function CheckAllRecords( form, mark )
{
        var ua = navigator.userAgent.toLowerCase();
        var isIE = (ua.indexOf('msie') != -1);
        var checkedCount = 0;
        var markState = 1;
    for( i = 0; i < form.elements.length; i++ )
    {
        var item = form.elements[ i ];
        if (item.id == 'selectAll') item.checked = mark;        

        if( item.type == "checkbox" && item.id != 'selectAll')
        {
                if (isIE && checkedCount == 100 && mark) 
                {
                        markState = 0;
                }
                if (markState)
        {
            item.checked = mark;
        }
                        checkedCount++;
        }
    }

    recordClick(form, 0);
    if (markState == 0)
    {
        alert('Your browser does not support a choice more than 100 records!');
    }
}


function getCheckedRecordsNum( form )
{
    num = 0;
    for( i = 0; i < form.elements.length; i++ )
    {
        var item = form.elements[ i ];
        if( item.type == "checkbox" && item.checked && item.id != "selectAll")
        {
            num++;
        }
    }

    return num;
}

function preprocessOperation( obj )
{
    var label = M_THIS_OPERATION;

    for( var i = 0; i < operationsNo; i++ )
    {
        if( arrOperations[i].id == obj.name )
        {
            label = "\"" + arrOperations[i].label + "\"";


            if( !isHttpUnit && obj.disabled )
            {
                var msg = M_AT_LEAST_ONE_RECORD;
                if( arrOperations[i].requiredRecordSetSize == 1 )
                    msg = M_EXACTLY_ONE_RECORD;

                alert(msg + " " + label + "!");
            }

            break;
        }
    }

    if( !isHttpUnit && obj.disabled )
        return false;

    return true;
}

function operation( id, requiredRecordSetSize, label)
{
    this.id = id;
    this.requiredRecordSetSize = requiredRecordSetSize;
    this.label = label;
    return this;
}


var operationsNo = 0;
var arrOperations = [];

function recordClick( form, checkID )
{
    var checkedRecordsNum = getCheckedRecordsNum(form);
        var ua = navigator.userAgent.toLowerCase();
        var isIE = (ua.indexOf('msie') != -1);
        if (isIE && checkedRecordsNum > 100 && checkID != 0)
        {
                var check = document.getElementById(checkID);
                check.checked = false;
                alert('Your browser does not support a choice more than 100 records!');
    }

    for( var i = 0; i < operationsNo; i++ )
    {
        //var item = form[arrOperations[i].id];
        var item = document.getElementById(arrOperations[i].id);

        if( item /*&& !arrOperations[i].isAlwaysDisabled*/ )
        {
            if( arrOperations[i].requiredRecordSetSize == 0 ||
                arrOperations[i].requiredRecordSetSize == -1 )
            {
                item.disabled = false;
            }

            else if( arrOperations[i].requiredRecordSetSize == 1 )
            {
                item.disabled = checkedRecordsNum != 1;
            }

            else
            {
                item.disabled = checkedRecordsNum == 0;
            }
        }
    }
        var pf = document.getElementById('pfbutton');
        if(pf)
        {
                pf.disabled = checkedRecordsNum == 0;
        }
}

function submitOperationForm(formId, operId, operName, target)
{
  var form = document.getElementById(formId);
  if (target) {
    form.target = target;
  }
  form['operation'].value = operName;
  form.submit();
}


function callOperationHandler(formId, operId, operName, target)
{
  if (window['operationHandlers']) {
    var operHandler = window['operationHandlers'][operId];
    if (operHandler) {
      operHandler.execute(formId);
    }
  }
}

function confirmDeleteRows()
{
  if (confirm ("Are you sure you want do delete checked rows?"))
  {
     form.submit();
  }
}

function operRemoveRows(form)
{
  if (confirm ("Are you sure you want to remove checked rows?"))
  {
    form['operation'].value = "remove";
    form.action = "result.cgi";
    form.submit();
  }
}

function operYesNo(form, message, actionForm, operation)
{
  if (confirm (message))
  {
    form['operation'].value = operation;
    form.action = actionForm;
    form.submit();
  }
}

