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Support FASTA input for calibration-library sequence matching #119

Description

@jspaezp

Title: Support FASTA input for calibration-library sequence matching

--calib-lib is now independent of the primary search source, including a
FASTA-predicted primary library. Calibration itself still accepts only a built
library.

Add --calib-fasta (and the matching configuration field). When sequence
features are available, match calibration peptides against predicted/search
sequences with a multi-pattern matcher such as Aho-Corasick instead of requiring
the user to materialize another spectral library.

Decide explicitly:

  • whether --calib-lib and --calib-fasta are mutually exclusive;
  • how modifications and I/L equivalence affect matching;
  • behavior when sequence features are unavailable;
  • whether calibration FASTA digestion settings share or override [library].

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