OpenMS
Loading...
Searching...
No Matches
ArrowSchemaRegistry.h
Go to the documentation of this file.
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#ifdef WITH_PARQUET
12
13#include <OpenMS/OpenMSConfig.h>
14#include <memory>
15#include <string>
16#include <vector>
17
18// Forward declarations
19namespace arrow
20{
21 class Schema;
22 class DataType;
23 class Table;
24}
25
26namespace OpenMS
27{
28
30 namespace ArrowSchemaValidation
31 {
33 enum class Mode
34 {
35 Strict,
36 Subset
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";
192 static constexpr const char* RANK = "rank";
193 static constexpr const char* PEPTIDE_IDENTIFICATION_INDEX = "peptide_identification_index";
194 static constexpr const char* PSM_METAVALUES = "psm_metavalues";
195 static constexpr const char* SPECTRUM_METAVALUES = "spectrum_metavalues";
196 static constexpr const char* RUN_IDENTIFIER = "run_identifier";
197
198 static std::shared_ptr<arrow::DataType> modificationsType();
199 static std::shared_ptr<arrow::DataType> additionalScoresType();
200 static std::shared_ptr<arrow::DataType> metavaluesType();
201 static std::shared_ptr<arrow::Schema> schema();
202 };
203
205 struct OPENMS_DLLAPI ConsensusFeatureExportSchema
206 {
207 static constexpr const char* SEQUENCE = "sequence";
208 static constexpr const char* PEPTIDOFORM = "peptidoform";
209 static constexpr const char* MODIFICATIONS = "modifications";
210 static constexpr const char* PRECURSOR_CHARGE = "precursor_charge";
211 static constexpr const char* CALCULATED_MZ = "calculated_mz";
212 static constexpr const char* OBSERVED_MZ = "observed_mz";
213 static constexpr const char* RT = "rt";
214 static constexpr const char* POSTERIOR_ERROR_PROBABILITY = "posterior_error_probability";
215 static constexpr const char* IS_DECOY = "is_decoy";
216 static constexpr const char* ADDITIONAL_SCORES = "additional_scores";
217 static constexpr const char* PREDICTED_RT = "predicted_rt";
218 static constexpr const char* REFERENCE_FILE_NAME = "reference_file_name";
219 static constexpr const char* CV_PARAMS = "cv_params";
220 static constexpr const char* SCAN = "scan";
221 static constexpr const char* ION_MOBILITY = "ion_mobility";
222 static constexpr const char* START_ION_MOBILITY = "start_ion_mobility";
223 static constexpr const char* STOP_ION_MOBILITY = "stop_ion_mobility";
224 static constexpr const char* INTENSITIES = "intensities";
225 static constexpr const char* ADDITIONAL_INTENSITIES = "additional_intensities";
226 static constexpr const char* PG_ACCESSIONS = "pg_accessions";
227 static constexpr const char* ANCHOR_PROTEIN = "anchor_protein";
228 static constexpr const char* UNIQUE = "unique";
229 static constexpr const char* PG_GLOBAL_QVALUE = "pg_global_qvalue";
230 static constexpr const char* GG_ACCESSIONS = "gg_accessions";
231 static constexpr const char* GG_NAMES = "gg_names";
232 static constexpr const char* SCAN_REFERENCE_FILE_NAME = "scan_reference_file_name";
233 static constexpr const char* RT_START = "rt_start";
234 static constexpr const char* RT_STOP = "rt_stop";
235 static constexpr const char* QUALITY = "quality";
236 static constexpr const char* SCORE = "score";
237 static constexpr const char* SCORE_TYPE = "score_type";
238 static constexpr const char* SPECTRUM_REFERENCE = "spectrum_reference";
239 static constexpr const char* FEATURE_METAVALUES = "feature_metavalues";
240
241 static std::shared_ptr<arrow::DataType> modificationsType();
242 static std::shared_ptr<arrow::DataType> additionalScoresType();
