Changes in version 1.4                         

Changes in 1.4.3

  - Fix addProcessing example in the vignette.

Changes in 1.4.2

  - Import query from AnnotationHub.
  - Fix examples and unit tests using QFeatures.

Changes in 1.4.1

  - Add possibility to select the spectra variable for retention time
    matching in matchSpectra (issue #98).

                         Changes in version 1.3                         

Changes in 1.3.2

  - Add mzR as suggested package to ensure package vignettes can be
    built.

Changes in 1.3.1

  - Small changes in matchSpectra to avoid unnecessary object creation.
  - Use backendBpparam to disable parallel processing of matchSpectra if
    the backend does not support it.

                         Changes in version 1.1                         

Changes in 1.1.6

  - scoreVariables function to return the names of the score variables
    in a Matched object.

Changes in 1.1.5

  - Fix issues on BioC build machines.

Changes in 1.1.4

  - matchSpectra: support a CompDb with parameter target.
  - Add CompAnnotionSource classes to support definition of references
    to annotation resources.
  - Add CompDbSource class defining a reference to a CompDb database.
  - matchSpectra: support for CompDbSource with parameter target.

Changes in 1.1.3

  - Extend filterMatches framework (issue #86). ScoreThresholdParam
    added to perform filtering the matches based on a threshold for the
    scores.

Changes in 1.1.2

  - lapply and endoapply methods (issue #84). lapply allows to apply any
    function to each subset of matches for each query element and
    returns the corresponding list of results. endoapply is similar but
    applies a function returning a Matched and returns a Matched
    representing updated matches.

Changes in 1.1.1

  - Extend filterMatches framework (issue #81). SelectMatchesParam and
    TopRankedMatchesParam added to perform respectively manual filtering
    and keeping only the best ranked matches for each query element.

                        Changes in version 0.99                         

Changes in 0.99.15

  - Highlight query and target spectra in different colors for
    validateMatchedSpectra.
  - query and/or target of type SummarizedExperiment supported for
    Matched objects.
  - MatchedSummarizedExperiment class removed.
  - query and/or target of type QFeatures supported for Matched objects.
  - Support SummarizedExperiment and QFeatures for both query and target
    parameters in matchValues.

Changes in 0.99.14

  - Improve plotly-based mirror plots in validateMatchedSpectra.

Changes in 0.99.13

  - Fix issue about matchedData not working for result objects of
    matchValues, Mz2MassParam and matchValues, Mz2MassRtParam (issue
    #69).

Changes in 0.99.12

  - Update plotly-based mirror plots in validateMatchedSpectra.

Changes in 0.99.11

  - Change matchMz into matchValues (issue #65).

Changes in 0.99.10

  - Add validateMatchedSpectra for manual inspection and validation of
    an MatchedSpectra object.

Changes in 0.99.9

  - Add setBackend for MatchedSpectra objects.

Changes in 0.99.8

  - Add matchMz, Mz2MassParam and matchMz, Mz2MassRtParam. (issue #56).

Changes in 0.99.7

  - Add formula matching functions.

Changes in 0.99.5

  - Add parameter ... to plotSpectraMirror.
  - Definitions of "score", "score_rt" changed to be the difference
    (with sign) between query and target m/z or retention time
    respectively.
  - "ppm_error" becomes error without sign.

Changes in 0.99.4

  - Add matches m/z error (variable "ppm_error") to the Matched object
    returned by matchMz.

Changes in 0.99.3

  - Address Herve's comments.

                         Changes in version 0.2                         

Changes in 0.2.11

  - Fix calculation of correct number of rows/columns of the plot in
    plotSpectraMirror.

Changes in 0.2.10

  - Add parameter toleranceRt to CompareSpectraParam to enable retention
    time-based pre-filtering (issue #35).

Changes in 0.2.9

  - Add support for manually defined adducts to Mass2MzParam (issue
    #41).

Changes in 0.2.8

  - Add parameter THRESHFUN_REVERSE to MatchForwardReverseParam to allow
    filtering results on forward and reverse score (issue #37).

Changes in 0.2.7

  - Performance improvement in matchSpectra if no precursor m/z filter
    is used (issue #38).
  - Report number of matching peaks in
    matchSpectra,MatchForwardReverseParam (issue #36).

Changes in 0.2.6

  - Fix bug in matchSpectra that was wrongly calculating the acceptable
    m/z difference if tolerance was > 0 (issue #34). Fix proposed by
    Hugo Varet (@hvaret).

Changes in 0.2.5

  - Improve performance of matchMz.
  - Rename queryColumn and targetColumn to queryColname and
    targetColname.

Changes in 0.2.4

  - Support data.frame, DataFrame and matrix in matchMz.
  - Add addMatches and filterMatches functions.

Changes in 0.2.3

  - Fixes in MatchedSpectra.

Changes in 0.2.2

  - Add MatchedSummarizedExperiment.

Changes in 0.2.1

  - Rename TargetMass2MzParam to Mass2MzParam.

Changes in 0.2.0

  - Add support for matching m/z against m/z and m/z in addition to
    retention times to matchMz.

                         Changes in version 0.0                         

Changes in 0.0.4

  - Fix vignette, documentations and unit tests.