score_all_epitopes: Given a list of scoring jobs, compute the similarities
In philliplab/EpitopeMatcher: Epitope Matcher

This function is mostly just a wrapper for score_epitope.

score_all_epitopes(
  the_scoring_jobs,
  query_alignment,
  range_expansion,
  update_progress_bar = NULL,
  substitutionMatrix = "BLOSUM50"
)

`the_scoring_jobs`	A list of scoring_jobs
`query_alignment`	The query alignment
`range_expansion`	After the epitope is found in the reference seqeuence, search in each of the query sequences for the same epitope, but expand the range with this number of amino acids
`update_progress_bar`	A closure passed in from a reactive shiny expression that allows a progress bar to be updated when using the shiny web ui.
`substitutionMatrix`	substitution matrix representing the fixed substitution scores for an alignment. It cannot be used in conjunction with patternQuality and subjectQuality arguments.