//Written by Paul Stothard, University of Alberta, Canada

function restDigest (theDocument) {	
	var newDna = "";
	var maxInput = 100000;

	if (testScript() == false) {
		return false;
	}

	var restrictionFragments = new Array();
	var restrictionFragment;

	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false))	{
		return false;
	}

	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);
	for (var i = 0; i < arrayOfFasta.length; i++)	{
		newDna = getSequenceFromFasta (arrayOfFasta[i]);
		title = getTitleFromFasta (arrayOfFasta[i]);
		newDna = removeNonDna(newDna);	
	
		//create restriction fragment objects from sequences and add them to array
		restrictionFragment = new RestrictionFragment (theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value, title, newDna, 1, newDna.length, "sequence start", "sequence end", newDna.length);
		restrictionFragments.push(restrictionFragment);		
	}
	
	restrictionFragments = digest(restrictionFragments, theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);
	restrictionFragments = digest(restrictionFragments, theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value);
	restrictionFragments = digest(restrictionFragments, theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value);

	restrictionFragments.sort(restrictionFragmentSorter);

	openWindow("Restriction Digest");
	openPre();
	for (var i = 0; i < restrictionFragments.length; i++)	{
		restrictionFragments[i].correctPositions();
		restrictionFragments[i].writeFragment(theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value);
	}
	closePre();
	closeWindow();
	return true;
}

function digest (arrayOfRestrictionFragments, enzyme) {

	if (enzyme == "") {
		return arrayOfRestrictionFragments;
	}

	var newFragments = new Array();
	var positions = new Array();
	var matchPosition = 0;
	var matchExp = enzyme.match(/\/.+\//).toString();
	matchExp = matchExp.replace(/\//g, "");
	matchExp = new RegExp (matchExp, "gi");
	var cutDistance = parseInt((enzyme.match(/\)\D*\d+/)).toString().replace(/\)\D*/,""));
	var enzymeName = ((enzyme.match(/\([^\(]+\)/)).toString()).replace(/\(|\)/g,"");
	var matchArray;
	var wasCut = false;
	var restrictionFragmentOne;
	var restrictionFragmentTwo;

	var previousCutPosition;
	var previousEnzyme;
	var previousStartPosition;

	var startRestrictionFragment;

	var lookAhead = 50;
	var lowerLimit;
	var upperLimit;
	var shiftValue;

	//go through each restriction fragment.
	for (var i = 0; i < arrayOfRestrictionFragments.length; i++)	{
	
		if (arrayOfRestrictionFragments[i].topology == "circular") {

			shiftValue = (arrayOfRestrictionFragments[i].sequence.substring(0, lookAhead)).length;
			var extendedSequence = arrayOfRestrictionFragments[i].sequence.substring(arrayOfRestrictionFragments[i].sequence.length - lookAhead, arrayOfRestrictionFragments[i].sequence.length) + arrayOfRestrictionFragments[i].sequence + arrayOfRestrictionFragments[i].sequence.substring(0, lookAhead);
			lowerLimit = 0 + shiftValue;
			upperLimit = arrayOfRestrictionFragments[i].sequence.length + shiftValue;	

			while (matchArray = matchExp.exec(extendedSequence)) {
				matchPosition = matchExp.lastIndex;
				matchPosition = matchPosition - cutDistance;
				if ((matchPosition >= lowerLimit) && (matchPosition < upperLimit))	{
					positions.push(matchPosition - shiftValue);
					wasCut = true;
				}
			}		
		}
		else {
		
			while (matchArray = matchExp.exec(arrayOfRestrictionFragments[i].sequence)) {
				matchPosition = matchExp.lastIndex;
				matchPosition = matchPosition - cutDistance;
				positions.push(matchPosition);
				wasCut = true;
			}
		}

		if (!(wasCut)) {
			newFragments.push(arrayOfRestrictionFragments[i]);
		}		
		else {
			wasCut = false;	
			
			//now go through positions
			previousCutPosition = 0;
			previousEnzyme = arrayOfRestrictionFragments[i].startEnzyme;
			previousStartPosition = arrayOfRestrictionFragments[i].start;
			for (var j = 0; j < positions.length; j++)	{

				if (arrayOfRestrictionFragments[i].topology == "circular") {

					arrayOfRestrictionFragments[i].topology = "linear";
					startRestrictionFragment = new RestrictionFragment("linear", arrayOfRestrictionFragments[i].sourceName, arrayOfRestrictionFragments[i].sequence.substring(previousCutPosition, positions[j]), previousStartPosition, previousStartPosition + arrayOfRestrictionFragments[i].sequence.substring(previousCutPosition, positions[j]).length - 1, previousEnzyme, enzymeName, arrayOfRestrictionFragments[i].originalLength);
					