243 static std::shared_ptr<arrow::DataType> intensitiesType();
244 static std::shared_ptr<arrow::DataType> metavaluesType();
245 static std::shared_ptr<arrow::Schema> schema();
246 };
247
249 struct OPENMS_DLLAPI SpectraLongSchema
250 {
251 static constexpr const char* MZ = "mz";
252 static constexpr const char* INTENSITY = "intensity";
253 static constexpr const char* RT = "rt";
254 static constexpr const char* ION_MOBILITY = "ion_mobility";
255 static constexpr const char* SPECTRUM_INDEX = "spectrum_index";
256 static constexpr const char* MS_LEVEL = "ms_level";
257 static constexpr const char* NATIVE_ID = "native_id";
258 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
259 static constexpr const char* PRECURSOR_CHARGE = "precursor_charge";
260 static constexpr const char* PRECURSOR_INTENSITY = "precursor_intensity";
261 static constexpr const char* ISOLATION_LOWER = "isolation_lower";
262 static constexpr const char* ISOLATION_UPPER = "isolation_upper";
263
264 static std::shared_ptr<arrow::Schema> schema();
265 };
266
268 struct OPENMS_DLLAPI SpectraSemiWideSchema
269 {
270 static constexpr const char* SPECTRUM_INDEX = "spectrum_index";
271 static constexpr const char* RT = "rt";
272 static constexpr const char* MS_LEVEL = "ms_level";
273 static constexpr const char* NATIVE_ID = "native_id";
274 static constexpr const char* MZ = "mz";
275 static constexpr const char* INTENSITY = "intensity";
276 static constexpr const char* ION_MOBILITY = "ion_mobility";
277 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
278 static constexpr const char* PRECURSOR_CHARGE = "precursor_charge";
279 static constexpr const char* PRECURSOR_INTENSITY = "precursor_intensity";
280 static constexpr const char* ISOLATION_LOWER = "isolation_lower";
281 static constexpr const char* ISOLATION_UPPER = "isolation_upper";
282
283 static std::shared_ptr<arrow::Schema> schema();
284 };
285
287 struct OPENMS_DLLAPI ChromatogramSchema
288 {
289 static constexpr const char* RT = "rt";
290 static constexpr const char* INTENSITY = "intensity";
291 static constexpr const char* CHROMATOGRAM_INDEX = "chromatogram_index";
292 static constexpr const char* NATIVE_ID = "native_id";
293 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
294 static constexpr const char* PRODUCT_MZ = "product_mz";
295
296 static std::shared_ptr<arrow::Schema> schema();
297 };
298
300 struct OPENMS_DLLAPI ChromatogramSemiWideSchema
301 {
302 static constexpr const char* CHROMATOGRAM_INDEX = "chromatogram_index";
303 static constexpr const char* NATIVE_ID = "native_id";
304 static constexpr const char* RT = "rt";
305 static constexpr const char* INTENSITY = "intensity";
306 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
307 static constexpr const char* PRODUCT_MZ = "product_mz";
308
309 static std::shared_ptr<arrow::Schema> schema();
310 };
311
313 struct OPENMS_DLLAPI OSWPrecursorSchema
314 {
315 static constexpr const char* PRECURSOR_ID = "precursor_id";
316 static constexpr const char* PRECURSOR_MZ = "precursor_mz";
317 static constexpr const char* CHARGE = "charge";
318 static constexpr const char* LIBRARY_RT = "library_rt";
319 static constexpr const char* LIBRARY_DRIFT_TIME = "library_drift_time";
320 static constexpr const char* DECOY = "decoy";
321 static constexpr const char* TRAML_ID = "traml_id";
322 static constexpr const char* MODIFIED_SEQUENCE = "modified_sequence";
323 static constexpr const char* UNMODIFIED_SEQUENCE = "unmodified_sequence";
324 static constexpr const char* PROTEIN_ACCESSIONS = "protein_accessions";
325
