motif_types = ['Yeast','JASPAR:Human','JASPAR:All'];

motif_list = [];
motif_list['Yeast'] = [
'ABF1','ACE2','ADR1','AFT2','ARR1','ASH1','AZF1','BAS1','CAD1','CBF1','CIN5','DAL80',
'DAL81','DAL82','DIG1','FHL1','FKH1','FKH2','GAL4','GAL80','GAT1','GCN4','GCR1','GLN3',
'GZF3','HAC1','HAP1','HAP2','HAP3','HAP4','HAP5','HSF1','INO2','INO4','LEU3','MAC1',
'MBP1','MCM1','MET31','MET32','MET4','MOT3','MSN2','MSN4','NDD1','NRG1','OPI1','PDR1',
'PDR3','PHD1','PHO2','PHO4','PUT3','RAP1','RCS1','RDS1','REB1','RFX1','RGT1','RIM101',
'RLM1','RLR1','ROX1','RPH1','RPN4','RTG3','SFP1','SIG1','SIP4','SKN7','SKO1','SMP1',
'SNT2','SOK2','SPT2','SPT23','STB1','STB4','STB5','STE12','STP1','SUM1','SUT1','SWI4',
'SWI5','SWI6','TEC1','THI2','TYE7','UGA3','UME1','UME6','XBP1','YAP1','YAP3','YAP5',
'YAP6','YAP7','YDR026c','YHP1','YOX1','ZAP1'
];

motif_list['JASPAR:Human'] = [
'MA0002','MA0003','MA0017','MA0018','MA0024','MA0025','MA0028','MA0030','MA0031','MA0032',
'MA0033','MA0036','MA0037','MA0042','MA0043','MA0048','MA0050','MA0051','MA0052','MA0055',
'MA0056','MA0057','MA0058','MA0059','MA0062','MA0065','MA0066','MA0069','MA0070','MA0071',
'MA0072','MA0073','MA0074','MA0076','MA0077','MA0079','MA0080','MA0081','MA0083','MA0084',
'MA0090','MA0091','MA0092','MA0093','MA0095','MA0101','MA0105','MA0106','MA0107'
];

motif_list['JASPAR:All'] = [
'MA0001','MA0002','MA0003','MA0004','MA0005','MA0006','MA0007','MA0008','MA0009','MA0010',
'MA0011','MA0012','MA0013','MA0014','MA0015','MA0016','MA0017','MA0018','MA0019','MA0020',
'MA0021','MA0022','MA0023','MA0024','MA0025','MA0026','MA0027','MA0028','MA0029','MA0030',
'MA0031','MA0032','MA0033','MA0034','MA0035','MA0036','MA0037','MA0038','MA0039','MA0040',
'MA0041','MA0042','MA0043','MA0044','MA0045','MA0046','MA0047','MA0048','MA0049','MA0050',
'MA0051','MA0052','MA0053','MA0054','MA0055','MA0056','MA0057','MA0058','MA0059','MA0061',
'MA0062','MA0063','MA0064','MA0065','MA0066','MA0067','MA0068','MA0069','MA0070','MA0071',
'MA0072','MA0073','MA0074','MA0075','MA0076','MA0077','MA0078','MA0079','MA0080','MA0081',
'MA0082','MA0083','MA0084','MA0085','MA0086','MA0087','MA0088','MA0089','MA0090','MA0091',
'MA0092','MA0093','MA0094','MA0095','MA0096','MA0097','MA0098','MA0099','MA0100','MA0101',
'MA0103','MA0104','MA0105','MA0106','MA0107','MA0108'
];


var seq = '>SMP1_V_433953_434536_1_[367]\r\n';
seq += 'AATAGATTCACGTCCTAAATCAAAGTTTAAAAAGGAAAATACTTATTAACAAGAAGAGTAGTAGAAGAAAAATACAAGAAACATAAACGTAGAAAACTTTTAGTCAATTCTTTAAGCGAAGAATACGAAAGAAACATCAAGAAAACAAAGGAAGATGCAATCATCACTCGTCATATACACAAATAATTCCCTTTAGTGCAACAAACCGCGAAAAAGCATAAGAAACATAAAAAAAATATAAAAAAAAGGAGATAATAATAAGATGTGAAGGATTTGAATTAGTGGAAAAATGATAAGTCTACACTATTATTATTAACGAAATGCAATTTTCCTTTATTTTCTTTTATTACTATTATCATTACTATTATTATTAGTATTATTATTTTTTTACTTATTTTTATATTAAACTATGTTAAATTACTATATTATTATTTTGTCTAACTCTATATTGAGGCTGTCTTTCGTTGCACTGTTAAGAATGGTCACGTCTTCCTTTGGCTTTGAACCCTTTTATAAACAAGTTGGCCAAATCATTTAGTCAATCACGTCAACCTGTCTAAAATAAGACAGGTAAAAAAGAAAA\r\n';
seq += '>SMP1_XII_903402_903722_1_[103]\r\n'
seq += 'AGGAAGCGTACTAGAAAATACCTCTATACTTTCTTTTCCTGTATATAGCATCAATAGTAAAGCCATTATAACGTTACAAAAACCTATTACCCGGAAAATTACTATTTATAGAAGCATTGGACCCATGCACCACATGCATTAGGACCCATTATTTCTTTTTTACAATTTTTCCGTTAATTTTTCACGAATTTTTCACCGTTTATAAACACTCTCGAACTTATAAACAAAGGGATGATAAATAGATTTCGCCAGTTGTTAATACACACAGGGTCAAAGCTCACAGCACTACTACACTCGTTCAACACTCGTTATATATTATC';


