// SLIKS-Alike Interactive Key Software (SAIKS)
// Inspired by SLIKS from http://stingersplace.com/SLIKS/ by Gerald F. Guala
// Copyright (c) 2006 Greg Alexander, to be distributed under the terms of
// the GPLv2 (COPYING)

//Modified by Brian C. O'Meara to allow automatic highlighting of useful
//   characters (depending on characters already selected, others might
//   not be informative)
//December 21, 2006. 
//My modifications have ADDED BY BCO before or after them.

// defaults for things that can be overriden in data.js
var binary = false;
var exclusive_mode = true;
var remove_mode = false;		// remove taxa instead of reddening

var first_row = 1;	// to skip chars[0] and items[0] for SLIKS compat
var char_flags = new Array();
// == 0   -->  initial state, is selectable
// == 1   -->  currently selected characteristic (click to unselect)
// == 2   -->  grayed out (obviated characteristic)
// == 3   -->  no longer useful characteristic //ADDED BY BCO
var taxa_flags = new Array();
// == 0   -->  not a possible match
// == 1   --> a possible match

// hopefully eliminate some downstream substring processing by caching
// single-value item characteristics
var item_cache = new Array();

// used instead of scanning char_flags[row] (as in any_in_row_selected())
var char_row_state = new Array();
// == 0       --> nothing selected
// == -1      --> several selected
// == 1-35    --> just that col selected (great for exclusive/binary mode!)

// these are initialized by *_table() to work around the fact that MSIE
// (et al?) have a distinct lack of document.getElementById()
var char_elems = new Array();
var taxa_elems = new Array();

// to support categories of characteristics
var char_titles = new Array();
var char_headers = new Array();
var char_header_run = new Array();
var any_char_headers = false;


function get_elem_by_tag_id(tag,id) {
	var elemlist = document.getElementsByTagName(tag);
	var len = elemlist.length;
	var i;
	for (i = 0; i < len; i++) {
		if (elemlist[i].id == id) {
			return elemlist[i];
		}
	}
}

// find width of characteristics table
function find_max_char_cols() {
	var i;
	var max=0;
	for (i = first_row; i < chars.length; i++) {
		if (chars[i].length > max) {
			max = chars[i].length;
		}
	}
	return max;
}

// emit characteristics table
function chars_table() {
	var max_char_cols = find_max_char_cols();
	var i;
	var j;
	var k;

	document.write("<table border=1 cellspacing=0 cellpadding=0 class=\"ct\">\n");

	for (i = first_row; i < chars.length; i++) {
		var percent;
		document.write("<tr>");
		if (any_char_headers) {
			if (char_header_run[i] > 0) {
				document.write("<td rowspan="+char_header_run[i]+"><div class=\"ct_cat\">"+char_headers[i]+"</div></td>\n");
			}
		}
		document.write("<td><div class=\"ct_title\">"+char_titles[i]+"</div></td>\n");
		document.write("<td><table border=1 cellspacing=0 width=100% class=\"ctt\"><tr>\n");
		percent = 100/(chars[i].length-1);
		for (j = 1; j < chars[i].length; j++) {
			document.write("<td width="+percent+"% id=\"char"+i+"m"+j+"\" onClick=\"toggle_char("+i+","+j+");\"><div class=\"ctt_char\">"+chars[i][j]+"</div></td>\n");
		}
		document.write("</tr></table></td></tr>\n");
	}

	document.write("</table>\n");

	// this could be improved slightly by getting just the tds
	// associated with the table we want, but it seems that simply not
	// referencing document.all is enough to guarantee decent performance,
	// even on firefox!
	var elemlist = document.getElementsByTagName("td");
	var len = elemlist.length;
	for (i = 0; i < len; i++) {
		if (elemlist[i].id.substr(0,4) == "char") {
			var s;
			s = elemlist[i].id.substr(4);
			k = s.indexOf("m");
			j = s.substr(0,k)-0;
			k = s.substr(k+1)-0;
			if (!char_elems[j]) {
				char_elems[j] = new Array();
			}
			char_elems[j][k] = elemlist[i];
		}
	}
}

