CHANGES IN VERSION 2.1.4 (October 19, 2021)
------------------------
+ Using non-linear fit to constrain similarity matrix.
+ Recalculate intensity for given peaks.
+ Direct alignment to root is added.
+ Multiple strategies for getting distance matrix and tree-agglomeration is added.
+ Remove peaks if not aligned.

CHANGES IN VERSION 2.1.0 (July 10, 2021)
------------------------
+ Added support for IPF based Post-translation Modification alignment.
+ Added Minimum Spanning Tree based alignment for reference-free approach.
+ Reintegrate area under the peak for low-confidence peaks.
+ Supporting Savitzky-Golay smoothing while calculating area.
+ Added input to select peptides which to align.
+ Speed improvement in progressive alignment by storing new featues in lists instead of data frames.

CHANGES IN VERSION 1.3.18 (February 21, 2021)
------------------------
+ Using data.table instead of data.frame for modify-in-place.
+ Added support for Metabolomics DIA data.
+ Hierarchical clustering based alignment.
+ Create a child run (features + chromatograms) from two parents.
+ Added support for sqMass files.

CHANGES IN VERSION 1.3.5 (January 03, 2021)
------------------------
+ Supporting transition level intensity for SAINTq
+ Added support for pyopenms.
+ Added support for sqMass files.
+ Added parallelization using BiocParallel.
+ Using context-specific qvalues to determine reference.
+ Alignment is done over multipeptide instead of multiprecursor.
+ Precursors of a peptides are forced to have same feature-RT.
+ Savitzky Golay smoothing in C++.
+ Fast and light global alignment functions.

CHANGES IN VERSION 1.1.5 (May 07, 2020)
------------------------
+ ananlyteFDR to limit features for multipeptide.
+ Removed decoy from features.
+ BugFix alignment if all intensities are zero.
+ Fixed printed stats.

CHANGES IN VERSION 0.99.26 (April 21, 2020)
  ------------------------
+ Fixed visualization function.
+ Calculating global alignment before iterating over multipeptides.
+ Added summary after the alignment.
+ Fixed area integrator for missing boundaries.

CHANGES IN VERSION 0.99.25 (April 19, 2020)
------------------------
+ Added filePath, Spectra file name, and RunID in one data frame. No need to pass datapath to each function.
+ Separate functions to get precursor IDs, OpenSWATH features and chromatogram indices for each precursor across runs.
+ Using multi-peptide and updating it in the parent frame.
+ Added Alignment rank column.
+ Copied C++ code for peak integration from OpenMS.

CHANGES IN VERSION 0.99.13 (March 31, 2020)
------------------------
+ Added as.list for S4 objects

CHANGES IN VERSION 0.99.12 (March 02, 2020)
------------------------
+ Added boxcar, Gaussian kernel and loess for chromatogram smoothing
+ Started documentation for C++ code
+ Added support for Microsoft Visual Studio compiler
+ Using lists instead of matrix while updating RT and intensities
+ Moved python code out of the src directory


CHANGES IN VERSION 0.99.11 (February 04, 2020)
------------------------
+ Made changes as suggested in initial review. Updated man/ pages associated with function.
+ Link to the file for generating example data is updated.


CHANGES IN VERSION 0.99.10 (January 22, 2020)
------------------------
+ Made changes as suggested in initial review. https://github.com/Bioconductor/Contributions/issues/1328#issuecomment-576806498

CHANGES IN VERSION 0.99.9
------------------------
+ Added option to include mz pointer in getOswFiles and getXIC4AlignObj


CHANGES IN VERSION 0.99.8
------------------------
+ Removed R version dependency, have rda files instead of Rdata


CHANGES IN VERSION 0.99.7
------------------------
+ Lowered R version dependency


CHANGES IN VERSION 0.99.4
------------------------
+ Upadted version number
+ Corrected tests
+ Updated tests to reflect mzR updates, included travis-CI build
+ Moved package to Bioconductor
