Transcriptomics/Digestion/OligoWithSetMods.cs 87.78% 20 Missing and 7 partials :warning:
mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs 88.23% 9 Missing and 3 partials :warning:
mzLib/Transcriptomics/NucleicAcid.cs 92.08% 6 Missing and 5 partials :warning:
...ProteomicsDatabases/Transcriptomics/RnaDbLoader.cs 93.71% 3 Missing and 7 partials :warning:
mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs 79.54% 6 Missing and 3 partials :warning:
mzLib/Transcriptomics/ClassExtensions.cs 93.84% 1 Missing and 3 partials :warning:
...zLib/Transcriptomics/Digestion/NucleolyticOligo.cs 96.39% 1 Missing and 3 partials :warning:
...roteolyticDigestion/PeptideWithSetModifications.cs 0.00% 3 Missing :warning:
...micsDatabases/Transcriptomics/RnaDecoyGenerator.cs 94.44% 1 Missing and 1 partial :warning:
...UsefulProteomicsDatabases/FastaHeaderFieldRegex.cs 88.88% 0 Missing and 1 partial :warning:
Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801/graphs/tree.svg?width=650&height=150&src=pr&token=1lXMC2BqYG&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?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 #801 +/- ## ========================================== + Coverage 75.52% 76.48% +0.96% ========================================== Files 202 211 +9 Lines 30945 31960 +1015 Branches 3129 3286 +157 ========================================== + Hits 23371 24446 +1075 + Misses 7040 6954 -86 - Partials 534 560 +26 ``` | [Files with missing lines](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?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/Chemistry/ClassExtensions.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FChemistry%2FClassExtensions.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvQ2hlbWlzdHJ5L0NsYXNzRXh0ZW5zaW9ucy5jcw==) | `100.00% <100.00%> (ø)` | | | [mzLib/MzLibUtil/MzLibException.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FMzLibUtil%2FMzLibException.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvTXpMaWJVdGlsL016TGliRXhjZXB0aW9uLmNz) | `100.00% <100.00%> (ø)` | | | [.../Fragmentation/Oligo/DissociationTypeCollection.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FOmics%2FFragmentation%2FOligo%2FDissociationTypeCollection.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvT21pY3MvRnJhZ21lbnRhdGlvbi9PbGlnby9EaXNzb2NpYXRpb25UeXBlQ29sbGVjdGlvbi5jcw==) | `100.00% <100.00%> (+100.00%)` | :arrow_up: | | [...ragmentation/Oligo/TerminusSpecificProductTypes.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FOmics%2FFragmentation%2FOligo%2FTerminusSpecificProductTypes.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvT21pY3MvRnJhZ21lbnRhdGlvbi9PbGlnby9UZXJtaW51c1NwZWNpZmljUHJvZHVjdFR5cGVzLmNz) | `100.00% <100.00%> (ø)` | | | [mzLib/Omics/IBioPolymerWithSetMods.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FOmics%2FIBioPolymerWithSetMods.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvT21pY3MvSUJpb1BvbHltZXJXaXRoU2V0TW9kcy5jcw==) | `95.23% <ø> (ø)` | | | [...ib/Transcriptomics/Digestion/RnaDigestionParams.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FTranscriptomics%2FDigestion%2FRnaDigestionParams.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvVHJhbnNjcmlwdG9taWNzL0RpZ2VzdGlvbi9SbmFEaWdlc3Rpb25QYXJhbXMuY3M=) | `100.00% <100.00%> (ø)` | | | [mzLib/Transcriptomics/Digestion/Rnase.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FTranscriptomics%2FDigestion%2FRnase.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvVHJhbnNjcmlwdG9taWNzL0RpZ2VzdGlvbi9SbmFzZS5jcw==) | `100.00% <100.00%> (ø)` | | | [mzLib/Transcriptomics/RNA.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FTranscriptomics%2FRNA.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvVHJhbnNjcmlwdG9taWNzL1JOQS5jcw==) | `100.00% <100.00%> (ø)` | | | [mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FUsefulProteomicsDatabases%2FProteinDbLoader.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvVXNlZnVsUHJvdGVvbWljc0RhdGFiYXNlcy9Qcm90ZWluRGJMb2FkZXIuY3M=) | `95.40% <ø> (ø)` | | | [...UsefulProteomicsDatabases/FastaHeaderFieldRegex.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree&filepath=mzLib%2FUsefulProteomicsDatabases%2FFastaHeaderFieldRegex.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvVXNlZnVsUHJvdGVvbWljc0RhdGFiYXNlcy9GYXN0YUhlYWRlckZpZWxkUmVnZXguY3M=) | `90.00% <88.88%> (-0.91%)` | :arrow_down: | | ... and [9 more](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/801/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)