# Updates values slot in featureSet and its feature-type specific slots (e.g. N, Shape, etc.)
setGeneric("updateValues<-",
function(object,value){standardGeneric("updateValues<-")})
setGeneric("updateErrors<-",
function(object,value){standardGeneric("updateErrors<-")})
setGeneric("updateZ<-",
function(object,value){standardGeneric("updateZ<-")})
setGeneric("updateSig<-",
function(object,value){standardGeneric("updateSig<-")})
# Get Generic Functions
setGeneric("getValues",
function(object,value){standardGeneric("getValues")})
setGeneric("getErrors",
function(object,value){standardGeneric("getErrors")})
setGeneric("getZ",
function(object,value){standardGeneric("getZ")})
setGeneric("getSig",
function(object,value){standardGeneric("getSig")})
setGeneric("getOldValues",
function(object,value){standardGeneric("getOldValues")})
setGeneric("getOldErrors",
function(object,value){standardGeneric("getOldErrors")})
setGeneric("getOldZ",
function(object,value){standardGeneric("getOldZ")})
setGeneric("getOldSig",
function(object,value){standardGeneric("getOldSig")})
setGeneric("getEquivMat",
function(object,value){standardGeneric("getEquivMat")})
setGeneric("getSeedLen",
function(object,value){standardGeneric("getSeedLen")})
setGeneric("getUpFootprintExtend",
function(object,value){standardGeneric("getUpFootprintExtend")})
setGeneric("getFsUpFootprintExtend",
function(object,value){standardGeneric("getFsUpFootprintExtend")})
setGeneric("getDownFootprintExtend",
function(object,value){standardGeneric("getDownFootprintExtend")})
setGeneric("getFsDownFootprintExtend",
function(object,value){standardGeneric("getFsDownFootprintExtend")})
setGeneric("getFpLen",
function(object,value){standardGeneric("getFpLen")})
setGeneric("getPositions",
function(object,value){standardGeneric("getPositions")})
setGeneric("getNumViews",
function(object,value){standardGeneric("getNumViews")})
setGeneric("getRcSymmetric",
function(object,value){standardGeneric("getRcSymmetric")})
setGeneric("getRounds",
function(object,value){standardGeneric("getRounds")})
setGeneric("getShapeParamsUsed",
function(object,value){standardGeneric("getShapeParamsUsed")})
setGeneric("getName",
function(object,value){standardGeneric("getName")})
setGeneric("getVarRegLen",
function(object,value){standardGeneric("getVarRegLen")})
setGeneric("getLeftFixedSeq",
function(object,value){standardGeneric("getLeftFixedSeq")})
setGeneric("getRightFixedSeq",
function(object,value){standardGeneric("getRightFixedSeq")})
setGeneric("getLeftFixedSeqOverlap",
function(object,value){standardGeneric("getLeftFixedSeqOverlap")})
setGeneric("getRightFixedSeqOverlap",
function(object,value){standardGeneric("getRightFixedSeqOverlap")})
setGeneric("getConsensusSeq",
function(object,value){standardGeneric("getConsensusSeq")})
setGeneric("getAffinityType",
function(object,value){standardGeneric("getAffinityType")})
setGeneric("getConfidenceLevel",
function(object,value){standardGeneric("getConfidenceLevel")})
setGeneric("getMinAffinity",
function(object,value){standardGeneric("getMinAffinity")})
setGeneric("getMissingValueSuppression",
function(object,value){standardGeneric("getMissingValueSuppression")})
setGeneric("getMinSeedValue",
function(object,value){standardGeneric("getMinSeedValue")})
setGeneric("getRegressionFormula",
function(object,value){standardGeneric("getRegressionFormula")})
setGeneric("getIteration",
function(object,value){standardGeneric("getIteration")})
setGeneric("getIncludeDNAstrand",
function(object,value){standardGeneric("getIncludeDNAstrand")})
setGeneric("getIncludeView",
function(object,value){standardGeneric("getIncludeView")})
setGeneric("getIncludeShape",
function(object,value){standardGeneric("getIncludeShape")})
setGeneric("getUseFixedValuesOffset.N",
