--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/formatRes.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,1542 @@
+// JScript source code
+/*************************new code begin *******************************************************/
+
+function getHiddenFieldVal(elemName) {
+    var val;
+    var elem = document.getElementsByName(elemName);
+    if (elem) {
+        val = (elem.length > 1) ? elem[0].value : elem.value;
+    }
+    return val;
+}
+
+function getHiddenFieldParamString(elemName) {
+    var ret = "";
+    var val = getHiddenFieldVal(elemName);
+    if (val) {
+        ret = "&" + elemName + "=" + val;
+    }
+    return ret;
+}
+
+function elementInViewport(el) {
+    if (!el) return;
+    var rect = el.getBoundingClientRect();
+
+    var myWidth = 0, myHeight = 0;
+    if (typeof (window.innerWidth) == 'number') {
+        //Non-IE
+        myWidth = window.innerWidth;
+        myHeight = window.innerHeight;
+    } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) {
+        //IE 6+ in 'standards compliant mode'
+        myWidth = document.documentElement.clientWidth;
+        myHeight = document.documentElement.clientHeight;
+    } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) {
+        //IE 4 compatible
+        myWidth = document.body.clientWidth;
+        myHeight = document.body.clientHeight;
+    }
+    //window.alert('Width = ' + myWidth);
+    //window.alert('Height = ' + myHeight);
+
+
+    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth)
+    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth)
+    return (rect.top >= 0 && rect.bottom <= myHeight);
+}
+
+function DisplayAlignFromDescription(elem) {
+    var alignView = $("FormatForm").ALIGNMENT_VIEW;
+    if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") {
+        DisplayDynamicAlign(elem);
+    }
+    else {
+        location.href = "#" + elem.getAttribute("seqID");        
+    }
+}	
+
+//<a class="deflnDesc" hsp=<hsp_num> ind="<index>" gi="<gi>" id="deflnDesc_gi" href="#AlnHdrgi">desc</a>
+//<div class="alnHdr" gi="<gi>" id="alnHdr_<index>">
+function DisplayDynamicAlign(elem) {
+    var currGi = elem.getAttribute("gi");
+    var currInd = elem.getAttribute("ind");
+    var stat = elem.getAttribute("stat");
+    if (!currInd || !currGi) return;
+    
+    if (!stat || stat == "") {
+        //Get 4(5) aligns before currInd and 4(5) aligns after
+        ReadCurrentSeqAligns(currInd, 5);        
+    }
+    else if (stat == "read") {
+        var indexes = getCurrIndexRange(currInd);
+        if (indexes) {
+            var msgID = "alnShow_" + indexes[0];
+            location.href = "#" + msgID;
+        }
+    }
+    else {
+        //error status handling        
+    }
+}
+
+
+function goToNextAlign(dtrID, next) {
+    var currInd = parseInt($(dtrID).getAttribute("ind"));
+    var rid = $("Rid").value;
+    nextInd = (next) ? currInd + 1 : currInd - 1;
+
+    if ($("deflnDesc_" + nextInd)) {
+        currGi = $("deflnDesc_" + nextInd).getAttribute("seqID");
+        scrollToGI = currGi;
+        if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") {
+
+            if (!next) {
+                ReadPrevSeqAligns(currInd, 5, scrollToGI);
+            }
+            else {
+                //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!!
+                ReadNextSeqAligns(currInd, 5, scrollToGI);
+            }
+
+        }
+        else {
+            location.href = "#" + scrollToGI;
+        }
+    }
+}
+
+function goToDefLine(dtrID) {
+    if ($("psiInp")) {
+        var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table
+        togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1";
+        jQuery($(togglerID)).ncbitoggler("open");
+    }
+}
+
+/*
+readAln.rid = rid;
+readAln.startIndex = parseInt(currInd);
+readAln.numSeq = parseInt(maxNumAligns);
+
+readAln.insertAfterID = insertAfterID;
+readAln.seqList = giList;
+readAln.scrollToSeqID = scrollToGI;
+*/
+function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) {
+    var lastDispIdx = 0;
+    var rid = $("Rid").value;
+
+    var readAln = new Object();
+    readAln.seqList = ""; //giList
+    readAln.rid = rid;
+
+    currInd = parseInt(currInd);
+
+    if (currInd != 0 && $("deflnDesc_" + currInd)) {
+        var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_<ind>
+        //alert(par.id);
+        if (par) par = utils.getParent(par); //"alnShow_<ind>
+        //alert(par.id);
+        if (par) readAln.insertAfterID = par.id;
+    }
+    else {
+        readAln.insertAfterID = "alnStart";
+    }
+
+
+
+    readAln.startIndex = currInd + 1;
+    readAln.numSeq = maxNumAligns;
+        
+    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next");
+        
+    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : "";
+    readAln.hspSort = 0;
+    ReadSeqAlignByIndex(readAln);
+}
+
+function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) {
+    var lastDispIdx = 0;
+    var rid = $("Rid").value;
+
+    var readAln = new Object();
+    readAln.seqList = ""; //giList
+    readAln.rid = rid;
+
+    currInd = parseInt(currInd);
+
+
+    //sets readAln.insertAfterID and returns lastDispIdx;
+    //Find the index of the previously displayed alignment
+    lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
+
+    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
+    readAln.numSeq = currInd - readAln.startIndex;    //stopIndex = currInd
+    
+    checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev");
+        
+    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID");
+    readAln.hspSort = 0;
+    ReadSeqAlignByIndex(readAln);
+}
+
+//When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd
+function ReadCurrentSeqAligns(currInd, maxNumAligns) {
+    var rid = $("Rid").value;
+    var readAln = new Object();
+    readAln.seqList = ""; //giList
+    readAln.rid = rid;
+
+    currInd = parseInt(currInd);
+
+
+    //sets readAln.insertAfterID and returns lastDispIdx;
+    //Find the index of the previously displayed alignment
+    var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
+
+    //lastDispIdx = parseInt(lastDispIdx);
+    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
+    readAln.numSeq = parseInt(maxNumAligns * 2);
+        
+    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr");
+        
