library(affycomp)
library(tools)
library(modreg)
dilution.ngenes <- 0
spikein.ngenes <- 0
spikein133.ngenes <- 0
###read in nickname and other info
affycomp.info <- read.table("info.txt",sep="\t",as.is=TRUE,quote="")
method.name <- affycomp.info[3,2]
verbose <- TRUE

# Read in the 3 files and perform assessments (if files exist).

f <- "dilution.csv"
if(file.exists(f)){
  d <- read.dilution(f)
  if(verbose) cat("Performing 3 assessments on dilution data...")
  dilution.assessment <- assessDilution(d,method.name=method.name)
 # added by HJ - Jan 13, 04
 tmp.assessment <- c(Dilution=list(dilution.assessment))
  if(verbose) cat("\n")
  dilution.ngenes <- nrow(exprs(d))
}
   
f <- "hgu95.csv"
if(file.exists(f)){
  s <- read.spikein(f,"hgu95a")
  spikein.assessment <-
    assessSpikeIn(s,verbose=verbose,method.name=method.name)
  if(exists("dilution.assessment")){
    tmp.assessment <- c(Dilution=list(dilution.assessment),spikein.assessment)
    tmp.assessment["what"] <- "All"
  }
  spikein.assessment2 <-
    assessSpikeIn2(s,verbose=verbose,method.name=method.name)
  spikein.ngenes <- nrow(exprs(s))
}

f <- "hgu133.csv"
if(file.exists(f)){
  s <- read.spikein(f,"hgu133a")
  spikein.assessment.133 <-
    assessSpikeIn(s,verbose=verbose,method.name=method.name)
  spikein.assessment2.133 <-
    assessSpikeIn2(s,verbose=verbose,method.name=method.name)
  spikein133.ngenes <- nrow(exprs(s))
}

# Now, if correct assessment lists exist we run Sweave and make tables.
dir <- paste(.path.package("affycomp"),"Rnw",sep="/")

F1 <- exists("dilution.assessment")
F2 <- exists("spikein.assessment")
F3 <- exists("spikein.assessment.133")

Table <- matrix(NA,23,1)

if(F1 & F2){
  Table <- tableAll(tmp.assessment)
  
  Table2 <- rbind(tableAll(spikein.assessment),
                  tableAll(spikein.assessment2))
  
  results2 <- "results2.txt"
  Table2 <- rbind(Table2,spikein.ngenes)
  write(Table2,file=results2,ncol=1)
  
  Sweave(paste(dir,"comparison.Rnw",sep="/"))
  Sweave(paste(dir,"simple.Rnw",sep="/"))
  Sweave(paste(dir,"complete-assessment.Rnw",sep="/"))
}

if(F1 & !F2){
  Table[1:6,] <- tableAll(dilution.assessment)
  
  Sweave(paste(dir,"dilution-assessment.Rnw",sep="/"))
}

if(!F1 & F2){
  Table[7:23,] <- tableAll(spikein.assessment)
  Table2 <- rbind(tableAll(spikein.assessment),
                  tableAll(spikein.assessment2))

  results2 <- "results2.txt"
  Table2 <- rbind(Table2,spikein.ngenes)
  write(Table2,file=results2,ncol=1)

  Sweave(paste(dir,"spike-in-assessment.Rnw",sep="/"))
}

if(F3){
  Table2.133 <- rbind(tableAll(spikein.assessment.133),
                      tableAll(spikein.assessment2.133))
  
  results2.133 <- "results2-133.txt"
  Table2.133 <- rbind(Table2.133,spikein133.ngenes)
  write(Table2.133,file=results2.133,ncol=1)
  Sweave(paste(dir,"spike-in-133-assessment.Rnw",sep="/"))
}
if(F1 | F2){
  Table <- rbind(Table,spikein.ngenes,dilution.ngenes)
  results <- "results.txt"
  write(Table,file=results,ncol=1)
}