diff NCBI Blast reference example_files/results.js @ 31:344cd76f6fd2

rename NCBI reference example

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBI Blast reference example_files/results.js	Thu May 15 16:59:18 2014 +0200
@@ -0,0 +1,649 @@
+// JScript source code
+
+//Display Reformat page button only after the whole page is loaded    
+
+function ReformatPageEvent()
+{
+	var refPageLink = document.getElementById("refPage");    	
+	
+	//alert(refPageLink);
+	//alert(refPageLink.getAttribute("submitForm"));
+	var submitForm = refPageLink.getAttribute("submitForm");
+	alert(submitForm);
+	if(refPageLink && submitForm) {
+		utils.addEvent(refPageLink, 
+					   "click", 
+					   function() {
+							document.getElementById(submitForm).submit();					
+						}, 
+						false);    
+	}	
+}
+
+
+function SubmitEvent(linkID)
+{
+	
+	var link = document.getElementById(linkID);    	
+	//alert(link.getAttribute("submitForm"));
+	var submitForm = link.getAttribute("submitForm");
+	if(link && submitForm) {
+		utils.addEvent(link, 
+					   "click", 
+					   function() {							
+							document.getElementById(submitForm).submit();					
+						}, 
+						false);    
+	}	
+}
+
+
+function SubmitEventSave(linkID)
+{
+	
+	var link = document.getElementById(linkID);    	
+	//alert(link.getAttribute("submitForm"));
+	var submitForm = link.getAttribute("submitForm");
+	if(link && submitForm) {
+		utils.addEvent(link, 
+					   "click", 
+					   function() {
+							//$(submitForm).CMD.value = "GetSaved";							
+							document.getElementById(submitForm).submit();					
+						}, 
+						false);    
+	}	
+}
+ 				
+ 				
+
+
+//This function creates submit form event on click
+//form submitted is defined in submitForm attribute
+//It also copies params from forms[0] (search paramateres) created by formatter
+function SubmitEventNew(linkID)
+{
+	
+	var link = document.getElementById(linkID);    	
+	//alert(link.getAttribute("submitForm"));
+	if(!link) return;
+	var submitForm = link.getAttribute("submitForm");
+	if(link && submitForm) {
+		utils.addEvent(link, 
+					   "click", 
+					   function() {					 
+							document.forms[0].CMD.value = "";  
+							if(document.forms[0].PAGE_TYPE) {
+								document.forms[0].PAGE_TYPE.value = "";  
+							}
+							var s = document.forms[0].innerHTML;														
+							var form = $(submitForm);							
+							form.innerHTML = s + form.innerHTML;							
+							form.submit();					
+						}, 
+						false);    
+	}	
+}
+
+function GetResults()
+{
+    form = $("results");    
+    form.QUERY_INDEX.value = $("queryList")[$("queryList").selectedIndex].value;
+    form.submit();   
+}
+
+function isIdIn(id, idArray){
+  var idSeen=false;
+
+  for(i=0; i<idArray.length; i++){
+    if(id==idArray[i]){
+      idSeen=true;
+      break;
+    }
+  }
+  return idSeen;
+}
+
+function GetSelectedSeqString(formName)
+{
+    var selSeqs = "";
+    var idArray=new Array();
+    forms = document.getElementsByName(formName);    
+    for(var j=0; j < forms.length; j++){
+      for(var i=0; i < forms[j].elements.length; i++){
+        var theElem=forms[j].elements[i];
+        if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"&&theElem.checked){      
+          if(!isIdIn(theElem.value, idArray)){            
+            idArray[idArray.length]=theElem.value;
+          }            
+        }      
+      }
+    }
+    selSeqs = idArray.join();
+    return selSeqs;
+}
+
+function ViewSelectedSeqs(e)
+{
+    var submitForm = $("submitterTop");
+    var targetForm = submitForm.getAttribute("seqsForm");
+    $("selSeqs").value = GetSelectedSeqString(targetForm);
+    submitForm.submit();
+    utils.preventDefault(e);
+}
+
+
+function ViewSelectedSeqTree()
+{
+    var submitForm = $("treesubmitterTop");
+    var targetForm = submitForm.getAttribute("seqsForm");
+    $("seqSet").value = GetSelectedSeqString(targetForm);
+    $("scrWidth").value = screen.width;
+    $("scrHeight").value = screen.height;
+    submitForm.submit();
+}
+
+function ViewTree(linkID) {
+    link = document.getElementById(linkID);
+    var target = link.target;
