NEWS

Version 0.1.2 (20200812)
--------------
- initial verison of annotation credential
o add authenticatePeakGroupCredential
o add convertSemiTargetedResult2LongTable
o add authenticateFormulaCredential
o add authenticateAnnotationCredential

Version 0.1.3 (20200815)
--------------
o fix bugs errors authenticatePeakGroupCredential & authenticateFormulaCredential
(errors: missing ms2 spec)


Version 0.1.4 (20200925)
--------------
o add function of RecursiveAnnotationInitialSeed (ms2Annotation in MetDNA1)


Verison 0.2.0 (20201006)
--------------
o add the frame of RecursiveAnnotationMRN (metABM and relate parts)
o fix some bugs in readMs2

Verison 0.2.1 (20201017)
--------------
o rewrite the frame of RecursiveAnnotationIniitialSeed
o combine annotationCredential with Recursive Annotation

Verison 0.2.2 (20201019)
--------------
o fit linux platform (GenForm)
o modify AnnotationCredential order (Seed first)
o fix some bugs in RescursiveAnnotationMRN
o fix bugs error report for adduct types 'M+' and 'M-' in checkElements

Version 0.2.3 (20201024)
--------------
o fix bugs in concisePeakGroup2PeakGroup (change peak name filter to peak group name filter)

Version 0.2.31 (20201027)
--------------
o fix bugs in prepare prepareMetDNA2 (correct "M+H-2H2O" to "M-2H2O+H")

Version 0.2.4 (20201103)
--------------
o add RT calibration (Update RT calibration table, and RT library)
o update cpd_emrn, lib_adduct_nl, lib_formula
o add a choice to select forward annotation as initial seed

Version 0.2.41 (20201105)
--------------
o add generateMetDNA2AnnotationResult part to merge initial annotation, recursive annotation and annotation credential results
o initial seed annotation: reserve candidates whose RT/CCS error within the tolerance or NA
o add plotNeighbor function in annotateNeighbor
o add package information export and data check part
o add pre-trained RT model for Amide12min and Amide23min

Version 0.2.42 (20201109)
--------------
o fix some bugs (obj missing)
o fix some bugs (correct tibble error)

Version 0.2.43 (20201110)
--------------
o fix versions of import packages
o fix bugs in formula prediction (replace rela_path with absolute_path)
o fix bugs in generateResultTable4AllAnnotation (fix column type)

Version 0.2.44 (20201113)
--------------
o Add a choice is_pred_formula_all for predict formula for all peak groups
o Add direction parameter in final result merge

Version 0.2.45 (20201117)
--------------
o Add sample-sample correlation (ssc) filtering for adductAnnotation, neutralLossAnnotation, but not apply for isotopeAnnotation and isfAnnotation
o Add rule limitation for adductAnnotation and neutralLossAnnotation
o Add a parameter to limit topN fragment of base peak for isfAnnotation
o Modify the mz match tolerance in credential (Old: 10pm, 500Da; New: 25ppm, 400Da)
o Change ms2 match function (Old: nl_ms2 vs base_ms2; New: base_ms2 vs nl_ms2)
o Remove peak groups first which not meet rule limitation (e.g. [2M+H]+ without [M+H]+), and defined as type0
o Update lib_adduct_nl (disable uncommon adduct and nl in credential)

Version 0.2.46 (20201124)
--------------
o Add base formula result into all peaks in the peak group during merge annotation results
o Add isotope column in id_merge
o Modify processing logic in is_credential_pg (assign TRUE when the label same with the annotated peak group, not base peak)
o Update formula result when is_pred_formula_all equals TRUE


Version 0.2.47 (20201130)
--------------
o Fix the bug in credential: perform the credential for annotations which are in initial seeds but not in KEGG
o Fix the bug in readInitialSeed: adduct error for annotation whoes KEGG_IDs is 'NA;NA;C00047'
o Fix the bug in MSP data importing and processing
o Fix the bug in plotNeighbor: feature with one fragment lead NULL ms2 score (skip it temporarily)


Version 0.2.5 (20201202)
--------------
o Update zhuMetLib (correct 48 error compound information, and add 5 compounds in 200STDs)
o Update md_zhumetlib
o Fix some bugs in credential: para dp_cutoff not passing

Version 0.2.51 (20201202)
--------------
o Modify absolute RT range to combined RT range (RT <= 500s, rt_tol=30s; RT>500, rt_tol=6%)


