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ArrowSchemaRegistry.h
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1// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2// SPDX-License-Identifier: BSD-3-Clause
3//
4// --------------------------------------------------------------------------
5// $Maintainer: Timo Sachsenberg $
6// $Authors: Timo Sachsenberg $
7// --------------------------------------------------------------------------
8
9#pragma once
10
11#include <OpenMS/OpenMSConfig.h>
12#include <memory>
13#include <string>
14#include <vector>
15
16// Forward declarations
17namespace arrow
18{
19 class Schema;
20 class DataType;
21 class Table;
22}
23
24namespace OpenMS
25{
26
28 namespace ArrowSchemaValidation
29 {
32 enum class Mode
33 {
34 Strict,
35 Subset,
36 Extensible
37 };
38
40 struct OPENMS_DLLAPI ValidationResult
41 {
42 bool valid = true;
43 std::vector<std::string> errors;
44 std::string toString() const;
45 };
46
48 OPENMS_DLLAPI ValidationResult validate(
49 const std::shared_ptr<arrow::Table>& table,
50 const std::shared_ptr<arrow::Schema>& expected_schema,
51 Mode mode = Mode::Strict);
52 }
53
55 struct OPENMS_DLLAPI ProteinSchema
56 {
57 static constexpr const char* ACCESSION = "accession";
58 static constexpr const char* SCORE = "score";
59 static constexpr const char* RANK = "rank";
60 static constexpr const char* COVERAGE = "coverage";
61 static constexpr const char* SEQUENCE = "sequence";
62 static constexpr const char* DESCRIPTION = "description";
63 static constexpr const char* IS_DECOY = "is_decoy";
64 static constexpr const char* RUN_IDENTIFIER = "run_identifier";
65 static constexpr const char* MODIFICATIONS = "modifications";
66 static constexpr const char* METAVALUES = "metavalues";
67
68 static std::shared_ptr<arrow::DataType> modificationsType();
69 static std::shared_ptr<arrow::DataType> metavaluesType();
70 static std::shared_ptr<arrow::Schema> schema();
71 };
72
74 struct OPENMS_DLLAPI ProteinGroupSchema
75 {
76 static constexpr const char* GROUP_TYPE = "group_type";
77 static constexpr const char* PROBABILITY = "probability";
78 static constexpr const char* ACCESSIONS = "accessions";
79 static constexpr const char* RUN_IDENTIFIER = "run_identifier";
80 static constexpr const char* GROUP_INDEX = "group_index";
81 static constexpr const char* FLOAT_DATA = "float_data";
82 static constexpr const char* STRING_DATA = "string_data";
83 static constexpr const char* INTEGER_DATA = "integer_data";
84
85 static std::shared_ptr<arrow::DataType> floatDataType();
86 static std::shared_ptr<arrow::DataType> stringDataType();
87 static std::shared_ptr<arrow::DataType> integerDataType();
88 static std::shared_ptr<arrow::Schema> schema();
89 };
90
92 struct OPENMS_DLLAPI SearchParamsSchema
93 {
94 static constexpr const char* RUN_IDENTIFIER = "run_identifier";
95 static constexpr const char* SEARCH_ENGINE = "search_engine";
96 static constexpr const char* SEARCH_ENGINE_VERSION = "search_engine_version";
97 static constexpr const char* INFERENCE_ENGINE = "inference_engine";
98 static constexpr const char* INFERENCE_ENGINE_VERSION = "inference_engine_version";
99 static constexpr const char* DATE = "date";
100 static constexpr const char* SCORE_TYPE = "score_type";
101 static constexpr const char* HIGHER_SCORE_BETTER = "higher_score_better";
102 static constexpr const char* SIGNIFICANCE_THRESHOLD = "significance_threshold";
103 static constexpr const char* DB = "db";
104 static constexpr const char* DB_VERSION = "db_version";
105 static constexpr const char* TAXONOMY = "taxonomy";
106 static constexpr const char* CHARGES = "charges";
107 static constexpr const char* MASS_TYPE = "mass_type";
108 static constexpr const char* PRECURSOR_MASS_TOLERANCE = "precursor_mass_tolerance";
109 static constexpr const char* PRECURSOR_MASS_TOLERANCE_PPM = "precursor_mass_tolerance_ppm";
110 static constexpr const char* FRAGMENT_MASS_TOLERANCE = "fragment_mass_tolerance";
111 static constexpr const char* FRAGMENT_MASS_TOLERANCE_PPM = "fragment_mass_tolerance_ppm";
112 static constexpr const char* DIGESTION_ENZYME = "digestion_enzyme";
113 static constexpr const char* ENZYME_TERM_SPECIFICITY = "enzyme_term_specificity";
114 static constexpr const char* MISSED_CLEAVAGES = "missed_cleavages";
115 static constexpr const char* FIXED_MODIFICATIONS = "fixed_modifications";
116 static constexpr const char* VARIABLE_MODIFICATIONS = "variable_modifications";
117 static constexpr const char* PRIMARY_MS_RUN_PATHS = "primary_ms_run_paths";
118 static constexpr const char* METAVALUES = "metavalues";
119 static constexpr const char* SP_METAVALUES = "sp_metavalues";
120
121 static std::shared_ptr<arrow::DataType> metavaluesType();
122 static std::shared_ptr<arrow::Schema> schema();
123 };
124
126 struct OPENMS_DLLAPI FeatureSchema
127 {
128 static constexpr const char* UNIQUE_ID = "unique_id";
129 static constexpr const char* PARENT_FEATURE_ID = "parent_feature_id";
130 static constexpr const char* DEPTH = "depth";
131 static constexpr const char* RT = "rt";
132 static constexpr const char* MZ = "mz";
133 static constexpr const char* INTENSITY = "intensity";
134 static constexpr const char* CHARGE = "charge";
135 static constexpr const char* QUALITY = "quality";
136 static constexpr const char* QUALITY_RT = "quality_rt";
137 static constexpr const char* QUALITY_MZ = "quality_mz";
138 static constexpr const char* WIDTH = "width";
139 static constexpr const char* RT_BB_MIN = "rt_bb_min";
