Introduced support for handling RNA data within the UsefulProteomicsDatabases project. Key changes include:

- Added `Transcriptomics\TestData` folder to `Test.csproj`.
- Changed access modifiers in `ProteinDbLoader.cs` to internal.
- Added `using` directives for `Transcriptomics` in `ProteinXmlEntry.cs`.
- Introduced methods `ParseRnaEndElement` and `ParseRnaEntryEndElement` in `ProteinXmlEntry.cs`.
- Modified `ParseAnnotatedMods` to check for RNA modifications.
- Added project reference to `Transcriptomics.csproj` in `UsefulProteomicsDatabases.csproj`.
- Added `ClassExtensions.cs` with `CreateNew` method for nucleic acids.
- Added `RnaDbLoader.cs` for RNA database loading.
- Added `RnaDecoyGenerator.cs` for generating decoy RNA sequences.

Updated `using` directives in `TestDigestion.cs` and `OligoWithSetMods.cs` to include necessary namespaces. Added assertions in `TestDigestion.cs` for `SequenceWithChemicalFormulas` and `FullSequenceWithMassShift`. Changed `namespace` in `OligoWithSetMods.cs` to `Transcriptomics.Digestion`. Implemented and cached `SequenceWithChemicalFormulas` property in `OligoWithSetMods.cs`.

- Added new files `ModomicsUnmodifiedTrimmed.fasta` and `ModomicsUnmodifiedTrimmed.fasta.gz` to `Test.csproj` with `CopyToOutputDirectory` set to `PreserveNewest`.
- Removed the `Transcriptomics\TestData` folder from `Test.csproj`.
- Introduced `Transcribe` method in `ClassExtensions.cs` for DNA to RNA transcription.
- Added summary comment to `NucleolyticOligo` class in `NucleolyticOligo.cs`.
- Added `ApplyRegex` method in `FastaHeaderFieldRegex.cs`.
- Introduced `ProteinDbWriter` class in `ProteinDbWriter.cs` for writing protein and nucleic acid databases.
- Modified `GetModsForThisProtein` to `GetModsForThisBioPolymer` in `ProteinDbWriter.cs`.
- Added `RnaDbLoader` class in `RnaDbLoader.cs` for RNA FASTA header detection and sequence loading.
- Updated user dictionary in `mzLib.sln.DotSettings` with new terms.
- Added test cases in `TestDbLoader.cs` for RNA database loading and header detection.
- Introduced `TestDecoyGeneration` class in `TestDecoyGenerator.cs` for RNA decoy generation tests.
- Added RNA sequence file `ModomicsUnmodifiedTrimmed.fasta` and its compressed version.

- Added `using` directives for `Transcriptomics.Digestion` and `UsefulProteomicsDatabases.Transcriptomics` in `TestDecoyGenerator.cs`.
- Introduced `TestCreateNew` in `TestDecoyGenerator.cs` to verify RNA and oligo creation.
- Added `using` directive for `MzLibUtil` in `TestDigestion.cs`.
- Added a test in `TestDigestion.cs` for exception handling with invalid sequences.
- Added `using` directives for `Omics` and related namespaces in `TestFragmentation.cs`.
- Modified `TestFragmentation_Modified` in `TestFragmentation.cs` to use `OligoWithSetMods` directly and added assertions.
- Updated `ClassExtensions.cs` to allow setting `isDecoy` in new `RNA` objects.
- Refactored `OligoWithSetMods.cs` to return a dictionary from `GetModsAfterDeserialization`.
- Updated `OligoWithSetMods.cs` to initialize `_allModsOneIsNterminus` using the returned dictionary.

…namespaces

…into RnaImplementation

Refactored constructors, improved exception handling, and added comprehensive tests across multiple files. Key changes include:

- `MzLibException.cs`: Updated constructor to include `innerException`.
- `TestDecoyGenerator.cs`: Added assertions for `CreateNew` method.
- `TestDigestion.cs`: Added assertions and new test for RNA digestion exception.
- Refactored modification lists and added various tests for modifications.
- `TestNucleicAcid.cs`: Refactored methods, adjusted precision, and updated terminus assignments.
- `NucleolyticOligo.cs`: Changed parameter types, updated comments, and improved variable names.
- `OligoWithSetMods.cs`: Enhanced exception messages and updated modification location checks.
- `NucleicAcid.cs`: Added `using` directive, changed exception type, and refactored methods.
- `mzLib.sln.DotSettings`: Updated user dictionary entries.

…into RnaImplementation

Added new test data files (`20mer1.fasta`, `20mer1.fasta.gz`, `20mer1.xml`, `20mer1.xml.gz`) to the `Transcriptomics\TestData` directory in the `Test.csproj` file, ensuring they are copied to the output directory. Introduced `TestDbReadingDifferentExtensions` in `TestDbLoader.cs` to verify RNA database reading from various formats. Added `TestDigestionMaxIsoforms` in `TestDigestion.cs` to test RNA sequence digestion with max isoforms. Updated `WriteNucleicAcidXmlDatabase` in `ProteinDbWriter.cs` with remarks for future implementation. Added a TODO in `RnaDecoyGenerator.cs` regarding palindromic sequences' impact on fragment ions. Included new RNA sequence data in test files for validation.