CoreMS 4.0.0__py3-none-any.whl

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Files changed (171) hide show
  1. corems/__init__.py +63 -0
  2. corems/chroma_peak/__init__.py +0 -0
  3. corems/chroma_peak/calc/ChromaPeakCalc.py +480 -0
  4. corems/chroma_peak/calc/__init__.py +0 -0
  5. corems/chroma_peak/calc/subset.py +196 -0
  6. corems/chroma_peak/factory/__init__.py +0 -0
  7. corems/chroma_peak/factory/chroma_peak_classes.py +1178 -0
  8. corems/encapsulation/__init__.py +0 -0
  9. corems/encapsulation/constant.py +1283 -0
  10. corems/encapsulation/factory/__init__.py +0 -0
  11. corems/encapsulation/factory/parameters.py +392 -0
  12. corems/encapsulation/factory/processingSetting.py +1244 -0
  13. corems/encapsulation/input/__init__.py +0 -0
  14. corems/encapsulation/input/parameter_from_json.py +579 -0
  15. corems/encapsulation/output/__init__.py +0 -0
  16. corems/encapsulation/output/parameter_to_dict.py +142 -0
  17. corems/encapsulation/output/parameter_to_json.py +332 -0
  18. corems/mass_spectra/__init__.py +0 -0
  19. corems/mass_spectra/calc/GC_Calc.py +84 -0
  20. corems/mass_spectra/calc/GC_Deconvolution.py +558 -0
  21. corems/mass_spectra/calc/GC_RI_Calibration.py +44 -0
  22. corems/mass_spectra/calc/MZSearch.py +249 -0
  23. corems/mass_spectra/calc/SignalProcessing.py +656 -0
  24. corems/mass_spectra/calc/__init__.py +0 -0
  25. corems/mass_spectra/calc/lc_calc.py +5790 -0
  26. corems/mass_spectra/calc/lc_calc_operations.py +1127 -0
  27. corems/mass_spectra/factory/GC_Class.py +791 -0
  28. corems/mass_spectra/factory/__init__.py +0 -0
  29. corems/mass_spectra/factory/chromat_data.py +51 -0
  30. corems/mass_spectra/factory/lc_class.py +2721 -0
  31. corems/mass_spectra/input/__init__.py +0 -0
  32. corems/mass_spectra/input/andiNetCDF.py +200 -0
  33. corems/mass_spectra/input/boosterHDF5.py +216 -0
  34. corems/mass_spectra/input/brukerSolarix.py +153 -0
  35. corems/mass_spectra/input/brukerSolarix_utils.py +73 -0
  36. corems/mass_spectra/input/corems_hdf5.py +1710 -0
  37. corems/mass_spectra/input/massList.py +133 -0
  38. corems/mass_spectra/input/mzml.py +668 -0
  39. corems/mass_spectra/input/parserbase.py +239 -0
  40. corems/mass_spectra/input/rawFileReader.py +1839 -0
  41. corems/mass_spectra/output/__init__.py +0 -0
  42. corems/mass_spectra/output/export.py +2800 -0
  43. corems/mass_spectrum/__init__.py +0 -0
  44. corems/mass_spectrum/calc/AutoRecalibration.py +237 -0
  45. corems/mass_spectrum/calc/Calibration.py +602 -0
  46. corems/mass_spectrum/calc/CalibrationCalc.py +253 -0
  47. corems/mass_spectrum/calc/KendrickGroup.py +239 -0
  48. corems/mass_spectrum/calc/MassErrorPrediction.py +436 -0
  49. corems/mass_spectrum/calc/MassSpectrumCalc.py +303 -0
  50. corems/mass_spectrum/calc/MeanResolvingPowerFilter.py +212 -0
  51. corems/mass_spectrum/calc/NoiseCalc.py +371 -0
  52. corems/mass_spectrum/calc/NoiseCalc_Bayes.py +93 -0
  53. corems/mass_spectrum/calc/PeakPicking.py +994 -0
  54. corems/mass_spectrum/calc/__init__.py +0 -0
  55. corems/mass_spectrum/factory/MassSpectrumClasses.py +1753 -0
  56. corems/mass_spectrum/factory/__init__.py +0 -0
  57. corems/mass_spectrum/input/__init__.py +0 -0
  58. corems/mass_spectrum/input/baseClass.py +531 -0
  59. corems/mass_spectrum/input/boosterHDF5.py +161 -0
  60. corems/mass_spectrum/input/coremsHDF5.py +475 -0
  61. corems/mass_spectrum/input/massList.py +402 -0
  62. corems/mass_spectrum/input/numpyArray.py +133 -0
  63. corems/mass_spectrum/output/__init__.py +0 -0
  64. corems/mass_spectrum/output/export.py +841 -0
  65. corems/molecular_formula/__init__.py +0 -0