140 static constexpr const char* RT_BB_MAX = "rt_bb_max";
141 static constexpr const char* MZ_BB_MIN = "mz_bb_min";
142 static constexpr const char* MZ_BB_MAX = "mz_bb_max";
143 static constexpr const char* CONVEX_HULLS = "convex_hulls";
144 static constexpr const char* METAVALUES = "metavalues";
145
146 static std::shared_ptr<arrow::DataType> convexHullType();
147 static std::shared_ptr<arrow::DataType> metavaluesType();
148 static std::shared_ptr<arrow::Schema> schema();
149 };
150
152 struct OPENMS_DLLAPI ConsensusFeatureSchema
153 {
154 static constexpr const char* UNIQUE_ID = "unique_id";
155 static constexpr const char* RT = "rt";
156 static constexpr const char* MZ = "mz";
157 static constexpr const char* INTENSITY = "intensity";
158 static constexpr const char* CHARGE = "charge";
159 static constexpr const char* QUALITY = "quality";
160 static constexpr const char* WIDTH = "width";
161 static constexpr const char* HANDLES = "handles";
162 static constexpr const char* METAVALUES = "metavalues";
163
164 static std::shared_ptr<arrow::DataType> handlesType();
165 static std::shared_ptr<arrow::DataType> metavaluesType();
166 static std::shared_ptr<arrow::Schema> schema();
167 };
168
170 struct OPENMS_DLLAPI PSMSchema
171 {
172 static constexpr const char* SEQUENCE = "sequence";
173 static constexpr const char* PEPTIDOFORM = "peptidoform";
174 static constexpr const char* MODIFICATIONS = "modifications";
175 static constexpr const char* PRECURSOR_CHARGE = "precursor_charge";
176 static constexpr const char* POSTERIOR_ERROR_PROBABILITY = "posterior_error_probability";
177 static constexpr const char* IS_DECOY = "is_decoy";
178 static constexpr const char* CALCULATED_MZ = "calculated_mz";
179 static constexpr const char* OBSERVED_MZ = "observed_mz";
180 static constexpr const char* ADDITIONAL_SCORES = "additional_scores";
181 static constexpr const char* PROTEIN_ACCESSIONS = "protein_accessions";
182 static constexpr const char* PREDICTED_RT = "predicted_rt";
183 static constexpr const char* REFERENCE_FILE_NAME = "reference_file_name";
184 static constexpr const char* CV_PARAMS = "cv_params";
185 static constexpr const char* SCAN = "scan";
186 static constexpr const char* RT = "rt";
187 static constexpr const char* ION_MOBILITY = "ion_mobility";
188 static constexpr const char* SPECTRUM_REFERENCE = "spectrum_reference";
189 static constexpr const char* SCORE = "score";
190 static constexpr const char* SCORE_TYPE = "score_type";
191 static constexpr const char* HIGHER_SCORE_BETTER = "higher_score_better";
195 static constexpr const char* HIT_INDEX = "hit_index";
196 static constexpr const char* PEPTIDE_IDENTIFICATION_INDEX = "peptide_identification_index";
197 static constexpr const char* PSM_METAVALUES = "psm_metavalues";
198 static constexpr const char* SPECTRUM_METAVALUES = "spectrum_metavalues";
199 static constexpr const char* RUN_IDENTIFIER = "run_identifier";
200 static constexpr const char* MZ_ARRAY = "mz_array";
201 static constexpr const char* INTENSITY_ARRAY = "intensity_array";
202 static constexpr const char* CHARGE_ARRAY = "charge_array";
203 static constexpr const char* ION_TYPE_ARRAY = "ion_type_array";
204
205 static std::shared_ptr<arrow::DataType> modificationsType();
206 static std::shared_ptr<arrow::DataType> additionalScoresType();
207 static std::shared_ptr<arrow::DataType> metavaluesType();
211 static std::shared_ptr<arrow::DataType> proteinAccessionsType();
212 static std::shared_ptr<arrow::Schema> schema();
213 };
214
219 struct OPENMS_DLLAPI QPXPSMSchema
220 {
222 static constexpr const char* PSM_ID = "psm_id";
224 static constexpr const char* FEATURE_ID = "feature_id";
225 static constexpr const char* SEQUENCE = "sequence";
226 static constexpr const char* PEPTIDOFORM = "peptidoform";
227 static constexpr const char* MODIFICATIONS = "modifications";
228 static constexpr const char* CHARGE = "charge";
229 static constexpr const char* POSTERIOR_ERROR_PROBABILITY = "posterior_error_probability";
230 static constexpr const char* IS_DECOY = "is_decoy";
231 static constexpr const char* CALCULATED_MZ = "calculated_mz";
232 static constexpr const char* OBSERVED_MZ = "observed_mz";
233 static constexpr const char* MASS_ERROR_PPM = "mass_error_ppm";
234 static constexpr const char* ADDITIONAL_SCORES = "additional_scores";
235 static constexpr const char* PREDICTED_RT = "predicted_rt";
236 static constexpr const char* RUN_FILE_NAME = "run_file_name";
237 static constexpr const char* CV_PARAMS = "cv_params";
238 static constexpr const char* SCAN = "scan";
239 static constexpr const char* RT = "rt";
240 static constexpr const char* ION_MOBILITY = "ion_mobility";
241 static constexpr const char* MISSED_CLEAVAGES = "missed_cleavages";
242 static constexpr const char* PROTEIN_ACCESSIONS = "protein_accessions";
243 static constexpr const char* CROSS_LINKS = "cross_links";
244 static constexpr const char* MZ_ARRAY = "mz_array";
245 static constexpr const char* INTENSITY_ARRAY = "intensity_array";
246 static constexpr const char* CHARGE_ARRAY = "charge_array";
247 static constexpr const char* ION_TYPE_ARRAY = "ion_type_array";
248 static constexpr const char* ION_MOBILITY_ARRAY = "ion_mobility_array";
249
251 static std::shared_ptr<arrow::DataType> modificationsType();
253 static std::shared_ptr<arrow::DataType> additionalScoresType();
255 static std::shared_ptr<arrow::DataType> cvParamsType();
257 static std::shared_ptr<arrow::DataType> crossLinksType();