// emit taxa table
function taxa_table() {
	document.write("<table class=\"tt\">");
	for (i = first_row; i < items.length; i++) {
		document.write("<tr><td id=\"taxa"+i+"\">");
		if (items[i][chars.length]) {
			document.write("<a class=\"tt_name\" href=\""+items[i][chars.length]+"\">"+items[i][0]+"</a>");
		} else {
			document.write(items[i][0]);
		}
		document.write("</td><td onClick=\"select_taxa("+i+");\"><img class=\"tt_show\" src=\"char-button.gif\"></td></tr>");
	}

	document.write("</table>");

	var elemlist = document.getElementsByTagName("td");
	var len = elemlist.length;
	for (i = 0; i < len; i++) {
		if (elemlist[i].id.substr(0,4) == "taxa") {
			taxa_elems[elemlist[i].id.substr(4)-0] = elemlist[i];
		}
	}
}

// inits the list of the currently selected characteristics
function init_char_flags() {
	var i;
	var j;
	for (i = first_row; i < chars.length; i++) {
		char_flags[i] = new Array();
		for (j = 1; j < chars[i].length; j++) {
			char_flags[i][j] = 0;
		}
		char_row_state[i] = 0;
	}
}

// toggles characteristic (i,j) in the table
function toggle_char(i, j) {
	var k;

	if (char_flags[i][j] == 1) {
		char_flags[i][j] = 0;
	} else {
		if (exclusive_mode) {
			// in exclusive mode, selecting something unselects
			// the other characteristics
			for (k = 1; k < char_flags[i].length; k++) {
				char_flags[i][k] = 0;
			}
		}
		char_flags[i][j] = 1;
	}

	// update char_row_state[i]
	char_row_state[i] = 0;
	for (k = 1; k < char_flags[i].length; k++) {
		if (char_flags[i][k] == 1) {
			if (char_row_state[i] == 0) {
				char_row_state[i] = k;
			} else {
				char_row_state[i] = -1;
			}
		}
	}

	update();
}

// sets the characteristics for a specific taxa
function select_taxa(i) {
	var j;
	var k;

	init_char_flags();		// reset everything to defaults first

	for (j = first_row; j < chars.length; j++) {
		var x = item_cache[i][j];
		if (x) {
			char_flags[j][x] = 1;
			char_row_state[j] = x;
		} else if (items[i][j] == "?") {
			// wildcard -- set them all
			for (k = 0; k < char_flags[j].length; k++) {
				char_flags[j][k] = 3; // MODIFIED BY BCO: changed to make these chars white
			}
			char_row_state[j] = -1;
		} else {
			// polymorphous subset...
			for (k = 0; k < items[i][j].length; k++) {
				char_flags[j][parseInt(items[i][j].charAt(k),36)] = 1;
			}
			char_row_state[j] = -1;
		}
	}

	update();
}

// do whatever appropriate browser magic to set the background color of
// the specified CSS ID
function set_bgcolor(elem, color) {
	var i;

	if (!elem) return;
	elem.setAttribute("bgColor",color);
}

// update the visual aspect of the characteristics table from char_flags
function update_chars() {
	var i;
	var j;

	for (i = first_row; i < chars.length; i++) {
		for (j = 1; j < char_flags[i].length; j++) {
			if (char_flags[i][j] == 2) {
				set_bgcolor(char_elems[i][j], "#7777AA");
			} else if (char_flags[i][j] == 1) {
				set_bgcolor(char_elems[i][j], "#00FF00");
			} else if (char_flags[i][j] == 0) {
				set_bgcolor(char_elems[i][j], "#AAAAFF");
			} else {  //ADDED BY BCO; MEANS char_flags ==3
				set_bgcolor(char_elems[i][j], "#FFFFFF");
			}
		}
	}
}

// see if anything in the characteristics row i is selected
function any_in_row_selected(i) {
	return (char_row_state[i] != 0);
}

