// Profile_AlignRef script by Christophe Leterrier
// very crude script to align a profiles table using a reference channel aligned table
// 19-06-14 Adapted to new Fiji with call to classes
// 09-07-14 Rebuilt to speed things up

importClass(Packages.ij.io.OpenDialog);
importClass(Packages.ij.IJ);
importClass(Packages.java.lang.Double);
importClass(Packages.java.io.File);
importClass(Packages.java.io.FileReader);
importClass(Packages.java.io.FileWriter);
importClass(Packages.java.io.FileReader);
importClass(Packages.java.io.FileWriter);
importClass(Packages.java.io.BufferedReader);
importClass(Packages.java.io.BufferedWriter);

var odi = new OpenDialog("Choose a file to align", "");
var odr = new OpenDialog("Choose a reference alignement file", "");

var startTime = new Date().getTime();
IJ.showStatus("start");

var inName = odi.getFileName();
var inDir = odi.getDirectory();
var inPath = inDir + inName;
var inString = IJ.openAsString(inPath);
var inArray = stringToArray(inString, true);

var inRows = inArray.length;
var inCols = inArray[0].length;
IJ.log("Input file: " + inPath);
IJ.log("Input file contains: " + inCols + " profiles with " + inRows + " points");

var refName = odr.getFileName();
var refDir = odr.getDirectory();
var refPath = refDir + refName;
var refFile = new File(refPath);

IJ.log("Ref file: " + inPath);

var alignPath = inDir + inName.substring(0, inName.length()-4) + "_Aligned.txt"
var alignFile = new File(alignPath);
if (!alignFile.exists()) {
		alignFile.createNewFile();
}

IJ.log("Align file: " + alignPath);

var br = new BufferedReader(new FileReader(refFile));
var bw = new BufferedWriter(new FileWriter(alignFile));

refLine = br.readLine();
bw.write(refLine);
bw.newLine();

var countLine = 1;
var countArray = new Array(inCols);
for (var i = 0; i < countArray.length; i++) countArray[i] = 0;

while ((refLine = br.readLine()) != null) {	
	
	var refCells = refLine.split("\t");
	var alignLine = refCells[0] + "\t" + refCells[1] + "\t";
	for (var c = 2; c < refCells.length; c++) {
		if (refCells[c] == "NaN") {
			alignLine = alignLine + "NaN" + "\t";
		}
		else {
			alignLine = alignLine + inArray[countArray[c]][c] + "\t";
			countArray[c]++;
		}
	}
	countLine ++;
	bw.write(alignLine);
	bw.newLine();
}

br.close();
bw.close();

var stopTime = new Date().getTime();
var Time = stopTime - startTime;

IJ.log(""+ countLine + " done after " + Time + " ms");

//**************************************

function stringToArray(st, head) {
	var rowsArray = st.split("\n");
	if (head == true) rowsArray.splice(0,1);
	mArray = new Array(rowsArray.length);
	for (var j = 0; j < rowsArray.length; j++) {
		mArray[j] = rowsArray[j].split("\t");	
	}
	return mArray;
}