Version 0.2.52 (20201212)
--------------
o Update zhuMetLib (correct meta info in different CE)


Version 0.3.00 (20201214)
--------------
o Modify general workflow: 1. merge initial seed result and recursive result; 2. assign confidence level; 3. perform annotation credential according to confidence level
o Add RecursiveAnnotationMerge part, MetDNA2Result part
o Add functions: mergeRecursiveAnnotation, generateMetDNA2AnnoClass, addInitialSeedResult2MetDNA2AnnoClass, addRecursiveResult2MetDNA2AnnoClass, addCredentialResult2MetDNA2AnnoClass, generateResultTable4AllAnnotation, generateMetDNA2AnnotationResult
o Add type_order for concisePeak2PeakGroup and concisePeakGroup2PeakGroup
o Export id_effective_with_credential_result
o Systemically modify the directory names of results

Version 0.3.01 (20201229)
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o add space check for path

Version 0.3.10 (20210105)
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o add fiehnHilicLib and md_fiehnHilicLib for obitrap data processing
o add checkPara function
o modify the related scripts to fit obitrap data processing
o fix the bugs: error title assign in the plot of initial seed match

Version 0.3.11 (20210107)
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o fix the bugs: error in annotation merge (GY)

Version 0.3.20 (20210111)
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o assign new confidence system into id_merge_modify and id_merge_modify_wide
o only keep the highest confidence level annotations in id_merge_modify
o export id_merge_modify_service for service projects
o fix some bugs in annotaiton credential

Version 0.4.00 (20210309)
--------------
o add module: BiologyInterpretation, BiologyInterpretation
o update libraries: reaction_pair_network, md_mrn_emrn, cpd_emrn, lib_formula
o add new libraries: lib_pathway
o add functions: runSpecMatch, interpretBiology, doStatAnalysis, doUniTest, calcuFoldChange, enrichPathway, mapInChIKey1ToKEGG, quantiPathway
o add plot functions: plotVolanco, plotPathwayScatter, plotPathwayBar, plotPathwayHeatmap, plotPathwayBoxplot, plotPathwayHeatmapMet
o change default spectra purification parameter: ppmPrecursor filter (500 -> 400)
o fix bugs: reverse score filtering but using forward score indeed

Version 0.4.01 (20210310)
--------------
o fix some bugs in BiologyInterpretation
o update in-house database: zhuMetlib (add new MS2), lib_rt (1230->1266), md_zhumetlib (2084->2105)
o add new in-house database: zhuMetlib_obitrap
o correct compound formula and information IDs for permanent charged metabolites

Version 0.4.02 (20210311)
--------------
o add parameters for zhuMetLib_obitrap


Version 0.4.03 (20210312)
--------------
o update zhuMetlib_orbitrap V2.2
o add [M-2H]- in lib_adduct_nl
o add the export of rt_calibration_result


Version 0.4.04 (20210315)
--------------
o update lib_ccs (add the pred_ccs for cpd_emrn)
o add functions: update lib_ccs (add the pred_ccs for cpd_emrn)
o export matchParam in recursive (matchParam_recursive)
o export shifted MS2 mirror plot in recursive annotation
o recode annotateMetaboliteMRN

Version 0.4.05 (20210317)
--------------
o recode annotateMetaboliteMRN
o fix the bugs in multi-threads running during metAnnotation
o fix some bugs in metAnnotation (Step -> step)
o modify the export of recursive report to fit IMMS data

Version 0.4.06 (20210318)
--------------
o modify functions: mergeRecursiveAnnotation, convertAnnotationTable2InitialId, authenticateAnnotationCredential and related functions
o add multi-thread runing in peak group annotation
o add CCS information in peak group annotation
o fix some bugs in peak group annotation (if multiple peaks annotated in peak group annotation, keep order follow: mass error > rt error > ccs error)
o modify the export of result table to fit IMMS data

Version 0.4.11 (20210319)
--------------
o fix some bugs for orbitrap data from GY
o fix some bugs for TIMS data from LMD

Version 0.4.12 (20210322)
--------------
o fix some bugs in CredentialPeakGroup for orbitrap data from GY
o fix some bugs in result table output

Version 0.4.13 (20210322)
--------------
o fix bugs in ms2 assignment: one ms2 matched multiple ms1, the ms2 was assigned the ms1 name of last index
o fix bugs in readMS2: passing `instrument` parameter into the readMS2 function

