/* A few helpful additions to manage the interaction with the new UI
 * Dominic Winsor, 22 Sept 2002
 */
 
//a few vars
var bad_characters_string = new String(); // bad characters found
var lastNterm = -1;


// this is a bit rubbish and it really breaks usability rules,
// but the user requires that n-term free is not an option for a radio set.
// should really convert to radio input, with "no modification" as default
function clearNterm( thisNterm ) {
	if (lastNterm != -1) {
		document.getElementById(lastNterm).checked = false;
	}
	lastNterm = thisNterm.id;
}

function startCalc() { // dominic's view controller
	resetCalc(); // tidy screen
	var sSeq = document.getElementById('aminoacids').value;
	var bOxidise = document.getElementById('opt_ox').checked;
	var bNAcetyl = document.getElementById('opt_acetyl').checked;
	var bCAmide = document.getElementById('opt_amide').checked;
	var bBiotin = document.getElementById('opt_biotin').checked;
	var bFluor = document.getElementById('opt_fluorescein').checked;
	OutputMass(sSeq,bOxidise,bNAcetyl,bCAmide,bBiotin,bFluor);
}

function resetCalc() {
	var output = document.getElementById('msgOut');
	var input = document.getElementById('aminoacids');
	output.value = new String();
	input.focus();	
}

function msgOut(message) { //dominic's wrapper for output
	var output = document.getElementById('msgOut');
	if (message) {
		output.value += message + "\n";
	}
	else {
		output.value += "\n";
	}
}

function copyParsedSeqToEdit( new_sequence ) { // copy string without bad chars back to edit box
	var input = document.getElementById('aminoacids');
	input.value = new_sequence.toUpperCase();
//	resetCalc();
//	startCalc();
}

// ------------------------------------------------------------




// Copyright © 1996 Ronald C. Beavis
// The author reserves all rights for the distribution and use
// of this script.
// Feel free to use this script in your own pages.  Please
// maintain this copyright notice on the script.
//
// Modified by Dominic Winsor of MenssanA web development 20 Sept 2002
//  - altered display code to fit site design.
//  - added facility to add phospho group to relevant amino acids.
//  - added Biotin and Fluorescein N-Term modifications
// www.get2dom.com
//
function Peptide(seq)	{
	this.sequence = "";
	this.OxidizeCysteines = OxidizeCysteines;
	this.sequence += CheckSequence(seq);
	this.length = CalculateLength(this.sequence);
	this.Mass = CalculateMass(this.sequence);
	this.ExactMass = CalculateExactMass(this.sequence);
}

function OxidizeCysteines(sequence)	{
	var string_length = sequence.length;
	var current = 0;
	var cysteines = 0;
	while(current < string_length)	{
		if(sequence.charAt(current) == 'c')
			cysteines++;
		current++;
	}
	var mass_change = -2*Math.floor(cysteines/2)*10000;
	return mass_change;
}
	
function FormatFloat(float_number,n)	{
	var temp_string = "";
	temp_string += float_number;
	var limit = temp_string.length;
	var current = 0;
	var output_string = "";
	var dot_found = false;
	var char_string = "";
	var decimal_places = 0;
	while(current < limit)	{
		char_string = temp_string.charAt(current);
		if(char_string == '.')
			dot_found = true;
		if(dot_found)	{
			if(decimal_places > n)
				break;
			decimal_places++;
		}
		output_string += char_string;
		current++;
	}
	return output_string;
}