259 static std::shared_ptr<arrow::Schema> schema();
260 };
261
266 struct OPENMS_DLLAPI QPXFeatureSchema
267 {
269 static constexpr const char* FEATURE_ID = "feature_id";
271 static constexpr const char* PSM_IDS = "psm_ids";
272 static constexpr const char* SEQUENCE = "sequence";
273 static constexpr const char* PEPTIDOFORM = "peptidoform";
274 static constexpr const char* MODIFICATIONS = "modifications";
275 static constexpr const char* CHARGE = "charge";
276 static constexpr const char* POSTERIOR_ERROR_PROBABILITY = "posterior_error_probability";
277 static constexpr const char* IS_DECOY = "is_decoy";
278 static constexpr const char* CALCULATED_MZ = "calculated_mz";
279 static constexpr const char* OBSERVED_MZ = "observed_mz";
280 static constexpr const char* MASS_ERROR_PPM = "mass_error_ppm";
281 static constexpr const char* ADDITIONAL_SCORES = "additional_scores";
282 static constexpr const char* PREDICTED_RT = "predicted_rt";
283 static constexpr const char* RUN_FILE_NAME = "run_file_name";
284 static constexpr const char* CV_PARAMS = "cv_params";
285 static constexpr const char* SCAN = "scan";
286 static constexpr const char* RT = "rt";
287 static constexpr const char* ION_MOBILITY = "ion_mobility";
288 static constexpr const char* MISSED_CLEAVAGES = "missed_cleavages";
289 static constexpr const char* INTENSITIES = "intensities";
290 static constexpr const char* ADDITIONAL_INTENSITIES = "additional_intensities";
291 static constexpr const char* PG_ACCESSIONS = "pg_accessions";
292 static constexpr const char* ANCHOR_PROTEIN = "anchor_protein";
293 static constexpr const char* UNIQUE = "unique";
294 static constexpr const char* PG_GLOBAL_QVALUE = "pg_global_qvalue";
295 static constexpr const char* PG_POSITIONS = "pg_positions";
296 static constexpr const char* ION_MOBILITY_START = "ion_mobility_start";
297 static constexpr const char* ION_MOBILITY_STOP = "ion_mobility_stop";
298 static constexpr const char* GG_ACCESSIONS = "gg_accessions";
299 static constexpr const char* GG_NAMES = "gg_names";
300 static constexpr const char* ID_RUN_FILE_NAME = "id_run_file_name";
301 static constexpr const char* RT_START = "rt_start";
302 static constexpr const char* RT_STOP = "rt_stop";
303
305 static std::shared_ptr<arrow::DataType> modificationsType();
307 static std::shared_ptr<arrow::DataType> additionalScoresType();
309 static std::shared_ptr<arrow::DataType> cvParamsType();
311 static std::shared_ptr<arrow::DataType> intensitiesType();
313 static std::shared_ptr<arrow::DataType> additionalIntensitiesType();
315 static std::shared_ptr<arrow::DataType> pgAccessionsType();
317 static std::shared_ptr<arrow::DataType> pgPositionsType();
319 static std::shared_ptr<arrow::Schema> schema();
320 };
321
332 struct OPENMS_DLLAPI QPXPgSchema
333 {
335 static constexpr const char* PG_ID = "pg_id";
336 static constexpr const char* PG_ACCESSIONS = "pg_accessions";
337 static constexpr const char* PG_NAMES = "pg_names";
338 static constexpr const char* GG_ACCESSIONS = "gg_accessions";
339 static constexpr const char* GG_NAMES = "gg_names";
340 static constexpr const char* GG_QVALUE = "gg_qvalue";
341 static constexpr const char* ANCHOR_PROTEIN = "anchor_protein";
342 static constexpr const char* GROUPED_RUNS = "grouped_runs";
343 static constexpr const char* GLOBAL_QVALUE = "global_qvalue";
344 static constexpr const char* PG_QVALUE = "pg_qvalue";
345 static constexpr const char* LABEL = "label";
346 static constexpr const char* INTENSITY = "intensity";
347 static constexpr const char* ADDITIONAL_INTENSITIES = "additional_intensities";
348 static constexpr const char* IS_DECOY = "is_decoy";
349 static constexpr const char* CONTAMINANT = "contaminant";
350 static constexpr const char* PEPTIDES = "peptides";
351 static constexpr const char* PEPTIDE_COUNTS = "peptide_counts";
352 static constexpr const char* FEATURE_COUNTS = "feature_counts";
353 static constexpr const char* SEQUENCE_COVERAGE = "sequence_coverage";
354 static constexpr const char* MOLECULAR_WEIGHT = "molecular_weight";
355 static constexpr const char* ADDITIONAL_SCORES = "additional_scores";
356 static constexpr const char* CV_PARAMS = "cv_params";
357
359 static std::shared_ptr<arrow::DataType> groupedRunsType();
361 static std::shared_ptr<arrow::DataType> additionalIntensitiesType();
363 static std::shared_ptr<arrow::DataType> peptidesType();
365 static std::shared_ptr<arrow::DataType> peptideCountsType();
367 static std::shared_ptr<arrow::DataType> featureCountsType();
369 static std::shared_ptr<arrow::DataType> additionalScoresType();
371 static std::shared_ptr<arrow::DataType> cvParamsType();
373 static std::shared_ptr<arrow::Schema> schema();
374 };
375
377 struct OPENMS_DLLAPI SpectraLongSchema
378 {
379 static constexpr const char* MZ = "mz";
380 static constexpr const char* INTENSITY = "intensity";
381 static constexpr const char* RT = "rt";
382 static constexpr const char* ION_MOBILITY = "ion_mobility";
383 static constexpr const char* SPECTRUM_INDEX = "spectrum_index";
384 static constexpr const char* MS_LEVEL = "ms_level";
385 static constexpr const char* NATIVE_ID = "native_id";
386 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
387 static constexpr const char* PRECURSOR_CHARGE = "precursor_charge";
388 static constexpr const char* PRECURSOR_INTENSITY = "precursor_intensity";
389 static constexpr const char* ISOLATION_LOWER = "isolation_lower";