				}

				else {
					restrictionFragmentOne = new RestrictionFragment("linear", arrayOfRestrictionFragments[i].sourceName, arrayOfRestrictionFragments[i].sequence.substring(previousCutPosition, positions[j]), previousStartPosition, previousStartPosition + arrayOfRestrictionFragments[i].sequence.substring(previousCutPosition, positions[j]).length - 1, previousEnzyme, enzymeName, arrayOfRestrictionFragments[i].originalLength);
					newFragments.push(restrictionFragmentOne);
				}

				if (j == (positions.length - 1)) {
					
					if (startRestrictionFragment == null) {
						restrictionFragmentTwo = new RestrictionFragment("linear", arrayOfRestrictionFragments[i].sourceName, arrayOfRestrictionFragments[i].sequence.substring(positions[j], arrayOfRestrictionFragments[i].sequence.length), previousStartPosition + arrayOfRestrictionFragments[i].sequence.substring(previousCutPosition, positions[j]).length, arrayOfRestrictionFragments[i].stop, enzymeName, arrayOfRestrictionFragments[i].stopEnzyme, arrayOfRestrictionFragments[i].originalLength);
						newFragments.push(restrictionFragmentTwo);
					}
					else {
						restrictionFragmentTwo = new RestrictionFragment("linear", arrayOfRestrictionFragments[i].sourceName, arrayOfRestrictionFragments[i].sequence.substring(positions[j], arrayOfRestrictionFragments[i].sequence.length) + startRestrictionFragment.sequence, previousStartPosition + arrayOfRestrictionFragments[i].sequence.substring(previousCutPosition, positions[j]).length, startRestrictionFragment.stop, enzymeName, startRestrictionFragment.stopEnzyme, arrayOfRestrictionFragments[i].originalLength);
						
						newFragments.push(restrictionFragmentTwo);	

					}
				}
				
				previousCutPosition = positions[j];
				previousEnzyme = enzymeName;
				previousStartPosition = arrayOfRestrictionFragments[i].start + positions[j];

			}
						
		}
		positions = new Array();
		startRestrictionFragment = null;
	}
	return newFragments;	
}

function restrictionFragmentSorter (a, b) {
   	if (a.sequence.length < b.sequence.length) {
      		return 1;
	}
   	if (a.sequence.length > b.sequence.length) {
      		return -1;
	}
	if (a.sequence.length == b.sequence.length) {
		if (a.start < b.start) {
			return -1;
		}
		if (a.start > b.start) {
			return 1;
		}
		else {
			// a must be equal to b
			return 0;
		}
	}
}

//RestrictionFragment writeFragment() method
function writeFragment(topology) {
	if (this.topology == "linear") {
		outputWindow.document.write ("&gt;" + this.sequence.length + " bp linear fragment from " + topology + " parent " + this.sourceName + ", base " + this.start + " to base " + this.stop + " (" + this.startEnzyme + " - " + this.stopEnzyme + ").\n");
	}
	else {
		outputWindow.document.write ("&gt;" + this.sequence.length + " bp circular molecule from " + topology + " parent " + this.sourceName + ".\n");
	}
	outputWindow.document.write (addReturns(this.sequence) + "\n\n");
}

//RestrictionFragment correctPositions() method
function correctPositions() {
	if (this.start > this.originalLength) {
		this.start = this.start - this.originalLength;
	}
	if (this.stop > this.originalLength) {
		this.stop = this.stop - this.originalLength;
	}
	if (this.stop == 0) {
		this.stop = this.originalLength;
	}
}

//RestrictionFragment class
function RestrictionFragment (topology, sourceName, sequence, start, stop, startEnzyme, stopEnzyme, originalLength) {
   	this.topology = topology;
   	this.sourceName = sourceName;
   	this.sequence = sequence;
	this.start = start;
	this.stop = stop;
	this.startEnzyme = startEnzyme;
	this.stopEnzyme = stopEnzyme;
	this.originalLength = originalLength;
}

//create and throw away a prototype object
new RestrictionFragment("", "", "", 0, 0, "", "", 0);

// define object methods
RestrictionFragment.prototype.writeFragment = writeFragment;
RestrictionFragment.prototype.correctPositions = correctPositions;