useDynLib("kebabs", .registration=TRUE)

import(methods)

import(Matrix)

import(e1071)

import(LiblineaR)

importFrom(stats, runif, hclust, dist, as.dendrogram,

delete.response, fitted, model.extract, model.matrix,

na.fail, na.omit, napredict, terms, var)

importFrom(graphics, axis, boxplot, frame, hist, layout,

lines, mtext, par, polygon, text, title)

importFrom(grDevices, col2rgb, dev.flush, dev.hold)

importFrom(utils, data, installed.packages, packageVersion,

sessionInfo)

importFrom(kernlab, ksvm, predict, kernelMatrix, as.kernelMatrix, kpar,

vanilladot, polydot, plot, SVindex)

importFrom(apcluster, heatmap)

import(Rcpp)

importFrom(XVector, subseq, width)

importFrom(S4Vectors, DataFrame, metadata, "metadata<-", elementMetadata,

"elementMetadata<-", mcols, "mcols<-")

import(Biostrings)

export(DNAVector, RNAVector, AAVector, genRandBioSeqs, annotationMetadata,

"annotationMetadata<-", annotationCharset, positionMetadata,

"positionMetadata<-", spectrumKernel, mismatchKernel, motifKernel,

gappyPairKernel, linearKernel, symmetricPairKernel, getKernelMatrix,

getExRep, getExRepQuadratic, getFeatureWeights, linWeight, expWeight,

gaussWeight, swdWeight, getSVMSlotValue, seqKernelAsChar,

computeROCandAUC, evaluatePrediction, showAnnotatedSeq, kebabsDemo,

kebabsCollectInfo)

exportClasses("DNAVector", "RNAVector", "AAVector", "SequenceKernel")

exportMethods(kbsvm, predict, show, kernelParameters, as.KernelMatrix,

getPredictionProfile, plot, profiles, baselines, sequences,

featureWeights, "featureWeights<-", modelOffset, "modelOffset<-",

cvResult, "cvResult<-", modelSelResult, "modelSelResult<-",

svmModel, "svmModel<-", probabilityModel, "probabilityModel<-",

gridRows, gridColumns, gridErrors, performance, selGridRow,

selGridCol, fullModel, length, width, names, "names<-", width,

performCrossValidation, auc, "auc<-", tpr, "tpr<-", fpr,

"fpr<-", trainSVM, predictSVM, SVindex, heatmap, folds,

isUserDefined, getFeatureSpaceDimension, getPredProfMixture)