### These are functions related to building an "Result Matrix" from a daCapo object.
"buildRMatrix" <-
function(dc,sumFun,...,whichLinkModels=1:length(dc$linkModels)) {
  ## We will create this object after the first call to FUN
  R <- NULL
  lmnames <- names(dc$linkModels[whichLinkModels])
  ## Calculate total number of variables which will determine the
  ## total number of rows  
  nrow <- do.call("sum",lapply(dc$linkModels[whichLinkModels],length))
  irow <- 1
  task <- character(0)
  EM <- character(0)
  observable <- character(0)
  for (alm in lmnames) {
    lmname <- splitlmn(alm)
    lmdat <- dc$linkModels[[alm]]
    task <- c(task,rep(lmname$task,length(lmdat)))
    EM <- c(EM,rep(lmname$EM,length(lmdat)))
    observable <- c(observable,getObservableVar(names(lmdat)))
    results <- t(sapply(lmdat,sumFun,...))
    if (is.null(R)) {
      ## Shape results matrix based on first row
      R <- results
    } else {
      R <- rbind(R,results)
    }
  }
  result <- data.frame(task=I(task),EM=I(EM),observable=I(observable),R)
  result
}

## Splits a link model name into two pieces,
## task name (accession number) and Evidence Model Name.
"splitlmn" <-
function(lmn) {
  sp1 <- regexpr("\\.[0-9]*_",lmn)
  sp1 <- sp1 + attr(sp1,"match.length")
  task <- substring(lmn,1,sp1-2)
  EM <- substring(lmn,sp1)
  list(task=task,EM=EM)
}


getObservableVar <-
function(obsParName) {
    sub(".CondMultParam","", sub(".betaLogAlpha","", obsParName))
}