function checkSequence() {
  var newWindow = document.getElementById('neww');
  var sequence = document.getElementById('sequence');
  var sequenceFile= document.getElementById('sequenceuserfile');
  var searchType = document.getElementById('searchtype');
  if(newWindow.checked)
  {
    document.getElementById('sform').target='_blank';
  }
  else
  {
    document.getElementById('sform').target='_self';
  }
  var legalCharacters = 0;
  var start = 0;
  if(sequence.value.charCodeAt(0) == 62) {
    start = sequence.value.indexOf("\n");
    if(start == -1)
      start = sequence.value.length;
    start++;
  }
  for (var i=start;i<sequence.value.length;i++)
  {
    if((sequence.value.charCodeAt(i) > 64 && sequence.value.charCodeAt(i) < 91)
       || (sequence.value.charCodeAt(i) > 96 && sequence.value.charCodeAt(i) < 123))
      legalCharacters++; 
  }
  if ((legalCharacters < 5) && (searchType.value == 'NT') && sequenceFile.value=="")
    {	
      alert('Translated queries needs at least 5 nucleotides');
      return false;
    }
  if ((legalCharacters < 1) && sequenceFile.value == "")
  {
    alert("Please fill in a legal query sequence");
    return false;
  }
 
}

function expectFrom(from) 
{
  var expectTo = document.getElementById('expectto');
  var index = expectTo.selectedIndex;
  for(i=0;i<expectTo.options.length;i++) 
  {
    if(expectTo.options[i].value>=from.value) 
    {
      expectTo.options[i].disabled=false;
    }
    else
    {
      expectTo.options[i].disabled=true;
    }
  }
  expectTo.selectedIndex=index;
}

function expectTo(to) 
{
  var expectFrom = document.getElementById('expectfrom');
  var index = expectFrom.selectedIndex;
  for(i=0;i<expectFrom.options.length;i++) 
  {
    if(expectFrom.options[i].value<=to.value) 
    {
      expectFrom.options[i].disabled=false;
    }
    else
    {
      expectFrom.options[i].disabled=true;
    }
  }
  expectFrom.selectedIndex=index;
}

function databaseOptions(searchType) 
{
  var databaseType = searchType.value;
  if (databaseType=='ND') 
  {
    searchType=1;
    document.getElementById('amino1').style.display="none";
    document.getElementById('amino2').style.display="none";
    document.getElementById('nucl1').style.display="block";
    document.getElementById('nucl2').style.display="block";
    document.getElementById('qstrand1').style.display="block";
    document.getElementById('qstrand2').style.display="block";
  }
  else 
  {
    if(databaseType=='NT') 
    {
      searchType=0;
      document.getElementById('nucl1').style.display="none";
      document.getElementById('nucl2').style.display="none";
      document.getElementById('amino1').style.display="block";
      document.getElementById('amino2').style.display="block";
      document.getElementById('qstrand1').style.display="block";
      document.getElementById('qstrand2').style.display="block";
    } 
    else 
    {
      searchType=0;
      document.getElementById('nucl1').style.display="none";
      document.getElementById('nucl2').style.display="none";
      document.getElementById('amino1').style.display="block";
      document.getElementById('amino2').style.display="block";
      document.getElementById('qstrand1').style.display="none";
      document.getElementById('qstrand2').style.display="none";
    }
  }
  var dblist = document.getElementById('db');
  var index = dblist.selectedIndex;

  for(i=0;i<dblist.options.length;i++)
  {
    if(searchType==1) 
    {	
      if(dblist.options[i].value.charAt(3) == "A")
	dblist.options[i].disabled = true;
    }	
    else
    {
      dblist.options[i].disabled = false;
    }
  }
  if(searchType==1)
  {
    if(dblist.selectedIndex < 5)
    {
      dblist.selectedIndex = 5;
    }
  }
}

function setRange() 
{
  var expectFrom = document.getElementById('expectfrom');
  var expectTo = document.getElementById('expectto');
  expectFrom.selectedIndex=0;
  expectTo.selectedIndex=5;
}

function noDisplay () 
{
  document.getElementById('newwspan').style.display="inline";
  document.getElementById('nucl1').style.display="none";
  document.getElementById('nucl2').style.display="none";
  document.getElementById('qstrand1').style.display="none";
  document.getElementById('qstrand2').style.display="none";
  return true;
}