todo.md

Unimplemented API Endpoints

This document lists the API endpoints and properties that are defined in the native-fisher-py codebase but currently lack implementation. They are ranked by importance for typical mass spectrometry data processing workflows.

1. Critical Importance (Core Data & MS/MS)

Missing foundational data required for standard LC-MS/MS analysis.

Class	Method / Property	Status
ScanEvent	get_isolation_width(index)	❌ Missing in Native & Python
ScanEvent	get_mass_range(index)	❌ Missing in Native & Python
Reaction	isolation_width	❌ Python Placeholder
Reaction	isolation_width_offset	❌ Python Placeholder
Reaction	precursor_range_is_valid	❌ Python Placeholder
ScanDependentDetails	precursor_mass_array	❌ Python Placeholder
ScanDependentDetails	isolation_width_array	❌ Python Placeholder

2. High Importance (Metadata & Run Stats)

Essential for file overview and scan tracking.

Class	Method / Property	Status
RunHeader	end_time	❌ Python Placeholder
RunHeader	expected_runtime	❌ Python Placeholder
RunHeader	high_mass / low_mass	❌ Python Placeholder
RunHeader	spectra_count	⚠️ Partially implemented in some subclasses
ScanStatistics	cycle_number	❌ Python Placeholder
ScanStatistics	segment_number	❌ Python Placeholder
ScanStatistics	scan_type	❌ Python Placeholder
ScanStatistics	spectrum_packet_type	❌ Python Placeholder

3. Medium Importance (Diagnostic & Advanced Info)

Useful for peak quality assessment and instrument status.

Class	Method / Property	Status
CentroidStream	base_peak_noise	✅ Implemented
CentroidStream	base_peak_resolution	✅ Implemented
CentroidStream	baselines	✅ Implemented
CentroidStream	charges	✅ Implemented
CentroidStream	noises	✅ Implemented
SampleInformation	injection_volume	✅ Implemented
SampleInformation	instrument_method_file	✅ Implemented
AutoSamplerInformation	tray_index / vial_index	✅ Implemented
AutoSamplerInformation	tray_name / tray_shape	✅ Implemented

4. Low Importance (Verbose Metadata)

Auxiliary information rarely used in downstream analysis.

Class	Method / Property	Status
ErrorLogEntry	message	❌ Python Placeholder
ErrorLogEntry	retention_time	❌ Python Placeholder
HeaderItem	is_numeric	❌ Python Placeholder
HeaderItem	format_value	❌ Python Placeholder
FileHeader	revision	❌ Python Placeholder
FileHeader	number_of_times_calibrated	❌ Python Placeholder
ScanEvent	is_custom	❌ Python Placeholder
ScanEvents	get_event_by_segment	❌ Python Placeholder

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Note: Many Python placeholders return default values when _IS_SPHINX is true to allow documentation builds, but will raise NotImplementedError during actual execution.