+    winRef = window.open(link.href + "&screenWidth=" + screen.width + "&screenHeight=" + screen.height, target);
+}
+
+function ViewSelectedSeqMultiAlign()
+{
+    var submitForm = $("multisubmitterTop");
+    var targetForm = submitForm.getAttribute("seqsForm");
+    $("seqSetM").value = GetSelectedSeqString(targetForm);    
+    submitForm.submit();
+}
+
+
+
+function selectAllSeqs()
+{
+    var formName = this.getAttribute("seqsForm");
+    forms = document.getElementsByName(formName);    
+    for(var j=0; j < forms.length; j++){
+        for(var i=0; i < forms[j].elements.length; i++){
+    //for(var i=0; i < document.forms[formName].elements.length; i++){
+            var theElem=forms[j].elements[i];
+            if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"){     
+                theElem.checked=this.checked;
+            }
+        } 
+    }
+    links = document.getElementsByName("selectAll");
+    for(var i=0; i < links.length;i++) {
+        if(links[i] != this)  links[i].checked = this.checked;
+    }       
+}
+
+
+function InitSeqAlignLinks()
+{
+    var links = document.getElementsByName("getSeqs");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",ViewSelectedSeqs,false);  
+    }
+    links = document.getElementsByName("treeView");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",ViewSelectedSeqTree,false);  
+    }    
+    links = document.getElementsByName("mltiAln");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",ViewSelectedSeqMultiAlign,false);  
+    }        
+    links = document.getElementsByName("selectAll");
+    for(var i=0; i < links.length;i++) {
+        utils.addEvent(links[i],"click",selectAllSeqs,false);  
+    }   
+    
+    if($("showAlign"))
+        utils.addEvent($("showAlign"),"click",showHideLinks,false);  
+}
+
+function InitDownLoad()
+{
+    var deltaBlast = ($("diThresh") && $("diThresh").value != "") ? true : false;
+    if (!deltaBlast && ($("stepNumber").value == "" || $("stepNumber").value < 2)) {        
+        utils.addClass($("dnPSSMPar"),"hidden");        
+    }
+}
+function Reformat()
+{
+    if(utils.hasClass($("FormatForm").FORMAT_ORGANISM,"orgHint"))  $("FormatForm").FORMAT_ORGANISM.value = "";
+    
+    $("FormatForm").submit();    
+}
+function InitCustomButton(bn)
+{
+  utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
+  utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
+  utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
+  utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);    
+}
+
+function InitAllCustomButtons()
+{
+    if($("go")) InitCustomButton($("go"));
+    if($("dn")) InitCustomButton($("dn"));
+    if($("onPageReformat")) InitCustomButton($("onPageReformat"));    
+}
+function showHideLinks()
+{
+    var links = document.getElementsByName("selectAll");
+    for(var i=0; i < links.length;i++) {
+        //This is done since IE does not recognize getElementsByName for span elem
+        var allLinks = utils.getParent(links[i]);
+        var removeClass,addClass;
+        if(utils.hasClass(allLinks,"shownInl")) {        
+            removeClass="shownInl";    
+            addClass="hidden";        
+        }
+        else {
+            removeClass="hidden";
+            addClass="shownInl";        
+        }    
+        utils.removeClass(allLinks,removeClass);
+        utils.addClass(allLinks,addClass);   
+    }
+}
+/*remove this function */
+function InitHelpLinks()
+{
+    for(var i=1; i <= 11;i++) {           
+        InitToggleEvent($("hlp" + i));      
+    }
+}
+//This function is used for collapsible deflines onmouseover="showInfo(this)"
+//Initialized in showdefline.cpp
+function showInfo(elem)
+{
+    var targetElem = $("info_" + elem.id);
+    if(!targetElem) return;
+    if(elem.getAttribute("init") == "on") return;
+    
+    Toggle.addTarget(elem, targetElem);  
+    elem.setAttribute("init","on");    
+}
+
+function InitPsiBlast()
+{
+    //utils.addEvent($("ttt"),"keyup",SetHitlistSize,false);  
+    var hts = document.getElementsByName("HITLIST_SIZE");
+    for(var i=0; i < hts.length;i++) {    
+        utils.addEvent(hts[i],"keyup",SetHitlistSize,false);  
+    } 
