--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/format.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,270 @@
+
+function UpdateDisplayTypes(displayTypes) {	
+    dispMenu = displayTypes.options;		
+    for(i=0; i < dispMenu.length; i++) {
+	    //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") ||
+	    if($("stepNumber").value == "" || $("stepNumber").value < 2) {	    	    
+			if(dispMenu[i].value.indexOf("PSSM") != -1) {
+				dispMenu[i--] = null;
+				//break;
+			}			
+		}		
+	}	    
+}
+
+function GetIndexByValue(selectElem,val) {	
+    var idx = 0;
+    var opts = selectElem.options;		
+    for(i=0; i < opts.length; i++) {
+        if(opts[i].value == val) {
+            idx = i;
+            break;
+        }
+    }	
+    return idx;	    
+}
+
+function resetAdvView(show)
+{
+    var advView = $("advView");    
+    if(show) {
+        if(utils.hasClass(advView, "hidden")) {
+            utils.removeClass(advView, "hidden");
+        }    
+    }
+    else {
+        utils.addClass(advView, "hidden");
+    }
+}
+
+
+function ShowOrHide(hide,elem)
+{
+    if(hide) {
+        if(!utils.hasClass(elem, "hidden")) {
+            utils.addClass(elem, "hidden");
+        }    
+    }
+    else {
+        if(utils.hasClass(elem, "hidden")) {
+            utils.removeClass(elem, "hidden");
+        }    
+    }
+}    
+
+function UpdateFormatTypes(form) {    
+    var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value;
+    var hideAdvView = false;
+    bioseqFormatHide = true;
+    pssmFormatHide = true;
+    pssmScFormatHide = true;
+    formatTypeHide = true;
+	if (selectedObjType == "Alignment") {
+		formatObjectSelectedIndex = 0; //HTML		
+		formatTypeHide = false;		
+		hideAdvView = true;
+	}
+    if (selectedObjType == "PSSM") {		
+		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text");	
+		pssmFormatHide = false;		
+    }
+    if (selectedObjType == "PSSM_Scoremat") {		
+		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");		
+		pssmScFormatHide = false;		
+    }    
+    else if (selectedObjType == "Bioseq") {		
+		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");		
+		bioseqFormatHide = false;		
+    }
+    form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex;     
+	ShowOrHide(formatTypeHide,form.FORMAT_TYPE);
+	if ($("bioseqFormat")) {
+	    ShowOrHide(bioseqFormatHide,$("bioseqFormat"));
+	    $("bioseqFormat").readOnly=true;		
+	}
+	if ($("pssmFormat")) {
+	    ShowOrHide(pssmFormatHide,$("pssmFormat"));
+	    $("pssmFormat").readOnly=true;	
+	}
+	if ($("pssmScFormat")) {
+	    ShowOrHide(pssmScFormatHide,$("pssmScFormat"));
+	    $("pssmScFormat").readOnly=true;	
+	}	
+	resetAdvView(hideAdvView);
+}	
+
+function ResetForm()
+{
+    //var defValNodes = cssQuery(".reset");	
+    defValNodes = $("FormatForm").elements;
+	for(i=0; i < defValNodes.length; i++) {	  	  
+	  if(utils.hasClass(defValNodes[i],"reset"))
+	                 setDefalValue(defValNodes[i]); 	  
+	}
+	if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
+	    UpdateFormatTypes($("FormatForm"));
+	    UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
+	}
+	if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH)
+	else $("FormatForm").I_THRESH.value="";
+	//resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
+	resetOrganismControls($("FormatForm").FORMAT_ORGANISM);
+	//TO DO: add threshold
+}
+
+function LimitByHitlistSize(list)
+{
+    var listBreak = false;
+    var optSel = false;
+    for(i=0; i < list.options.length; i++) {    
+        var optVal = parseInt(list.options[i].value ,10);
+        var hitListSize = parseInt($("maxNumSeq").value ,10);                
+        if(list.options[i].selected) optSel = true;
+        if(optVal >= hitListSize)  {
+            if(!optSel) {list.options[i].selected = true;}
+            list.options.length = i + 1; 
+            break;
+        }                
+    }             
+}
+
+function AddFormatOrgField(e) {
+    AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE");
+}
+
+function initSubmit() {
+
+
+}
+
+function adjustFormatOptions() 
+{
+    var alignView = $("FormatForm").ALIGNMENT_VIEW;
+    var formatType = $("FormatForm").FORMAT_TYPE;
+    var queryAnch =  formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
