Commented out Carbamidomethyl filtering in MZIdentMLReader.
Most recent version I have.
Loading still not 100% complete, but is almost there. Charges are getting loaded and NET renamed to AverageNet for greater clarity
Merge branch 'master' into Sam's_Recommendations
-- Revert some changes in the object mappings - other work needs to be done to fix the duplicate key problem; Changed the output path of one test to the TestData directory; updating the mtdb test files.
Added PTM object to hold location, mass and eventually formula
Merge branch 'Sam's_Recommendations' of https://github.com/PNNL-Comp-Mass-Spec/MTDB-Creator into local/Sam's_Recommendations
PTMs are saved and loaded from the database back into the objects. (both consensus and evidences)
Add files to begin supporting UNIMOD xml parsing and data access
-Updated schema for database to hold the sequence
-ConsensusTarget constructor now creates EncodedNumericSequence and EncodedNonNumericSequence automatically
-Clarified naming of variables in MtdbCreator.cs
-Added check to prevent same dataset from being processed across multiple runs
-Added check where if no new data is given through the API, it will simply return the existing database
Most work on Unimod data parser done; still does not work, but does compile. Test currently fails.
Adding clean sequence back in
Merge remote-tracking branch 'origin-github/Sam's_Recommendations' into Sam's_Recommendations
- Added reader.ReadStartElement() calls at the beginning of each data builder to digest the start element node
- Added loop for each data builder so the ReadElement style method need only be called once (not sure if this is the right way to do it)
- Commented out reader call inside UniModData, which causes datafile to be read multiple times
Forgot to move initialization of list into the loop. Was creating bad formula for every mod and amino acid
Unimod reader is functional, further changes pending.
More work on UniMod data reader and object. Also storing mod bricks now.
Fleshed out the test for the UniMod data. Now testing multiple units of each type.
Further work will include data access changes - changing some data to private.
More cleanup of UniModData, Reader, and tests.
Implemented a preferred output order of elements in the chemical formula.
Consolidated DatabaseReaderFactory into DatabaseCreatorFactory and renamed to DatabaseFactory.
Made necessary changes to other classes to work as previously did.
Passes all current unit tests.
More cleanup - added some comments, removed some debugging output, cleaned up namespaces.
Uncommented the database reader, and made changes to make it functional again.
- Updated Evidences to also have the NonNumericSequence
- Updated Clusterer to cluster based on the NonNumericSequence from evidences
    - Doing this preserves Evidences (especially from MzIdent format files) which have the same sequence, but with modifications
- Added a flag to LcmsDataSet for if the dataset had been analyzed previously to address duplicate analysis
- Updated ConsensusTarget
    - CleanSequence is the sequence stored in the database
    - All sequences are rebuild upon addition of an evidence