  66. corems/molecular_formula/calc/MolecularFormulaCalc.py +885 -0
  67. corems/molecular_formula/calc/__init__.py +0 -0
  68. corems/molecular_formula/factory/MolecularFormulaFactory.py +895 -0
  69. corems/molecular_formula/factory/__init__.py +0 -0
  70. corems/molecular_formula/input/__init__.py +0 -0
  71. corems/molecular_formula/input/masslist_ref.py +355 -0
  72. corems/molecular_id/__init__.py +0 -0
  73. corems/molecular_id/calc/ClusterFilter.py +251 -0
  74. corems/molecular_id/calc/MolecularFilter.py +122 -0
  75. corems/molecular_id/calc/SpectralSimilarity.py +632 -0
  76. corems/molecular_id/calc/__init__.py +0 -0
  77. corems/molecular_id/calc/math_distance.py +1637 -0
  78. corems/molecular_id/data/FAMES_REF.msp +980 -0
  79. corems/molecular_id/data/PNNLMetV20191015.msp +157267 -0
  80. corems/molecular_id/factory/EI_SQL.py +650 -0
  81. corems/molecular_id/factory/MolecularLookupTable.py +914 -0
  82. corems/molecular_id/factory/__init__.py +0 -0
  83. corems/molecular_id/factory/classification.py +884 -0
  84. corems/molecular_id/factory/lipid_molecular_metadata.py +50 -0
  85. corems/molecular_id/factory/molecularSQL.py +827 -0
  86. corems/molecular_id/factory/spectrum_search_results.py +119 -0
  87. corems/molecular_id/input/__init__.py +0 -0
  88. corems/molecular_id/input/nistMSI.py +148 -0
  89. corems/molecular_id/search/__init__.py +0 -0
  90. corems/molecular_id/search/compoundSearch.py +214 -0
  91. corems/molecular_id/search/database_interfaces.py +1527 -0
  92. corems/molecular_id/search/findOxygenPeaks.py +330 -0
  93. corems/molecular_id/search/lcms_spectral_search.py +348 -0
  94. corems/molecular_id/search/molecularFormulaSearch.py +1117 -0
  95. corems/molecular_id/search/priorityAssignment.py +723 -0
  96. corems/ms_peak/__init__.py +0 -0
  97. corems/ms_peak/calc/MSPeakCalc.py +1010 -0
  98. corems/ms_peak/calc/__init__.py +0 -0
  99. corems/ms_peak/factory/MSPeakClasses.py +542 -0
  100. corems/ms_peak/factory/__init__.py +0 -0
  101. corems/transient/__init__.py +0 -0
  102. corems/transient/calc/TransientCalc.py +362 -0
  103. corems/transient/calc/__init__.py +0 -0
  104. corems/transient/factory/TransientClasses.py +457 -0
  105. corems/transient/factory/__init__.py +0 -0
  106. corems/transient/input/__init__.py +0 -0
  107. corems/transient/input/brukerSolarix.py +461 -0
  108. corems/transient/input/midasDatFile.py +172 -0
  109. corems-4.0.0.dist-info/METADATA +475 -0
  110. corems-4.0.0.dist-info/RECORD +171 -0
  111. corems-4.0.0.dist-info/WHEEL +5 -0
  112. corems-4.0.0.dist-info/licenses/LICENSE +22 -0
  113. corems-4.0.0.dist-info/top_level.txt +4 -0
  114. examples/archive/scripts/CoreMS_tutorial.py +94 -0
  115. examples/archive/scripts/DI HR-MS Halogens Bruker.py +196 -0
  116. examples/archive/scripts/DI HR-MS MassList.py +385 -0
  117. examples/archive/scripts/GC-MS MetabRef.py +213 -0
  118. examples/archive/scripts/GC-MS NetCDF.py +217 -0
  119. examples/archive/scripts/HR-MS Thermo Raw 21T.py +136 -0
  120. examples/archive/scripts/LC-ICPMS_metal_peaks.py +297 -0
  121. examples/archive/scripts/LCMS-Thermo.py +460 -0
  122. examples/archive/scripts/LCMS_isotopes.py +283 -0
  123. examples/archive/scripts/MSParams_example.py +21 -0
  124. examples/archive/scripts/Molecular Formula Data Aggreation.py +84 -0
  125. examples/archive/scripts/Single Mz Search.py +69 -0
  126. examples/test_notebooks.py +145 -0
  127. ext_lib/ChemstationMSFileReader.dll +0 -0
  128. ext_lib/ChemstationMSFileReader.xml +126 -0
  129. ext_lib/RawFileReaderLicense.doc +0 -0