function(object,value){standardGeneric("getUseFixedValuesOffset.N")})
setGeneric("getUseFixedValuesOffset.Shape",
function(object,value){standardGeneric("getUseFixedValuesOffset.Shape")})
setGeneric("getExUpBases",
function(object,value){standardGeneric("getExUpBases")})
setGeneric("getExDownBases",
function(object,value){standardGeneric("getExDownBases")})
setGeneric("getShapeTable",
function(object,value){standardGeneric("getShapeTable")})
setGeneric("getFeatures",
function(object,value){standardGeneric("getFeatures")})
setGeneric("getVerbose",
function(object,value){standardGeneric("getVerbose")})
setGeneric("getDateInitialized",
function(object,value){standardGeneric("getDateInitialized")})
setGeneric("getDateLastModified",
function(object,value){standardGeneric("getDateLastModified")})
setGeneric("getDateBetasLastAdded",
function(object,value){standardGeneric("getDateBetasLastAdded")})
setGeneric("getGlmFits",
function(object,value){standardGeneric("getGlmFits")})
setGeneric("getDesignMatrixSummary",
function(object,value){standardGeneric("getDesignMatrixSummary")})
setGeneric("getN",
function(object,value){standardGeneric("getN")})
setGeneric("getIntercept",
function(object,value){standardGeneric("getIntercept")})
setGeneric("getShape",
function(object,value){standardGeneric("getShape")})
setGeneric("getDesignMatrix",
function(object,design){standardGeneric("getDesignMatrix")})
setGeneric("getFeatureDesign",
function(object,...){standardGeneric("getFeatureDesign")})
setGeneric("getPlotValues",
function(object,...){standardGeneric("getPlotValues")})
setGeneric("getPSAM",
function(object, ...){standardGeneric("getPSAM")})
setGeneric("getTopSeqLabels",
function(object, ...){standardGeneric("getTopSeqLabels")})
# Set Generic Functions
setGeneric("setValues<-",
function(object,value){standardGeneric("setValues<-")})
setGeneric("setErrors<-",
function(object,value){standardGeneric("setErrors<-")})
setGeneric("setZ<-",
function(object,value){standardGeneric("setZ<-")})
setGeneric("setSig<-",
function(object,value){standardGeneric("setSig<-")})
setGeneric("setOldValues<-",
function(object,value){standardGeneric("setOldValues<-")})
setGeneric("setOldErrors<-",
function(object,value){standardGeneric("setOldErrors<-")})
setGeneric("setOldZ<-",
function(object,value){standardGeneric("setOldZ<-")})
setGeneric("setOldSig<-",
function(object,value){standardGeneric("setOldSig<-")})
setGeneric("setEquivMat<-",
function(object,value){standardGeneric("setEquivMat<-")})
setGeneric("setSeedLen<-",
function(object,value){standardGeneric("setSeedLen<-")})
setGeneric("setUpFootprintExtend<-",
function(object,value){standardGeneric("setUpFootprintExtend<-")})
setGeneric("setFsUpFootprintExtend<-",
function(object,value){standardGeneric("setFsUpFootprintExtend<-")})
setGeneric("setDownFootprintExtend<-",
function(object,value){standardGeneric("setDownFootprintExtend<-")})
setGeneric("setFsDownFootprintExtend<-",
function(object,value){standardGeneric("setFsDownFootprintExtend<-")})
setGeneric("setFpLen<-",
function(object,value){standardGeneric("setFpLen<-")})
setGeneric("setPositions<-",
function(object,value){standardGeneric("setPositions<-")})
setGeneric("setNumViews<-",
function(object,value){standardGeneric("setNumViews<-")})
setGeneric("setRcSymmetric<-",
function(object,value){standardGeneric("setRcSymmetric<-")})
setGeneric("setRounds<-",
function(object,value){standardGeneric("setRounds<-")})
setGeneric("setShapeParamsUsed<-",
function(object,value){standardGeneric("setShapeParamsUsed<-")})
setGeneric("setName<-",
function(object,value){standardGeneric("setName<-")})
setGeneric("setVarRegLen<-",
function(object,value){standardGeneric("setVarRegLen<-")})
setGeneric("setLeftFixedSeq<-",
function(object,value){standardGeneric("setLeftFixedSeq<-")})
