Add SpectrumParser virtual class

[jorainer]

This is a small proposal to help unifying the API for the spectrum parsers. The idea is to have a virtual class SpectrumParser with a defined set of methods. Parser implementations should extend this class and implement all of its methods.

We would have to agree also on a common set of methods and its input and result arguments. I've added one method so far, but more (or different ones) might be helpful.

• importSpectrum takes a SpectrumParser object and a file, reads its content, maps its properties to the standard fields (using the schema) and returns a Spectra object.

If this method or the return type makes sense needs to be discussed further. I just wanted to propose one way how a single API for the user could be defined that uses different parsers to read data from different sources.

An example workflow to read data from a single file would be the following (based on the toy MassbankParser object extending SpectrumParser I've implemented):

library(MSnio)
## Create and intialize a parser; this should read/import the corresponding schema
prs <- MassbankParser()
## Spectrum file
fl <- system.file("spectra/massbank/EA016614.txt", package="MSnio")
res <- importSpectrum(prs, fl)

## res should then ideally be a `Spectra` object - or the new `Spectrum` object.

Let's discuss now.

[jorainer]

Just realized I can't request any reviewers - so please @meowcat , @michaelwitting @Treutler , have a look at it and let's discuss.

[meowcat]

Thanks for the input. It looks good already, but do we want a SpectrumParser or do we want a more general FormatHandler (or whatever) which has both import (parser) and export (writer)?

[meowcat]

We can of course have them separate, but ideally for any format the Parser and the Writer implementation would successfully round-trip (and we could use this as a unit test) and ideally also use the same schema definitions...

[jorainer]

Good point! I just don't like the name yet. What about SpectrumRecord and e.g. MassbankRecord?

[meowcat]

I also don't like the name :) But Record is also so-so because it describes the entity of a record more than the facility to handle it.

By the way, for this class I suggest we also specify something like the "subset of fields it can successfully round-trip", because not all formats will be able to handle everything lossless for import and export (even though we would like it). The validation / unittest procedure would then possibly be:

• Take a sample record
• crop it to supported fields
• export it
• (check the exported file)
• import it back
• check the identity of the re-imported record to the cropped original record.

[jorainer]

An alternative would be to set all the not-supported fields to NA. That's at least what we have e.g. in mzR as not all input files provide all spectrum metadata.

[meowcat]

A field can be NA if there is no data in the file, regardless of whether the file format actually supports the field or not. E.g. for MassBank records there is a vast amount of optional fields. I think specifying the supported fields per file format will be important when it comes to reproducibility/testing.

[jorainer]

Agree. And that's exactly the point. I will try to define a schema for hmdb an importer, unit tests etc and then make a pull request (or actually change this one).

[jorainer]

Name: SpectrumAccessor, MassbankAccessor???

[Treutler]

Our FormatAdapter (or whatever) is similar to a BridgeDb IDMapper. A FormatAdapter could have

• a supported record format
• a set of supported input fields (the fields from the general format which are readable from file)
• a set of supported output fields (the fields from the general format which are writeable to file)
• any other format-specific information we want

The FormatAdapter would than do the import and export and map the fields from file to the fields from the general format and vice versa.

[meowcat]

Other name ideas: SpectrumTranslator SpectrumConverter But @jorainer for now you can use what you like best, changing the name will be the smallest problem if we don't like it.