code wiki / (root) / nx_chem_peak_list.nx

nx_chem_peak_list.nx

buildroot/runtime/nx_chem_peak_list.nx

15504 B404 linesdepth 7pulls 9 transitivereach 11 importersview sourcekind librarytopic chem

docs dependencies structs consts functions

about

nx_chem_peak_list.nx -- C5.0 milestone: text-format peak list parser. A lab analyst's LC-MS output (after peak picking) is typically a list of "m/z [intensity] [retention_time]" entries. This module parses that format into a PeakList struct that composes directly with C4.0 adulterant_db_lookup_mh_plus. Supported format (whitespace-separated, '#' comments): # comment line ignored m/z [intensity] [rt_seconds] 280.1826 10000 742.3 102.1274 8500 45.2 195.0875 15000 234.1 166.1223 5000 89.5 Decimals are parsed to Q4 (4 fractional digits) for m/z; rt stored as Q3 milliseconds. Intensity stored as raw nx_int. Honest gaps (deferred): - mzML/mzXML parsing (XML-based standard): too complex without full XML parser in substrate; C5.1. - JCAMP-DX (NMR/IR/spectra format): C5.2. - Centroided vs profile-mode discrimination: caller responsibility. - Adduct/charge state assignment heuristics (a la CAMERA): C5.3.

dependencies 3 imports · 11 importers

diagram shows first 10 each side; +0 more imports, +1 more importers in the complete lists below.

imports: nx_chem.nxnx_syscalls.nxnx_loop.nx

imported by: nx_chem_adulterant_db.nxnx_chem_adulterant_db_test.nxnx_chem_peak_list_test.nxnx_chem_report_csv.nxnx_chem_report_csv_test.nxnx_chem_report_json.nxnx_chem_report_json_test.nxnx_supplement.nxnx_supplement_batch.nxnx_supplement_check.nxnx_supplement_csv.nx

structs

31	struct PeakObservation
38	struct PeakList

consts

36	const NX_PEAK_OBS_BYTES: nx_int = 24
43	const NX_PEAK_LIST_BYTES: nx_int = 24

functions

48	func nx_chem_peak_list_new(cap: nx_int) -> *PeakList called by 7: nx_chem_peak_list_parse nx_chem_peak_list_read_file e_full_report run_csv_demo g_full_json_report run_json_demo+1 calls 1: sys_mmap
59	func nx_chem_peak_list_add(pl: *PeakList, mz_q4: nx_int, intensity_q4: nx_int, rt_q3: nx_int) -> nx_int called by 6: nx_chem_peak_list_parse e_full_report run_csv_demo g_full_json_report run_json_demo cmd_validate
80	func nx_chem_parse_decimal_q4(buf: u8, offset: nx_int, len: nx_int, out_value: nx_int) -> nx_int called by 7: nx_chem_load_rt_calibration nx_chem_peak_list_parse a_parse_decimal b_parse_short_decimal c_parse_int d_parse_no_digit+1 calls 3: nx_loop_begin nx_loop_step nx_loop_break
149	func nx_chem_is_hspace(c: nx_int) -> nx_int called by 2: nx_chem_load_rt_calibration nx_chem_peak_list_parse
159	func nx_chem_is_lineterm(c: nx_int) -> nx_int called by 3: nx_chem_load_rt_calibration nx_chem_load_compounds_from_file nx_chem_peak_list_parse
176	func nx_chem_peak_list_parse(buf: u8, len: nx_int) -> PeakList called by 6: nx_chem_peak_list_read_file f_parse_two_peaks g_parse_comments_and_blanks h_parse_three_col l_csv_peak_format run_pipeline_demo calls 8: nx_chem_peak_list_new nx_loop_begin nx_loop_step nx_loop_break nx_chem_is_lineterm nx_chem_parse_decimal_q4+2
289	func nx_chem_peak_list_read_file(path: u8) -> PeakList called by 9: i_file_roundtrip j_missing_file cmd_check cmd_selftest process_one_sample_batch process_one_csv_row+3 calls 3: sys_read_file nx_chem_peak_list_new nx_chem_peak_list_parse
306	func nx_chem_write_file(path: u8, buf: u8, len: nx_int) -> nx_int called by 3: o_load_compounds m_load_rt_calibration i_file_roundtrip calls 3: sys_openat_wr sys_write sys_close
335	func nx_chem_path_from_literal(literal: u8) -> u8 called by 1: cmd_selftest calls 4: sys_mmap nx_loop_begin nx_loop_step nx_loop_break
366	func nx_chem_basename(path: u8, out_buf: u8) -> nx_int called by 7: k_basename cmd_check process_one_sample_batch process_one_csv_row process_one_sample main+1 calls 3: nx_loop_begin nx_loop_step nx_loop_break