## IMPORTS
import(DBI, RSQLite, methods, Matrix, rjson)
importFrom("XML", xmlTreeParse, xpathSApply, xmlValue, free)
importFrom("BiocGenerics", organism, "organism<-")
importFrom("stats", "pbeta", "sd")
importClassesFrom("ChemmineR", FPset)

## EXPORTS
## S4 Classes
exportClasses(
    "BioassayDB",
    "bioassay",
    "bioassaySet"
)

## Methods
exportMethods(
    "queryBioassayDB", "show",
    "aid", "source_id", "assay_type", "organism", "scoring", "targets", "target_types", "scores",
    "aid<-", "source_id<-", "assay_type<-", "organism<-", "scoring<-", "targets<-", "target_types<-", "scores<-",
    "activity", "sources", "source_id", "scoring",
    "activity<-", "sources<-", "source_id<-", "scoring<-"
)

## Functions
export(
    "connectBioassayDB", 
    "addDataSource", 
    "loadBioassay", 
    "dropBioassay", 
    "disconnectBioassayDB", 
    "newBioassayDB",
    "addBioassayIndex",
    "dropBioassayIndex",
    "activeTargets", 
    "inactiveTargets", 
    "activeAgainst",
    "selectiveAgainst",
    "getAssay",
    "getAssays",
    "parsePubChemBioassay",
    "getBioassaySetByCids",
    "perTargetMatrix",
    "targetSelectivity",
    "screenedAtLeast",
    "loadIdMapping",
    "translateTargetId",
    "assaySetTargets",
    "allCids",
    "allTargets",
    "bioactivityFingerprint",
    "scaleBioassaySet",
    "crossReactivityProbability",
    "crossReactivityPrior",
    "trinarySimilarity"
)