+    readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID");
+    readAln.hspSort = 0;
+    ReadSeqAlignByIndex(readAln);
+    g_DisableAutoCheck = true;
+    location.href = "#alnShow_" + readAln.startIndex;
+}
+
+
+
+
+function setupDynHSPParams(readAln) 
+{
+    var currSeqInd = readAln.startIndex;
+    hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp"));
+    alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len"));
+    var maxDispLen = parseInt($("maxDispAlnLen").value);//20000
+    var minDispLen = parseInt($("minDispAlnLen").value);//2000
+    if (alnLen > maxDispLen) {
+        var lenPerMatch = alnLen / hspNum;        
+        readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch);
+        readAln.AlignDbPageNum = 0;
+        $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize);
+    }
+}
+
+
+
+function getCurrSeqsAlnLen(currSeqInd) 
+{
+    var alnLen = 0;
+    if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) {
+        alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len");            
+    }
+    alnLen = (alnLen) ? parseInt(alnLen) : 0;
+    return alnLen;
+}
+
+function checkTotalAlignLen(startIndex,stopIndex)
+{
+    var dispAlnLen = 0;
+    var maxDispLen = parseInt($("maxDispAlnLen").value);    
+    for (var i = startIndex; i <= stopIndex; i++) {
+        alnLen = getCurrSeqsAlnLen(i);
+        if (alnLen == 0) break;
+        dispAlnLen += alnLen;        
+    }
+    return dispAlnLen;
+}
+//Get total align length for seq currSeqInd and
+//"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs
+function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType) 
+{
+    var startIndex = readAln.startIndex;
+    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
+    if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current                
+        startIndex = Math.max(startIndex, currSeqInd - countSeqs);        
+        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs);        
+    }
+    else if(dispType == "prev") {        
+        startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs);
+        stopIndex = currSeqInd - 1;        
+    }
+    else {//next                                
+        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1);
+    }
+    var totAlnLen = checkTotalAlignLen(startIndex,stopIndex);
+    return totAlnLen;
+}
+
+function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType) 
+{
+    var maxDispLen = parseInt($("maxDispAlnLen").value);
+    var totAlnLen = 0;
+    var exc = false;
+    for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) {
+        totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType);
+        if(totAlnLen > maxDispLen) {
+            break;
+        }
+    }
+    if (totAlnLen > maxDispLen) {
+        if (numSeq != 0) numSeq--;      
+        if (dispType == "curr") {
+            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq);
+            //prev + 1(curr) + next            
+            readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq;
+        }
+        else if (dispType == "prev") {
+            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq);
+            readAln.numSeq = numSeq + 1;
+        }
+        else { //"next" - readAln.startIndex stays
+            readAln.numSeq = numSeq + 1;
+        }
+        
+        if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") {
+            setupDynHSPParams(readAln);            
+        } 
+                   
+        exc = true;   
+    }
+    return exc;
+}
+
+
+//readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set
+function ReadSeqAlignByIndex(readAln) {
+    var numAligns = 0;
+    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
+
+        if (!$("deflnDesc_" + i)) {
+            break;
+        }
+        if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") {            
+            currGi = $("deflnDesc_" + i).getAttribute("seqFSTA");
+            if (readAln.seqList != "") readAln.seqList += ",";
+            readAln.seqList += currGi;
+            numAligns++;
+        }
+        else {
+            break;
+        }
+    }
+    if (readAln.seqList != "") {        
+        readAln.numSeq = parseInt(numAligns);
+        ReadSeqAlignForSeqList(readAln);
+    }
+}
+
+
+var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2...
+//Find the range of indexes of displayed alignments for currAlnInd
+//Returns array of 2 startIndex, stopIndex
+function getCurrIndexRange(currAlinInd) {
+    var currRange;
+    var ranges = g_DisplayeAlignsRanges.split(",");
+    for (var i = 0; i < ranges.length; i++) {
+        var indexes = ranges[i].split("-");
+        if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) {
+            currRange = indexes;
+            break;
+        }
+    }
+    return currRange;
+}
+
+
+//Find the index of the previous  displayed alignment
+function getPrevDisplyedAlignInfo(currInd, readAln) {
+    readAln.insertAfterID = "alnStart";
+    lastDispIdx = 0;
+    for (var i = currInd - 1; i >= 1; i--) {
+        indexes = getCurrIndexRange(i);
+        if (indexes) {
+            lastDispIdx = indexes[1];
+            readAln.insertAfterID = "alnShow_" + indexes[0];
+            break;
+        }
+    }
+    return parseInt(lastDispIdx);
+}
+
+
+//setReadStatus
+function setSeqAlnReadStatus(readAln, status) {
+    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
+        if ($("deflnDesc_" + i)) {
+            jQuery($($("deflnDesc_" + i))).attr("stat", status);
+            if (status == "disp") {
+                g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex;
+            }
+        }
+    }
+}
+
+/*
+readAln.rid = rid;
+readAln.seqList = giList;
+readAln.startIndex = parseInt(idx);
+readAln.insertAfterID = insertAfterID;
+readAln.numSeq = parseInt(numSeq);
+readAln.scrollToSeqID = scrollToGI;
+*/
+function SendReadSeqAlinRequest(readAln) {        
+    blastUrl = "t2g.cgi";
+    
+    var rp = new RemoteDataProvider(blastUrl);
+
+
+    rp.onSuccess = function(obj) {
+        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
+
+        if ($("alnShow_" + readAln.startIndex)) {
+            var moreHspsLink = getNextHspsLink(readAln);            
+            jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, {
+                'widgets': ['ncbipopper', 'ncbitoggler'],
+                'configs': {