// update the taxa table to visually match the taxa_flags array
function update_taxa() {
	var i;
	var j;

	for (i = first_row; i < items.length; i++) {
		if (remove_mode) {
			// XXX - to make remove_mode work, I think we change
			// taxa table to not be a table, but rather a list of
			// divs...and then we can do this display="none" hack.
			if (taxa_flags[i] == 1) {
				set_bgcolor(taxa_elems[i], "#0088ff");
				taxa_elems[i].display = "block";
			} else {
				taxa_elems[i].style.display = "none";
				set_bgcolor(taxa_elems[i], "#888800");
			}
		} else {
			if (taxa_flags[i] == 1) {
				set_bgcolor(taxa_elems[i], "#00FF00");
			} else {
				set_bgcolor(taxa_elems[i], "#FF4444");
			}
		}
	}
}

// given the current state of char_flags, compute taxa_flags
// (possible matching taxa)
function compute_taxa() {
	var i;
	var j;
	var k;
	var disp;
	var sub_disp;

	for (i = first_row; i < items.length; i++) {
		disp = 1;
		for (j = first_row; j < chars.length; j++) {
			if (char_row_state[j] == 0) {
				// nothing selected, assume match
			} else if (item_cache[i][j]) {
				if (char_flags[j][item_cache[i][j]] != 1) {
					disp = 0;
				}
			} else if (items[i][j] == "?") {
				// wildcard, matches everything
			} else {
				// disp remains only if the corresponding
				// element of char_flags is set
				sub_disp = 0;
				for (k = 0; k < items[i][j].length; k++) {
					if (char_flags[j][parseInt(items[i][j].charAt(k),36)] == 1) {
						sub_disp = 1;
					}
				}
				if (sub_disp == 0) {
					disp = 0;
				}
			}

		}
		taxa_flags[i] = disp;
	}
}

// some selections obviate others (set char_flags to 2 for obviated ones)
function compute_obviates_binary() {
	var i;
	var j;
	var k;

	for (i = first_row; i < chars.length; i++) {
		if (char_row_state[i] == 0) {
			var poss;
			poss = 0;
				// == 1  --> Yes
				// == 2  --> No
				// == 3  --> Either
			for (j = first_row; j < items.length; j++) {
				if (taxa_flags[j] == 1) {
					var x = item_cache[j][i];
					if (x) {
						poss |= x;
						if (poss == 3) {
							// yes and no both possible
							break;
						}
					} else {
						// must be "?"
						poss = 3;
						break;
					}
				}
			}
			for (j = first_row; j < char_flags[i].length; j++) {
				if (poss & j) {
					char_flags[i][j] = 0;
				} else {
					char_flags[i][j] = 2;
				}
			}
		}
	}
}

function compute_obviates() {
	var i;
	var j;
	var k;
	var match_everything;

	if (binary) {
		// use optimized version instead
		compute_obviates_binary();
		return;
	}

	for (i = first_row; i < chars.length; i++) {
		if (char_row_state[i] == 0) {
	// really instead of using a private array for the possibilities, we
	// could use a bitmask...but frankly I don't trust javascript binary
	// arithmetic, so use the poss[] array instead
			var poss;
			poss = new Array();
			match_everything = false;
			// first mark all possibilities
			for (j = first_row; j < items.length; j++) {
				if (taxa_flags[j] == 1) {
					if (item_cache[j][i]) {
						poss[item_cache[j][i]] = true;
					} else if (items[j][i] == "?") {
						// wildcard - match everything
						match_everything = true;
						break;
					} else {
						for (k = 0; k < items[j][i].length; k++) {
							poss[parseInt(items[j][i].charAt(k), 36)] = true;
						}
					}
				}
			}

			// now mark remaining unpossibilities
			for (j = first_row; j < char_flags[i].length; j++) {
				if (match_everything || poss[j]) {
					char_flags[i][j] = 0;
				} else {
					char_flags[i][j] = 2;
				}
			}
		}
	}
}

function compute_redundants() { //Function ADDED BY BCO
	var i; // i is index of char
	var j; // j is index of taxon 
	var k; // k is index of char state
	var observed_state_array = new Array();
	var change_to_redundant; // if ==1, then change the char_flag for this row to 3
	var is_unique_item;
	for (i = first_row; i < chars.length; i++) {

