Changes in version 1.11 Changes in version 1.11.1 - Complete unit test coverage. Changes in version 1.9 Changes in version 1.9.5 - Add new extractByIndex() method. Changes in version 1.9.4 - compound_tbl_lipidblast supports now parallel processing and extracts more information from MoNA's JSON format (thanks to Prateek Arora for contribution). Changes in version 1.9.3 - compound_tbl_lipidblast: ensure exactmass is of type numeric. Changes in version 1.9.2 - compound_tbl_lipidblast: add parameter n to support reading and processing MoNA json files in sets (chunks) of lines at a time and hence reduce memory demand for very large files. Changes in version 1.9.1 - Allow CompDb to store that database name as alternative to an active database connection. This allows to serialize and load an object to/from disk (serializing an active database connection would not be possible) . Each call to extract data from the database will however open (and close) its own connection. Changes in version 1.7 Changes in version 1.7.2 - Import method generics from ProtGenerics. Changes in version 1.7.1 - Adapt script to create CompDb from MassBank to new MassBank database format. Changes in version 1.3 Changes in version 1.3.3 - Add backendBpparam to define (disable) parallel processing for the MsBackendCompDb backend. Changes in version 1.3.2 - Evaluate validity of the MsBackendCompDb using the full test suite from the Spectra package. Changes in version 1.3.2 - Add parameter nonStop to compound_tbl_sdf that is passed to parameter skipErrors of ChemmineR::read.SDFset. Issue #110 Changes in version 1.3.0 - Bioconductor 3.17 developmental version. Changes in version 1.1 Changes in version 1.1.6 - CompDb tests also for NA input. Changes in version 1.1.5 - MsBackendCompDb always returns collisionEnergy as numeric. Changes in version 1.1.4 - Add script to create a CompDb from a MassBank database. Changes in version 1.1.3 - Expand vignette with examples to create CompDb databases from scratch. Changes in version 1.1.2 - Add insertCompound and deleteCompound functions to add or remove compounds from a CompDb or IonDb. Changes in version 1.1.1 - Fix wrong warning message in deleteIon. - Change database data type for internal ion_id from character to integer. Changes in version 0.99 Changes in version 0.99.12 - Add mass2mz method for CompDb databases. Changes in version 0.99.11 - Add peaksVariables method. Changes in version 0.99.10 - Add parameter columns to peaksData. Changes in version 0.99.9 - Add parameter dbFile to createCompDb and add an example on how to create a CompDb database from custom input. Changes in version 0.99.8 - Add citation. Changes in version 0.99.7 - Add bug reports link to DESCRIPTION. Changes in version 0.99.6 - MsBackendCompDb extends Spectra::MsBackendCached instead of Spectra::MsBackendDataFrame. Changes in version 0.99.5 - No updates, just version bump to cause a new build. Changes in version 0.99.4 - Address more comments from @jianhong. Changes in version 0.99.3 - Fix BiocCheck warnings. Changes in version 0.99.2 - Fix BiocCheck warnings. Changes in version 0.99.1 - Address comments/change requests from @jianhong. Changes in version 0.99.0 - Preparing for Bioconductor submission. Changes in version 0.9 Changes in version 0.9.4 - Add deleteIon and deleteSpectra allowing to delete ions or spectra. Changes in version 0.9.3 - insertIons supports adding additional database columns. Changes in version 0.9.2 - Add instertSpectra method to add MS/MS spectra from a Spectra object to the database. Changes in version 0.9.1 - Add IonDb constructor methods. - Expand documentation and examples. - Add and fix unit tests. Changes in version 0.9.0 - Add IonDb class as extension of CompDb (to allow adding ion information to the database) and the functionalities to create such object. - Add insertIon to allow adding new ions to an IonDb object - Add ionVariables, ions functions to access the ions data in the