perf: remove unnecessary string copy in MSA output

[nh13]

Summary

Remove unnecessary string copy when outputting MSA sequences.

Background

From code review (research.md §2.1, LOW severity):
The code was copying each string to a local variable before calling c_str().

Changes

• src/caller.cpp: Use it.c_str() directly instead of copying to a new string

Test plan

• CI workflow passes
• MSA output unchanged

Closes #33

🤖 Generated with Claude Code

Summary by CodeRabbit

• Refactor
  • Optimized internal code for improved efficiency with no change to user-facing functionality.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

A single-line optimization in the MSA output loop removes an unnecessary temporary string copy, replacing a string variable assignment with direct element access for cleaner code.

Changes

Cohort / File(s)	Change Summary
MSA Output Optimization src/caller.cpp	Removed unnecessary string copy in loop; now prints iterator element directly via it.c_str() instead of intermediate std::string sequence variable. No functional change to output format.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Poem

🐰 A string once needlessly cloned,
Now prints with elegance shown—
Direct from the loop, no copy kept,
Where efficiency softly crept.
Hop, hop! ✨

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and specifically describes the main change: removing an unnecessary string copy in MSA output for performance.
Linked Issues check	✅ Passed	The changes directly address issue #33 by removing the unnecessary std::string copy and using it.c_str() directly in the fprintf call.
Out of Scope Changes check	✅ Passed	The changes are narrowly scoped to the specific objective stated in issue #33 with no additional modifications outside the stated scope.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/33-remove-string-copy

---

📜 Recent review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 6125727 and b72c119.

📒 Files selected for processing (1)

• src/caller.cpp

🔇 Additional comments (1)

src/caller.cpp (1)

244-246: Clean and correct optimization. 👍

Removing the unnecessary temporary string copy improves performance by eliminating a heap allocation per loop iteration while maintaining identical output semantics. The range-based for loop with const auto& it correctly binds it to a const reference, and it.c_str() is a valid and safe call.

---

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[nh13]

@coderabbitai review

[coderabbitai]

✅ Actions performed

Review triggered.

Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.