+                    'ncbipopper': { hasArrow: true, arrowDirection: 'top' }
+                }
+            }); 
+            setSeqAlnReadStatus(readAln, "disp");
+            jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");        
+            //Saves start and stop indexes of loaded alignments in global variables
+            saveIdxesForAutomaticLoad(readAln);
+            jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) {
+                var seqID = this.getAttribute("seqID");
+                if(seqID) initAlignBatch(seqID);
+            });
+
+        }
+
+        if (readAln.scrollToSeqID) {
+            location.href = "#" + readAln.scrollToSeqID;
+        }
+
+    };
+    rp.onError = function(obj) {        
+        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
+        jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
+        $("alnShowReal_" + readAln.startIndex).innerHTML = "<div class=\"erm\" id=\"erm_" + readAln.startIndex + "\">Error loading alignment ...<span class=\"db\">requests:" + this.iActiveRequests + " status:" + obj.status +
+                          "</span><a class=\"gbd\" href=\"#\" onclick=\"ReSubmitReadSeqAligns(event," + readAln.startIndex + ")\">Try again<\a></div>";
+    }
+    var params = constructURLParams(readAln);
+    if (readAln.numSeq == 1) {
+        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
+    }
+    params += "&SEQ_LIST_START=" + readAln.startIndex;    
+    
+    var formatParams = constructFormatParams();
+    params += formatParams;    
+    
+    //alert(params);
+    rp.Request(params);
+}
+
+
+function constructURLParams(readAln) {
+    var params;
+
+    if ($("useAlignDB") && $("useAlignDB").value == "true") {
+
+        var alignDbParams = "&USE_ALIGNDB=true";
+        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
+        if (batchID) {
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID");
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS");
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST");
+            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH");
+        }
+        alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList;
+        alignDbParams += "&HSP_SORT=" + readAln.hspSort;
+
+        if (readAln.hasOwnProperty("AlignDbPageNum")) {
+            alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum;
+            alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize;
+            alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum;
+        }
+
+        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams;
+    }
+    else {
+        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort;
+    }    
+    if ($("phiPtInd")) {
+        params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value;
+    }
+    return params;
+}
+
+/*
+readAln.rid = rid;
+readAln.seqList = giList;
+readAln.startIndex = parseInt(idx);
+readAln.insertAfterID = insertAfterID;
+readAln.numSeq = parseInt(numSeq);
+readAln.scrollToSeqID = scrollToGI;
+*/
+/*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes
+2. Insert another div with id="alnShowReal_index and class="alnMsgR"
+3. For "alnShow_index" set atrr indexes="startInd-stopInd"
+4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this 
+5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes
+6. Send read request
+*/
+
+function ReadSeqAlignForSeqList(readAln) {
+    var text = "<div id=\"alnShow_" + readAln.startIndex + "\" class=\"alnMsg\"><div class=\"alnMsgS\" id=\"alnMsg_" + readAln.startIndex + "\">Loading alignment...<span class=\"db\"> for sequences " + readAln.seqList;
+    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
+    var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : "";
+    text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "</span></div>";
+    text += "<div id=\"alnShowReal_" + readAln.startIndex + "\" class=\"alnMsgR\"></div></div>";
+    var debugControl = "<div id=\"debug\"></div>";
+    if (!$("debug")) {
+        jQuery($($("descriptions"))).before(debugControl);
+    }
+    if (!$("alnShow_" + readAln.startIndex)) {        
+        jQuery($($(readAln.insertAfterID))).after(text);
+        jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex);
+        jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList);
+        g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex;
+        setSeqAlnReadStatus(readAln, "read");
+        $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex;
+
+        if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ",";
+        g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex;
+
+        SendReadSeqAlinRequest(readAln);
+    }
+    else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) {
+        jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden");
+        jQuery($("erm_" + readAln.startIndex)).remove();        
+        SendReadSeqAlinRequest(readAln);
+    }
+}
+
+
+function ReSubmitReadSeqAligns(e,currInd) {
+    var rid = $("Rid").value;
+    if ($("alnShow_" + currInd)) {
+        var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes");
+        var range = indexRange.split("-");
+
+
+        var readAln = new Object();
+        readAln.seqList = ""; //giList
+        readAln.rid = rid;
+        readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist");
+        readAln.startIndex = parseInt(range[0]);
+        readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1;
+        readAln.hspSort = 0;
+        ReadSeqAlignForSeqList(readAln);
+        utils.preventDefault(e);
+    }
+}
+
+
+var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read"
+var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N
+var g_DisableAutoCheck = false;
+
+var g_autoStartIdx = new Array();
+var g_autoStopIdx = new Array();
+
+function saveIdxesForAutomaticLoad(readAln) {
+    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
+    g_autoStartIdx.push(readAln.startIndex); //1,20,25
+    g_autoStopIdx.push(stopIndex);  //4,24,29    
+    $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex;
+}
+
+function getNextHspsLink(readAln)
+{
+    var moreHspsLink = ""
+    if (readAln.hasOwnProperty("AlignDbPageNum")) {
+        var nextPageNum = readAln.AlignDbPageNum + 1;
+        var currHspInd = readAln.AlignDbPageSize * nextPageNum;
+        var argstring = readAln.startIndex + "," + currHspInd;                
