var TimerID; 
var FastTimerID; 
var HighlightStart = "<SPAN class=RealTimePCRHighlight>";
var HighlightEnd = "</SPAN>";
var isIE = document.all?true:false;
var isNS = document.layers?true:false;
//var LocktbSelectionStart = false;
var oCaretPosHold = 0;
var oCaretPosHoldEnd = -1;
  
//For Input
function InputOnload()
{
    var AccessionUpload = "AccessionFileUp";
    var SequenceFileUp = "SequenceFileUp";
    var btnViewAccessionList = "btnViewAccessionList";
    var btnViewSequenceList = "btnViewSequenceList";
    var btnSavedRequests = "btnSavedRequests";
    var btnRefSeqLookup = "btnRefSeqLookup";

    $get(AccessionUpload).style.display = 'none'; 
    $get(SequenceFileUp).style.display = 'none';
    $get(btnViewAccessionList).style.display = 'none';
    $get(btnViewSequenceList).style.display = 'none'; 
    $get(btnSavedRequests).style.display = 'block';  
    $get(btnRefSeqLookup).style.display = 'block';  

}

function UploadAccessionFile()
{
    var AccessionUpload = "AccessionFileUp";    
    var AccessionHeader = "AccessionHeader";
    var tbAccessionIDs = "tbAccessionIDs";
    var btnUploadAccessionList = "btnUploadAccessionList";
    var SequenceHeader = "SequenceHeader";
    var tdOr = "tdOr";
    var tbSequences = "tbSequences";
    var btnUploadSequenceList = "btnUploadSequenceList";
    var btnViewAccessionList = "btnViewAccessionList";
    var btnClearEntry = "btnClearEntry";    
    var btnSavedRequests = "btnSavedRequests";
    var btnRefSeqLookup = "btnRefSeqLookup";
    
    $get(AccessionUpload).style.display = 'block';
    $get(tbAccessionIDs).style.display = 'none';
    $get(btnUploadAccessionList).style.display = 'none';
    $get(SequenceHeader).style.display = 'none';
    $get(tdOr).style.display = 'none';
    $get(tbSequences).style.display = 'none';
    $get(btnUploadSequenceList).style.display = 'none';
    $get(btnViewAccessionList).style.display = 'block';
    $get(btnClearEntry).style.display = 'none';  
    $get(btnSavedRequests).style.display = 'none';  
    $get(btnRefSeqLookup).style.display = 'none';  
    $get("tblAdditional").style.display = 'none';  
    $get(AccessionHeader).innerHTML = 'Enter the path for the text file of accession numbers';
 }
 
 function ViewAccessionList()
 {
    var AccessionUpload = "AccessionFileUp";    
    var AccessionHeader = "AccessionHeader";
    var tbAccessionIDs = "tbAccessionIDs";
    var btnUploadAccessionList = "btnUploadAccessionList";
    var SequenceHeader = "SequenceHeader";
    var tdOr = "tdOr";    
    var tbSequences = "tbSequences";
    var btnUploadSequenceList = "btnUploadSequenceList";
    var btnViewAccessionList = "btnViewAccessionList";
    var btnClearEntry = "btnClearEntry";    
    var btnSavedRequests = "btnSavedRequests";
    var btnRefSeqLookup = "btnRefSeqLookup";
    
    $get("trAccessionFileUp").style.display = 'block';
    $get(AccessionUpload).style.display = 'none';
    $get(tbAccessionIDs).style.display = 'block';
    $get(btnUploadAccessionList).style.display = 'block';
    $get(SequenceHeader).style.display = 'block';
    $get(tdOr).style.display = 'block';
    $get(tbSequences).style.display = 'block';
    $get(btnUploadSequenceList).style.display = 'block';
    $get(btnViewAccessionList).style.display = 'none';
    $get(btnClearEntry).style.display = 'block';   
    $get(btnSavedRequests).style.display = 'none';  
    $get(btnRefSeqLookup).style.display = 'none'; 
    $get("tblAdditional").style.display = 'block';   
    $get(AccessionHeader).innerHTML = 'Enter gene sequence accession numbers of interest (comma separated)';