Version 0.4.14 (20210323)
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o fix the format of column in credential

Version 0.4.15 (20210323)
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o remove parameter `instrument` in the readMS2 and readMGF function
o change parameter name in combineMs1Ms2: mz_tol->mz_tol_combine_ms1_ms2, rt_tol->rt_tol_combine_ms1_ms2, ccs_tol->ccs_tol_combine_ms1_ms2

Version 0.4.16 (20210324)
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o fix bugs in annotateInitialSeed function ('version1' mode)
o fix bugs in plotNeighbor

Version 0.4.17 (20210326)
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o add `test_old_mrn` parameter in annotateMRN function to evaluate the effect of MRN change

Version 0.4.18 (20210326)
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o upate MRN v0.5 (remove the limitation of similarity 0.7 for known reaction pairs)

Version 0.4.19 (20210330)
--------------
o upate zhuMetlib_obitrap (v3)

Version 0.4.20 (20210331)
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o add MetDNA2Report module to export html/pdf report file

Version 0.4.21 (20210401)
--------------
o modify report template

Version 0.4.22 (20210402)
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o open mz_tol_combine_ms1_ms2 and rt_tol_combine_ms1_ms2 for QE
o add 'Exploris' instrument item
o split report template into 'MetDNA2' and 'MetDNA2Extension'

Version 0.4.23 (20210403)
--------------
o add generateBioInterpSummary4Report in report template
o move intermediate data "annotation_initial", "ms2_data.msp", "ms2_data.RData" and peak_table.csv to 03_credential directory
o update compound information in zhuMetlib and zhuMetlib_obitrap

Version 0.4.24 (20210406)
--------------
o change s4 function to s3 in report generation

Version 0.5.00 (20210406)
--------------
o remove the intermidiate data in report generation
o add test_adduct_version for trouble shooting in annotateMRN

Version 0.5.10 (20210407)
--------------
o fix bugs in matchMs2WithSpecLib: all fragments larger than the precursor
o fix bugs in checkQuality: add IMMS instrument
o fix bugs in checkQuality: generate error if sample information contains >2 groups

Version 0.5.11 (20210408)
--------------
o add test_adduct_version in initial seed annotation

Version 0.5.12 (20210408)
--------------
o change instrument parameter 'IMMS' to "AgilentDTIMMS", "BrukerTIMS", "Exploris" to "ThermoExploris"
o change library parameter 'zhuMetLib_obitrap' to "zhuMetLib_orbitrap"
o add conditional chunk in Rmd report: is_rt_calibration and is_bio_intepret

Version 0.5.13 (20210423)
--------------
o add as_seed and as_seed_round in the addInitialSeedResult2MetDNA2AnnoClass, addCredentialResult2MetDNA2AnnoClass, generateResultTable4AllAnnotation, generateMetDNA2AnnotationResult, modifyOutputResult
o add "test_rm_extra_anno_from_ini_seed" parameter in modifyOutputResult function. It controls whether remove extra annotation records if this feature has adduct or isotope annotations are directly from initial seeds.
o fix bugs in report generation: if rt calibration or biology interpretation not performed, some intermidate missing.
o fix bugs in plotNeighbor function.

Version 0.5.20 (20210429)
--------------
o fix the bugs in function 'runSpecMatch`: mathced fragment falsely assigned for multiple candidates

Version 0.5.21 (20210508)
--------------
o update SpectralTools v0.2.3

Version 0.5.22 (20210510)
--------------
o passing mz_tol_ms2 parameter (verion1: 30ppm, version2: 25ppm)
o update README.md
o add documents with pkgdown
o add vignettes 'instruction_of_metdna2'
o add CIATION file

Version 0.5.23 (20210515)
--------------
o add rt_filter and related functions in readInitialAnnotation
o update version 1 MD (md_mrn_emrn$version1 object)
o remove test_old_mrn parameter

Version 0.5.24 (20210518)
--------------
o fix bugs in parameter passing 'candidate_num'

Version 0.5.25 (20210520)
--------------
o fix bugs in uncompleted 'generateMetDNA2Report' call in major function

Version 0.5.26 (20210522)
--------------
o fix bugs: correct parameter 'zhuMetLib_obitrap' to 'zhuMetLib_orbitrap', 'Exploris' to 'ThermoExploris'