  130. ext_lib/ThermoFisher.CommonCore.BackgroundSubtraction.dll +0 -0
  131. ext_lib/ThermoFisher.CommonCore.BackgroundSubtraction.xml +2307 -0
  132. ext_lib/ThermoFisher.CommonCore.Data.dll +0 -0
  133. ext_lib/ThermoFisher.CommonCore.Data.xml +28974 -0
  134. ext_lib/ThermoFisher.CommonCore.MassPrecisionEstimator.dll +0 -0
  135. ext_lib/ThermoFisher.CommonCore.MassPrecisionEstimator.xml +241 -0
  136. ext_lib/ThermoFisher.CommonCore.RawFileReader.dll +0 -0
  137. ext_lib/ThermoFisher.CommonCore.RawFileReader.xml +31174 -0
  138. ext_lib/__init__.py +0 -0
  139. ext_lib/dotnet/OpenMcdf.Extensions.dll +0 -0
  140. ext_lib/dotnet/OpenMcdf.dll +0 -0
  141. ext_lib/dotnet/OpenMcdf.xml +1154 -0
  142. ext_lib/dotnet/System.IO.FileSystem.AccessControl.dll +0 -0
  143. ext_lib/dotnet/System.IO.FileSystem.AccessControl.xml +506 -0
  144. ext_lib/dotnet/System.Security.AccessControl.dll +0 -0
  145. ext_lib/dotnet/System.Security.AccessControl.xml +2043 -0
  146. ext_lib/dotnet/System.Security.Principal.Windows.dll +0 -0
  147. ext_lib/dotnet/System.Security.Principal.Windows.xml +1011 -0
  148. ext_lib/dotnet/ThermoFisher.CommonCore.BackgroundSubtraction.dll +0 -0
  149. ext_lib/dotnet/ThermoFisher.CommonCore.BackgroundSubtraction.xml +2307 -0
  150. ext_lib/dotnet/ThermoFisher.CommonCore.Data.dll +0 -0
  151. ext_lib/dotnet/ThermoFisher.CommonCore.Data.xml +29148 -0
  152. ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.dll +0 -0
  153. ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.xml +241 -0
  154. ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.dll +0 -0
  155. ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.xml +31492 -0
  156. ext_lib/version +18 -0
  157. support_code/atom_parsers/AtomsDescription.py +359 -0
  158. support_code/atom_parsers/CreateAtomsDescription.py +56 -0
  159. support_code/nmdc/filefinder.py +90 -0
  160. support_code/nmdc/lipidomics/lipidomics_workflow.py +748 -0
  161. support_code/nmdc/lipidomics/manifest_examples.py +49 -0
  162. support_code/nmdc/metabolomics/gcms_workflow.py +158 -0
  163. support_code/nmdc/metabolomics/lcms_metabolomics_targeted_search.py +59 -0
  164. support_code/nmdc/metabolomics/lcms_metabolomics_workflow.py +248 -0
  165. support_code/nmdc/metabolomics/metabolomics_collection.py +628 -0
  166. support_code/nmdc/metadata/dms_api.py +42 -0
  167. support_code/nmdc/nom/archived_scripts/nmdc_metadata_gen.py +288 -0
  168. support_code/nmdc/nom/archived_scripts/nom_grow_workflow.py +209 -0
  169. support_code/nmdc/nom/nom_workflow.py +312 -0
  170. support_code/windows_only_importers/BrukerCompassXtract.py +180 -0
  171. support_code/windows_only_importers/ThermoMSFileReader.py +405 -0
ext_lib/ThermoFisher.CommonCore.MassPrecisionEstimator.xml ADDED
@@ -0,0 +1,241 @@
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+ <?xml version="1.0"?>
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+ <doc>
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+ <assembly>
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+ <name>ThermoFisher.CommonCore.MassPrecisionEstimator</name>
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+ </assembly>
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+ <members>
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+ <member name="T:ThermoFisher.CommonCore.MassPrecisionEstimator.EstimatorResults">
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+ <summary>
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+ Class to hold mass precision estimator results for individual mass/intensity points
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+ in a scan.