390 static constexpr const char* ISOLATION_UPPER = "isolation_upper";
391
392 static std::shared_ptr<arrow::Schema> schema();
393 };
394
396 struct OPENMS_DLLAPI SpectraSemiWideSchema
397 {
398 static constexpr const char* SPECTRUM_INDEX = "spectrum_index";
399 static constexpr const char* RT = "rt";
400 static constexpr const char* MS_LEVEL = "ms_level";
401 static constexpr const char* NATIVE_ID = "native_id";
402 static constexpr const char* MZ = "mz";
403 static constexpr const char* INTENSITY = "intensity";
404 static constexpr const char* ION_MOBILITY = "ion_mobility";
405 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
406 static constexpr const char* PRECURSOR_CHARGE = "precursor_charge";
407 static constexpr const char* PRECURSOR_INTENSITY = "precursor_intensity";
408 static constexpr const char* ISOLATION_LOWER = "isolation_lower";
409 static constexpr const char* ISOLATION_UPPER = "isolation_upper";
410
411 static std::shared_ptr<arrow::Schema> schema();
412 };
413
415 struct OPENMS_DLLAPI ChromatogramSchema
416 {
417 static constexpr const char* RT = "rt";
418 static constexpr const char* INTENSITY = "intensity";
419 static constexpr const char* CHROMATOGRAM_INDEX = "chromatogram_index";
420 static constexpr const char* NATIVE_ID = "native_id";
421 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
422 static constexpr const char* PRODUCT_MZ = "product_mz";
423
424 static std::shared_ptr<arrow::Schema> schema();
425 };
426
428 struct OPENMS_DLLAPI ChromatogramSemiWideSchema
429 {
430 static constexpr const char* CHROMATOGRAM_INDEX = "chromatogram_index";
431 static constexpr const char* NATIVE_ID = "native_id";
432 static constexpr const char* RT = "rt";
433 static constexpr const char* INTENSITY = "intensity";
434 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
435 static constexpr const char* PRODUCT_MZ = "product_mz";
436
437 static std::shared_ptr<arrow::Schema> schema();
438 };
439
441 struct OPENMS_DLLAPI OSWPrecursorSchema
442 {
443 static constexpr const char* PRECURSOR_ID = "precursor_id";
444 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
445 static constexpr const char* CHARGE = "charge";
446 static constexpr const char* LIBRARY_RT = "library_rt";
447 static constexpr const char* LIBRARY_DRIFT_TIME = "library_drift_time";
448 static constexpr const char* DECOY = "decoy";
449 static constexpr const char* TRAML_ID = "traml_id";
450 static constexpr const char* MODIFIED_SEQUENCE = "modified_sequence";
451 static constexpr const char* UNMODIFIED_SEQUENCE = "unmodified_sequence";
452 static constexpr const char* PROTEIN_ACCESSIONS = "protein_accessions";
453
454 static std::shared_ptr<arrow::Schema> schema();
455 };
456
458 struct OPENMS_DLLAPI OSWTransitionSchema
459 {
460 static constexpr const char* TRANSITION_ID = "transition_id";
461 static constexpr const char* PRECURSOR_ID = "precursor_id";
462 static constexpr const char* TRAML_ID = "traml_id";
463 static constexpr const char* PRODUCT_MZ = "product_mz";
464 static constexpr const char* CHARGE = "charge";
465 static constexpr const char* TYPE = "type";
466 static constexpr const char* ANNOTATION = "annotation";
467 static constexpr const char* ORDINAL = "ordinal";
468 static constexpr const char* DETECTING = "detecting";
469 static constexpr const char* IDENTIFYING = "identifying";
470 static constexpr const char* QUANTIFYING = "quantifying";
471 static constexpr const char* LIBRARY_INTENSITY = "library_intensity";
472 static constexpr const char* DECOY = "decoy";
473
474 static std::shared_ptr<arrow::Schema> schema();
475 };
476
478 struct OPENMS_DLLAPI OSWFeaturePrecursorSchema
479 {
480 static constexpr const char* FEATURE_ID = "feature_id";
481 static constexpr const char* RUN_ID = "run_id";
482 static constexpr const char* PRECURSOR_ISOTOPE = "precursor_isotope";
483 static constexpr const char* PRECURSOR_AREA_INTENSITY = "precursor_area_intensity";
484 static constexpr const char* PRECURSOR_APEX_INTENSITY = "precursor_apex_intensity";
485
486 static std::shared_ptr<arrow::Schema> schema();
487 };
488
490 struct OPENMS_DLLAPI OSWRunSchema
491 {
492 static constexpr const char* RUN_ID = "run_id";
493 static constexpr const char* FILENAME = "filename";
494
495 static std::shared_ptr<arrow::Schema> schema();
496 };
497
499 struct OPENMS_DLLAPI OSWFeatureSchema
500 {
501 static constexpr const char* FEATURE_ID = "feature_id";
502 static constexpr const char* RUN_ID = "run_id";
503 static constexpr const char* PRECURSOR_ID = "precursor_id";
504 static constexpr const char* EXP_RT = "exp_rt";
505 static constexpr const char* EXP_IM = "exp_im";
506 static constexpr const char* NORM_RT = "norm_rt";
507 static constexpr const char* DELTA_RT = "delta_rt";
508 static constexpr const char* LEFT_WIDTH = "left_width";
509 static constexpr const char* RIGHT_WIDTH = "right_width";
510 static constexpr const char* EXP_IM_LEFTWIDTH = "exp_im_leftwidth";
511 static constexpr const char* EXP_IM_RIGHTWIDTH = "exp_im_rightwidth";
512 static constexpr const char* MS1_AREA_INTENSITY = "ms1_area_intensity";
513 static constexpr const char* MS1_APEX_INTENSITY = "ms1_apex_intensity";
514 static constexpr const char* MS1_EXP_IM = "ms1_exp_im";
515 static constexpr const char* MS1_DELTA_IM = "ms1_delta_im";
516 static constexpr const char* VAR_MS1_MASSDEV_SCORE = "var_ms1_massdev_score";
517 static constexpr const char* VAR_MS1_IM_MS1_DELTA_SCORE = "var_ms1_im_ms1_delta_score";
518 static constexpr const char* VAR_MS1_MI_SCORE = "var_ms1_mi_score";