Version 0.5.27 (20210526)
--------------
o fix bugs: modify default absolute cps filtering to 30 from 0 in 'version1' parameter
o fix bugs: add '[M-H2O-H]-' type under recursiveAnnotationMRN 'version1' condition

Version 0.5.28 (20210527)
--------------
o add checkElement to remove unrational formula and adduct pair in annotateMetaboliteMRN function

Version 0.5.29 (20210531)
--------------
o fix bugs: unconsist length of confidence/group.group with ids
o fix bugs: incorrect mz calculation for [M-2H]2-

Version 0.5.30 (20210601)
--------------
o fix bugs: add nmol and ncharge parameter in calculateMz to correct mz calculation for [M-2H]2-
o fix bugs: falsely extract double/triple charge state in calculateMz function

Version 0.5.31 (20210601)
--------------
o use m/z in peak_table instead of m/z in MS2 for metAnnotation

Version 0.5.32 (20210602)
--------------
o remove [M+CH3COO]- adduct form in version1 condition during recursive annotation

Version 0.6.00 (20210609)
--------------
o add peak_group_id in concisePeakGroup2Annotation function
o modify kept digit in initial seed annotation: mz error (1), rt error (1), ccs error (1), msms score (4)
o modify MetDNA2Result module to exported files

Version 0.6.10 (20210615)
--------------
o update lib_adduct_nl: modify M+ to [M]+, M- to [M]-, [M-H3N+H]+ to [M-NH3+H]+, [M-H3N-H]- to [M-NH3-H]-
o update zhuMetLib and zhuMetLib_orbitrap to add cation information
o add adduct/NL/ISF label for isotope annotation using recursive way
o rename recursive_type to iden_type, id to id_kegg
o add iden_type label 'MS1 + RT + ExpLib Match' and 'MS1 + ExpLib Match' for level1 and level2 identification respectively
o keep NA in id_kegg column for identification not included in KEGG
o only add abc suffix for base peak with more than 1 candidates
o add quanti information in table_identification_unique

Version 0.6.11 (20210616)
--------------
o fix bugs: errors in change [M]+ to M+ in readInitialSeed
o fix bugs: false base adduct extraction for 2M/3M adducts in generateExportTable function
o add is_check_cation in initial seed annotation
o uncheck [M]+ in recursive annotation

Version 0.6.12 (20210618)
--------------
o keep inchikey1 redundancy in final result export
o add stereo_isomer_id, stereo_isomer_name in table_identification

Version 0.6.13 (20210621)
--------------
o update zhuMetlib and zhuMetlib_orbitrap (v20210621)
o apply predicted rt filter for seed selection in version2 condition

Version 0.6.14 (20210624)
--------------
o fix bugs: inconsist credential format in generateMetDNA2Annotation function

Version 0.6.15 (20210627)
--------------
o fix bugs: return a blank identification table if no metabolite identified in initial seed annotation
o replace interpretBiology with MetBioInterpretation package
o modify the exported report to fit the revised exported report
o add runMetDNA2 to support both positive and negative data analysis
o add 'both' parameter in generateMetDNA2Report
o add 'MetDNA2BothPolarity' and 'MetDNA2ExtensionBothPolarity' report template
o fix bugs: unmatched information for some peaks in mrn.annotation.result file (reported by WHM)
o modify readMSP function to fit new version MSDIAL software

Version 0.6.16 (20210629)
--------------
o add "WatersQTOF" and "WatersTWIMMS" options in instrument parameters
o update cpd_emrn: add compound names for in-silico metabolites in KEGG
o replace KEGG ID and compound name for some known in-silico metabolites
o rename exported tables: "table1_identification.csv", "table2_peak_group.csv", "table3_identification_pair.csv"

Version 0.6.17 (20210630)
--------------
o fix bugs: the change of readMSP caused name missing for credentialFormula
o fix bugs: the error polarity in exported MSP files in credential
o fix bugs: not find 'table.identification.pair.csv' file

Version 0.6.18 (20210701)
--------------
o add a parameter to remove intermediate data
o fix bugs: inconsist column type in mergeRecursiveAnnotation for MSDIAL data
o fix bugs: inconsist column type in peak group generation

Version 0.6.19 (20210702)
--------------
o fix bugs: not find 'table.identification.pair.csv' file in both mode
o fix bugs: errors in html report generation for MetDNA2ExtensionBothPolarity