		if (char_row_state[i] == 0) { // only care if char still not assigned
			change_to_redundant=1;
			var observed_state_array = new Array();
			for (j = first_row; j < items.length; j++) {
				if (taxa_flags[j]==1) { // only look at taxa still displayed
					if (items[j][i] == "?") {
						//Do nothing: redundant change is indicated
					}
					else if (item_cache[j][i]) {
							change_to_redundant=0;
					} else {
						if (observed_state_array.length == 0) {
							for (k = 0; k < items[j][i].length; k++) {
								observed_state_array[k]=items[j][i].charAt(k);
							}
						}
						else if (observed_state_array.length != items[j][i].length) {
							change_to_redundant=0;
						}
						else {
							for (k = 0; k < items[j][i].length; k++) {
								if (observed_state_array[k] != items[j][i].charAt(k)) { // Assumes that states are written in same order in file
									change_to_redundant=0;	
								}
							}
						}
					}
				}
			}
			if (change_to_redundant == 1) {
				for (k = first_row; k < char_flags[i].length; k++) {
					char_flags[i][k]=3;
				}
			}
		}
	}
}


var dbg_elem;
function dbg_out(s) {
	if (!dbg_elem) {
		dbg_elem = get_elem_by_tag_id("div","dbg");
	}
	dbg_elem.innerHTML += "<p>"+s+"</p>\n";
}
function dbg_reset() {
	if (!dbg_elem) {
		dbg_elem = get_elem_by_tag_id("div","dbg");
	}
	dbg_elem.innerHTML = "";
}

var last_timeout = 0;
function timeout(s) {
return;
	var t = (new Date()).getTime();
	dbg_out(""+s+":"+(t-last_timeout)+";\n");
	last_timeout = t;
}

function update() {
	timeout("upd1");
	compute_taxa();
	timeout("upd2");
	compute_obviates();
	timeout("upd3"); //ADDED BY BCO
	compute_redundants(); //ADDED BY BCO
	timeout("upd4");
	update_chars();
	timeout("upd4");
	update_taxa();
	timeout("upd6");
}

function do_reset() {
	init_char_flags();
	update();
}

function cache_items() {
	var i;
	var j;

	for (i = first_row; i < items.length; i++) {
		item_cache[i] = new Array();
		for (j = first_row; j < items[i].length; j++) {
			var x = items[i][j];
			if (x != "?" && x.length == 1) {
				item_cache[i][j] = parseInt(x,36);
			}
		}
	}
}

// initialize the char_headers and char_titles arrays
function setup_char_headers() {
	var i;
	var last_i;
	for (i = 0; i < chars.length; i++) {
		var s = chars[i][0];
		var x = s.indexOf("|");
		if (x == -1) {
			// no header
			char_headers[i] = "";
			char_titles[i] = s;
		} else {
			any_char_headers = true;
			char_headers[i] = s.substr(0,x);
			char_titles[i] = s.substr(x+1);
		}
	}
	last_i = 0;
	for (i = 0; i < chars.length; i++) {
		if (char_headers[i] == char_headers[last_i]) {
			char_header_run[last_i] = (i+1)-last_i;
		} else {
			last_i = i;
			char_header_run[i] = 1;
		}
	}
}

function gotouse() {
	window.location = "use.html";
}


function main() {
	cache_items();

	if (binary) {
		// binary is exclusive-only
		exclusive_mode = true;
	}

	setup_char_headers();

	// output the button bar along the top
	document.write("<form onSubmit=\"return false;\">\n");
	document.write("<table width=100%><tr>\n");
	document.write("<td width=10%><input type=\"submit\" value=\"RESET\" onClick=\"do_reset();\"></td>\n");
	document.write("<td align=right width=100%><input type=\"submit\" value=\"How to use SAIKS\" onClick=\"gotouse();\"></td>\n");
	document.write("</table></form><br>\n");
	document.write("</form>\n");

	document.write("<table width=100%><tr><td width=70% valign=top align=center>\n");
	chars_table();
	document.write("</td><td width=30% valign=top align=center>\n");
	taxa_table();
	document.write("</td></tr></table>\n");

	init_char_flags();
	update();
}