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.EstimatorResults.Intensity">
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+ <summary>
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+ Gets or sets the intensity value
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.EstimatorResults.Mass">
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+ <summary>
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+ Gets or sets the mass value
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.EstimatorResults.MassAccuracyInMmu">
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+ <summary>
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+ Gets or sets the mass accuracy in MMU value
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.EstimatorResults.MassAccuracyInPpm">
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+ <summary>
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+ Gets or sets the mass accuracy in PPM value
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.EstimatorResults.Resolution">
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+ <summary>
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+ Gets or sets the resolution value
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+ </summary>
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+ </member>
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+ <member name="T:ThermoFisher.CommonCore.MassPrecisionEstimator.IPrecisionEstimate">
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+ <summary>
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+ The interface class for the Mass Precision Estimate (MPE) code
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.IPrecisionEstimate.Rawfile">
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+ <summary>
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+ Sets the RAW file.
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.IPrecisionEstimate.ScanNumber">
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+ <summary>
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+ Sets the scan number.
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+ </summary>
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+ <value> The scan number. </value>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.IPrecisionEstimate.GetIonTime(ThermoFisher.CommonCore.Data.FilterEnums.MassAnalyzerType,ThermoFisher.CommonCore.Data.Business.Scan,System.Collections.Generic.List{System.String},System.Collections.Generic.List{System.String})">
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+ <summary>
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+ Calculate the ion time - fill (traps and FT) or dwell time (quads)
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+ based upon the type of instrument.
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+ </summary>
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+ <param name="analyzerType">The analyzer type</param>
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+ <param name="scan">The scan to process</param>
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+ <param name="trailerHeadings">The trailer headings.</param>
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+ <param name="trailerValues">The trailer values.</param>
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+ <returns>The calculated ion time</returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.IPrecisionEstimate.GetMassPrecisionEstimate(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.FilterEnums.MassAnalyzerType,System.Double,System.Double)">
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+ <summary>
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+ Gets the mass precision estimate for the data in the provided scan. The information is passed through the
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+ arguments in this method.
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+ </summary>
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+ <param name="scan">The scan to process</param>
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+ <param name="analyzerType">The analyzer type for the provided scan</param>
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+ <param name="ionTime">The ion time for the provided scan</param>
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+ <param name="resolution">the resolution for the provided scan</param>
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+ <returns>The list of EstimatorResults objects</returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.IPrecisionEstimate.GetMassPrecisionEstimate">
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+ <summary>
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+ Gets mass precision estimate for the provided scan number. The information needed to process the scan is passed through
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+ the properties in the class when using this method.
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+ </summary>
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+ <returns>The list of EstimatorResults objects</returns>
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+ </member>
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+ <member name="T:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate">
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+ <summary>
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+ Class to calculate the mass precision estimates (MPE) for a specific scan
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+ </summary>
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+ </member>
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+ <member name="T:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.TrapScanType">
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+ <summary>
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+ Values that represent the ion trap scan types.
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.TrapScanType.Normal">
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+ <summary>
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+ The type for a normal scan
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.TrapScanType.Enhanced">
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+ <summary>
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+ The type for an enhanced scan
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.TrapScanType.Zoom">
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+ <summary>
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+ The type for a zoom scan
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.TrapScanType.UltraZoom">
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+ <summary>
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+ The type for an ultra zoom scan
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate._estimatorResults">
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+ <summary>
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+ List containing the results from the mass precision estimate calculation.
