columninput<-function(n,a){
	scanwhat<-list()
	for (i in 1:n){
		if (a[i]==0){
			textnums<-0
		}
		else {
			textnums<-""
		}
	scanwhat[[i]]<-textnums
	}
	scanwhat
}

##############################################################################################
croporcompletedata<-function(n,inp){
cropdata<-yesno("Do you wish to analyse a proportion of the highest data points? ")

if(cropdata==2){
	print("Complete data set used.")
	keeppercent<-0
	}
else if(cropdata==1){
	keeppercent<-readline("Enter the percentage of top data points you wish to retain as a decimal. ")
	keeppercent<-as.numeric(keeppercent)
	print(keeppercent)
	}
else {
	print("Incorrect choice.")
	print("Complete data set used. ")
	keeppercent<-0
	}
	keeptoppercent(n,keeppercent,inp)
}

##############################################################################################
filelayout<-function(){
	defaultyn<-yesno("Are the text files in the default layout? ")
	if (defaultyn==1){
		b<-c(1,0,0)
		n<-3
		noskiplines<-18
	}
	else {
		n<-readline("Please input the number of columns in the text file up to and including the one of interest. ")
		n<-as.numeric(n)
		b<-vector(length=n)
		for (i in 1:n){
			b[i]<-readline(paste("For column ",i," enter 0 for numeric data and 1 for non-numeric data. ", sep=""))
			b[i]<-as.numeric(b[i])
		}
		noskiplines<-readline("Please enter the number of lines to be skipped. ")
		noskiplines<-as.numeric(noskiplines)
	}
	scanwhat<-columninput(n,b)
	
	scaninfo<-list(scanwhat,n,noskiplines)
}

##############################################################################################
getfilenames<-function(n,extra=" "){
	filenm<-vector(length=n)
	for (i in 1:n){
		filenm[i]<-readline(paste("Enter file location ",i,extra,sep=""))
	}
	filenm
	print(filenm)
}

##############################################################################################
getmultistrstrdata<-function(filenm,n,scaninfo){
	filenmt<-vector(length=n)
	scanwhat<-scaninfo[[1]]
	g<-scaninfo[[2]]
	for (i in 1:n){
		filenmt[i]<-paste(filenm[i],".txt",sep="")
	}
	vm<-list()
		for (i in 1:n){
		inp<-scan(file=filenmt[i],what=scanwhat,skip=scaninfo[[3]],flush=TRUE)
		vm[[i]]<-inp[[g]]
	}

	inpall<-vm
}

##############################################################################################
getnofiles<-function(){
	numfiles<-readline("Enter the number of files for comparison " )
	numfiles<-as.numeric(numfiles)
}

##############################################################################################
getpermultidata<-function(d){
	valsfun<-function(x){
		vals<-quantile(x,probs=c(0.25,0.5,0.75,0.9,0.95,0.98,0.99,0.999))
		vals
		}
	percvals<-sapply(d,valsfun)
	meansdvals<-matrix(nrow=4,byrow=TRUE,data=c(sapply(d,min),sapply(d,mean),sapply(d,sd),sapply(d,max)))
	allstatsvals<-rbind(meansdvals,percvals)
	print(allstatsvals)
	allstatsvals
}

##############################################################################################
getreducedmultidata<-function(n,inp,pt,i){
	p<-as.numeric(pt[i])
	print(paste("pt is",p))
	lengthsinitial<-vector(length=n)
	lengthsnew<-vector(length=n)
	inp1<-lapply(inp,sort)

	lengthsinitial<-sapply(inp1,length)
	lengthsinitial<-p*lengthsinitial

	for (i in 1:n){
		lengthsnew[i]<-floor(lengthsinitial[i])
		inp1[[i]]<-inp1[[i]][1:lengthsnew[i]]
	}
	inpall<-inp1
}

##############################################################################################
gettoppercentsmultidata<-function(n,inp,keeppercent){
	print(keeppercent)
	lengthsinitial<-vector(length=n)
	lengthsnew<-vector(length=n)
	inp1<-lapply(inp,sort,decreasing=TRUE)
	lengthsinitial<-sapply(inp1,length)
	print(lengthsinitial)
	lengthsinitial<-keeppercent*lengthsinitial

	for (i in 1:n){
		lengthsnew[i]<-ceiling(lengthsinitial[i])
		inp1[[i]]<-inp1[[i]][1:lengthsnew[i]]
	}
	inpall<-inp1
	inpall
	