326 static std::shared_ptr<arrow::Schema> schema();
327 };
328
330 struct OPENMS_DLLAPI OSWTransitionSchema
331 {
332 static constexpr const char* TRANSITION_ID = "transition_id";
333 static constexpr const char* PRECURSOR_ID = "precursor_id";
334 static constexpr const char* TRAML_ID = "traml_id";
335 static constexpr const char* PRODUCT_MZ = "product_mz";
336 static constexpr const char* CHARGE = "charge";
337 static constexpr const char* TYPE = "type";
338 static constexpr const char* ANNOTATION = "annotation";
339 static constexpr const char* ORDINAL = "ordinal";
340 static constexpr const char* DETECTING = "detecting";
341 static constexpr const char* IDENTIFYING = "identifying";
342 static constexpr const char* QUANTIFYING = "quantifying";
343 static constexpr const char* LIBRARY_INTENSITY = "library_intensity";
344 static constexpr const char* DECOY = "decoy";
345
346 static std::shared_ptr<arrow::Schema> schema();
347 };
348
350 struct OPENMS_DLLAPI OSWFeaturePrecursorSchema
351 {
352 static constexpr const char* FEATURE_ID = "feature_id";
353 static constexpr const char* RUN_ID = "run_id";
354 static constexpr const char* PRECURSOR_ISOTOPE = "precursor_isotope";
355 static constexpr const char* PRECURSOR_AREA_INTENSITY = "precursor_area_intensity";
356 static constexpr const char* PRECURSOR_APEX_INTENSITY = "precursor_apex_intensity";
357
358 static std::shared_ptr<arrow::Schema> schema();
359 };
360
362 struct OPENMS_DLLAPI OSWRunSchema
363 {
364 static constexpr const char* RUN_ID = "run_id";
365 static constexpr const char* FILENAME = "filename";
366
367 static std::shared_ptr<arrow::Schema> schema();
368 };
369
371 struct OPENMS_DLLAPI OSWFeatureSchema
372 {
373 static constexpr const char* FEATURE_ID = "feature_id";
374 static constexpr const char* RUN_ID = "run_id";
375 static constexpr const char* PRECURSOR_ID = "precursor_id";
376 static constexpr const char* EXP_RT = "exp_rt";
377 static constexpr const char* EXP_IM = "exp_im";
378 static constexpr const char* NORM_RT = "norm_rt";
379 static constexpr const char* DELTA_RT = "delta_rt";
380 static constexpr const char* LEFT_WIDTH = "left_width";
381 static constexpr const char* RIGHT_WIDTH = "right_width";
382 static constexpr const char* EXP_IM_LEFTWIDTH = "exp_im_leftwidth";
383 static constexpr const char* EXP_IM_RIGHTWIDTH = "exp_im_rightwidth";
384 static constexpr const char* MS1_AREA_INTENSITY = "ms1_area_intensity";
385 static constexpr const char* MS1_APEX_INTENSITY = "ms1_apex_intensity";
386 static constexpr const char* MS1_EXP_IM = "ms1_exp_im";
387 static constexpr const char* MS1_DELTA_IM = "ms1_delta_im";
388 static constexpr const char* VAR_MS1_MASSDEV_SCORE = "var_ms1_massdev_score";
389 static constexpr const char* VAR_MS1_IM_MS1_DELTA_SCORE = "var_ms1_im_ms1_delta_score";
390 static constexpr const char* VAR_MS1_MI_SCORE = "var_ms1_mi_score";
391 static constexpr const char* VAR_MS1_MI_CONTRAST_SCORE = "var_ms1_mi_contrast_score";
392 static constexpr const char* VAR_MS1_MI_COMBINED_SCORE = "var_ms1_mi_combined_score";
393 static constexpr const char* VAR_MS1_ISOTOPE_CORRELATION_SCORE = "var_ms1_isotope_correlation_score";
394 static constexpr const char* VAR_MS1_ISOTOPE_OVERLAP_SCORE = "var_ms1_isotope_overlap_score";
395 static constexpr const char* VAR_MS1_XCORR_COELUTION = "var_ms1_xcorr_coelution";
396 static constexpr const char* VAR_MS1_XCORR_COELUTION_CONTRAST = "var_ms1_xcorr_coelution_contrast";
397 static constexpr const char* VAR_MS1_XCORR_COELUTION_COMBINED = "var_ms1_xcorr_coelution_combined";