+        var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId");
+        var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs");        
+        var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
+        var prevHspInd = readAln.AlignDbPageSize * nextPageNum;
+        var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize);        
+        var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1);
+
+        moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID);        
+        moreHspsLink = moreHspsLink.replace(/@accs@/g, accs);
+        moreHspsLink = moreHspsLink.replace("@argstring@", argstring);
+        moreHspsLink = moreHspsLink.replace(/@segs@/g, segs);
+        moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps);        
+        moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize);
+        moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd);
+        moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi);
+    }
+    return moreHspsLink;
+}
+
+
+function ReadNextHSPSet(currSeqInd, currHSPNum) {
+    var readAln = new Object();
+
+    readAln.rid = $("Rid").value;
+    readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA");
+    readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId");
+    dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps");
+    readAln.startIndex = currSeqInd;
+    readAln.numSeq = 1;
+    if (dynHsps) {
+        readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps);
+        readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve
+    }
+    if (currHSPNum != 0) {
+        readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1);
+        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum;
+    }
+    var sortLink = $("sa_" + readAln.gi);
+    readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0;
+    SendReadSeqAlinSortHSPRequest(readAln);
+}
+
+function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) {
+    ReadNextHSPSet(currSeqInd, currHSPNum);    
+    utils.preventDefault(e);
+}
+
+
+
+function checkAutoAlignArray() {
+    var stop = false;
+    var start = false;
+    var currAlignViewPos = $("alignView").getBoundingClientRect().top;
+    if (currAlignViewPos < g_alignViewPos) {//scrolling down
+        g_alignViewPos = currAlignViewPos;
+        if (g_DisableAutoCheck) {
+            g_DisableAutoCheck = false;
+            return;
+        }        
+        for (i = 0; i < g_autoStopIdx.length; i++) {
+            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) {
+                //alert("Reading more aligns scrolling down!");
+                var nextInd = parseInt(g_autoStopIdx[i] + 1);
+                var currInd = g_autoStopIdx[i];
+                if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) {
+                    ReadNextSeqAligns(currInd, 5);
+                    stop = true;
+                    break;
+                }
+            }
+        }
+        if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array
+    }
+    else if (currAlignViewPos > g_alignViewPos) {//scrolling up
+        g_alignViewPos = currAlignViewPos;
+        //here maybe return if autoStop found!!!
+        /* commenting automic read when scroll up */
+        for (i = 0; i < g_autoStartIdx.length; i++) {
+            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) {
+                //alert("Reading more aligns scrolling up!");
+                var currInd = g_autoStartIdx[i];
+                //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!!
+                if (currInd > 1) {
+                    ReadPrevSeqAligns(currInd, 5);
+                    start = true;
+                    break;
+                }
+            }
+        }
+        if (start) g_autoStartIdx.splice(i, 1);
+    }
+    /*end of comment*/
+}
+
+var g_alignViewPos = 0;
+
+function checkAutoAlignLoad() {
+
+
+    checkAutoAlignArray();
+
+    if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) {
+        //alert("bottom!");       
+
+        if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") {
+            //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex
+            ReadNextSeqAligns(g_MaxDisplayedIndex, 5);
+        }
+    }
+}
+
+
+function GetPatternLocResults()
+{
+    form = $("results");
+    if (!form.PHI_PTTRN_INDEX) {
+        var el = document.createElement("input");
+        el.name = "PHI_PTTRN_INDEX";
+        el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
+        form.appendChild(el);
+    }
+    else {
+        form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
+    }
+    form.submit();
+}
+
+function goToNextHSP(elem, next) {    
+    var par = jQuery(elem).parent(); //parent span with class="alnParLinks"
+    var parts = par[0].id.split("_"); //"hsp<seqid>_hspnum "hsp207524544_2"
+    if (parts[0].indexOf("nxHsp") != -1) {
+        parts[0] = parts[0].replace("nxHsp", "hsp");
+    }
+    nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1)
+    
+    gotoElem = jQuery($(nextID));
+    if (gotoElem[0]) {
+        a = jQuery(gotoElem).offset();
+        window.scroll(0, a.top);
+    }
+    
+    else {
+        retrieveNextHSP(parts[0],parts[1]);
+    }
+    
+}
+
+
+//parts[0]//hsp<seqid>,    parts[1] hspnum
+function retrieveNextHSP(currLinkID, currHSPNum) 
+{
+    var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id
+    var currSeqInd, totalHsps;
+    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
+        currSeqInd = parseInt(this.getAttribute("ind"));
+        totalHsps = parseInt(this.getAttribute("hsp"));
+        dynHsps = this.getAttribute("dynHsps");
+    });
+    currHSPNum = parseInt(currHSPNum);
+    if (currHSPNum < totalHsps && dynHsps) {        
+        ReadNextHSPSet(currSeqInd, currHSPNum);
+    }
+}
+/********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/
+function getUrlCompForEntryField(elem) {
+    var url = "";
+    if (elem && elem.value != "") {
+        url = "&" + elem.name + "=" + escape(elem.value);
+    }
+    return url;
+}
+
+
+function getUrlCompForCheckedField(elem) {
+    var url = "";
+    if (elem && elem.checked) {
+        url = "&" + elem.name + "=" + elem.value;
+    }
+    return url;
+
+}
+
+function getUrlCompForOptionsField(elem) {
+    var url = "";
+    if (elem) {
+        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