setGeneric("setRightFixedSeq<-",
function(object,value){standardGeneric("setRightFixedSeq<-")})
setGeneric("setLeftFixedSeqOverlap<-",
function(object,value){standardGeneric("setLeftFixedSeqOverlap<-")})
setGeneric("setRightFixedSeqOverlap<-",
function(object,value){standardGeneric("setRightFixedSeqOverlap<-")})
setGeneric("setConsensusSeq<-",
function(object,value){standardGeneric("setConsensusSeq<-")})
setGeneric("setAffinityType<-",
function(object,value){standardGeneric("setAffinityType<-")})
setGeneric("setConfidenceLevel<-",
function(object,value){standardGeneric("setConfidenceLevel<-")})
setGeneric("setMinAffinity<-",
function(object,value){standardGeneric("setMinAffinity<-")})
setGeneric("setMissingValueSuppression<-",
function(object,value){standardGeneric("setMissingValueSuppression<-")})
setGeneric("setMinSeedValue<-",
function(object,value){standardGeneric("setMinSeedValue<-")})
setGeneric("setRegressionFormula<-",
function(object,value){standardGeneric("setRegressionFormula<-")})
setGeneric("setIteration<-",
function(object,value){standardGeneric("setIteration<-")})
setGeneric("setIncludeDNAstrand<-",
function(object,value){standardGeneric("setIncludeDNAstrand<-")})
setGeneric("setIncludeView<-",
function(object,value){standardGeneric("setIncludeView<-")})
setGeneric("setIncludeShape<-",
function(object,value){standardGeneric("setIncludeShape<-")})
setGeneric("setUseFixedValuesOffset.N<-",
function(object,value){standardGeneric("setUseFixedValuesOffset.N<-")})
setGeneric("setUseFixedValuesOffset.Shape<-",
function(object,value){standardGeneric("setUseFixedValuesOffset.Shape<-")})
setGeneric("setExUpBases<-",
function(object,value){standardGeneric("setExUpBases<-")})
setGeneric("setExDownBases<-",
function(object,value){standardGeneric("setExDownBases<-")})
setGeneric("setShapeTable<-",
function(object,value){standardGeneric("setShapeTable<-")})
setGeneric("setFeatures<-",
function(object,value){standardGeneric("setFeatures<-")})
setGeneric("setVerbose<-",
function(object,value){standardGeneric("setVerbose<-")})
setGeneric("setDateInitialized<-",
function(object,value){standardGeneric("setDateInitialized<-")})
setGeneric("setDateLastModified<-",
function(object,value){standardGeneric("setDateLastModified<-")})
setGeneric("setDateBetasLastAdded<-",
function(object,value){standardGeneric("setDateBetasLastAdded<-")})
setGeneric("setGlmFits<-",
function(object,value){standardGeneric("setGlmFits<-")})
setGeneric("setDesignMatrixSummary<-",
function(object,value){standardGeneric("setDesignMatrixSummary<-")})
setGeneric("finalizeFeatureBetas",
function(object){standardGeneric("finalizeFeatureBetas")})
setGeneric("setN<-",
function(object,value){standardGeneric("setN<-")})
setGeneric("setIntercept<-",
function(object,value){standardGeneric("setIntercept<-")})
setGeneric("setShape<-",
function(object,value){standardGeneric("setShape<-")})
setGeneric("buildSymmetricEquivalenceMatrix",
function(object){standardGeneric("buildSymmetricEquivalenceMatrix")})
setGeneric("buildSymSquaredEquivalenceMatrix",
function(object){standardGeneric("buildSymSquaredEquivalenceMatrix")})
setGeneric("buildNullEquivalenceMatrix",
function(object){standardGeneric("buildNullEquivalenceMatrix")})
setGeneric("formatEquivalenceMatrix",
function(object){standardGeneric("formatEquivalenceMatrix")})
setGeneric("addSeedPsam<-",
function(object, value){standardGeneric("addSeedPsam<-")})
setGeneric (
name = "seedTable2psam",
def = function(object, seedTable){standardGeneric("seedTable2psam")}
)
setGeneric("addNewBetas",
function(object, design, value,...){standardGeneric("addNewBetas")})
setGeneric("plotZs",
function(object, ...){standardGeneric("plotZs")})
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