519 static constexpr const char* VAR_MS1_MI_CONTRAST_SCORE = "var_ms1_mi_contrast_score";
520 static constexpr const char* VAR_MS1_MI_COMBINED_SCORE = "var_ms1_mi_combined_score";
521 static constexpr const char* VAR_MS1_ISOTOPE_CORRELATION_SCORE = "var_ms1_isotope_correlation_score";
522 static constexpr const char* VAR_MS1_ISOTOPE_OVERLAP_SCORE = "var_ms1_isotope_overlap_score";
523 static constexpr const char* VAR_MS1_XCORR_COELUTION = "var_ms1_xcorr_coelution";
524 static constexpr const char* VAR_MS1_XCORR_COELUTION_CONTRAST = "var_ms1_xcorr_coelution_contrast";
525 static constexpr const char* VAR_MS1_XCORR_COELUTION_COMBINED = "var_ms1_xcorr_coelution_combined";
526 static constexpr const char* VAR_MS1_XCORR_SHAPE = "var_ms1_xcorr_shape";
527 static constexpr const char* VAR_MS1_XCORR_SHAPE_CONTRAST = "var_ms1_xcorr_shape_contrast";
528 static constexpr const char* VAR_MS1_XCORR_SHAPE_COMBINED = "var_ms1_xcorr_shape_combined";
529 static constexpr const char* MS2_AREA_INTENSITY = "ms2_area_intensity";
530 static constexpr const char* MS2_TOTAL_AREA_INTENSITY = "ms2_total_area_intensity";
531 static constexpr const char* MS2_APEX_INTENSITY = "ms2_apex_intensity";
532 static constexpr const char* MS2_EXP_IM = "ms2_exp_im";
533 static constexpr const char* MS2_EXP_IM_LEFTWIDTH = "ms2_exp_im_leftwidth";
534 static constexpr const char* MS2_EXP_IM_RIGHTWIDTH = "ms2_exp_im_rightwidth";
535 static constexpr const char* MS2_DELTA_IM = "ms2_delta_im";
536 static constexpr const char* MS2_TOTAL_MI = "ms2_total_mi";
537 static constexpr const char* VAR_MS2_BSERIES_SCORE = "var_ms2_bseries_score";
538 static constexpr const char* VAR_MS2_DOTPROD_SCORE = "var_ms2_dotprod_score";
539 static constexpr const char* VAR_MS2_INTENSITY_SCORE = "var_ms2_intensity_score";
540 static constexpr const char* VAR_MS2_ISOTOPE_CORRELATION_SCORE = "var_ms2_isotope_correlation_score";
541 static constexpr const char* VAR_MS2_ISOTOPE_OVERLAP_SCORE = "var_ms2_isotope_overlap_score";
542 static constexpr const char* VAR_MS2_LIBRARY_CORR = "var_ms2_library_corr";
543 static constexpr const char* VAR_MS2_LIBRARY_DOTPROD = "var_ms2_library_dotprod";
544 static constexpr const char* VAR_MS2_LIBRARY_MANHATTAN = "var_ms2_library_manhattan";
545 static constexpr const char* VAR_MS2_LIBRARY_RMSD = "var_ms2_library_rmsd";
546 static constexpr const char* VAR_MS2_LIBRARY_ROOTMEANSQUARE = "var_ms2_library_rootmeansquare";
547 static constexpr const char* VAR_MS2_LIBRARY_SANGLE = "var_ms2_library_sangle";
548 static constexpr const char* VAR_MS2_LOG_SN_SCORE = "var_ms2_log_sn_score";
549 static constexpr const char* VAR_MS2_MANHATTAN_SCORE = "var_ms2_manhattan_score";
550 static constexpr const char* VAR_MS2_MASSDEV_SCORE = "var_ms2_massdev_score";
551 static constexpr const char* VAR_MS2_MASSDEV_SCORE_WEIGHTED = "var_ms2_massdev_score_weighted";
552 static constexpr const char* VAR_MS2_MI_SCORE = "var_ms2_mi_score";
553 static constexpr const char* VAR_MS2_MI_WEIGHTED_SCORE = "var_ms2_mi_weighted_score";
554 static constexpr const char* VAR_MS2_MI_RATIO_SCORE = "var_ms2_mi_ratio_score";
555 static constexpr const char* VAR_MS2_NORM_RT_SCORE = "var_ms2_norm_rt_score";
556 static constexpr const char* VAR_MS2_XCORR_COELUTION = "var_ms2_xcorr_coelution";
557 static constexpr const char* VAR_MS2_XCORR_COELUTION_WEIGHTED = "var_ms2_xcorr_coelution_weighted";
558 static constexpr const char* VAR_MS2_XCORR_SHAPE = "var_ms2_xcorr_shape";
559 static constexpr const char* VAR_MS2_XCORR_SHAPE_WEIGHTED = "var_ms2_xcorr_shape_weighted";
560 static constexpr const char* VAR_MS2_YSERIES_SCORE = "var_ms2_yseries_score";
561 static constexpr const char* VAR_MS2_ELUTION_MODEL_FIT_SCORE = "var_ms2_elution_model_fit_score";
562 static constexpr const char* VAR_MS2_IM_XCORR_SHAPE = "var_ms2_im_xcorr_shape";
563 static constexpr const char* VAR_MS2_IM_XCORR_COELUTION = "var_ms2_im_xcorr_coelution";
564 static constexpr const char* VAR_MS2_IM_DELTA_SCORE = "var_ms2_im_delta_score";
565 static constexpr const char* VAR_MS2_IM_LOG_INTENSITY = "var_ms2_im_log_intensity";
566
567 static std::shared_ptr<arrow::Schema> schema();
568 };
569
571 struct OPENMS_DLLAPI OSWFeatureTransitionSchema
572 {
573 static constexpr const char* FEATURE_ID = "feature_id";
574 static constexpr const char* RUN_ID = "run_id";
575 static constexpr const char* TRANSITION_ID = "transition_id";
576 static constexpr const char* AREA_INTENSITY = "area_intensity";
577 static constexpr const char* TOTAL_AREA_INTENSITY = "total_area_intensity";
578 static constexpr const char* APEX_INTENSITY = "apex_intensity";
579 static constexpr const char* APEX_RT = "apex_rt";
580 static constexpr const char* RT_FWHM = "rt_fwhm";
581 static constexpr const char* MASSERROR_PPM = "masserror_ppm";
582 static constexpr const char* TOTAL_MI = "total_mi";
583 static constexpr const char* VAR_INTENSITY_SCORE = "var_intensity_score";
584 static constexpr const char* VAR_INTENSITY_RATIO_SCORE = "var_intensity_ratio_score";
585 static constexpr const char* VAR_LOG_INTENSITY = "var_log_intensity";
586 static constexpr const char* VAR_XCORR_COELUTION = "var_xcorr_coelution";
587 static constexpr const char* VAR_XCORR_SHAPE = "var_xcorr_shape";
588 static constexpr const char* VAR_LOG_SN_SCORE = "var_log_sn_score";
589 static constexpr const char* VAR_MASSDEV_SCORE = "var_massdev_score";
590 static constexpr const char* VAR_MI_SCORE = "var_mi_score";