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate._rawFile">
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+ <summary>
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+ The RAW file object.
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate._scanResolution">
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+ <summary>
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+ The scan resolution.
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate._ionTime">
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+ <summary>
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+ The ion time.
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+ </summary>
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+ </member>
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+ <member name="F:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate._scanNumber">
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+ <summary>
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+ The scan number.
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.Rawfile">
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+ <summary>
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+ Sets the raw file as an open IRawData objects.
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+ </summary>
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+ </member>
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+ <member name="P:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.ScanNumber">
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+ <summary>
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+ Sets the scan number of the scan to be analyzed
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+ </summary>
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+ <value> The scan number. </value>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.GetIonTrapScanType(System.String)">
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+ <summary>
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+ Gets the ion trap scan type.
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+ </summary>
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+ <param name="scanFilter">
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+ The scan filter to process
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+ </param>
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+ <returns>
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+ The ion trap scan type as an enumerated value.
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+ </returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.#ctor">
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+ <summary>
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+ Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate"/> class.
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+ </summary>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.Dispose">
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+ <summary>
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+ Performs application-defined tasks associated with freeing, releasing, or resetting
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+ unmanaged resources.
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+ </summary>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.GetIonTime(ThermoFisher.CommonCore.Data.FilterEnums.MassAnalyzerType,ThermoFisher.CommonCore.Data.Business.Scan,System.Collections.Generic.List{System.String},System.Collections.Generic.List{System.String})">
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+ <summary>
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+ Calculate the ion time (fill (traps and FT) or dwell time (quads))
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+ </summary>
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+ <param name="analyzerType">The analyzer type</param>
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+ <param name="scan">The scan to process</param>
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+ <param name="trailerHeadings">The trailer extra data headings</param>
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+ <param name="trailerValues">The trailer extra data values</param>
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+ <returns> The calculated ion time</returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.GetMassPrecisionEstimate(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.FilterEnums.MassAnalyzerType,System.Double,System.Double)">
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+ <summary>
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+ Gets mass precision estimate and stores them in a class property list of classes
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+ This method will throw an Exception or ArgumentException if a problem occurs
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+ during processing.
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+ </summary>
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+ <param name="scan">
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+ The scan to process
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+ </param>
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+ <param name="analyzerType">
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+ The analyzer type for the scan
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+ </param>
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+ <param name="ionTime">
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+ The ion time for the scan
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+ </param>
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+ <param name="resolution">
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+ The resolution for the scan
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+ </param>
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+ <returns>
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+ Returns the list of Mass Precision Estimation results
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+ </returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.GetMassPrecisionEstimate">
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+ <summary>
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+ Gets mass precision estimate and stores them in a class property list of classes
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+ This method will throw an Exception or ArgumentException if a problem occurs
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+ during processing.
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+ </summary>
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+ <returns>
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+ Returns the list of Mass Precision Estimation results
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+ </returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.PopulateScanData(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.FilterEnums.MassAnalyzerType)">
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+ <summary>
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+ Populate the mass precision estimator data list from raw or label data
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+ as appropriate for the scan data.
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+ </summary>
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+ <param name="scan">The scan</param>
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+ <param name="analyzerType"> The analyzer type </param>
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+ <returns>Returns true or false based upon if the scan could be filled in</returns>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.CalculateMassPrecisionEstimateFromFormula">
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+ <summary>
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+ Calculate the MPE for the scan from formula.
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+ </summary>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.CompareMassAccuracyToTables(ThermoFisher.CommonCore.Data.FilterEnums.MassAnalyzerType,System.String)">
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+ <summary>
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+ Compare the calculated MPE to tables of information from Alexander and Jae
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+ </summary>
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+ <param name="analyzerType"> the analyzer type. </param>
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+ <param name="scanFilter"> the scan filter. </param>
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+ </member>
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+ <member name="M:ThermoFisher.CommonCore.MassPrecisionEstimator.PrecisionEstimate.GetScanResolution">
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+ <summary>
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+ Gets the scan resolution from the file header
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+ </summary>
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+ <returns>The resolution from the run header.</returns>
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+ </member>
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+ </members>
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+ </doc>