Changes in version 1.2                         

Changes in 1.2.2

  - Fix error message in setBackend displaying the wrong class name
    (issue #217).

Changes in 1.2.1

  - Fix bug in plotSpectra and plotSpectraMirror causing an error if a
    spectrum contains a single peak and labels are provided.

                         Changes in version 1.1                         

Changes in 1.1.20

  - Fix concatenating empty spectra (issue #200).

Changes in 1.1.19

  - New filterPrecursorCharge() method.

Changes in 1.1.18

  - Define plotSpectraMirror as a method.

Changes in 1.1.17

  - Fix issue #187.
  - Add function concatenateSpectra to allow concatenating Spectra
    objects and list of Spectra objects.

Changes in 1.1.16

  - Support arbitrary spectra variables to be passed to the functions
    provided/added with addProcessing; issue #182.

Changes in 1.1.15

  - Pass spectras' precursor m/z to the MAPFUN in compareSpectra; issue
    #171.
  - Add joinPeaksGnps to perform a peak matching between spectra similar
    to the one performed in GNPS (issue #171).

Changes in 1.1.14

  - Support plotting of empty spectra (issue 175).

Changes in 1.1.13

  - Move ProcessingStep to ProtGenerics.

Changes in 1.1.12

  - Fix show method for Spectra to list only the 3 most recent
    processing steps (issue 173).
  - Add processingLog function to display the log messages of all
    processing steps of a Spectra object.

Changes in 1.1.11

  - Add support for ... to pickPeaks and smooth (issue 168).

Changes in 1.1.10

  - Import filterIntensity from ProtGenerics.

Changes in 1.1.9

  - Fix label in plotSpectra.

Changes in 1.1.8

  - filterIntensity supports passing of additional parameters to the
    used filter function (issue 164).

Changes in 1.1.7

  - Fix bug in show,ProcessingStep (issue 162).

Changes in 1.1.6

  - New joinSpectraData() function.

Changes in 1.1.5

  - Add [[,Msbackend and [[<-,MsBackend methods (issue 149).
  - Add [[,Spectra and [[<-,Spectra methods.

Changes in 1.1.4

  - Fix issue with labelCol in plotSpectra (issue #157).

Changes in 1.1.3

  - Implement a generic Spectra,ANY constructor replacing
    Spectra,DataFrame and Spectra,character.

Changes in 1.1.2

  - Fix problem in export to mzML files that failed for empty spectra
    (issue #145)

Changes in 1.1.1

  - Round retention time in figure titles.
  - Document differences between spectrumId (spectrumID), acquisitionNum
    and scanIndex.

Changes in 1.1.0

  - New Bioc devel version

                        Changes in version 0.99                         

Changes in 0.99.11

  - Re-add mz and intensity as core spectra variables.

Changes in 0.99.10

  - Fix in spectraData<-,Spectra to avoid removing m/z and intensity
    values (issue #146).
  - Add default implementations of filter functions for MsBackend.

Changes in 0.99.9

  - Fix in Spectra,character constructor to ensure the backend is
    changed even if source inherits from backend (issue #143).

Changes in 0.99.8

  - combineSpectra applies data processing steps in the processing queue
    prior to combination (issue #140).

Changes in 0.99.7

  - Fix problem in dropNaSpectraVariables that would also drop m/z and
    intensity values for most backends (issue #138.

Changes in 0.99.6

  - Support intensity in filterIntensity method to be a function to
    enable peak intensity-based filtering of spectra (issue #126).

Changes in 0.99.5

  - Add filterMzRange and filterMzValues to filter spectra based on an
    m/z range or a list of target m/z values, respectively.

Changes in 0.99.4

  - Add export,MsBackendMzR to export spectra data to mzML or mzXML
    file(s).
  - Add an export,MsBackend method to allow backends to take care of
    data export.
  - Refactor export,Spectra to use the MsBackend class to export the
    data.
  - Change parameter source in Spectra,character to MsBackendMzR and set
    parameter backend = source. Thus by default, the import backend will
    also be used to store the data.

Changes in 0.99.3

  - Replace lapply,Spectra with spectrapply,Spectra.

Changes in 0.99.2

  - Replace asDataFrame,MsBackend with spectraData,MsBackend.
  - Replace asDataFrame<-,MsBackend with spectraData<-,MsBackend.
  - Replace as.list,MsBackend with peaksData,MsBackend.
  - Replace replaceList<-,MsBackend with peaksData<-,MsBackend.
  - Replace as.list,Spectra with peaksData,Spectra and add methods to
    coerce a Spectra to a list or SimpleList.

Changes in 0.99.0

  - Add reset method.
  - Add processing by chunk to compareSpectra.