Version 0.6.20 (20210703)
--------------
o fix bugs: adduct 'M' in 'version1' recursive_result leads error in credential
o modify default candidate_num to 5
o remove test_adduct_version parameter in MetDNA2 and runMetDNA2 functions
o rename directory 'POS_and_NEG' to 'BOTH' to keep consist with MetDNA


Version 0.6.21 (20210705)
--------------
o add "version1" parameter to read MRN result for biology interpretation (keep same with MetDNA1)
o fix bugs: only use significant metabolites in pathway quantafication
o fix bugs: no pathway name showed in pathway enrichment plot

Version 0.6.22 (20210708)
--------------
o modify calibrateRT function to fit the new version RT_recalibration_table
o judge ms2_type in the working directory instead of 'mgf' (default) in runMetDNA2 function

Version 0.6.23 (20210709)
--------------
o change default parameters: dir_Genform to '/GenForm', is_rm_intermediate_data to TRUE

Version 0.6.24 (20210709)
--------------
o fix bugs: zhulab candidates (not in KEGG) were falsely deplicated when merging initial seed annotation and recursive annotation
o fix bugs: '[M]+' and '[M-2H]-' adduct of initial seed were not reserved during credential

Version 0.6.25 (20210710)
--------------
o fix bugs: errors in check format for 'RT_recalibration_file.csv'
o fix bugs: '[M]+' and '[M-2H]-' calculate twice calling convertMz2Adduct for defined '[M]+'

Version 0.6.26 (20210712)
--------------
o update depends packages
o define ZZWtool function in report template instead of calling ZZWtool package

Version 0.6.27 (20210713)
--------------
o fix bugs: remove intermediate data for single mode
o add a parameter is_webserver: force 'extention_step' as '0', turn off all plot functions

Version 0.6.28 (20210715)
--------------
o extract ms2_file names with recursive function to keep compatibility with MetProcess2
o change defalut threads to 4

Version 0.6.30 (20210721)
--------------
o add test_evaluation parameter for perform 200STD incubation experiment analysis
o fix bugs: errors in readMSP for MSP from MetAnalyzer

Version 0.6.31 (20210722)
--------------
o modify default use_redun_rm_result parameter as TRUE, and export this parameter

Version 0.6.32 (20210722)
--------------
o fix bugs: lib parameters was not changed for orbitrap data

Version 0.6.33 (20210724)
--------------
o fix bugs: no significant metabolites leads pathway enrichment error
o fix bugs: no pathway has > 3 metabolites leads error

Version 0.6.34 (20210724)
--------------
o fix bugs: id were falsely replaced for metabolites in zhulab
o fix bugs: no class enriched leads error

Version 0.6.35 (20210726)
--------------
o fix bugs: one group has only one sample cause plot error

Version 0.6.36 (20210727)
--------------
o fix bugs: one group has only one sample cause plot error (for negative modes and both modes)

Version 0.6.37 (20210815)
-------------
o fix bugs: peak_names were falsely replaced in table 3
o modify default parameter: is_plot_ms2 to TRUE

Version 0.6.40 (20210823)
-------------
o add test_evaluation parameter for perform 46STD and S9 fraction incubation experiment analysis

Version 0.6.41 (20210928)
-------------
o update lib_rt and rt_ref to emcompass metlin RP rts
o add 'MetlinRP' parameter in method_lc variable, and related functions

Version 0.6.42 (20211001)
-------------
o fix bugs in no conflict feature group leads error (reported by ZhouYiyang)

Version 0.6.43 (20211015)
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o fix bugs in the character '-' existed in name column (reported by ChenJunMiao)
o fix bugs 'record_rule_filter_peak_group' not found in credential (reported by QiangJia)

Version 0.6.44 (20211018)
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o stop the program if feature table contains all-zero features (reported by CaiYuping)
o ms2 file size shows NA in data importing (reported by CaiYuping)

Version 0.6.50 (20211028)
-------------
o add zhuRPLab and zhulabRP RTs

Version 0.6.51 (20211028)
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o fix bugs in quantiPathway in both mode (reported by LiuGuangxue)

Version 0.6.52 (20211031)
-------------
o fix bugs in zhuRPLab and zhulabRP RTs

Version 0.6.53 (20211101)
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o fix bugs in zhuRPLib: character type of monoisotopic mass

Version 0.6.54 (20211101)
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o slient bug report in intepretBiology and report