591 static constexpr const char* VAR_MI_RATIO_SCORE = "var_mi_ratio_score";
592 static constexpr const char* VAR_ISOTOPE_CORRELATION_SCORE = "var_isotope_correlation_score";
593 static constexpr const char* VAR_ISOTOPE_OVERLAP_SCORE = "var_isotope_overlap_score";
594 static constexpr const char* EXP_IM = "exp_im";
595 static constexpr const char* EXP_IM_LEFTWIDTH = "exp_im_leftwidth";
596 static constexpr const char* EXP_IM_RIGHTWIDTH = "exp_im_rightwidth";
597 static constexpr const char* DELTA_IM = "delta_im";
598 static constexpr const char* VAR_IM_DELTA_SCORE = "var_im_delta_score";
599 static constexpr const char* VAR_IM_LOG_INTENSITY = "var_im_log_intensity";
600 static constexpr const char* VAR_IM_XCORR_COELUTION_CONTRAST = "var_im_xcorr_coelution_contrast";
601 static constexpr const char* VAR_IM_XCORR_SHAPE_CONTRAST = "var_im_xcorr_shape_contrast";
602 static constexpr const char* VAR_IM_XCORR_COELUTION_COMBINED = "var_im_xcorr_coelution_combined";
603 static constexpr const char* VAR_IM_XCORR_SHAPE_COMBINED = "var_im_xcorr_shape_combined";
604 static constexpr const char* START_POSITION_AT_5 = "start_position_at_5";
605 static constexpr const char* END_POSITION_AT_5 = "end_position_at_5";
606 static constexpr const char* START_POSITION_AT_10 = "start_position_at_10";
607 static constexpr const char* END_POSITION_AT_10 = "end_position_at_10";
608 static constexpr const char* START_POSITION_AT_50 = "start_position_at_50";
609 static constexpr const char* END_POSITION_AT_50 = "end_position_at_50";
610 static constexpr const char* TOTAL_WIDTH = "total_width";
611 static constexpr const char* TAILING_FACTOR = "tailing_factor";
612 static constexpr const char* ASYMMETRY_FACTOR = "asymmetry_factor";
613 static constexpr const char* SLOPE_OF_BASELINE = "slope_of_baseline";
614 static constexpr const char* BASELINE_DELTA_2_HEIGHT = "baseline_delta_2_height";
615 static constexpr const char* POINTS_ACROSS_BASELINE = "points_across_baseline";
616 static constexpr const char* POINTS_ACROSS_HALF_HEIGHT = "points_across_half_height";
617
618 static std::shared_ptr<arrow::Schema> schema();
619 };
620
622 struct OPENMS_DLLAPI XICSchema
623 {
624 static constexpr const char* RUN_ID = "RUN_ID";
625 static constexpr const char* SOURCE_FILE = "SOURCE_FILE";
626 static constexpr const char* MS_LEVEL = "MS_LEVEL";
627 static constexpr const char* PRECURSOR_ID = "PRECURSOR_ID";
628 static constexpr const char* TRANSITION_ID = "TRANSITION_ID";
629 static constexpr const char* MODIFIED_SEQUENCE = "MODIFIED_SEQUENCE";
630 static constexpr const char* PRECURSOR_CHARGE = "PRECURSOR_CHARGE";
631 static constexpr const char* PRODUCT_CHARGE = "PRODUCT_CHARGE";
632 static constexpr const char* DETECTING_TRANSITION = "DETECTING_TRANSITION";
633 static constexpr const char* PRECURSOR_DECOY = "PRECURSOR_DECOY";
634 static constexpr const char* PRODUCT_DECOY = "PRODUCT_DECOY";
635 static constexpr const char* TRANSITION_ORDINAL = "TRANSITION_ORDINAL";
636 static constexpr const char* TRANSITION_TYPE = "TRANSITION_TYPE";
637 static constexpr const char* ANNOTATION = "ANNOTATION";
638 static constexpr const char* RT_DATA = "RT_DATA";
639 static constexpr const char* INTENSITY_DATA = "INTENSITY_DATA";
640 static constexpr const char* RT_COMPRESSION = "RT_COMPRESSION";
641 static constexpr const char* INTENSITY_COMPRESSION = "INTENSITY_COMPRESSION";
642
643 static std::shared_ptr<arrow::Schema> schema();
644 };
645
647 struct OPENMS_DLLAPI XIMSchema
648 {
649 static constexpr const char* RUN_ID = "RUN_ID";
650 static constexpr const char* SOURCE_FILE = "SOURCE_FILE";
651 static constexpr const char* MS_LEVEL = "MS_LEVEL";
652 static constexpr const char* MOBILOGRAM_TYPE = "MOBILOGRAM_TYPE";
653 static constexpr const char* PRECURSOR_ID = "PRECURSOR_ID";
654 static constexpr const char* TRANSITION_ID = "TRANSITION_ID";
655 static constexpr const char* FEATURE_ID = "FEATURE_ID";
656 static constexpr const char* FEATURE_RT = "FEATURE_RT";
657 static constexpr const char* MODIFIED_SEQUENCE = "MODIFIED_SEQUENCE";
658 static constexpr const char* PRECURSOR_CHARGE = "PRECURSOR_CHARGE";
659 static constexpr const char* PRODUCT_CHARGE = "PRODUCT_CHARGE";
660 static constexpr const char* DETECTING_TRANSITION = "DETECTING_TRANSITION";
661 static constexpr const char* PRECURSOR_DECOY = "PRECURSOR_DECOY";
662 static constexpr const char* PRODUCT_DECOY = "PRODUCT_DECOY";
663 static constexpr const char* TRANSITION_ORDINAL = "TRANSITION_ORDINAL";
664 static constexpr const char* TRANSITION_TYPE = "TRANSITION_TYPE";
665 static constexpr const char* ANNOTATION = "ANNOTATION";
666 static constexpr const char* MOBILITY_DATA = "MOBILITY_DATA";
667 static constexpr const char* INTENSITY_DATA = "INTENSITY_DATA";
668 static constexpr const char* MOBILITY_COMPRESSION = "MOBILITY_COMPRESSION";
669 static constexpr const char* INTENSITY_COMPRESSION = "INTENSITY_COMPRESSION";
670
671 static std::shared_ptr<arrow::Schema> schema();
672 };
673
683 struct OPENMS_DLLAPI XIPMSchema
684 {
685 static constexpr const char* RUN_ID = "RUN_ID";
686 static constexpr const char* SOURCE_FILE = "SOURCE_FILE";
687 static constexpr const char* MS_LEVEL = "MS_LEVEL";
688 static constexpr const char* PEAKMAP_TYPE = "PEAKMAP_TYPE";
689 static constexpr const char* PRECURSOR_ID = "PRECURSOR_ID";
690 static constexpr const char* TRANSITION_ID = "TRANSITION_ID";
691 static constexpr const char* MODIFIED_SEQUENCE = "MODIFIED_SEQUENCE";