function ChangeHitsOnPage(form)
{
    form['operation'].value = 'ChangeHits';
    form.action = "result.cgi";
    form.submit();
}

function goToPage(form)
{
  var txtPage = document.getElementById('page');
  var pageNum = txtPage.value;
  var re = /^[0-9]*$/;
  if (!re.test(pageNum) || parseInt(pageNum)<=0 || pageNum=='' ) return;
  
  form.action = "result.cgi";
  form.submit();
}

var swfMovie;
function findSWF(movieName) {
    if (navigator.appName.indexOf("Microsoft")!= -1) {
          return window[movieName];
    } else {
          return document[movieName];
    }
}
var w1 = null;
function getSelectedAccessions() 
{
    var resultRows = document.getElementsByName("resultRows");
    var acc = '';
    var i;
    for (i = 0; i < resultRows.length; i++) {
        var row = resultRows[i];
        if (row.checked) {            
            acc += id2acc[row.value] + ","
        }
    }
        if(!acc)
        {
            acc = readCookie('globAcc');
        }
		else
		{
			createCookie("globAcc", acc);
		}
	//alert("Sending " + acc + " to Pathfinder");
    swfMovie = findSWF('lzapp');
    swfMovie.sendAccToViewer(acc);
    //eraseCookie('globAcc');
}

function launchSWFViewer(url)
{
  url += escape("&ret=0");
  w1 = window.open(url, 'Workspace');
  //getSelectedAccessions();
}

function addSWFViewer(url)
{
         if (navigator.appName.indexOf("Microsoft")!= -1) {
               if (w1) {
                  getSelectedAccessions();
                  w1.focus();
               } else {
                  launchSWFViewer(url);
               }
         } else {
               if (w1 && !w1.closed) {
                  getSelectedAccessions();
               } else {
                  launchSWFViewer(url);
               }
         }
  //getSelectedAccessions();
}

function visualizeChain( accession, cgi_path, html_path, transpath_path )
{
        acc = accession;
    url = html_path + '/swf/graph.lzx.swf?srv=' + transpath_path + '/bin/graph.cgi&pl=' + transpath_path + '/bin/pathwaylist.cgi&etr=' + cgi_path + '/get.cgi&dstup1=2&dstdown1=2&id=' + acc;
    launchSWFViewer( url );
}

function visualizeSWF( accession, cgi_path, html_path, transpath_path ) {
    acc = accession;
    url = html_path + '/swf/graph.lzx.swf?srv=' + transpath_path + '/bin/graph.cgi&pl=' + transpath_path + '/bin/pathwaylist.cgi&etr=' + cgi_path + '/get.cgi&dstup1=2&dstdown1=2&id=';
        url = cgi_path + '/BKLPathfinder.cgi?viewer=' + escape(url);
        launchSWFViewer( url );
}

