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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

What Is Comet

Comet is an open-source tandem mass spectrometry (MS/MS) sequence database search engine written in C/C++. It searches experimental MS/MS spectra against protein sequence databases to identify peptides.

Build Commands

Linux / macOS

make          # Full build (MSToolkit + AScorePro + CometSearch + Comet.exe)
make clean    # Full clean including MSToolkit and AScorePro
make cclean   # Quick clean: only CometSearch and root object files

Windows (Visual Studio)

  • Load Comet.sln in Visual Studio 2022 (build tools v143)
  • Set configuration to Release / x64
  • Right-click the Comet project → Build
  • Output: x64/Release/Comet.exe

The build requires Thermo's MSFileReader to be installed first (Windows only).

CometSearch library only

cd CometSearch && make

Repository Structure

Comet/                      # Top-level: main entry point (Comet.cpp), solution files
CometSearch/                # Core C++ search library (compiled to libcometsearch.a)
CometWrapper/               # C++/CLI managed wrapper (CometWrapper.dll) bridging C++ to C#
RealtimeSearch/             # C# application layer for real-time (RTS) searches
AScorePro/                  # AScore phosphosite localization library (git submodule-like)
MSToolkit/                  # Mass spec file format reader library (Mike Hoopmann)
extern/                     # Third-party dependencies (expat, zlib)
docs/                       # Architecture docs, coding style, threading design records

Architecture

The codebase has three layers:

  1. Native C++ core (CometSearch/): The search engine library. Key classes:

    • CometSearchManager — implements ICometSearchManager; top-level orchestrator
    • CometSearch — fragment index querying, XCorr scoring, peptide matching
    • CometPreprocess — spectrum preprocessing (binning, noise reduction)
    • CometPostAnalysis — SP score, E-value, delta-Cn, AScorePro localization
    • CometFragmentIndex / CometPeptideIndex — index building and lookup
    • CometSpecLib — MS1 spectral library loading and search
    • CometAlignment — MS1 RT alignment

  2. C++/CLI wrapper (CometWrapper/): CometSearchManagerWrapper (ref class) marshals data between managed C# and native C++. CometDataWrapper.h defines managed wrapper types (ScoreWrapper, FragmentWrapper, etc.).

  3. C# application (RealtimeSearch/): SearchMS1MS2.cs drives concurrent real-time searches by launching parallel C# Task threads that call into the wrapper.

Key Globals (CometSearch)

Global Thread-safe? Notes
g_staticParams ✅ Read-only after init All search parameters
g_iFragmentIndex, g_vFragmentPeptides, g_vRawPeptides ✅ Read-only after init Fragment index
g_pvProteinNames, g_pvProteinsList ✅ Read-only after init
g_vSpecLib ✅ Read-only after init MS1 spectral library
g_pvQuery ❌ Shared mutable Batch search path only
g_pvQueryMS1 ❌ Shared mutable Batch MS1 path only
g_cometStatus ❌ Shared mutable Error reporting

Threading Model (RTS path)

The real-time search (DoSingleSpectrumSearchMultiResults and DoMS1SearchMultiResults) is designed for concurrent calls from C# Task threads:

  • MS2 RTS: PreprocessSingleSpectrumThreadLocal() creates a caller-owned Query*; CometSearch::RunSearch(Query*, time_point) searches against the read-only fragment index; thread-local CalculateSP/CalculateEValue/CalculateDeltaCn(Query*) do post-analysis. No g_pvQuery access.
  • MS1 RTS: PreprocessMS1SingleSpectrumThreadLocal() creates a caller-owned QueryMS1*; RunMS1Search(QueryMS1*, ...) scores against read-only g_vSpecLib. No g_pvQueryMS1 access. Reference library is loaded once in InitializeSingleSpectrumMS1Search().
  • Batch search: Still uses g_pvQuery / g_pvQueryMS1 with the original mutex-guarded path.

Coding Style

From docs/CometCodingStyleGuidelines.md:

  • Allman brace style: opening brace on its own line at the same indentation as the control structure
  • 3 spaces per indentation level (no tabs)
  • Windows-style line endings (\r\n)
  • Use // for inline comments (reserve /* */ for commenting out blocks)
  • Systems Hungarian Notation for variable names (e.g., iCount, dMass, szName, bFlag, p prefix for pointers)
  • No trailing whitespace
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