NEWS/CHANGELOG

R4RNA_1.0.0 2015-10-27 (Daniel Lai <jujubix {at} cs.ubc.ca>)
- Now accepts Biostrings XStringSet as valid multiple sequence alignment input
- Removed readFasta and writeFasta functions, please use readBStringSet
  and writeXStringSet instead.
- colourByValue handles single value and empty helix cases
- isConflictingHelix, isDuplicatingHelix and isOverlapping helix now return a
    decimal value from 0 to 1 instead of a FALSE or TRUE value when faced
    classifying a single helix with multiple basepairs.  This leaves the
    thresholding up to the user and the functions are also A LOT faster.
- added asp option to plots

R4RNA_0.1.4.tar.gz 2012-03-21 (Daniel Lai <jujubix {at} cs.ubc.ca>)
- Addition of structureMismatchScore and sequencePercentGaps
- Added "pad" parameter for specifying padding in blankPlot
- Added "no.par" option to blankPlot, to allow for par(mfrow = ...), etc
- Replaced conflict.filter for conflict.col and conflict.lty in plotCovariance
- Fixed bug in collapseHelix

R4RNA_0.1.3.tar.gz 2012-02-16 (Daniel Lai <jujubix [at] cs.ubc.ca>)
- Updated vignette, obtained via vignette("R4RNA")

R4RNA_0.1.2.tar.gz 2012-02-15 (Daniel Lai <jujubix [at] cs.ubc.ca>)
- Improved colourBy functions (default arguments + get option)
- Addition of basepairFrequency and colourByBasepairFrequency
- Addition of log space operations, logseq, logfloor, logceiling
- Updated examples in manual to reflect changes

R4RNA_0.1.1.tar.gz 2012-02-14 (Daniel Lai <jujubix [at] cs.ubc.ca>)
- Package revised for publication in NAR Method Online
- Functions streamlined for improved user experience
- Addition of various "ColourBy" functions
- Addition of alignment statistics functions
- File reading functions made robust and able to handle multiple entries
- Various format conversion functions to and from helix
- Addition of plotDoubleCovariance and plotOverlapCovariance functions
- Addition of a lot of fine-tuning paramters for plotCovariance
- Expanded role and functionality of blankPlot
- Allows for direct output as png or pdf files
- Improved and expanded documentation

R4RNA_0.1.0.tar.gz 2011-12-16 (Daniel Lai <jujubix [at] cs.ubc.ca>)
- Initial public release
