Refactored function names in msa.R | networks_domarch.R | networks_gencontext.R

[teddyCodex]

Description

Refactored specified function names in multiple files based on issue #7

R/msa.R

Original	Modified	User Facing
msa_pdf	createMSA_PDF	✅
generate_msa	createMSA_Kalign	✅

R/networks_domarch.R

Original	Modified	User Facing
domain_network	createDomainNetwork	✅
BinaryDomainNetwork	createBinaryDomainNetwork	✅

R/networks_gencontext.R

Original	Modified	User Facing
gc_undirected_network	createUndirectedDomainNetwork	✅
GenContextNetwork	createGenomicContextNetwork	✅

Fixes issue #49

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

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• I have read and followed the CONTRIBUTING.md guidelines.
• I have searched for existing content to ensure this is not a duplicate.
• I have performed a self-review of these additions (including spelling, grammar, and related).
• I have added comments to my code to help provide understanding.
• I have added a test which covers the code changes found within this PR.
• I have deleted all non-relevant text in this pull request template.
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[the-mayer]

Thanks, sending to main!