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

function rangeExtract (theDocument) {	
	var newDna = "";
	var maxInput = 500000;
	var matchFound = false;
	var ranges = new Array();

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

	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false) || (checkFormElement (theDocument.forms[0].elements[1]) == false))	{
		return false;
	}

	var arrayOfRanges = theDocument.forms[0].elements[1].value.split(/,/);
	var arrayOfStartAndEnd;
	for (var i=0; i < arrayOfRanges.length; i++) {
		arrayOfStartAndEnd = arrayOfRanges[i].split(/\.\.|\-/);
		if ((arrayOfStartAndEnd.length == 1) && (arrayOfStartAndEnd[0].search(/\d/) != -1)) {
			matchFound = true;
			ranges.push(new Range(arrayOfStartAndEnd[0], arrayOfStartAndEnd[0]));
		}
		else if ((arrayOfStartAndEnd.length == 2) && (arrayOfStartAndEnd[0].search(/\d/) != -1) && (arrayOfStartAndEnd[1].search(/\d/) != -1)) {
			matchFound = true;
			ranges.push(new Range(arrayOfStartAndEnd[0], arrayOfStartAndEnd[1]));
		}				
	}
	if (matchFound == false) {
		alert ("No ranges were entered.");
		return false;
	}	

	openWindow("Range Extractor Protein");	
	openPre();
	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);
	for (var i = 0; i < arrayOfFasta.length; i++)	{
		newProtein = getSequenceFromFasta (arrayOfFasta[i]);
		title = getTitleFromFasta (arrayOfFasta[i]);
		newProtein = removeNonProtein(newProtein);
		outputWindow.document.write(getFastaTitleFromTitleAndSequence(title, newProtein));
		writeSequenceRanges (newProtein, ranges, theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);
	}
	closePre();
	closeWindow();
	return true;
}

function writeSequenceRanges (sequence, ranges, segmentType)	{

	var rangeGroup = new RangeGroup(segmentType);

	for (var i=0; i < ranges.length; i++) {
		rangeGroup.addRange(ranges[i]);			
	}
	rangeGroup.writeRanges(sequence);
}

//Range class getSequence() method
function getSequence(sequence) {
	var problem = false;
	var warnings = new Array();

	if (this.start == this.stop) {
		if (this.start < 1) {
			problem = true;
			warnings.push("position value of " + this.start + " is less than 1");
		}

		if (this.start > sequence.length) {
			problem = true;
			warnings.push("position value of " + this.start + " is greater than the sequence length");		
		}

	}
	else {
		if (this.start < 1) {
			problem = true;
			warnings.push("position value of " + this.start + " is less than 1");
		}
		if (this.stop < 1) {
			problem = true;
			warnings.push("position value of " + this.stop + " is less than 1");		
		}
		if (this.start > sequence.length) {
			problem = true;
			warnings.push("position value of " + this.start + " is greater than the sequence length");		
		}
		if (this.stop > sequence.length) {
			problem = true;
			warnings.push("position value of " + this.stop + " is greater than the sequence length");		
		}
		if (this.start > this.stop) {
			problem = true;
			warnings.push("stop position is less than start position in range " + this.start + " to " + this.stop);		
		}
	}



	if (problem) {
		alert ("An entry was skipped because of the following:\n" + warnings.join(",\n"));
		return false;
	}
	else if (this.start == this.stop) {
		return sequence.charAt(this.start - 1);
	}
	else {
		return sequence.substring(this.start - 1, this.stop);
	}
}

//Range class getTitle() method
function getTitle() {
	if (this.start == this.stop) {
		return "&gt;base " + this.start;
	}
	else {
		return "&gt;base " + this.start + " to " + this.stop;
	}
}

//Range class
function Range (start, stop) {
	this.start = parseInt(start);
	this.stop = parseInt(stop);
}

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

// define object methods
Range.prototype.getSequence = getSequence;
Range.prototype.getTitle = getTitle;

//RangeGroup class addRange() method
function addRange(range) {
	this.ranges.push(range);
}

//RangeGroup class writeRanges() method
function writeRanges(sequence) {
	var sequenceArray = new Array();
	
	if (this.type == "new_sequence") {
		
		for (var i = 0; i < this.ranges.length; i++) {
			if (this.ranges[i].getSequence(sequence) != "") {
				sequenceArray.push(this.ranges[i].getSequence(sequence));
			}		
		}
		outputWindow.document.write(addReturns(sequenceArray.join("")) + "\n\n");
		return true;	
	}

	if (this.type == "separate") {

		for (var i = 0; i < this.ranges.length; i++) {
			if (this.ranges[i].getSequence(sequence) != "") {
				outputWindow.document.write(this.ranges[i].getTitle() + "\n");
				outputWindow.document.write(addReturns(this.ranges[i].getSequence(sequence)) + "\n\n");
			}		
		}
		return true;
	}

	if (this.type == "uppercased") {
		var re;
		sequence = sequence.toLowerCase();
		for (var i = 0; i < this.ranges.length; i++) {
			if (this.ranges[i].getSequence(sequence) != "") {
				if (this.ranges[i].start > 1) {
					re = "(.{" + (this.ranges[i].start - 1) + "})\\B(.{" + (this.ranges[i].stop - this.ranges[i].start + 1) + "})";
					re = new RegExp(re);
					sequence = sequence.replace(re, 
                    				function (str, p1, p2, offset, s) {
                      					return p1 + p2.toUpperCase();
                   				}
        				);					
				}
				else {
					re = "(.)";
					re = new RegExp(re);
					sequence = sequence.replace(re, 
                    				function (str, p1, offset, s) {
                      					return p1.toUpperCase();
                   				}
        				);	
				}
			}		
		}
		outputWindow.document.write(addReturns(sequence) + "\n\n");
		return true;			
	}

	if (this.type == "lowercased") {
		var re;
		sequence = sequence.toUpperCase();
		for (var i = 0; i < this.ranges.length; i++) {
			if (this.ranges[i].getSequence(sequence) != "") {
				if (this.ranges[i].start > 1) {
					re = "(.{" + (this.ranges[i].start - 1) + "})\\B(.{" + (this.ranges[i].stop - this.ranges[i].start + 1) + "})";
					re = new RegExp(re);
					sequence = sequence.replace(re, 
                    				function (str, p1, p2, offset, s) {
                      					return p1 + p2.toLowerCase();
                   				}
        				);					
				}
				else {
					re = "(.)";
					re = new RegExp(re);
					sequence = sequence.replace(re, 
                    				function (str, p1, offset, s) {
                      					return p1.toLowerCase();
                   				}
        				);	
				}
			}		
		}
		outputWindow.document.write(addReturns(sequence) + "\n\n");
		return true;			
	}	
}

//RangeGroup class
function RangeGroup (type) {
	this.type = type;
	this.ranges = new Array();
}

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

// define object methods
RangeGroup.prototype.addRange = addRange;
RangeGroup.prototype.writeRanges = writeRanges;