Index

A

Agilent_Test (class in test_MSAnalysis) (class in test_MSRawData) AgilentColumnName_to_SciexColumnName() (MSRawData.SciexMSRawData method)

AgilentMSRawData (class in MSRawData) Annotation module

B

Bad_Annotation_Test (class in test_BadInput)

Bad_Input_File_Test (class in test_BadInput) Bad_Input_Json_Test (class in test_BadInput)

C

check_duplicated_columns_in_wide_data() (in module MSDuplicateCheck) check_duplicated_sample_names_in_wide_data() (in module MSDuplicateCheck) Concatenation_By_Column_Test (class in test_ConcatenationColumn)

Concatenation_By_Row_Test (class in test_ConcatenationRow) create_ISTD_report() (MSDataReport.MSDataReport_PDF method) create_parameters_report() (MSDataReport.MSDataReport_PDF method) create_Transition_Name_dict() (MSCalculate.ISTD_Operations method)

D

df_to_file() (MSDataOutput.MSDataOutput method) (MSDataOutput.MSDataOutput_csv method) (MSDataOutput.MSDataOutput_Excel method)

df_to_file_preparation() (MSDataOutput.MSDataOutput method) Duplicate_Input_Test (class in test_DuplicateInput)

E

end_writer() (MSDataOutput.MSDataOutput_Excel method)

expand_Transition_Name_df() (MSCalculate.ISTD_Operations method)

G

get_Analyte_Concentration() (MSAnalysis.MS_Analysis method) get_from_Input_Data() (MSAnalysis.MS_Analysis method) get_Long_Table() (MSAnalysis.MS_Analysis method)

get_Normalised_Area() (MSAnalysis.MS_Analysis method) get_table() (MSRawData.AgilentMSRawData method) (MSRawData.SciexMSRawData method) getConc_by_ISTD() (MSCalculate.ISTD_Operations method)

I

ISTD_Operations (class in MSCalculate)

ISTDAnnot_Test (class in test_ISTDAnnot)

M

module Annotation MSAnalysis MSCalculate MSDataOutput MSDataReport MSDuplicateCheck MSRawData test_BadInput test_ConcatenationColumn test_ConcatenationRow test_DuplicateInput test_ISTDAnnot test_MSAnalysis test_MSRawData test_NoConcatenation test_SampleAnnot test_TransitionNameAnnot MS_Analysis (class in MSAnalysis)

MS_Template (class in Annotation) MSAnalysis module MSCalculate module MSDataOutput module MSDataOutput (class in MSDataOutput) MSDataOutput_csv (class in MSDataOutput) MSDataOutput_Excel (class in MSDataOutput) MSDataReport module MSDataReport (class in MSDataReport) MSDataReport_PDF (class in MSDataReport) MSDuplicateCheck module MSRawData module MSRawData (class in MSRawData)

N

NoConcatenation_Test (class in test_NoConcatenation)

normalise_by_ISTD() (MSCalculate.ISTD_Operations method)

O

output_to_PDF() (MSDataReport.MSDataReport_PDF method)

P

parse_MSOrganiser_args() (in module MSParser)

R

Read_ISTD_Annot_Sheet() (Annotation.MS_Template method) read_ISTD_map() (MSCalculate.ISTD_Operations method) read_Sample_Annot() (MSCalculate.ISTD_Operations method)

Read_Sample_Annot_Sheet() (Annotation.MS_Template method) Read_Transition_Name_Annot_Sheet() (Annotation.MS_Template method) remove_whiteSpaces() (Annotation.MS_Template method) (MSRawData.MSRawData method)

S

SampleAnnot_Test (class in test_SampleAnnot) SciexMSRawData (class in MSRawData) setUp() (test_ConcatenationColumn.Concatenation_By_Column_Test method) (test_ConcatenationRow.Concatenation_By_Row_Test method) (test_DuplicateInput.Duplicate_Input_Test method) (test_ISTDAnnot.ISTDAnnot_Test method) (test_MSAnalysis.Agilent_Test method) (test_MSRawData.Agilent_Test method) (test_NoConcatenation.NoConcatenation_Test method) (test_SampleAnnot.SampleAnnot_Test method) (test_TransitionNameAnnot.TransitionNameAnnot_Test method)

start_writer() (MSDataOutput.MSDataOutput method) (MSDataOutput.MSDataOutput_Excel method)