function OutputMass(input_sequence,oxidize,n_acetyl,c_amide,n_biotin,n_fluor)	{

	var sequence_string = "";
	var current = 0;
	CurrentPeptide = new Peptide(input_sequence);
	if(CurrentPeptide.sequence.length == 0)	{
		msgOut("Error");
		msgOut("The sequence contains no valid residues.");
		msgOut("Re-enter the sequence or click in the text window.");
		return false;
	}
	var mass_change = 0;
	if(oxidize)	{
		mass_change = CurrentPeptide.OxidizeCysteines(CurrentPeptide.sequence);
		CurrentPeptide.Mass += 	mass_change;
		CurrentPeptide.ExactMass += mass_change;
	}
	if(n_acetyl)	{
		CurrentPeptide.Mass += 420373;
		CurrentPeptide.ExactMass += 420106;
	}
	if(n_biotin)	{
		CurrentPeptide.Mass += 2260000;
		CurrentPeptide.ExactMass += 2260000;
	}
	if(n_fluor)	{
		CurrentPeptide.Mass += 3580000;
		CurrentPeptide.ExactMass += 3580000;
	}
	if(c_amide)	{
		CurrentPeptide.Mass += -9847;
		CurrentPeptide.ExactMass += -9840;
	}
	while(current < CurrentPeptide.sequence.length)	{
		sequence_string += CurrentPeptide.sequence.substring(current,current+30);
		sequence_string += "\n";
		current += 30;
	}
	sequence_string = sequence_string.toUpperCase();
	
	
	//echo sequence
	msgOut("Sequence ("+CurrentPeptide.length+" amino acids)");
	msgOut(sequence_string);	
	
	//echo mass
	msgOut("Mass");
	msgOut(FormatFloat(CurrentPeptide.Mass/10000,3)+" (av.) ");
	msgOut(FormatFloat(CurrentPeptide.ExactMass/10000,3)+" (mono.)");
	msgOut();
	
	//echo seq. length
//	msgOut("Length: "+CurrentPeptide.length);
//	msgOut();
	
	//echo characteristics
	msgOut("Characteristics");
	if(oxidize)
		msgOut(" * Cys oxidized");
	else
		msgOut(" * Cys reduced");
	if(n_acetyl)
		msgOut(" * N-term acetyl");
	else if(n_biotin)
		msgOut(" * N-term biotin");
	else if(n_fluor)
		msgOut(" * N-term fluorescein");
	else
		msgOut(" * N-term free");
	if(c_amide)
		msgOut(" * C-term amide");
	else
		msgOut(" * C-term free");

	//echo break
//	msgOut("-------------------");
	return true;
}



function CalculateMass(input_sequence)	{
	var sequence = input_sequence;
	sequence += " ";
	var string_length = sequence.length;
	var current = 0;
	var mass = 180000;
	var aamass = 0;
	while(current < string_length)	{
		aamass = AAMass(sequence.charAt(current));
		if(aamass > 10000)
			mass += aamass;
		current += 1;
	}
	if(mass < 190000)
		return 0;
	return mass;
}
function CalculateExactMass(input_sequence)	{
	var sequence = input_sequence;
	sequence += " ";
	var string_length = sequence.length;
	var current = 0;
	var mass = 180000;
	var aamass = 0;
	while(current < string_length)	{
		aamass = ExactAAMass(sequence.charAt(current));
		if(aamass > 10000)
			mass += aamass;
		current += 1;
	}
	if(mass < 190000)
		return 0;
	return mass;
}

function CalculateLength(input_sequence)	{
	var sequence = input_sequence;
	sequence += " ";
	var string_length = sequence.length;
	var current = 0;
	var aamass = 0;
	var length = 0;
	while(current < string_length)	{
		aamass = AAMass(sequence.charAt(current));
		if(aamass > 10000 && (sequence.charAt(current)!="*") ) // * does not add length, it is a modifier (see below)
			length++;
		current += 1;
	}
	return length;
}

function CheckSequence(input_sequence)	{
	var output_sequence = new String();
	var sequence = input_sequence.toLowerCase();
	var string_length = sequence.length;
	var current = 0;
	var aamass = 0;
	var bad_characters = 0;
	bad_characters_string = "";
	
	while(current < string_length)	{
		aamass = AAMass(sequence.charAt(current));
		if(aamass == 0)	{
			bad_characters++;
			bad_characters_string += sequence.charAt(current)+",";
		}