398 static constexpr const char* VAR_MS1_XCORR_SHAPE = "var_ms1_xcorr_shape";
399 static constexpr const char* VAR_MS1_XCORR_SHAPE_CONTRAST = "var_ms1_xcorr_shape_contrast";
400 static constexpr const char* VAR_MS1_XCORR_SHAPE_COMBINED = "var_ms1_xcorr_shape_combined";
401 static constexpr const char* MS2_AREA_INTENSITY = "ms2_area_intensity";
402 static constexpr const char* MS2_TOTAL_AREA_INTENSITY = "ms2_total_area_intensity";
403 static constexpr const char* MS2_APEX_INTENSITY = "ms2_apex_intensity";
404 static constexpr const char* MS2_EXP_IM = "ms2_exp_im";
405 static constexpr const char* MS2_EXP_IM_LEFTWIDTH = "ms2_exp_im_leftwidth";
406 static constexpr const char* MS2_EXP_IM_RIGHTWIDTH = "ms2_exp_im_rightwidth";
407 static constexpr const char* MS2_DELTA_IM = "ms2_delta_im";
408 static constexpr const char* MS2_TOTAL_MI = "ms2_total_mi";
409 static constexpr const char* VAR_MS2_BSERIES_SCORE = "var_ms2_bseries_score";
410 static constexpr const char* VAR_MS2_DOTPROD_SCORE = "var_ms2_dotprod_score";
411 static constexpr const char* VAR_MS2_INTENSITY_SCORE = "var_ms2_intensity_score";
412 static constexpr const char* VAR_MS2_ISOTOPE_CORRELATION_SCORE = "var_ms2_isotope_correlation_score";
413 static constexpr const char* VAR_MS2_ISOTOPE_OVERLAP_SCORE = "var_ms2_isotope_overlap_score";
414 static constexpr const char* VAR_MS2_LIBRARY_CORR = "var_ms2_library_corr";
415 static constexpr const char* VAR_MS2_LIBRARY_DOTPROD = "var_ms2_library_dotprod";
416 static constexpr const char* VAR_MS2_LIBRARY_MANHATTAN = "var_ms2_library_manhattan";
417 static constexpr const char* VAR_MS2_LIBRARY_RMSD = "var_ms2_library_rmsd";
418 static constexpr const char* VAR_MS2_LIBRARY_ROOTMEANSQUARE = "var_ms2_library_rootmeansquare";
419 static constexpr const char* VAR_MS2_LIBRARY_SANGLE = "var_ms2_library_sangle";
420 static constexpr const char* VAR_MS2_LOG_SN_SCORE = "var_ms2_log_sn_score";
421 static constexpr const char* VAR_MS2_MANHATTAN_SCORE = "var_ms2_manhattan_score";
422 static constexpr const char* VAR_MS2_MASSDEV_SCORE = "var_ms2_massdev_score";
423 static constexpr const char* VAR_MS2_MASSDEV_SCORE_WEIGHTED = "var_ms2_massdev_score_weighted";
424 static constexpr const char* VAR_MS2_MI_SCORE = "var_ms2_mi_score";
425 static constexpr const char* VAR_MS2_MI_WEIGHTED_SCORE = "var_ms2_mi_weighted_score";
426 static constexpr const char* VAR_MS2_MI_RATIO_SCORE = "var_ms2_mi_ratio_score";
427 static constexpr const char* VAR_MS2_NORM_RT_SCORE = "var_ms2_norm_rt_score";
428 static constexpr const char* VAR_MS2_XCORR_COELUTION = "var_ms2_xcorr_coelution";
429 static constexpr const char* VAR_MS2_XCORR_COELUTION_WEIGHTED = "var_ms2_xcorr_coelution_weighted";
430 static constexpr const char* VAR_MS2_XCORR_SHAPE = "var_ms2_xcorr_shape";
431 static constexpr const char* VAR_MS2_XCORR_SHAPE_WEIGHTED = "var_ms2_xcorr_shape_weighted";
432 static constexpr const char* VAR_MS2_YSERIES_SCORE = "var_ms2_yseries_score";
433 static constexpr const char* VAR_MS2_ELUTION_MODEL_FIT_SCORE = "var_ms2_elution_model_fit_score";
434 static constexpr const char* VAR_MS2_IM_XCORR_SHAPE = "var_ms2_im_xcorr_shape";
435 static constexpr const char* VAR_MS2_IM_XCORR_COELUTION = "var_ms2_im_xcorr_coelution";
436 static constexpr const char* VAR_MS2_IM_DELTA_SCORE = "var_ms2_im_delta_score";
437 static constexpr const char* VAR_MS2_IM_LOG_INTENSITY = "var_ms2_im_log_intensity";
438
439 static std::shared_ptr<arrow::Schema> schema();
440 };
441
443 struct OPENMS_DLLAPI OSWFeatureTransitionSchema
444 {