Version 0.6.55 (20211129)
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o update zhuRPLib (v3.4) and zhulabRP RTs

Version 0.6.56 (20211201)
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o update zhulabRP RTs (fix bug update of v0.6.55)

Version 0.6.57 (20211213)
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o fix bugs in excluded_adduct in annotateInitialSeed

Version 0.6.60 (20220115)
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o add a parameter adduct_limit_specLib in MetDNA2 function to limit the adduct types in initial seed annotation
o add a test_force_filtering_rt in annotateInitialSeed function to enforce filtering RT in final table
o add a whether_use_predRT in annotateMRN related functions to ignore RT match

Version 0.6.61 (20220117)
-------------
o major changed parameter: adduct_limit_specLib, test_force_filtering_rt, use_pretrained_model, remove_conflict_seed_from_final_table
o add groupRT2 function to use recursive way to group RTs instead of region division in merge annotation record part (recursive annotation)
o add trainRandomForestWithCaret function to update randomForest model with Caret
o add removeReplicateSeedAnnotationFromFinalTable to remove replicated annotations between seed annotation and recursive annotations

Version 0.6.62 (20220119)
-------------
o modify the order when keep record in redundancy removal (metAnnotation > isotopeAnnotaion > adductAnnotation)
o modify the annotation report in generateExporTableIden (when keep the highest confidence level, the level3.1 and level3.2 have same priority)

Version 0.6.63 (20220121)
-------------
o open mz_ppm_thr parameter in the MetDNA2 function

Version 0.6.64 (20220122)
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o add whether_link_frag parameter in the MetDNA2 function. This parameter controls whether perform annotation propagation with matched fragment number higher than the cutoff

Version 1.0.0 (20220215)
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o modify default parameters for submitted manuscript: test_force_filtering_rt (NULL to 20), adduct_limit_specLib ('all' to c('[M+H]+', '[M+Na]+') or c('[M-H]-', '[M-2H]-')), whether_link_frag (FALSE to TRUE), matched_frag_cutoff (1 to 4), candidate_num (1 to 10), remove_conflict_seed_from_final_table (FALSE to TRUE)
o open the parameter extended_step on web server
o open global peak correlation network function on web server

Version 1.0.01 (20220221)
-------------
o modify method_lc 'zhulabRP' to 'RP12min'
o update rt_ref for RP12min

Version 1.0.02 (20220224)
-------------
o update some typo in report

Version 1.1.00 (20220226)
-------------
o use MetLib functions to replace loadDB
o add skip credential and MRN sections

Version 1.1.01 (20220302)
-------------
o add adduct_limit_specLib decision for local runing, and default use 'limited' (POS:  c('[M+H]+', '[M+Na]+'), NEG: c('[M-H]-', '[M-2H]-'))
o adjust parameter mz_tol and mz_ppm_thr according to instrument. (Default: QTOF: 15ppm & 400; QE: 15ppm & 0)
o fix some bugs
o modify logic of analysis report generation (Only all function enabled)

Version 1.1.11 (20220303)
-------------
o modify default tolerance_rt_range as 25s
o remove test_force_filtering_rt parameter

Version 1.1.12 (20220322)
-------------
o modify bugs: manually given adduct list 

Version 1.1.13 (20220415)
-------------
o modify bugs: addRecursiveResult2MetDNA2AnnoClass: add structure information into recursive annotation (id_kegg redirection)
o set adduct_limit_specLib default 'limited' (POS:  c('[M+H]+', '[M]+', '[M-H2O+H]+), NEG: c('[M-H]-', '[M-2H]-', '[M-H2O-H]-))

Version 1.1.15 (20220421)
-------------
o fix bugs: mz_ppm_thr parameter was not passed in matchMs2WithNeighbor
o change annotateAdductMRN as single thread

Version 1.1.16 (20220421)
-------------
o recode the function to call annotateAdductMRN with multiple threads 

Version 1.1.17 (20220423)
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o modify bugs: addRecursiveResult2MetDNA2AnnoClass: id_kegg redirection

Version 1.2 / 1.1.18 (20220427)
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o modify bugs: addRecursiveResult2MetDNA2AnnoClass: id_kegg redirection from lib_kegg (181214)
o cancel 1.1.13[1] and 1.1.17 modification

Version 1.2.10 (20220506)
-------------
o fix bugs: ignore electron mass in adduct m/z calculation during recursive annotation