+    }
+    return url;
+}
+/****************************************/
+
+function constructFormatParams() {
+    var formatParams = "";
+
+    if ($("queryList")) {
+        formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value;
+    }
+
+    
+    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT);
+    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE);
+    formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI);
+    formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW);
+    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR);
+    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR);    
+    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW);
+    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH);
+    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW);
+    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH);
+    formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH);
+    
+
+    formatParams += getHiddenFieldParamString("BUILD_NAME");
+    
+    var serviceType = "";
+    if ($("serviceType").value == "sra") {
+        serviceType = "sra";
+    }
+    else if ($("clientType").value == "TMSmart_restricted") {
+        serviceType = "restricted";
+    }
+    if (serviceType != "") {
+        formatParams += "&BOBJSRVC=" + serviceType;
+    }
+    if ($("currQuery").value != "") {
+        formatParams += "&CURR_QUERY_ID=" + $("currQuery").value;
+    }
+    
+    return formatParams;
+}
+
+//readAln.seqList contains one gi only for this
+function SendReadSeqAlinSortHSPRequest(readAln) {
+    blastUrl = "t2g.cgi";    
+    var rp = new RemoteDataProvider(blastUrl);
+
+
+    rp.onSuccess = function(obj) {
+        var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : "";        
+        var alnHtml = obj.responseText + moreHspsLink;
+        initHSPRequest(readAln, obj.responseText + moreHspsLink,false);        
+        if (readAln.scrollToSeqID) {
+            location.href = "#" + readAln.scrollToSeqID;
+        }                
+    };
+    rp.onError = function(obj) {        
+        var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
+        var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
+        if (!$(msgID)) {
+            var msg = "<div class=\"erm\" att=\"1\" id=\"" + msgID + "\">Error loading alignment ...<span class=\"db\">status:" + obj.status +
+                          "</span><a class=\"gbd\" href=\"#\" onclick=\"ReadNextHSPSetEvt(event," + readAln.startIndex + "," + currHspInd + 
+                          ")\">Try again <span class=\"attmt\"></span> <\a></div>";
+            initHSPRequest(readAln, msg, true);
+        }
+        else {
+            var attNum = parseInt($(msgID).getAttribute("att")) + 1;
+            $(msgID).setAttribute("att", attNum);
+            jQuery($(msgID)).find(".attmt").each(function(index) {
+                jQuery(this).html(", attempt " + attNum);
+            });
+        }
+    }
+    
+    var params = constructURLParams(readAln);
+    if (readAln.AlignDbPageSize) {    
+        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
+    }    
+    params += "&SORT_ONE_ALN=on";
+    var formatParams = constructFormatParams();
+        
+    params += formatParams;
+    
+    //alert(params);
+    rp.Request(params);
+}
+function initHSPRequest(readAln, alnHtml, err) {
+    var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;    
+    if (currHspInd != 0) {
+        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd;
+        jQuery($(readAln.insertAfterID)).after(alnHtml);
+        moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1);
+        jQuery($(moreHspsID)).remove();
+        if (!err) {
+            errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
+            jQuery($(errMsgID)).remove();            
+        }
+    }
+    else {
+        jQuery($("alnAll_" + readAln.gi)).html(alnHtml);
+    }    
+}
+
+function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544"
+    var readAln = new Object();
+
+    
+    var desLineID = sortLink.id.replace("sa", "dtr"); //tr id
+    var seqInd;
+
+    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {        
+        seqInd = this.getAttribute("ind");
+    });    
+    
+    ReadNextHSPSet(parseInt(seqInd), 0);
+}
+
+
+function configDescriptions(e,btn,dlgId) 
+{
+    var suffix = PsiBelowThresh(dlgId);    
+    var colmnsInfId = "cfcDsInf" + suffix;
+    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
+    var showAllColId = "shcl" + suffix;    
+    var chkBoxes = $C("checkbox", "type", $(dlgId), "input");
+    if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = "";    
+    for (i = 0; i < chkBoxes.length; i++) {
+        var check;
+        if (utils.hasClass(btn, "cnc")) {//cancel
+            if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) {
+                check = true;
+            }
+            else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) {
+                check = false;
+            }
+        }
+        else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) {
+            check = true;
+        }
+        if (typeof (check) != 'undefined') {
+            chkBoxes[i].checked = check;
+            showHideCol(tblID,parseInt(chkBoxes[i].value), !check);
+        }
+        if (!utils.hasClass(btn, "cnc")) {
+            if (chkBoxes[i].checked) { //OK
+                if ($(colmnsInfId).value != "") $(colmnsInfId).value += ",";
+                $(colmnsInfId).value += chkBoxes[i].value;
+            }
+        }
+    }
+    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
+        jQuery($(showAllColId)).removeClass("hidden");
+    }
+    else {
+        jQuery($(showAllColId)).addClass("hidden");
+    }
+
+    var chConfig = $("cfcDsSave").value != $(colmnsInfId).value;
+    
+    var cfds = document.getElementsByName("CONFIG_DESCR");        
+    if (cfds) {
+        for (i = 0; i < cfds.length; i++) {
+            cfds[i].value = $(colmnsInfId).value;
+        }
+    }    
+    $("cfcDsSave").value = $(colmnsInfId).value;
+    if (chConfig) SaveConfigTable();
+    jQuery(document.body).click();
+    utils.preventDefault(e);
+}
+
+
+
+function initDescConfig() 
+{
+    initConfigColumns("dsConfig");
+    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
+        initConfigColumns("dsConfig_psiw");