T

tearDown() (test_ConcatenationColumn.Concatenation_By_Column_Test method) (test_ConcatenationRow.Concatenation_By_Row_Test method) (test_DuplicateInput.Duplicate_Input_Test method) (test_ISTDAnnot.ISTDAnnot_Test method) (test_MSAnalysis.Agilent_Test method) (test_MSRawData.Agilent_Test method) (test_NoConcatenation.NoConcatenation_Test method) (test_SampleAnnot.SampleAnnot_Test method) (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_BadInput module test_CompoundData() (test_MSRawData.Agilent_Test method) test_CompoundData_Qualifier() (test_MSRawData.Agilent_Test method) test_concatenate_by_columns() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_LongTable() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_LongTable_with_Annot() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_multiple_ISTD() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_multiple_ISTD_LongTable() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_multiple_ISTD_LongTable_with_Annot() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_multiple_ISTD_transpose() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_columns_transpose() (test_ConcatenationColumn.Concatenation_By_Column_Test method) test_concatenate_by_rows() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_LongTable() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_LongTable_with_Annot() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_multiple_ISTD() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_multiple_ISTD_LongTable() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_multiple_ISTD_LongTable_with_Annot() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_multiple_ISTD_transpose() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_concatenate_by_rows_transpose() (test_ConcatenationRow.Concatenation_By_Row_Test method) test_ConcatenationColumn module test_ConcatenationRow module test_DuplicateInput module test_function_duplicate_column() (test_DuplicateInput.Duplicate_Input_Test method) test_function_duplicate_column_multipleISTD() (test_DuplicateInput.Duplicate_Input_Test method) test_function_duplicate_row() (test_DuplicateInput.Duplicate_Input_Test method) test_function_duplicate_row_multipleISTD() (test_DuplicateInput.Duplicate_Input_Test method) test_getAnalyteConcTable() (test_MSAnalysis.Agilent_Test method) test_getLongTable() (test_MSAnalysis.Agilent_Test method) test_getLongTable_with_Annot() (test_MSAnalysis.Agilent_Test method) test_getnormAreaTable() (test_MSAnalysis.Agilent_Test method) test_input_agilent_compound_table_file_no_name() (test_BadInput.Bad_Input_File_Test method) test_input_agilent_file_no_data_file() (test_BadInput.Bad_Input_File_Test method) test_input_annotation_cannot_be_found() (test_BadInput.Bad_Annotation_Test method) test_input_annotation_is_a_folder() (test_BadInput.Bad_Annotation_Test method) test_input_annotation_wrong_file_extention() (test_BadInput.Bad_Annotation_Test method) test_input_file_cannot_be_found() (test_BadInput.Bad_Input_File_Test method) test_input_file_empty() (test_BadInput.Bad_Input_File_Test method) test_input_file_is_a_folder() (test_BadInput.Bad_Input_File_Test method) test_input_invalid_output_option() (test_BadInput.Bad_Input_File_Test method) test_input_valid_output_option_agilent_no_data_csv() (test_BadInput.Bad_Input_File_Test method) test_input_valid_output_option_agilent_no_data_excel() (test_BadInput.Bad_Input_File_Test method)

test_invalid_agilent_dataform() (test_BadInput.Bad_Input_File_Test method) test_invalid_json_file() (test_BadInput.Bad_Input_Json_Test method) test_ISOEncodedData() (test_MSRawData.Agilent_Test method) test_ISTDAnnot module test_MSAnalysis module test_MSRawData module test_no_concatenate() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_LongTable() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_LongTable_with_Annot() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_multiple_ISTD() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_multiple_ISTD_LongTable() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_multiple_ISTD_LongTable_with_Annot() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_multiple_ISTD_transpose() (test_NoConcatenation.NoConcatenation_Test method) test_no_concatenate_transpose() (test_NoConcatenation.NoConcatenation_Test method) test_NoConcatenation module test_SampleAnnot module test_SciexData() (test_MSRawData.Agilent_Test method) test_TransitionNameAnnot module test_validation_CustomUnit() (test_ISTDAnnot.ISTDAnnot_Test method) test_validation_DuplicateData() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_validation_DuplicateISTD() (test_ISTDAnnot.ISTDAnnot_Test method) test_validation_EmptyData() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_validation_EmptyTransitionName() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_validation_InvalidSheetName() (test_ISTDAnnot.ISTDAnnot_Test method) (test_SampleAnnot.SampleAnnot_Test method) (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_validation_Missing_DataFile_Or_SampleName() (test_SampleAnnot.SampleAnnot_Test method) test_validation_MissingColumnNames() (test_ISTDAnnot.ISTDAnnot_Test method) (test_SampleAnnot.SampleAnnot_Test method) (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_validation_MSFilePath_with_NoSampleAnnot() (test_SampleAnnot.SampleAnnot_Test method) test_validation_RawDataFileName() (test_SampleAnnot.SampleAnnot_Test method) test_warn_BlankISTD() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_warn_ISTD_in_ISTD_Annot_but_not_in_Transition_Name_Annot() (test_ISTDAnnot.ISTDAnnot_Test method) test_warn_ISTD_in_Transition_Name_Annot_but_not_in_Input_Data() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_warn_ISTD_in_Transition_Name_Annot_but_not_in_Input_Data_multiple_ISTD() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_warn_ISTD_in_Transition_Name_Annot_but_not_in_ISTD_Annot() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_warn_sample_in_MSFilePath_but_not_in_SampleAnnot() (test_SampleAnnot.SampleAnnot_Test method) test_warn_TransitionName_in_Input_Data_but_not_in_Transition_Name_Annot() (test_TransitionNameAnnot.TransitionNameAnnot_Test method) test_WideData() (test_MSRawData.Agilent_Test method) test_WideData_Qualifier() (test_MSRawData.Agilent_Test method) test_WideDataLarge() (test_MSRawData.Agilent_Test method) test_workflow_column_concatenate_duplicate_column() (test_DuplicateInput.Duplicate_Input_Test method) test_workflow_no_concatenate_duplicate_column() (test_DuplicateInput.Duplicate_Input_Test method) test_workflow_no_concatenate_duplicate_row() (test_DuplicateInput.Duplicate_Input_Test method) test_workflow_row_concatenate_duplicate_row() (test_DuplicateInput.Duplicate_Input_Test method) test_wrong_file_extention() (test_BadInput.Bad_Input_File_Test method) TransitionNameAnnot_Test (class in test_TransitionNameAnnot) transpose_MSdata() (MSDataOutput.MSDataOutput method)