}

##############################################################################################
getwritefile<-function(extra=""){
	filenmin<-readline(paste("Enter the file name to which the",extra," statistical summary will be saved. ",sep=""))
	filenm<-paste(filenmin,".xls",sep="")
	filenm
}

##############################################################################################
keeppercentages<-function(n){
	yesno<-yesno("Do you wish to use the existing 99%, 97% and 95% data retention levels? ")
	if (yesno==1) {
	pt<-c(0.99,0.97,0.95,1)
	}
	else if (yesno==2){
		pt<-vector(length=3)
		for (i in 1:3){
			pt[i]<-readline(paste("Please enter percentage ",i," as a decimal. ", sep=""))
		}
		pt<-as.numeric(pt)
		pt<-c(pt,1)
	}
	else {
		pt<-c(0.99,0.97,0.95,1)

	}
	pt
}

##############################################################################################
keeptoppercent<-function(n,keeppercent,inp){
	print(keeppercent)
	if(keeppercent==0){
		print("Complete data set used.")
		inpall<-list(inp,keeppercent)
	}
	else{
	inp1<-gettoppercentsmultidata(n,inp,keeppercent)
	inpall<-list(inp1,keeppercent)
	}
	inpall
}

##############################################################################################
makematricx<-function(n,a1,a2,a3,inp1,tofile,filenm,keeppercent,pt){
	datarownames<-c("min          ","mean         ","sd.          ","max          ","25th value   ","50th value   ","75th value   ","90th value   ","95th value   ","98th value   ","99th value   ","99.9th value ")
	datawrite<-list(a1,a2,a3,inp1)
	datacolheader<-filenm
	datamats<-matrix(ncol=n,nrow=15)
	pt<-pt*100
	print(pt)
	keeppercent<-100*keeppercent
	if (keeppercent==0){
		dataheader<-c(paste(pt[1],"% of data",sep=""), paste(pt[2],"% of data",sep=""),paste(pt[3],"% of data",sep=""),paste("All data",sep=""))	
	}
	else {
	dataheader<-c(paste(keeppercent,"% of ",pt[1],"% of data",sep=""), paste(keeppercent,"% of ",pt[2],"% of data",sep=""),paste(keeppercent,"% of ",pt[3],"% of data",sep=""),paste(keeppercent,"% of all data",sep=""))	
	}
	for (i in 1:4){
		
		datamats<-datawrite[[i]]
		rownames(datamats)<-datarownames
		colnames(datamats)<-datacolheader
		datamatsf<-format(datamats,trim=FALSE,scientific=TRUE)
	
		write.table(dataheader[i],file=tofile,sep="\t",append=TRUE,quote=FALSE,col.names=NA)

		write.table(datamatsf,file=tofile,sep="\t",append=TRUE,quote=FALSE,col.names=NA)
	}
}

##############################################################################################
removelowervalues<-function(inp,n){
	rlm<-yesno("Do you wish to remove data below a certain value? ")
	if(rlm==2){
		rlm<-"No."
		print(rlm)
		inp1<-inp
	}
	else if(rlm==1){
	x<-readline("Please input the value from which all data lesser than shall be removed. ")
	x<-as.numeric(x)
	inp1<-lapply(inp,sort)
	for (i in 1:n){
		inp1[[i]]<-inp1[[i]][inp1[[i]]>x]
	}
	inp1
	}
	else {
		rlm<-"No."
		print(rlm)
		inp1<-inp
	}
	inp1
}

##############################################################################################
yesno<-function(question){
	yesno<-readline(paste(question,"Enter 1 for yes and 2 for no. ",sep=""))
	yesno<-as.numeric(yesno)
	yesno
}

##############################################################################################
summaries<-function(){
	graphics.off()
	n<-getnofiles()
	filenm<-getfilenames(n)
	pt<-keeppercentages(n)
	print(pt)
	tofile1<-getwritefile()
	scanwhat<-filelayout()
	inp<-getmultistrstrdata(filenm,n,scanwhat)
	inp1<-removelowervalues(inp,n)
	inpall<-croporcompletedata(n,inp1)
	inp<-inpall[[1]]
	a1<-getreducedmultidata(n,inp,pt,1)
	a2<-getreducedmultidata(n,inp,pt,2)
	a3<-getreducedmultidata(n,inp,pt,3)
	vm1<-getpermultidata(a1)
	vm2<-getpermultidata(a2)
	vm3<-getpermultidata(a3)
	vminp1<-getpermultidata(inp1)
	statsvalsvm<-getpermultidata(inp)

	
	statsmatrix1<-makematricx(n,vm1,vm2,vm3,vminp1,tofile1,filenm,inpall[[2]],pt)

}