+    }        
+}
+
+
+function initConfigColumns(cnfDlgID) 
+{
+    var suffix = PsiBelowThresh(cnfDlgID);
+    //cnfDlgID is "dsConfig[_psiw]"
+    var colmnsInfId = "cfcDsInf" + suffix;
+    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
+    var showAllColId = "shcl" + suffix;
+    
+    if (navigator.userAgent.match(/ie/i)) {
+        if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") {        
+            jQuery($(tblID)).find("th.c1").each(function(index) {            
+                db = getHiddenFieldVal("DATABASE");
+                var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em";
+                jQuery(this).css("width", width);
+            });        
+        }
+    }
+
+    jQuery($(tblID)).find("tr.first").each(function(index) {
+        jQuery(this).find("a.dcs").each(function(index) {        
+           jQuery(this).bind("click", function(e) { checkConfig(this); });           
+        });
+    });
+
+    jQuery($(cnfDlgID)).find("button").each(function(index) {
+        jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); });
+    });
+
+        
+    jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); });
+
+    $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR");
+    if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") {
+        $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval");
+    }
+    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
+        jQuery($(showAllColId)).removeClass("hidden");
+    }    
+    else {
+        jQuery($(showAllColId)).addClass("hidden");
+    }
+    var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input")
+    for (i = 0; i < chkBoxes.length; i++) {
+        jQuery(chkBoxes[i]).bind("click", configColumn);
+        if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) {
+            chkBoxes[i].checked = true;
+        }
+        else {
+            //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value);
+            showHideCol($(tblID), chkBoxes[i].value, true); 
+        }
+    }
+}
+function showAllCol(e,elem) 
+{
+    var suffix = PsiBelowThresh(elem.id);
+    var rdf = "dscRsDf" + suffix;
+    jQuery($(rdf)).click();//click "restore defaults'
+    utils.preventDefault(e);
+}
+
+
+function configColumn() {
+    var suffix = PsiBelowThresh(this.id);
+    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
+    
+    cCls = "c" + this.value;
+    if (this.checked) {//show        
+        showHideCol(tblID,parseInt(this.value), false);        
+    }
+    else {
+        showHideCol(tblID,parseInt(this.value), true);        
+    }
+}
+
+function showHideCol(tblID, columnIndex, hide) {
+
+    if ($("Transcr")) {
+        colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden");
+        hide = hide && !colHidden;
+        show = !hide && colHidden;
+    }
+    else {
+        show = !hide;
+    }    
+    if (hide) {
+        jQuery($(tblID)).ncbigrid("hideColumn", columnIndex);        
+    }
+    else if (show) {
+        jQuery($(tblID)).ncbigrid("showColumn", columnIndex);    
+    }
+    if ($("Transcr") && (hide || show) ) {
+        var colsp = parseInt($("Transcr").getAttribute("colspan"));
+        colsp = (hide) ? colsp - 1 : colsp + 1;
+        $("Transcr").setAttribute("colSpan", colsp);
+        if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp);
+    }
+}
+
+function checkConfig(lnk) {
+    var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value;
+    lnk.href = lnk.href + cnfCol + "#sort_mark";    
+}
+
+function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists
+{
+    var dflLineLinks = $C(seqID, "gi", document, "a");    
+    for (i = 0; i < dflLineLinks.length; i++) {
+        jQuery(dflLineLinks[i]).click();
+        break;
+    }    
+    location.href = dflLineLinks[i].href;
+}
+
+
+
+function initDescSelect() 
+{
+
+    jQuery("#cntDesc").find("a").each(function(index) {
+        jQuery(this).bind("click", configDescrSelect);
+    });
+    jQuery("#cntSelN").click();
+    jQuery("#descTblCtrl").find("a[view]").each(function(index) {
+        jQuery(this).bind("click", DisplaySelectedView);
+    });
+    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
+        jQuery("#cntDesc_psiw").find("a").each(function(index) {
+            jQuery(this).bind("click", configDescrSelect);
+        });
+        jQuery("#cntSelN_psiw").click();
+        jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) {
+            jQuery(this).bind("click", DisplaySelectedView);
+        });
+    }
+    
+    
+    //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });??
+
+}
+
+function DisplaySelectedView(e) {
+    if (this.getAttribute("view") == "graph") {    //seqviewer
+        ViewSelectedSeqViewer(e,this);
+    }
+    else {
+        if (this.getAttribute("view") == "tree") {    //seqviewer
+            $("scrWidth").value = screen.width;
+            $("scrHeight").value = screen.height;
+        }
+        ViewSelectedSeqsEx(e, this);
+    }
+}
+
+function PsiBelowThresh(elemID) 
+{
+    var suffix = "";
+    if (elemID.indexOf("_psiw") != -1) {
+        suffix = "_psiw";
+    }
+    return suffix;
+}
+
+function ViewSelectedSeqsEx(e,elem) {
+    var sbmForm = elem.getAttribute("frm");
+    var seqList = elem.getAttribute("seqList");
+
+    var cnfElem = utils.getParent(elem); //.cnf div    
+    var suffix = PsiBelowThresh(cnfElem.id);
+    var tblID = "dscTable" + suffix;
+
+    $(seqList).value = createSelseqString(tblID,true);
+    $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces
+    if ($(seqList).value.indexOf("dbSNP") != -1) {
+        $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp
+        elem.href = $(sbmForm).action + $(seqList).value;
+        elem.target = "new";
+    }
+    else {
+        $(sbmForm).submit();
+        utils.preventDefault(e);
+    }    
+}
+
+function ViewSelectedSeqsTree(e) {
+    $("scrWidth").value = screen.width;
+    $("scrHeight").value = screen.height;
+}
+
+function initSeqViewerGet(seqList) {
+    if (seqList.length >= 2000) {    
+        seqList = seqList.substr(0,2000);
+        lastComma = seqList.lastIndexOf(",");
+        seqList = seqList.substr(0,lastComma);             
+    }
+    $("seqViewParams").name = "RID";
+    $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]";
+}
+
+function ViewSelectedSeqViewer(e, elem) 
+{
