import(Biostrings)

export(
    as.helix,
    is.helix,
    
    blankPlot,
    maxHeight,

    collapseHelix,
    expandHelix,

    defaultPalette,
    colourByValue,
    colourByCount,
    colourByConservation,
    colourByCovariation,
    colourByCanonical,
    colourByBasepairFrequency,
    colourByUnknottedGroups,
    
    unknottedGroups,
    basepairFrequency,

    alignmentPercentGaps,

    alignmentConservation,
    alignmentCovariation,
    alignmentCanonical,
    
    helixCovariation,
    helixConservation,
    helixCanonical,
    
    basepairCovariation,
    basepairConservation,
    basepairCanonical,
    
    baseConservation,
    
    isConflictingHelix,
    isDuplicatingHelix,
    isOverlappingHelix,

    plotCovariance,
    plotDoubleCovariance,
    plotOverlapCovariance,
    
    plotArc,
    plotArcs,
    plotHelix,
    plotDoubleHelix,
    plotOverlapHelix,

    readConnect,
    readHelix,
    readVienna,
    readBpseq,

    viennaToHelix,
    helixToVienna,
    helixToBpseq,
    helixToConnect,
    
    writeHelix,

    logseq,
    logceiling,
    logfloor,

    structureMismatchScore
)
