obitools4/autodoc/docmd/pkg/obiapat/pattern_test.md

Semantic Description of obiapat Package Functionality

The obiapat package provides utilities for constructing and representing approximate sequence patterns—flexible biological or symbolic string templates supporting mismatches, insertions, and deletions.

Core Functionality

• MakeApatPattern(pattern string, errormax int, allowsIndel bool)
  Parses a pattern specification (e.g., "A[T]C!GT") and returns an internal representation (*ApatPattern) suitable for approximate matching.

  • pattern: A string where:
    • Standard characters (e.g., 'A', 'C') denote exact matches.
    • Brackets [X] indicate optional or variable positions, e.g., ambiguity (like IUPAC codes).
    • Exclamation ! marks positions where errors (substitutions) are permitted.
  • errormax: Maximum number of allowed errors (mismatches or indels, depending on flags).
  • allowsIndel: Boolean flag enabling/disabling insertion/deletion operations.

Behavior & Semantics

• Returns a compiled pattern object (non-nil) on success; errors may arise from malformed input or invalid parameters.
• Supports three modes:
  • Exact matching (errormax = 0, allowsIndel = false).
  • Substitution-only approximation (errormax > 0, allowsIndel = false).
  • Full approximate matching with indels (errormax > 0, allowsIndel = true).

Testing Coverage

The provided test suite validates:

• Valid pattern parsing across different configurations.
• Correct handling of nil vs. non-nil output pointers.
• Robustness against error conditions (e.g., invalid inputs would trigger expected errors).

In summary, obiapat enables efficient definition and handling of approximate regular expressions tailored for sequence analysis in bioinformatics or pattern recognition contexts.