+    var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch;
+    dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities");    
+    
+    UpdateDescriptions(dynFormatPW);
+    if (dynFormatPW) {
+        jQuery("#frmAln").addClass("hidden");
+        if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
+        jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE
+        jQuery("#scf").removeClass("hidden");//show CDS_FEAT
+        $("FormatForm").SHOW_LINKOUT.checked = true;        
+    }
+    else {
+        if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex;
+        
+        jQuery("#frmAln").removeClass("hidden");
+        if (dynFormatQA) {
+            if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
+        }
+        else {
+            jQuery("#shl").removeClass("hidden");
+        } 
+        if (queryAnch) {
+            jQuery("#scf").addClass("hidden"); //hide CDS_FEAT
+        }
+        else {//pairwise old_view=false
+            jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT
+        }
+        jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE
+    }
+    if ($("blastSpec").value == "VecScreen") {
+        adjustVecscreen(dynFormatPW);
+    }
+}
+
+function adjustVecscreen(dynFormatPW) 
+{
+    var dfltDescrInd = 0; //0
+    var dfltDynDescrInd = 5; //1000
+    var dfltAlnInd = 6; //1000
+    if (dynFormatPW) {
+        utils.addClass($("lr"), "hidden");
+        $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd;        
+    }
+    else {
+        utils.removeClass($("lr"), "hidden");
+        $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd;
+    }
+    $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd;
+}
+
+
+function UpdateDescriptions(removeZero) 
+{
+    if (removeZero) {        
+        dispMenu = $("FormatForm").DESCRIPTIONS;
+        dispMenu.remove(0);
+    }
+    else {
+        dispMenu = $("FormatForm").DESCRIPTIONS;        
+        if (dispMenu.options[0].value != "0") {            
+            if (navigator.userAgent.match(/ie/i)) {
+                dispMenu.add(new Option("0", "0"), 0);
+            }
+            else {
+                dispMenu.add(new Option("0", "0"), dispMenu[0]);
+            }
+        }
+	}
+}
+
+function InitDynFormatOptions() 
+{
+    if ($("OLD_VIEW")) {
+        utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false);
+        utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false);
+        utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false);
+        adjustFormatOptions();
+    }
+}
+
+function InitFormatPage()
+{
+    if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
+        UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);    
+        UpdateFormatTypes($("FormatForm"));
+        list = $("FormatForm").FORMAT_OBJECT;
+        utils.addEvent(list, "change", function() {
+            UpdateFormatTypes($("FormatForm"));
+                               },
+	                           false);
+    }
+    utils.addEvent($("resetAll"), "click",  ResetForm, false);         
+    if($("maxNumSeq") != null) {
+    if($("maxNumSeq").value != "") {
+        LimitByHitlistSize($("FormatForm").DESCRIPTIONS);
+        LimitByHitlistSize($("FormatForm").ALIGNMENTS);
+        LimitByHitlistSize($("FormatForm").NUM_OVERVIEW);        
+    }
+    }    
+    setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
+    utils.addEvent($("FormatForm"), "submit", function() {
+                            adjustOrgVal($("FormatForm").FORMAT_ORGANISM);},
+                    false);
+                    
+    if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false);
+    InitDynFormatOptions();    
+	/* add this code if decide image for View Report
+	var imgButtons = jQuery("[class='viewReport']");
+    for (var i = 0; i < imgButtons.length; i++) {
+      var l = imgButtons[i];
+      utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false);          
+      utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false);
+      utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false);
+      utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false);
+      utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false);
+   }  
+   */ 
+}
+
+utils.addEvent(window, 'load', InitFormatPage, false);
+
+
+
+
+
+