// validate that form entries are filled in
var html_root = "/genome_browser";
function ValidateForm() {
//alert (typeof(document.genomeform.bacteriagenome.options[document.genomeform.bacteriagenome.selectedIndex]));
//alert (document.genomeform.bacteriagenome.options[document.genomeform.bacteriagenome.selectedIndex].value);
//alert (document.genomeform.virusgenome.selectedIndex.value);
//alert (document.genomeform.feature_list.value);

if ((document.genomeform.bacteriagenome.value == ""  &&  document.genomeform.virusgenome.value == "")){
	alert ("Please select a genome.");
	return false;
}
else if (document.genomeform.bacteriagenome.value != ""  &&  document.genomeform.virusgenome.value != ""){
	alert ("Please press 'Start Over' and select just one genome.");
	return false;
}
else if (document.genomeform.keywords.value == ""){
	alert ("Please enter at least one keyword.");
	return false;
}
else if ((document.genomeform.feature_list.value == "") || (document.genomeform.feature_list.value ==null) || (document.genomeform.feature_list.value == "Pick a Feature")){
	alert ("Please select a feature to search.");
	return false;
}
	
else {
	var source= html_root + "/images/clock.gif";
	parent.document.clock.src=source;
	return true;}
}
function swapOptions(filename, genome_type)
{
    var xml_file= "";
    if (genome_type == "virus"){
        xml_file = html_root + "/viral_genome_fields.xml"
    }
    else if (genome_type == "bacteria"){
        xml_file = html_root + "/bacterial_genome_fields.xml"
    }
    var field_array = new Array();
    $.ajax({
          type: "GET",
          url: xml_file,
          dataType: "xml",
          success: function(xml) { 
              var find_string = "genome[name='" + filename + "']";
              var genome = $(xml).find(find_string);
              $(genome).find("field").each(function(){
                 field_array.push($(this).text());
              });
              setOptionText(document.genomeform.feature_list, field_array);
          }
    });
	
}

function setOptionText (the_select, the_array)

{

	//remove old options
	the_select.options.length = 0;

	//add new options
	for (loop=0; loop < the_array.length; loop++){
		the_select.options[the_select.options.length] = new Option(the_array[loop], the_array[loop]);
	}
	the_select.options[the_select.options.length] = new Option ('----------','----------');
}
function changeimg (imageSrc){
	parent.document.clock.src=imageSrc;
}
$(document).ready(function(){
    if (document.images) {
        a = new Image()
        a.src = html_root + '/images/clock.gif';
    }
    /* load the bacterial genomes into the form*/
    if ($('#plasmids').is(":checked")){
        $('#bacterial_genomes').load('/cgi-bin/genome_browser/generate_bacterial_select_box_from_xml.cgi?genomes=all');
    }
    else{
        $('#bacterial_genomes').load('/cgi-bin/genome_browser/generate_bacterial_select_box_from_xml.cgi?genomes=partial');
    }
    
    /* load the virus genomes into the form*/
    $('#viral_genomes').load('/cgi-bin/genome_browser/generate_viral_select_box_from_xml.cgi');
    

    /* function to allow plasmids to be turned on or off*/
    $("#plasmids").click(function(){
        if ($('#plasmids').is(":checked")){
            $('#bacterial_genomes').load('/cgi-bin/genome_browser/generate_bacterial_select_box_from_xml.cgi?genomes=all');
        }
        else{
            $('#bacterial_genomes').load('/cgi-bin/genome_browser/generate_bacterial_select_box_from_xml.cgi?genomes=partial');
        }
        });
 });