CHANGES IN VERSION 1.1.17
-------------------------
USER UNVISIBLE CHANGES

    o removed file argument in genSwathIonLib function

CHANGES IN VERSION 1.1.16
-------------------------
USER UNVISIBLE CHANGES

    o added unit test for genSwathIonLib



CHANGES IN VERSION 1.1.15
-------------------------
USER UNVISIBLE CHANGES

    o added circle plots to specLSet plot method
    o added breaks argument in genSwathIonLib methode


CHANGES IN VERSION 1.1.14
-------------------------
USER UNVISIBLE CHANGES

  o LinkedTo Rcpp; added C++ STL lower bound function 
  which is reqired for determining overlapping q1 and q3 SWATH windows

CHANGES IN VERSION 1.1.13
-------------------------
USER VISIBLE CHANGES

  o fixed man pages 

CHANGES IN VERSION 1.1.12
-------------------------
USER VISIBLE CHANGES

  o impoved package vignette

CHANGES IN VERSION 1.1.11
-------------------------
USER VISIBLE CHANGES

    o modified default parameters of genSwathIonLib
    o add content to vignette 

CHANGES IN VERSION 1.1.10
-------------------------
USER VISIBLE CHANGES

    o added generate.consensus

CHANGES IN VERSION 1.1.9
-------------------------
USER VISIBLE CHANGES

    o new features in specLSet 'summary' plot

USER UNVISIBLE CHANGES

    o refactored merge.specLSet; merge by group_id 
    o added unit test for merge.specLSet

CHANGES IN VERSION 1.1.8
-------------------------
USER VISIBLE CHANGES

    o renamed annotateProteinID to annotate.protein_id
    o added graphics on plot.specLSet method

USER UNVISIBLE CHANGES

    o refactored merge
    

CHANGES IN VERSION 1.1.7
-------------------------
USER VISIBLE CHANGES

    o introduce peakplot for bibliospec object
    o introduce LCMS map for bibliospec object
    o vignette cosmetics


CHANGES IN VERSION 1.1.6
-------------------------
USER VISIBLE CHANGES

    o introduce specL_bibliospec summary method

CHANGES IN VERSION 1.1.5
-------------------------
USER VISIBLE CHANGES

    o specLSet merge function 

    o work on specLSet summary method


CHANGES IN VERSION 1.1.4
-------------------------
USER VISIBLE CHANGES

    o summary method of specLSet class 

USER UNVISIBLE CHANGES

    o unit test for data containing no iRT peptides

CHANGES IN VERSION 1.1.3
-------------------------

USER VISIBLE CHANGES

    o renamed write.Spectronaut to write.spectronaut

    o write.spectronaut writes filename 

    o added benchmark section in package vignette

CHANGES IN VERSION 1.1.2
-------------------------

USER VISIBLE CHANGES

    o uses modSeq in group_id iff existing

CHANGES IN VERSION 1.1.1
-------------------------

USER VISIBLE CHANGES

    o streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK 
    for compatibility with peakView V2.0


CHANGES IN VERSION 0.99.23
-------------------------

USER VISIBLE CHANGES

    o added methods for specLSet class: 
        ionlibrary, rt.input, rt.normalized

    o fixed Sys.time() units in message.

USER UNVISIBLE CHANGES

    o genSwathIonLib using bpmapply



CHANGES IN VERSION 0.99.22
-------------------------

USER VISIBLE CHANGES

    o specLSet plot method

CHANGES IN VERSION 0.99.21
-------------------------

USER VISIBLE CHANGES

    o specLSet class

    o replace print by show and write.Spectronaut method in specL and specLSet classes
CHANGES IN VERSION 1.1.5
-------------------------
USER VISIBLE CHANGES

    o specLSet merge function 

    o work on specLSet summary method


CHANGES IN VERSION 1.1.4
-------------------------
USER VISIBLE CHANGES

    o summary method of specLSet class 

USER UNVISIBLE CHANGES

    o unit test for data containing no iRT peptides

CHANGES IN VERSION 1.1.3
-------------------------

USER VISIBLE CHANGES

    o renamed write.Spectronaut to write.spectronaut

    o write.spectronaut writes filename 

    o added benchmark section in package vignette

CHANGES IN VERSION 1.1.2
-------------------------

USER VISIBLE CHANGES

    o uses modSeq in group_id iff existing

CHANGES IN VERSION 1.1.1
-------------------------

USER VISIBLE CHANGES

    o streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK 
    for compatibility with peakView V2.0


CHANGES IN VERSION 0.99.23
-------------------------

USER VISIBLE CHANGES

    o added methods for specLSet class: 
        ionlibrary, rt.input, rt.normalized

    o fixed Sys.time() units in message.

USER UNVISIBLE CHANGES

    o genSwathIonLib using bpmapply



CHANGES IN VERSION 0.99.22
-------------------------

USER VISIBLE CHANGES

    o specLSet plot method

CHANGES IN VERSION 0.99.21
-------------------------

USER VISIBLE CHANGES

    o specLSet class

    o replace print by show and write.Spectronaut method in specL and specLSet classes

CHANGES IN VERSION 0.99.20
-------------------------

USER VISIBLE CHANGES

    o replaced mclapply by BiocParalle::bplapply

    o print method

    o include iRTpeptide data