/*
Copyright (c) Copyright (c) 2007, Carl S. Yestrau All rights reserved.
Code licensed under the BSD License: http://www.featureblend.com/license.txt
Version: 1.0.2
*/
var FlashDetect = new function(){
        var self = this;
        self.installed = false;
        self.major = -1;
        self.minor = -1;
        self.revision = -1;
        self.revisionStr = "";
        self.activeXVersion = "";
        var activeXDetectRules = [
                {
                        "name":"ShockwaveFlash.ShockwaveFlash.7",
                        "version":function(obj){
                                return getActiveXVersion(obj);
                        }
                },
                {
                        "name":"ShockwaveFlash.ShockwaveFlash.6",
                        "version":function(obj){
                                var version = "6,0,21";
                                try{
                                        obj.AllowScriptAccess = "always";
                                        version = getActiveXVersion(obj);
                                }catch(err){}
                                return version;
                        }
                },
                {
                        "name":"ShockwaveFlash.ShockwaveFlash",
                        "version":function(obj){
                                return getActiveXVersion(obj);
                        }
                }
        ];
        var getActiveXVersion = function(activeXObj){
                var version = -1;
                try{
                        version = activeXObj.GetVariable("$version");
                }catch(err){}
                return version;
        };
        var getActiveXObject = function(name){
                var obj = -1;
                try{
                        obj = new ActiveXObject(name);
                }catch(err){}
                return obj;
        };
        var parseActiveXVersion = function(str){
                var versionArray = str.split(",");//replace with regex
                return {
                        "major":parseInt(versionArray[0].split(" ")[1], 10),
                        "minor":parseInt(versionArray[1], 10),
                        "revision":parseInt(versionArray[2], 10),
                        "revisionStr":versionArray[2]
                };
        };
        var parseRevisionStrToInt = function(str){
                return parseInt(str.replace(/[a-zA-Z]/g, ""), 10) || self.revision;
        };
        self.majorAtLeast = function(version){
                return self.major >= version;
        };
        self.FlashDetect = function(){
                if(navigator.plugins && navigator.plugins.length>0){
                        var type = 'application/x-shockwave-flash';
                        var mimeTypes = navigator.mimeTypes;
                        if(mimeTypes && mimeTypes[type] && mimeTypes[type].enabledPlugin && mimeTypes[type].enabledPlugin.description){
                                var desc = mimeTypes[type].enabledPlugin.description;
                                var descParts = desc.split(' ');//replace with regex
                                var majorMinor = descParts[2].split('.');
                                self.major = parseInt(majorMinor[0], 10);
                                self.minor = parseInt(majorMinor[1], 10); 
                                self.revisionStr = descParts[3];
                                self.revision = parseRevisionStrToInt(self.revisionStr);
                                self.installed = true;
                        }
                }else if(navigator.appVersion.indexOf("Mac")==-1 && window.execScript){
                        var version = -1;
                        for(var i=0; i<activeXDetectRules.length && version==-1; i++){
                                var obj = getActiveXObject(activeXDetectRules[i].name);
                                if(typeof obj == "object"){
                                        self.installed = true;
                                        version = activeXDetectRules[i].version(obj);
                                        if(version!=-1){
                                                var versionObj = parseActiveXVersion(version);
                                                self.major = versionObj.major;
                                                self.minor = versionObj.minor; 
                                                self.revision = versionObj.revision;
                                                self.revisionStr = versionObj.revisionStr;
                                                self.activeXVersion = version;
                                        }
                                }
                        }
                }
        }();
};
FlashDetect.release = "1.0.2";

function readCookie(name) {
        var nameEQ = name + "=";
        var ca = document.cookie.split(';');
        for(var i=0;i < ca.length;i++) {
                var c = ca[i];
                while (c.charAt(0)==' ') c = c.substring(1,c.length);
                if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length,c.length);
        }
        return null;
}

function BKLPathfinder(gifurl, accession, cgi_path, html_path, transpath_path, isSearch)
{
        if(accession)
        {
                accession = accession + ',';
        }
        // Flash not detected, redirect to GIF visualization
        if(!FlashDetect.installed)
        {
                // If it is a call from a search result
                if(isSearch)
                {
                        submitOperationForm('rForm', 'op_2', 'Visualize GIF', '_blank');
                }
                else
                {
                        window.open(gifurl);
                }
        }
        // Flash deteced, open / add-to viewer
        else
        {
                // Viewer window not open
                if(!readCookie('viewerOpen'))
                {
                        visualizeSWF(accession, cgi_path, html_path, transpath_path);
                        if(accession)
                        {
                                createCookie('globAcc',accession);
                        }
                        // If it is a search results page, then we need to fetch the checked records
                        if(isSearch)
                        {
                                // alert("Search result");
                                getSelectedAccessions();
                        }
                }
                // Viewer window already open
                else
                {
                        // Search result - fetch checked rows
                        if(isSearch)
                        {
                                getSelectedAccessions();
                        }
                        // Not a search result - send accession to viewer
                        else
                        {
                                swfMovie = findSWF('lzapp');
                                swfMovie.sendAccToViewer(accession);
                        }
                }
        }
}

function createCookie(name,value,days) {
        if (days) {
                var date = new Date();
                date.setTime(date.getTime()+(days*24*60*60*1000));
                var expires = "; expires="+date.toGMTString();
        }
        else var expires = "";
        document.cookie = name+"="+value+expires+"; path=/";
}

function eraseCookie(name) {
        createCookie(name,"",-1);
}