database. - Add filters: IonIdFilter, IonAdductFilter, IonMzFilter, IonRtFilter. Changes in version 0.8 Changes in version 0.8.1 - Import spectra type (MS level) and precursor type from MoNa. Changes in version 0.8.0 - Rename database table name compound into ms_compound issue #74. Changes in version 0.7 Changes in version 0.7.0 - Remove mass2mz and mz2mass function in favour of the functions implemented in MetaboCoreUtils. Changes in version 0.6 Changes in version 0.6.6 - Import compounds method from ProtGenerics. Changes in version 0.6.5 - Add parameter onlyValid to compound_tbl_sdf to allow importing of only valid elements issue #69. Changes in version 0.6.4 - Add additional filters: MassFilter, FormulaFilter, InchiFilter and InchikeyFilter. Changes in version 0.6.3 - Add metadata, spectraVariables and compoundVariables functions. Changes in version 0.6.2 - Support creation of databases without specifying the organism. - Ensure database columns are mapped correctly to Spectra variable names. Changes in version 0.6.1 - Add SpectrumIdFilter to support filtering by spectrum IDs. Changes in version 0.6.0 - Rename column names: compound_name -> name, mass -> exactmass, inchi_key -> inchikey. Changes in version 0.5 Changes in version 0.5.0 - Replace as.list with peaksData. - Replace asDataFrame with spectraData. Changes in version 0.4 Changes in version 0.4.3 - Updated to match new LIPID MAPS field names. Changes in version 0.4.2 - Fix bug in as.list,MsBackendCompDb which returned a SimpleList instead of a list. Changes in version 0.4.0 - Rename method spectraData for MsBackendCompDb into asDataFrame (adapting to the changes in Spectra). Changes in version 0.3 Changes in version 0.3.2 - Import also smiles from SDF files. Changes in version 0.3.1 - Move package Spectra from Depends to Imports Changes in version 0.3.0 - Change from MSnbase to RforMassSpectrometry packages (Spectra and MsCoreUtils). - Store MS/MS spectra in two tables, msms_spectrum and msms_spectrum_peak. Changes in version 0.2 Changes in version 0.2.3 - Add instrument and precursor_mz spectra data columns (issue #32). Changes in version 0.2.2 - Add adduct information from Jan Stanstrup's commonMZ package. - Add matchWithPpm function to match numeric values allowing for a small difference. - Add adducts function to retrieve adduct definitions. - Add mass2mz and mz2mass to convert between mass and m/z for provided adducts. - Add annotateMz method to annotate m/z values. Changes in version 0.2.1 - Change field collision_energy to character to support values from MoNa (issue #31). - Add functions import_mona_sdf and msms_spectra_mona functions to enable import of spectrum data from MoNa SDF files (issue #30). - Add support for MoNa SDF files (issue #30). Changes in version 0.2.0 - Add hasMz,Spectrum and hasMz,Spectra methods to look for m/z values within spectra (issue #28). - Add MsmsMzRangeMinFilter and MsmsMzRangeMaxFilter (issue #29). - Re-use Spectra object from MSnbase. - Add supportedFilters,CompDb method. Changes in version 0.1 Changes in version 0.1.1 - Add precursorMz, precursorCharge, precursorIntensity, acquisitionNum, scanIndex, peaksCount, msLevel, tic, ionCount, collisionEnergy, fromFile, polarity, smoothed, isEmpty, centroided and isCentroided methods for Spectrum2List. Changes in version 0.1.0 - Add expandMzIntensity function. - Add spectra method to extract spectra from the CompDb database. - Add functionality to store MS/MS spectra in a CompDb database (m/z and intensity values stored as BLOB). - Add functionality to load MS/MS spectra from HMDB xml files. Changes in version 0.0 Changes in version 0.0.3 - Add CompoundIdFilter and CompoundNameFilter classes and filtering framework. Changes in version 0.0.2 - Define CompDb class and all functionality to create CompDb databases. - createCompDb supports file names as input and create a database including annotations from all files. - Add create-compounddb vignette.