+    var cnfElem = utils.getParent(elem); //.cnf div    
+    var suffix = PsiBelowThresh(cnfElem.id);
+    var tblID = "dscTable" + suffix;
+
+    //change to false when new verison of seqVier is installed in production
+    var seqList = createSelseqString(tblID, false);
+    $("sbmtGraphics").action = $("seqViewUrl").value;
+    
+    var rp = new RemoteDataProvider("url2nc.cgi");
+    rp.onSuccess = function(obj) {
+        var jsnResp = JSON.parse(obj.responseText);
+        ncid = jsnResp.ncid;
+
+        if (ncid != "") {
+            $("seqViewParams").name = "rkey";
+            $("seqViewParams").value = ncid;
+        }
+        else {
+            initSeqViewerGet(seqList);
+        }
+        $("sbmtGraphics").submit();        
+    };
+    rp.onError = function(obj) {
+        initSeqViewerGet(seqList);
+        $("sbmtGraphics").submit();
+        utils.preventDefault(e);   
+    }
+    var params = $("ridParam").value + "[" + seqList + "]";    
+    rp.Request(params, "POST");
+    utils.preventDefault(e);   
+}
+
+function configDescrSelect(e) {    
+    var sel = this.getAttribute("sel");    
+    if (sel) {
+        var selNum = 0;
+        var check = (sel == "all") ? true : false;
+
+        var suffix = PsiBelowThresh(this.id);
+        var tblID = "dscTable" + suffix;
+        var toolbarID = "descTblCtrl" + suffix;
+        var selElID = "slcNum" + suffix;
+
+        jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
+            jQuery(this)[0].checked = check;
+            if (check) selNum++;
+        });
+        enableDescrLinks(selNum, toolbarID, selElID);        
+    }     
+    utils.preventDefault(e);
+}
+
+
+
+function enableDescrLinks(selNum, toolbarID, selElID) {
+    jQuery($(toolbarID)).find("a[minSlct]").each(function(index) {
+        var minSelected = this.getAttribute("minSlct");
+        minSelected = parseInt(minSelected);
+        if (selNum >= minSelected) {
+            this.removeAttribute("disabled");
+        }
+        else {
+            this.setAttribute("disabled", "disabled");
+        }
+    });    
+    $(selElID).innerHTML = selNum;
+}
+
+
+
+function configDescrLinks(e, elem) 
+{
+
+    ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false");     
+    var par = jQuery(elem).parents(".jig-ncbigrid");//parent table
+    if (par) {
+        var suffix = PsiBelowThresh(par[0].id);
+        var tblID = "dscTable" + suffix;
+        var toolbarID = "descTblCtrl" + suffix;
+        var selElID = "slcNum" + suffix;
+        
+        var currSelNum = parseInt($(selElID).innerHTML);
+        var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1;
+        enableDescrLinks(selNum, toolbarID, selElID);
+    }
+}
+/***Download code begin****/
+
+function initDownLoadPopup(dwnDialog) {
+
+    jQuery(dwnDialog).find("button").each(function(index) {        
+        jQuery(this).bind("click", execDownLoad);        
+    });
+
+    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
+}
+
+function initDescDownLoad() {
+    initDownLoadPopup($("dsDownload"));
+
+    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
+        initDownLoadPopup($("dsDownload_psiw"));        
+    }
+}
+
+function initAlignDownLoad(navObj) 
+{
+    var seqID = navObj.seqID;
+    var dwnDialog = $("dlgDwnl_" + seqID);
+    jQuery(dwnDialog).find("button").each(function(index) {        
+        jQuery(this).bind("click", execDownLoad);        
+    });
+
+    var dwnFSTW = $("dwFST_" + seqID);//whole seq
+    var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions
+    
+    if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID); 
+    if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID); 
+    
+    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });    
+}
+
+    
+function execDownLoad(e) {
+    if (!utils.hasClass(this, "cnc")) {
+        par = utils.getParent(this);
+        dwnDialog = utils.getParent(par); //parent dialog with popDl class
+        var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false;
+        jQuery(dwnDialog).find("input").each(function(index) {
+            if (this.checked) {
+                submitDownLoad(this, descr);
+            }
+        });
+    }
+    jQuery(document.body).click();
+    utils.preventDefault(e);      
+}
+
+function submitDownLoad(radioElem, descr) {    
+    var toolURL = radioElem.getAttribute("url");
+    if (toolURL) {
+        if (descr) {
+            var getGi = radioElem.getAttribute("getGi");
+            getGi = (getGi) ? true : false;
+            
+            var tblID = "dscTable";
+            var suffix = PsiBelowThresh(radioElem.id);
+            tblID += suffix;
+
+            $("selDnSeqs").value = createSelseqString(tblID,getGi);
+        }
+        else {
+            var seqfsta = radioElem.getAttribute("seqfsta");
+            $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi");
+        }
+        var addParams = "";
+        if (radioElem.getAttribute("addParam")) {
+            addParams = addDwnlParams();
+        }
+        var submitName = radioElem.getAttribute("sbName")
+        $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST";
+        $("dwdlSubmit").action = toolURL + addParams;
+        $("dwdlSubmit").submit();
+    }       
+    else {
+        var sbFunction = radioElem.getAttribute("sbFunc");        
+        if (sbFunction) {
+            eval(sbFunction + "(radioElem, descr)");
+        }        
+    }
+}
+
+
+function initDownLoadFSTA(radioElem, descr) 
+{
+    if (descr) {
+    
+        var tblID = "dscTable";
+        var suffix = PsiBelowThresh(radioElem.id);
+        tblID += suffix;
+
+        $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false);
+    }
+    else {        
+        $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta");
+    }
+    $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType");
+    
+    $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE");
+    if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox    
+        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
+        if (batchID) {
+            $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID");
+            $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS");
+            $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST");
+            $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH");
+        }
