Some overloads violate function intent

[timholy]

Some of the overloads of Base methods violate the intended API of the function. For example, print(x, y, z...) should print all of x, y, and z to the terminal, yet we have methods that add a format argument that isn't displayed:

• MIToS.jl/src/MSA/FASTA.jl

  Line 97 in 717d6f9

  Base.print(msa::AbstractMatrix{Residue}, format::Type{FASTA}) = print(stdout, msa, FASTA)

• MIToS.jl/src/MSA/Raw.jl

  Line 72 in 717d6f9

  Base.print(msa::AbstractMatrix{Residue}, format::Type{Raw}) = print(stdout, msa, Raw)

• MIToS.jl/src/PDB/PDBParser.jl

  Line 301 in 717d6f9

  Base.print(reslist::AbstractVector{PDBResidue},format::Type{PDBFile}) = print(stdout, reslist, format)

By comparison:

julia> print("Hello", Float32)
HelloFloat32

The way that Base intends you to customize output of print is with an IOContext wrapper around the io object.

[diegozea]

Hi @timholy !

I think I will change the read , parse and write and print for (something, FileFormat), to read_file, parse_file, print_file, and write_file, respectively. Do you think that's a better approach?

Cheers,

[diegozea]

Hi!

MIToS 2.18 now defines the read_file, parse_file, print_file, and write_file functions for reading and writing in specific file formats—subtypes of FileFormat—instead of overloading the functions from Base. The signatures and behaviors don't change, so the migration will require replacing read with read_file and so on. So, for example read(msafile, FASTA) becomes read_file(msafile, FASTA).

Cheers