692 static constexpr const char* PRECURSOR_CHARGE = "PRECURSOR_CHARGE";
693 static constexpr const char* PRODUCT_CHARGE = "PRODUCT_CHARGE";
694 static constexpr const char* DETECTING_TRANSITION = "DETECTING_TRANSITION";
695 static constexpr const char* PRECURSOR_DECOY = "PRECURSOR_DECOY";
696 static constexpr const char* PRODUCT_DECOY = "PRODUCT_DECOY";
697 static constexpr const char* TRANSITION_ORDINAL = "TRANSITION_ORDINAL";
698 static constexpr const char* TRANSITION_TYPE = "TRANSITION_TYPE";
699 static constexpr const char* ANNOTATION = "ANNOTATION";
700 static constexpr const char* TARGET_MZ = "TARGET_MZ";
701 static constexpr const char* TARGET_RT = "TARGET_RT";
702 static constexpr const char* TARGET_ION_MOBILITY = "TARGET_ION_MOBILITY";
703 static constexpr const char* RT_START = "RT_START";
704 static constexpr const char* RT_END = "RT_END";
705 static constexpr const char* MZ_DATA = "MZ_DATA";
706 static constexpr const char* RT_DATA = "RT_DATA";
707 static constexpr const char* MOBILITY_DATA = "MOBILITY_DATA";
708 static constexpr const char* INTENSITY_DATA = "INTENSITY_DATA";
709 static constexpr const char* MZ_COMPRESSION = "MZ_COMPRESSION";
710 static constexpr const char* RT_COMPRESSION = "RT_COMPRESSION";
711 static constexpr const char* MOBILITY_COMPRESSION = "MOBILITY_COMPRESSION";
712 static constexpr const char* INTENSITY_COMPRESSION = "INTENSITY_COMPRESSION";
713
714 static std::shared_ptr<arrow::Schema> schema();
715 };
716
717} // namespace OpenMS
OpenMS::ArrowSchemaValidation::validate
ValidationResult validate(const std::shared_ptr< arrow::Table > &table, const std::shared_ptr< arrow::Schema > &expected_schema, Mode mode=Mode::Strict)
Validate an Arrow table's schema against an expected schema.
OpenMS::ArrowSchemaValidation::Mode
Mode
Validation strictness: Strict requires exact match, Subset allows missing and extra columns,...
Definition ArrowSchemaRegistry.h:33
OpenMS
Main OpenMS namespace.
Definition openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
OpenMS::DIM_UNIT::RT
@ RT
RT in seconds.
arrow
Definition ArrowIOHelpers.h:28
OpenMS::ArrowSchemaValidation::ValidationResult
Result of schema validation containing validity flag and error messages.
Definition ArrowSchemaRegistry.h:41
OpenMS::ArrowSchemaValidation::ValidationResult::errors
std::vector< std::string > errors
Definition ArrowSchemaRegistry.h:43
OpenMS::ChromatogramSchema
Schema for chromatograms in long (one row per data point) format.
Definition ArrowSchemaRegistry.h:416
OpenMS::ChromatogramSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::ChromatogramSemiWideSchema
Schema for chromatograms in semi-wide (one row per chromatogram, list columns) format.
Definition ArrowSchemaRegistry.h:429
OpenMS::ChromatogramSemiWideSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::ConsensusFeatureSchema
Schema for consensus feature table (ConsensusMap features)
Definition ArrowSchemaRegistry.h:153
OpenMS::ConsensusFeatureSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::ConsensusFeatureSchema::handlesType
static std::shared_ptr< arrow::DataType > handlesType()
OpenMS::ConsensusFeatureSchema::metavaluesType
static std::shared_ptr< arrow::DataType > metavaluesType()
OpenMS::FeatureSchema
Schema for LC-MS feature table (FeatureMap features)
Definition ArrowSchemaRegistry.h:127
OpenMS::FeatureSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::FeatureSchema::metavaluesType
static std::shared_ptr< arrow::DataType > metavaluesType()
OpenMS::FeatureSchema::convexHullType
static std::shared_ptr< arrow::DataType > convexHullType()
OpenMS::OSWFeaturePrecursorSchema
Schema for OpenSWATH feature-level precursor intensity table.
Definition ArrowSchemaRegistry.h:479
OpenMS::OSWFeaturePrecursorSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::OSWFeatureSchema
Schema for OpenSWATH feature scoring results table.
Definition ArrowSchemaRegistry.h:500
OpenMS::OSWFeatureSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::OSWFeatureTransitionSchema
Schema for OpenSWATH per-transition feature scoring results table.
Definition ArrowSchemaRegistry.h:572
OpenMS::OSWFeatureTransitionSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::OSWPrecursorSchema
Schema for OpenSWATH precursor (peptide query) table.
Definition ArrowSchemaRegistry.h:442
OpenMS::OSWPrecursorSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::OSWRunSchema
Schema for OpenSWATH run metadata table.
Definition ArrowSchemaRegistry.h:491
OpenMS::OSWRunSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::OSWTransitionSchema
Schema for OpenSWATH transition (fragment ion) table.
Definition ArrowSchemaRegistry.h:459
OpenMS::OSWTransitionSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::PSMSchema
Schema for peptide-spectrum match (PSM) results table.
Definition ArrowSchemaRegistry.h:171
OpenMS::PSMSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::PSMSchema::additionalScoresType
static std::shared_ptr< arrow::DataType > additionalScoresType()
OpenMS::PSMSchema::modificationsType
static std::shared_ptr< arrow::DataType > modificationsType()
OpenMS::PSMSchema::metavaluesType
static std::shared_ptr< arrow::DataType > metavaluesType()
OpenMS::PSMSchema::proteinAccessionsType
static std::shared_ptr< arrow::DataType > proteinAccessionsType()
Arrow type for protein_accessions: list<struct{accession, aa_before, aa_after, start,...
OpenMS::ProteinGroupSchema
Schema for protein group (indistinguishable group) results table.
