function ChangeSelection(value, type) {
	var species = ["hs", "mm", "dm", "ce", "at", "os", "sp"];
	var id;
	for (var i = 0; i < species.length; i++) {
		var query;
		if (type == 1) {
			if (species[i] != "sp") {
				query = ["transcript", "gene_symbol", "gene_ID"];
			} else {
				query = ["swissprot", "gene_symbol_sp"];
			}
		} else if (type == 2) {
			query = ["gene_symbol", "gene_ID", "transcript"];
		}
		for (var j = 0; j < query.length; j++) {
			if (species[i] != "sp") {
				id = query[j] + "_" + species[i];
			} else {
				id = query[j];
			}
			if (document.getElementById(id) != null) {
				document.getElementById(id).style.display = "none";
			}
		}
	}
	if (type == 1) {
		if (value != "sp") {
			document.getElementById('q_search').id_type.options[0] = new Option("Transcript ID", "transcript");
			document.getElementById('q_search').id_type.options[1] = new Option("Gene Symbol", "gene_symbol");
			document.getElementById('q_search').id_type.options[2] = new Option("Entrez Gene ID", "gene_ID");
			id = "transcript_" + value;
		} else {
			document.getElementById('q_search').id_type.options[0] = new Option("Swiss-Prot ID", "swissprot");
			document.getElementById('q_search').id_type.options[1] = new Option("Gene Symbol", "gene_symbol");
			document.getElementById('q_search').id_type.options[2] = null;
			id = "swissprot";
		}
	} else if (type == 2) {
		document.getElementById('q_search').id_type.options[0] = new Option("Gene Symbol", "gene_symbol");
		document.getElementById('q_search').id_type.options[1] = new Option("Entrez Gene ID", "gene_ID");
		document.getElementById('q_search').id_type.options[2] = new Option("Transcript ID", "transcript");
		id = "gene_symbol_" + value;
	}
	document.getElementById(id).style.display = "inline";
}

function ChangeExample(value) {
	var species = ["hs", "mm", "dm", "ce", "at", "os", "sp"];
	var id;
	for (var i = 0; i < species.length; i++) {
		var query;
		if (species[i] != "sp") {
			query = ["transcript", "gene_symbol", "gene_ID"];
		} else {
			query = ["swissprot", "gene_symbol_sp"];
		}
		for (var j = 0; j < query.length; j++) {
			if (species[i] != "sp") {
				id = query[j] + "_" + species[i];
			} else {
				id = query[j];
			}
			if (document.getElementById(id) != null) {
				document.getElementById(id).style.display = "none";
			}
		}
	}
	if (value != "swissprot") {
		id = value + "_" + document.getElementById('q_search').sp.value;
	} else {
		id = value;
	}
	document.getElementById(id).style.display = "inline";
}

function ChangeRNASeqImage(sp, contig_ID, rev_f, max, min, value) {
	source = "./obi_rnaseq.php?sp=" + sp + "&contig_ID=" + contig_ID + "&rev=" + rev_f + "&max=" + max + "&min=" + min + "&source=" + value;

	document.getElementById('RNASeq_Image').src = source;
}

function ShowUninformativeTranscripts() {
	document.getElementById('uninformative').style.display = 'table-row-group';
	document.getElementById('uninformative_legend').style.display = 'inline';
	document.getElementById('hide_uninformative_button').style.display = 'table-row';
	document.getElementById('show_uninformative_button').style.display = 'none';
}

function HideUninformativeTranscripts() {
	document.getElementById('uninformative').style.display = 'none';
	document.getElementById('uninformative_legend').style.display = 'none';
	document.getElementById('hide_uninformative_button').style.display = 'none';
	document.getElementById('show_uninformative_button').style.display = 'table-row';
}

function ChangeDomainDefinition(value) {
	var ids = Array("SSF", "PF", "G3D", "TM");
	for (var i = 0; i < ids.length; i++) {
		document.getElementById(ids[i]).style.display = "none";
	}
	document.getElementById(value).style.display = "block";
}