function addExample() {
	document.getElementById('seq').value = seq;
}  

function makeListBoxes() {
  //Table 1
  var table1 = document.getElementById('motif_table1');

  var listbox = document.createElement('select');
  listbox.id = 'select1';
  listbox.name = 'select1';
  listbox.onchange = changeListBox1;

  for (var i = 0; i < motif_types.length; i++) {
	var listitem = document.createElement('option');
	listitem.text = motif_types[i];
	listbox.appendChild(listitem);
  }


  
  //var dummy = document.getElementById('select1');
  //dummy.parentNode.appendChild(listbox);
  //dummy.parentNode.removeChild(dummy);
  document.getElementById('pos1').appendChild(listbox);
  //table1.childNodes[1].firstChild.childNodes[2].appendChild(listbox);
  

  //Table 2
  var table2 = document.getElementById('motif_table2');
  
  var listbox = document.createElement('select');
  listbox.id = 'select2';
  listbox.name = 'select2';
  listbox.onchange = changeListBox2;
  
  var listitem = document.createElement('option');
  listitem.text = 'All';
  listbox.appendChild(listitem);
  
  
  for (var i = 0; i < motif_list['Yeast'].length; i++) {
	var listitem = document.createElement('option');
	listitem.text = motif_list['Yeast'][i];
	listbox.appendChild(listitem);
  }

  document.getElementById('pos2').appendChild(listbox);
  //table2.childNodes[1].firstChild.childNodes[2].appendChild(listbox);
}


function changeListBox1() {
  var motif_type = document.getElementById('select1').value;

  var link_posn = document.getElementById('link_posn');

  try {
	link_posn.removeChild(link_posn.childNodes[0]);
	//link_posn.removeChild(link_posn.childNodes[1]);
	//link_posn.parentNode.removeChild(link_posn);
  }
  catch (e) {
	;//alert(e);
  }


  var elem = document.getElementById('select2');
  elem.parentNode.removeChild(elem);

  //Table 2
  var table2 = document.getElementById('motif_table2');

  var listbox = document.createElement('select');
  listbox.id = 'select2';
  listbox.name = 'select2';
  listbox.onchange = changeListBox2;

  var listitem = document.createElement('option');
  listitem.text = 'All';
  listbox.appendChild(listitem);


  for (var i = 0; i < motif_list[motif_type].length; i++) {
	var listitem = document.createElement('option');
	listitem.text = motif_list[motif_type][i];
	listbox.appendChild(listitem);
  }
  


  document.getElementById('pos2').appendChild(listbox);
  //table2.childNodes[1].childNodes[0].childNodes[1].appendChild(listbox);

}

function changeListBox2() {
  var motif_type = document.getElementById('select1').value;

  var motif = document.getElementById('select2').value;

  var link_posn = document.getElementById('link_posn');


  try {
	link_posn.removeChild(link_posn.childNodes[0]);
	//link_posn.removeChild(link_posn.childNodes[1]);
	//link_posn.parentNode.removeChild(link_posn);
  }
  catch (e) {
	;//alert(e);
  }

  if (motif == 'All') {
	return;
  }

  //var link = document.getElementById('link');
  //link.parentNode.removeChild(link);

  var lnk = document.createElement('div');
  
  var link = document.createElement('a');
  link.id = 'link';


  if (motif_type.substring(0,6) == 'JASPAR') {
	link.href = 'http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl?ID='+motif+'&rm=present';
  }
  else if (motif_type.substring(0,5) == 'Yeast') {
	link.href = 'http://jura.wi.mit.edu/fraenkel/download/release_v24/final_set/Final_Motifs/'+motif+'_data/'
  }


  link.innerHTML = motif;

  lnk.appendChild(link);

  document.getElementById('link_posn').appendChild(lnk);
}