		//validate the prefix to a '*' modifier (phospho)
		if( sequence.charAt(current)=="*" ) {
			var prefix_error = true;
			var prev_char = sequence.charAt(current-1);
			if( prev_char == "s" || prev_char == "t" || prev_char == "y" ) prefix_error = false;
			if (prefix_error) {
				msgOut("Phospho error");
				msgOut("'*' must follow S, T or Y amino acid");
				msgOut();
			}
		}
		
		if(aamass > 10000 )	{
			output_sequence += sequence.charAt(current);
		}
		current += 1;
	}
	if(bad_characters > 0)	{
		// this is silly, but formats a nice english sentence
		var format_s = "s";
		var format_was = "were";
		if (bad_characters==1) {
			format_s = "";
			format_was = "was";
		}
		bad_characters_string = bad_characters_string.substr(0, (bad_characters_string.length-1));
		msgOut('Note\n'+bad_characters+' non-standard abbreviation'+format_s+' ('+bad_characters_string+') '+format_was+' deleted from this sequence.');
		msgOut();
	} 
	
	copyParsedSeqToEdit( output_sequence ); // automatically update sequence without bad chars.
	return output_sequence;
}

function ExactAAMass(aa)	{
	var mass = 0;	
	if(aa == 'a')	mass =  710371;
	if(aa == 'r')	mass = 1561011;
	if(aa == 'n')	mass = 1140429;
	if(aa == 'd')	mass = 1150269;
	if(aa == 'k')	mass = 1280950;
   	if(aa == 'c')	mass = 1030092;
	if(aa == 'e')	mass = 1290426;
	if(aa == 'q')	mass = 1280586;
	if(aa == 'g')	mass =  570215;
	if(aa == 'h')	mass = 1370589;
	if(aa == 'i')	mass = 1130841;
	if(aa == 'l')	mass = 1130841;
	if(aa == 'm')	mass = 1310405;
   	if(aa == 'f')	mass = 1470684;
	if(aa == 'p')	mass =  970528;
	if(aa == 's')	mass =  870320;
	if(aa == 't')	mass = 1010477;
	if(aa == 'w')	mass = 1860793;
 	if(aa == 'y')	mass = 1630633;
	if(aa == 'v')	mass =  990684;
   	if(aa == 'b')	mass = 1145000;
	if(aa == 'z')	mass = 1285000;
	if(aa == 'x')	mass = 1110000;
	if(aa == '*')	mass =  800000; //this is for phospho group, which may only appear on a S, T or Y group.
	if(aa == ' ')	mass = 1;
	if(aa == '\t')	mass = 1;
	if(aa == '\n')	mass = 1;
	if(aa == '\r')	mass = 1;
	return mass;
}

function AAMass(aa)	{
	var mass = 0;
	if(aa == 'a')	mass =  710787;
	if(aa == 'r')	mass = 1561872;
	if(aa == 'n')	mass = 1141036;
	if(aa == 'd')	mass = 1150883;
	if(aa == 'k')	mass = 1281738;
	if(aa == 'c')	mass = 1031426;
	if(aa == 'e')	mass = 1291152;
	if(aa == 'q')	mass = 1281305;
	if(aa == 'g')	mass =  570518;
	if(aa == 'h')	mass = 1371407;
	if(aa == 'i')	mass = 1131593;
	if(aa == 'l')	mass = 1131593;
	if(aa == 'm')	mass = 1311963;
	if(aa == 'f')	mass = 1471759;
	if(aa == 'p')	mass =  971164;
	if(aa == 's')	mass =  870780;
	if(aa == 't')	mass = 1011049;
	if(aa == 'w')	mass = 1862124;
	if(aa == 'y')	mass = 1631753;
	if(aa == 'v')	mass =  991323;
	if(aa == 'b')	mass = 1145000;
	if(aa == 'z')	mass = 1285000;
	if(aa == '*')	mass =  800000; //this is for phospho group, which may only appear on a S, T or Y group.
	if(aa == ' ')	mass = 1;
	if(aa == '\t')	mass = 1;
	if(aa == '\n')	mass = 1;
	if(aa == '\r')	mass = 1;
	return mass;
}