445 static constexpr const char* FEATURE_ID = "feature_id";
446 static constexpr const char* RUN_ID = "run_id";
447 static constexpr const char* TRANSITION_ID = "transition_id";
448 static constexpr const char* AREA_INTENSITY = "area_intensity";
449 static constexpr const char* TOTAL_AREA_INTENSITY = "total_area_intensity";
450 static constexpr const char* APEX_INTENSITY = "apex_intensity";
451 static constexpr const char* APEX_RT = "apex_rt";
452 static constexpr const char* RT_FWHM = "rt_fwhm";
453 static constexpr const char* MASSERROR_PPM = "masserror_ppm";
454 static constexpr const char* TOTAL_MI = "total_mi";
455 static constexpr const char* VAR_INTENSITY_SCORE = "var_intensity_score";
456 static constexpr const char* VAR_INTENSITY_RATIO_SCORE = "var_intensity_ratio_score";
457 static constexpr const char* VAR_LOG_INTENSITY = "var_log_intensity";
458 static constexpr const char* VAR_XCORR_COELUTION = "var_xcorr_coelution";
459 static constexpr const char* VAR_XCORR_SHAPE = "var_xcorr_shape";
460 static constexpr const char* VAR_LOG_SN_SCORE = "var_log_sn_score";
461 static constexpr const char* VAR_MASSDEV_SCORE = "var_massdev_score";
462 static constexpr const char* VAR_MI_SCORE = "var_mi_score";
463 static constexpr const char* VAR_MI_RATIO_SCORE = "var_mi_ratio_score";
464 static constexpr const char* VAR_ISOTOPE_CORRELATION_SCORE = "var_isotope_correlation_score";
465 static constexpr const char* VAR_ISOTOPE_OVERLAP_SCORE = "var_isotope_overlap_score";
466 static constexpr const char* EXP_IM = "exp_im";
467 static constexpr const char* EXP_IM_LEFTWIDTH = "exp_im_leftwidth";
468 static constexpr const char* EXP_IM_RIGHTWIDTH = "exp_im_rightwidth";
469 static constexpr const char* DELTA_IM = "delta_im";
470 static constexpr const char* VAR_IM_DELTA_SCORE = "var_im_delta_score";
471 static constexpr const char* VAR_IM_LOG_INTENSITY = "var_im_log_intensity";
472 static constexpr const char* VAR_IM_XCORR_COELUTION_CONTRAST = "var_im_xcorr_coelution_contrast";
473 static constexpr const char* VAR_IM_XCORR_SHAPE_CONTRAST = "var_im_xcorr_shape_contrast";
474 static constexpr const char* VAR_IM_XCORR_COELUTION_COMBINED = "var_im_xcorr_coelution_combined";
475 static constexpr const char* VAR_IM_XCORR_SHAPE_COMBINED = "var_im_xcorr_shape_combined";
476 static constexpr const char* START_POSITION_AT_5 = "start_position_at_5";
477 static constexpr const char* END_POSITION_AT_5 = "end_position_at_5";
478 static constexpr const char* START_POSITION_AT_10 = "start_position_at_10";
479 static constexpr const char* END_POSITION_AT_10 = "end_position_at_10";
480 static constexpr const char* START_POSITION_AT_50 = "start_position_at_50";
481 static constexpr const char* END_POSITION_AT_50 = "end_position_at_50";
482 static constexpr const char* TOTAL_WIDTH = "total_width";
483 static constexpr const char* TAILING_FACTOR = "tailing_factor";
484 static constexpr const char* ASYMMETRY_FACTOR = "asymmetry_factor";
485 static constexpr const char* SLOPE_OF_BASELINE = "slope_of_baseline";
486 static constexpr const char* BASELINE_DELTA_2_HEIGHT = "baseline_delta_2_height";
487 static constexpr const char* POINTS_ACROSS_BASELINE = "points_across_baseline";
488 static constexpr const char* POINTS_ACROSS_HALF_HEIGHT = "points_across_half_height";
489
490 static std::shared_ptr<arrow::Schema> schema();
491 };
492
494 struct OPENMS_DLLAPI XICSchema
495 {
496 static constexpr const char* RUN_ID = "RUN_ID";
497 static constexpr const char* SOURCE_FILE = "SOURCE_FILE";
498 static constexpr const char* MS_LEVEL = "MS_LEVEL";