function ShowAssignResult(value) {
	var ids = Array("top_hit", "hit_100", "hit_90", "hit_80", "hit_70", "hit_60", "hit_50", "hit_40", "hit_30", "hit_20", "hit_10");
	if (value == ids[0]) {
		for (var i = 1; i < ids.length; i++) {
			var elem = document.getElementById(ids[i]);
			if (elem != null) {
				elem.style.display = "none";
			}
		}
	} else {
		var flag = 0;
		for (var i = 1; i < ids.length; i++) {
			var elem = document.getElementById(ids[i]);
			if (elem != null) {
				if (flag == 1) {
					elem.style.display = "none";
				} else {
					elem.style.display = "table-row-group";
				}
			}
			if (ids[i].substring(4) == value) {
				flag = 1;
			}
		}
	}
}

function ToggleObi(tag) {
	if (document.getElementById("check_" + tag).checked == true) {
		document.getElementById(tag).style.display = '';
	} else {
		document.getElementById(tag).style.display = 'none';
	}
}

function LaunchJmol(f) {
	var width = 600;
	var height = 600;
	var X = (window.screen.width-width)/3;
	var Y = (window.screen.height-height)/3;
	var url = "view_3D.php?sp=" + f.sp.value + "&ref_ID=" + f.ref_ID.value + "&var_ID=" + f.var_ID.value + "&PDB_ID=" + f.PDB_ID.value + "&chain=" + f.chain.value + "&PDB_st=" + f.PDB_st.value + "&PDB_ed=" + f.PDB_ed.value + "&PDB_AS_st=" + f.PDB_AS_st.value + "&PDB_AS_ed=" + f.PDB_AS_ed.value;
	if (f.work.value != '') {
		url = url + "&work=" + f.work.value;
	}	
	var option = "toolbar=no,scrollbars=yes,resizable=yes,location=no,directories=no,menubar=no,status=no,width=" + width + ",height=" + height + ",screenX=" + X + ",screenY=" + Y;
	window.open(url, "", option);
}

function jmolCheckbox2(tag, scriptWhenChecked, scriptWhenUnchecked,
                       labelHtml, isChecked, id, title)
{
	_jmolInitCheck();
	if (id == undefined || id == null)
		id = "jmolCheckbox" + _jmol.checkboxCount;
	++_jmol.checkboxCount;
	if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
	    scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
		alert("jmolCheckbox requires two scripts");
		return;
	}
	if (labelHtml == undefined || labelHtml == null) {
		alert("jmolCheckbox requires a label");
		return;
	}
	var indexChecked = _jmolAddScript(scriptWhenChecked);
	var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
	var eospan = "</span>"
	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
	    "' onClick='_jmolCbClick(this," +
	    indexChecked + "," + indexUnchecked + _jmol.targetText +
	    "); ShowAnnotation(\"" + tag + "\",\"" + id + "\");' onMouseover='_jmolCbOver(this," + indexChecked + "," +
	    indexUnchecked +
	    ");return true' onMouseout='_jmolMouseOut()' " +
	    (isChecked ? "checked " : "") + _jmol.checkboxCssText + "/>";
	if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
		t += eospan
		eospan = "";
	}
	t += labelHtml +eospan;
	if (_jmol.debugAlert)
		alert(t);
	return _jmolDocumentWrite(t);
}

function ChangeTranscripts(value) {
	var elem = document.getElementById('generate');
	for (var i = 0; i < elem.childNodes.length; i++) {
		if (elem.childNodes[i].nodeName == "DIV") {
			elem.childNodes[i].style.display = "none";
		}
	}
	document.getElementById(value).style.display = "block";
/*	document.getElementById('transcript_id').value = value; */
}

function PasteSeq() { 
	var elem = document.getElementById('gen_seq');
	var textarea = document.getElementById('sequence');
	textarea.value = elem.firstChild.nodeValue;
}

function ShowRNASeq() {
	document.getElementById('expression').style.display = "table-row";
	document.getElementById('show_RNASeq').style.display = "none";
	document.getElementById('hide_RNASeq').style.display = "inline";
}

function HideRNASeq() {
	document.getElementById('expression').style.display = "none";
	document.getElementById('show_RNASeq').style.display = "inline";
	document.getElementById('hide_RNASeq').style.display = "none";
}