Definition ArrowSchemaRegistry.h:75
OpenMS::ProteinGroupSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::ProteinGroupSchema::floatDataType
static std::shared_ptr< arrow::DataType > floatDataType()
OpenMS::ProteinGroupSchema::stringDataType
static std::shared_ptr< arrow::DataType > stringDataType()
OpenMS::ProteinGroupSchema::integerDataType
static std::shared_ptr< arrow::DataType > integerDataType()
OpenMS::ProteinSchema
Schema for protein identification results table.
Definition ArrowSchemaRegistry.h:56
OpenMS::ProteinSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::ProteinSchema::modificationsType
static std::shared_ptr< arrow::DataType > modificationsType()
OpenMS::ProteinSchema::metavaluesType
static std::shared_ptr< arrow::DataType > metavaluesType()
OpenMS::QPXFeatureSchema
Schema for QPX feature view (quantms Parquet eXchange format)
Definition ArrowSchemaRegistry.h:267
OpenMS::QPXFeatureSchema::schema
static std::shared_ptr< arrow::Schema > schema()
Complete Arrow schema for QPX feature table (33 fields)
OpenMS::QPXFeatureSchema::pgAccessionsType
static std::shared_ptr< arrow::DataType > pgAccessionsType()
Arrow type for protein group accessions: list<struct{accession, start, end, pre, post}>
OpenMS::QPXFeatureSchema::additionalScoresType
static std::shared_ptr< arrow::DataType > additionalScoresType()
Arrow type for additional scores (delegates to QPXPSMSchema::additionalScoresType)
OpenMS::QPXFeatureSchema::additionalIntensitiesType
static std::shared_ptr< arrow::DataType > additionalIntensitiesType()
Arrow type for additional intensities: list<struct{label, intensities: list<struct{....
OpenMS::QPXFeatureSchema::intensitiesType
static std::shared_ptr< arrow::DataType > intensitiesType()
Arrow type for intensities: list<struct{label, intensity}>
OpenMS::QPXFeatureSchema::modificationsType
static std::shared_ptr< arrow::DataType > modificationsType()
Arrow type for modifications (delegates to QPXPSMSchema::modificationsType)
OpenMS::QPXFeatureSchema::cvParamsType
static std::shared_ptr< arrow::DataType > cvParamsType()
Arrow type for CV params (delegates to QPXPSMSchema::cvParamsType)
OpenMS::QPXFeatureSchema::pgPositionsType
static std::shared_ptr< arrow::DataType > pgPositionsType()
Arrow type for protein group positions: list<struct{protein_accession, start, end}>
OpenMS::QPXPSMSchema
Schema for QPX PSM export (quantms Parquet eXchange format, PSM table)
Definition ArrowSchemaRegistry.h:220
OpenMS::QPXPSMSchema::schema
static std::shared_ptr< arrow::Schema > schema()
Complete Arrow schema for QPX PSM table (26 fields)
OpenMS::QPXPSMSchema::crossLinksType
static std::shared_ptr< arrow::DataType > crossLinksType()
Arrow type for cross-links: list<struct{xl_type, partner_sequence, ...}>
OpenMS::QPXPSMSchema::additionalScoresType
static std::shared_ptr< arrow::DataType > additionalScoresType()
Arrow type for additional scores: list<struct{score_name, score_value, higher_better}>
OpenMS::QPXPSMSchema::modificationsType
static std::shared_ptr< arrow::DataType > modificationsType()
Arrow type for modifications: list<struct{name, accession, positions: list<struct{position,...
OpenMS::QPXPSMSchema::cvParamsType
static std::shared_ptr< arrow::DataType > cvParamsType()
Arrow type for CV params: list<struct{cv_name, cv_value}>
OpenMS::QPXPgSchema
Schema for QPX protein group export (quantms Parquet eXchange format, pg table)
Definition ArrowSchemaRegistry.h:333
OpenMS::QPXPgSchema::schema
static std::shared_ptr< arrow::Schema > schema()
Complete Arrow schema for QPX pg table (22 fields)
OpenMS::QPXPgSchema::additionalScoresType
static std::shared_ptr< arrow::DataType > additionalScoresType()
Arrow type for additional scores (delegates to QPXPSMSchema::additionalScoresType)
OpenMS::QPXPgSchema::additionalIntensitiesType
static std::shared_ptr< arrow::DataType > additionalIntensitiesType()
Arrow type for additional intensities: list<struct{label, intensities: list<struct{....
OpenMS::QPXPgSchema::peptidesType
static std::shared_ptr< arrow::DataType > peptidesType()
Arrow type for peptides: list<struct{protein_name, peptide_count}>
OpenMS::QPXPgSchema::cvParamsType
static std::shared_ptr< arrow::DataType > cvParamsType()
Arrow type for CV params (delegates to QPXPSMSchema::cvParamsType)
OpenMS::QPXPgSchema::featureCountsType
static std::shared_ptr< arrow::DataType > featureCountsType()
Arrow type for feature_counts: struct{unique_features, total_features}.
OpenMS::QPXPgSchema::peptideCountsType
static std::shared_ptr< arrow::DataType > peptideCountsType()
Arrow type for peptide_counts: struct{unique_sequences, total_sequences}.
OpenMS::QPXPgSchema::groupedRunsType
static std::shared_ptr< arrow::DataType > groupedRunsType()
Arrow type for grouped_runs: list<utf8> — the raw files of one quantification unit.
OpenMS::SearchParamsSchema
Schema for search engine parameters and settings table.
Definition ArrowSchemaRegistry.h:93
OpenMS::SearchParamsSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::SearchParamsSchema::metavaluesType
static std::shared_ptr< arrow::DataType > metavaluesType()
OpenMS::SpectraLongSchema
Schema for spectra in long (one row per peak) format.
Definition ArrowSchemaRegistry.h:378
OpenMS::SpectraLongSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::SpectraSemiWideSchema
Schema for spectra in semi-wide (one row per spectrum, list columns for peaks) format.
Definition ArrowSchemaRegistry.h:397
OpenMS::SpectraSemiWideSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::XICSchema
Schema for extracted ion chromatogram (XIC) data table.
Definition ArrowSchemaRegistry.h:623
OpenMS::XICSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::XIMSchema
Schema for extracted ion mobilogram (XIM) data table.
Definition ArrowSchemaRegistry.h:648
OpenMS::XIMSchema::schema
static std::shared_ptr< arrow::Schema > schema()
OpenMS::XIPMSchema
Schema for extracted ion peak-map (XIPM) data table.
Definition ArrowSchemaRegistry.h:684
OpenMS::XIPMSchema::schema
static std::shared_ptr< arrow::Schema > schema()