499 static constexpr const char* PRECURSOR_ID = "PRECURSOR_ID";
500 static constexpr const char* TRANSITION_ID = "TRANSITION_ID";
501 static constexpr const char* MODIFIED_SEQUENCE = "MODIFIED_SEQUENCE";
502 static constexpr const char* PRECURSOR_CHARGE = "PRECURSOR_CHARGE";
503 static constexpr const char* PRODUCT_CHARGE = "PRODUCT_CHARGE";
504 static constexpr const char* DETECTING_TRANSITION = "DETECTING_TRANSITION";
505 static constexpr const char* PRECURSOR_DECOY = "PRECURSOR_DECOY";
506 static constexpr const char* PRODUCT_DECOY = "PRODUCT_DECOY";
507 static constexpr const char* TRANSITION_ORDINAL = "TRANSITION_ORDINAL";
508 static constexpr const char* TRANSITION_TYPE = "TRANSITION_TYPE";
509 static constexpr const char* ANNOTATION = "ANNOTATION";
510 static constexpr const char* RT_DATA = "RT_DATA";
511 static constexpr const char* INTENSITY_DATA = "INTENSITY_DATA";
512 static constexpr const char* RT_COMPRESSION = "RT_COMPRESSION";
513 static constexpr const char* INTENSITY_COMPRESSION = "INTENSITY_COMPRESSION";
514
515 static std::shared_ptr<arrow::Schema> schema();
516 };
517
519 struct OPENMS_DLLAPI XIMSchema
520 {
521 static constexpr const char* RUN_ID = "RUN_ID";
522 static constexpr const char* SOURCE_FILE = "SOURCE_FILE";
523 static constexpr const char* MS_LEVEL = "MS_LEVEL";
524 static constexpr const char* MOBILOGRAM_TYPE = "MOBILOGRAM_TYPE";
525 static constexpr const char* PRECURSOR_ID = "PRECURSOR_ID";
526 static constexpr const char* TRANSITION_ID = "TRANSITION_ID";
527 static constexpr const char* FEATURE_ID = "FEATURE_ID";
528 static constexpr const char* FEATURE_RT = "FEATURE_RT";
529 static constexpr const char* MODIFIED_SEQUENCE = "MODIFIED_SEQUENCE";
530 static constexpr const char* PRECURSOR_CHARGE = "PRECURSOR_CHARGE";
531 static constexpr const char* PRODUCT_CHARGE = "PRODUCT_CHARGE";
532 static constexpr const char* DETECTING_TRANSITION = "DETECTING_TRANSITION";
533 static constexpr const char* PRECURSOR_DECOY = "PRECURSOR_DECOY";
534 static constexpr const char* PRODUCT_DECOY = "PRODUCT_DECOY";
535 static constexpr const char* TRANSITION_ORDINAL = "TRANSITION_ORDINAL";
536 static constexpr const char* TRANSITION_TYPE = "TRANSITION_TYPE";
537 static constexpr const char* ANNOTATION = "ANNOTATION";
538 static constexpr const char* MOBILITY_DATA = "MOBILITY_DATA";
539 static constexpr const char* INTENSITY_DATA = "INTENSITY_DATA";
540 static constexpr const char* MOBILITY_COMPRESSION = "MOBILITY_COMPRESSION";
541 static constexpr const char* INTENSITY_COMPRESSION = "INTENSITY_COMPRESSION";
542
543 static std::shared_ptr<arrow::Schema> schema();
544 };
545
546} // namespace OpenMS
547
548#endif // WITH_PARQUET
OpenMS::Constants::UserParam::SIGNIFICANCE_THRESHOLD
const std::string SIGNIFICANCE_THRESHOLD
Definition Constants.h:624
OpenMS::Constants::UserParam::SPECTRUM_REFERENCE
const std::string SPECTRUM_REFERENCE
Definition Constants.h:350
OpenMS::Constants::UserParam::ION_MOBILITY
const std::string ION_MOBILITY
Definition Constants.h:251
OpenMS::Constants::UserParam::RANK
const std::string RANK
Definition Constants.h:629
OpenMS::Internal::ClassTest::validate
bool validate(const std::vector< std::string > &file_names)
Validates the given files against the XML schema (if available)
OpenMS::StringConversions::toString
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition StringConversions.h:141
OpenMS
Main OpenMS namespace.
Definition openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
OpenMS::DIM_UNIT::RT
@ RT
RT in seconds.