 }

function UploadSequenceFile()
{
    var SequenceFileUp = "SequenceFileUp";
    var AccessionHeader = "AccessionHeader";
    var tbAccessionIDs = "tbAccessionIDs";
    var btnUploadAccessionList = "btnUploadAccessionList";
    var SequenceHeader = "SequenceHeader";
    var tdOr = "tdOr";
    var tbSequences = "tbSequences";
    var btnUploadSequenceList = "btnUploadSequenceList";
    var btnViewSequenceList = "btnViewSequenceList";
    var btnClearEntry = "btnClearEntry";
    var btnSavedRequests = "btnSavedRequests";
    var btnRefSeqLookup = "btnRefSeqLookup";
    
    $get(tbAccessionIDs).style.display = 'none';
    $get(btnUploadAccessionList).style.display = 'none';
    $get(SequenceHeader).style.display = 'block';
    $get(tdOr).style.display = 'none';
    $get(tbSequences).style.display = 'none';
    $get(btnUploadSequenceList).style.display = 'none';
    $get(btnViewSequenceList).style.display = 'block';
    $get(AccessionHeader).style.display = 'none';
    $get(btnClearEntry).style.display = 'none';  
    $get(btnSavedRequests).style.display = 'none';  
    $get(btnRefSeqLookup).style.display = 'none';  
    $get("tblAdditional").style.display = 'none';  
    $get(SequenceHeader).innerHTML = 'Enter the path for the text file of FASTA formatted sequences';       
    $get(SequenceFileUp).style.display = 'block'; 
    $get("trAccessionFileUp").style.display = 'none';
}
  
function LinkOnMouseOver(aControl)
{   
    $get(aControl.id).className = 'SciToolError';
}

function LinkOnMouseOut(aControl)
{
    $get(aControl.id).className = 'SciToolHeader';
}

function UpdateRefSeq(aControl, AccessionID)
{
    IsChecked = $get(aControl.id).checked;
    hfAccessionID = $get("hfAccessionID");  
    if(IsChecked)//add accession id
    {
        if(hfAccessionID.value == "")
        {
            hfAccessionID.value = AccessionID;
        }
        else
        {
            hfAccessionID.value = hfAccessionID.value + "," + AccessionID;
        }
    }
    else
    {
        //remove accession id   
        if(hfAccessionID.value == AccessionID)
        {
            hfAccessionID.value = "";
        }
        else
        {
            hfAccessionID.value = replace(hfAccessionID.value, "," + AccessionID, "");
            hfAccessionID.value = replace(hfAccessionID.value, AccessionID + ",", ""); 
        }       
    }    
}

function ViewObj(ObjID, DisplayType)
{
    $get(ObjID).style.display = DisplayType;
}

function ManualSeqEntry(aObject)
{
    $get('trManualEntry').style.display = 'block';
}

function CollapseSort(ObjectID, TargetID)
{
    var theObject = $get(ObjectID);
    var EListID = theObject.id.replace(ObjectID, TargetID);
    $get(EListID).style.display = 'none'; 
    theObject.src = "/Scitools/Images/general/Expand_Off.gif";
    theObject.onclick = function(){ExpandSort(ObjectID, TargetID);}
    theObject.onmouseover = function(){this.src='/Scitools/Images/general/Expand_On.gif'}
    theObject.onmouseout = function(){this.src='/Scitools/Images/general/Expand_Off.gif'}
    theObject.alt = "Click to Expand";
}
function ExpandSort(ObjectID, TargetID)
{
    var theObject = $get(ObjectID);
    var EListID = theObject.id.replace(ObjectID, TargetID)
    $get(EListID).style.display = 'block';  
    theObject.onclick = function(){CollapseSort(ObjectID, TargetID);}
    theObject.src = "/Scitools/Images/general/Collapse_Off.gif";     
    theObject.onmouseover = function(){this.src='/Scitools/Images/general/Collapse_On.gif';}
    theObject.onmouseout = function(){this.src='/Scitools/Images/general/Collapse_Off.gif';}
    theObject.alt = "Click to Collapse";
}

function TranscriptView(aObject, AccessionID, ViewState)
{
    var ParentID = aObject.id.replace("lblTranscript_" + AccessionID, "");
    var aTableCell = $get(ParentID + "td_" + AccessionID);
    
    if(ViewState == 'Hide')
    {
        aObject.innerHTML = 'View Transcript Image';
        aTableCell.style.display = 'none';
        aObject.onclick = function(){TranscriptView(this, AccessionID, 'View');}   
    }
    else
    {
        aObject.innerHTML = 'Hide Transcript Image';
        aTableCell.style.display = '';
        aObject.onclick = function(){TranscriptView(this, AccessionID, 'Hide');}         
    }
}