+    }
+    $("sbmtFASTA").submit();    
+}
+
+function createSelseqString(tblID,getGi) {    
+    var selSeqs = "";
+    jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
+        if (jQuery(this)[0].checked) {
+            if (selSeqs != "") selSeqs += ",";
+            if (getGi) {
+                selSeqs += jQuery(this)[0].value;
+            }
+            else {
+                var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc");
+                selSeqs += $(linkID).getAttribute("seqFSTA");
+            }
+        }
+    });
+    return selSeqs;
+}
+
+/***Download code end****/
+
+/***Init navigation code begin **/
+
+function initNavigation(navObj) {    
+    initNextAlnLink(navObj, true);
+    initNextAlnLink(navObj, false);        
+}
+
+
+function initNavInfo(navObj) {
+    var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind"));
+    nextInd = currInd + 1;
+    prevInd = currInd - 1;
+    
+    navObj.currSeqID = "";
+    navObj.nextSeqID = "";
+    navObj.prevSeqID = "";
+        
+    if ($("deflnDesc_" + nextInd)) {
+        navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs");
+        if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA");
+    }
+    if ($("deflnDesc_" + prevInd)) {
+        navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs");
+        if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA");
+    }
+    if ($("deflnDesc_" + currInd)) {
+        navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA");        
+    }
+}
+
+
+function initNextAlnLink(navObj, next) {
+
+    var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID);
+    var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID;
+    
+    if (nextLinkEl) {
+        if (nextSeqid != "") {
+            var text = (next) ? "next" : "previous";
+            nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid);
+        }
+        else {
+            nextLinkEl.setAttribute("disabled", "disabled");
+        }
+    }
+}
+function scan(link) {
+    var init = link.getAttribute("init");
+    if (!init) {
+        ncbi.sg.scanLinks(link);
+        link.setAttribute("init","on");
+    }
+}
+
+function initWidth(seqID) {
+    var lineLengthElem = $("FormatForm").LINE_LENGTH;
+    var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
+    if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
+    
+    var relWidth = (lineLength > 90) ? "12%" : "15%";
+    var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
+    lineLength = (lineLength + parseInt(17)) * charWidth;
+    var width = lineLength + "px";
+    jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) {
+        jQuery(this).css("width", width);
+    });
+    jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) {
+        jQuery(this).css("width", width);
+    });    
+    jQuery($("relInf_" + seqID)).css("width", relWidth);
+}
+
+
+/***Init navigation code end **/
+function initAlignBatch(seqID)
+{
+    var navObj = new Object();
+    navObj.seqID = seqID;
+    initNavInfo(navObj);
+
+    initAlignDownLoad(navObj);
+    initNavigation(navObj);
+    ncbi.sg.scanLinks($("alnNxt_" + seqID));
+    ncbi.sg.scanLinks($("alnPrv_" + seqID));
+    if ($("serviceType").value == "vecscreen") {
+        utils.addClass($("alnDsc_" + seqID), "hidden");
+    }
+    ncbi.sg.scanLinks($("alnDwnld_" + seqID));
+    jQuery($("csLinks_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("relInf_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("rng_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("dln_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    initWidth(seqID); 
+/*        
+    jQuery($("alnHdr_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+    jQuery($("aln_" + seqID)).find("a").each(function(index) {
+        ncbi.sg.scanLinks(this);
+    });
+*/    
+}
+
+function SaveConfigTable() {
+    blastUrl = "fmtsave.cgi";
+    
+
+    var rp = new RemoteDataProvider(blastUrl);
+
+
+    rp.onSuccess = function(obj) {
+        //alert("success");
+    };
+    rp.onError = function(obj) {
+        //alert("error");
+    }    
+
+    var program = getHiddenFieldVal("PROGRAM");
+    var rid = getHiddenFieldVal("RID");
+    var blastSpec = getHiddenFieldVal("BLAST_SPEC");
+    var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value;
+    if(blastSpec) {
+        params += "&BLAST_SPEC=" + blastSpec;
+    }     
+    rp.Request(params,"POST");
+}
+
+function removeRID() {
+    var rid = document.getElementsByName("RID");
+    for (var i = 0; i <= rid.length; i++) {
+        jQuery(rid[i]).remove();        
+    }
+}
+
+function initAdvancedView()
+{
+    if ($("dsConfig")) {
+    
+        var alnView = getHiddenFieldVal("ALIGNMENT_VIEW");
+        if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") {
+            var rid = getHiddenFieldVal("RID");        
+            ReadNextSeqAligns(0, 5);            
+            g_alignViewPos = $("alignView").getBoundingClientRect().top;
+            utils.addEvent(window, "scroll", checkAutoAlignLoad, false);
+        }
+        list = $("phiPtInd");
+        if (list) {
+            utils.addEvent(list, "change", GetPatternLocResults, false);
+        }                
+        initDescConfig();
+        initDescSelect();
+        initDescDownLoad();
+        if ($("psiInp")) {
+            var nextIter = document.getElementsByName("NEXT_I");
+            for (var i = 0; i < nextIter.length; i++) {
+                utils.addEvent(nextIter[i], "click", removeRID, false);
+            }
+        }
+    }
+}
+
+//takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4"
+function initjQry() 
+{
+    var oldCreate = jQuery.ui.ncbipopper.prototype._create;
+    jQuery.ui.ncbipopper.prototype._create = function() {
+        var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash");
+        this.options.destSelector = destSelector.replace(/\./g, "\\.");
+        oldCreate.apply(this, arguments);
+    }
+}
+utils.addEvent(window,
+				"load", initAdvancedView,
+				false);
+
+initjQry()
+
+/* If user agent has "safari" in it, include safari-specific stylesheet. */
+if (navigator.userAgent.match(/ie/i)) {
+    document.write("<link rel='stylesheet' type='text/css' href='css/ie-descriptions.css'  media='screen'/>");
+}
+/*****************************new code end*********************************************************************/