+    if($("psiInp")) {
+        var numSubsets = $("psiInp").getAttribute("numSubsets");
+        for(var i=1; i <= numSubsets;i++) {
+            if ($("alnPos" + i)) InitToggleEvent($("alnPos" + i));  
+            if ($("deflnG" + i)) InitToggleEvent($("deflnG" + i));
+            if ($("deflnB" + i)) InitToggleEvent($("deflnB" + i));        
+        }         
+    }
+}
+
+function SetHitlistSize()
+{
+    var hts = document.getElementsByName("HITLIST_SIZE");
+    for(var i=0; i < hts.length;i++) {    
+        if(this != hts[i]) {
+            hts[i].value = this.value;
+        }
+    }    
+}
+function InitToggleEvent(toggleNode)
+{
+    if(toggleNode) {
+        var srcid = toggleNode.getAttribute("toggle");
+        if(srcid) Toggle.addTarget(srcid, toggleNode);  
+    }
+} 				
+
+function InitIFrameLinks()
+{
+    CheckIframe($("RSIFrameNoRes"),"prlink");
+    CheckIframe($("RSIFrameDesc"),"prlink");
+    CheckIframe($("RSIFrameAln"),"prlink");
+}
+
+function CheckIframe(iframe,contentElemID)
+{
+    if(!iframe) return;
+    
+    var iframeDoc;
+    
+    if(iframe.contentDocument) {//Firefox
+        iframeDoc = iframe.contentDocument;                
+    }
+    else if (iframe.contentWindow) {//IE
+        iframeDoc = iframe.contentWindow.document;                
+    }
+    else if(iframe.document) {
+        iframeDoc = iframe.document;                
+    }
+    if(iframeDoc){        
+        if(iframeDoc.getElementById(contentElemID)) {                        
+            utils.addClass(iframe,"shown");
+            utils.removeClass(iframe,"hidden");        
+        }           
+     }
+}    
+
+
+function InitHitMatrix()
+{
+    if($("bl2seImg")) {
+    
+        utils.addEvent($("hitmtImg"),"load",
+                        function() {                              
+						    utils.addClass($("bl2seImg"),"shown");
+                            utils.removeClass($("bl2seImg"),"hidden");                  
+                           
+						}, 
+						false);          
+        utils.addEvent($("showHitMatrix"),"click",
+                        function() {                            
+                            $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
+                            if(utils.hasClass($("htmb"),"shown")) {	                                
+							    utils.addClass($("htmb"),"hidden");
+                                utils.removeClass($("htmb"),"shown");                  
+                            }
+                            else {                                
+                                utils.addClass($("htmb"),"shown");
+                                utils.removeClass($("htmb"),"hidden");                  
+                            }
+						}, 
+						false);          
+        
+        if($("blastSpec") && $("blastSpec").value=="GlobalAln") {            
+            $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
+        }        
+    }   
+}    
+    
+    
+    
+	
+ 				
+function SetFormSubmitEvent()
+{
+    var el = $("refPage");
+    if(el) {
+	    SubmitEventNew("refPage");	
+	}
+	SubmitEventNew("frmPage");	
+	el = $("searchOptions");
+	if(el) {
+	    SubmitEventNew("searchOptions");	
+	}
+	el = $("saveSearchOptions");
+	if(el) {
+	    SubmitEventNew("saveSearchOptions");	
+	}
+	//SubmitEventNew("breadCrSearchOptions");	
+	list = $("queryList");
+	if(list) {
+        utils.addEvent(list,"change",GetResults,false);  
+    }
+    
+    list = $("go");
+	if(list) {
+        utils.addEvent(list,"click",GetResults,false);  
+    }
+    
+    
+    list= $("onPageReformat");
+    if(list) {
+        utils.addEvent(list,"click",Reformat,false);  
+    }
+
+    if ($("cddResults") && $("statInfo")) {
+        jQuery($("cddResults")).ncbitoggler('toggle');
+    }
+    //New design still uses toggle    
+    if ($("showCDD")) {
+        InitToggleEvent($("cddInfo"));
+    }
+    InitToggleEvent($("refInfo"));
+    InitToggleEvent($("resStat"));
+    InitToggleEvent($("dbDetails"));
+    InitToggleEvent($("graphicInfo"));
+    InitToggleEvent($("descrInfo"));
+    InitToggleEvent($("alignInfo"));
+    InitToggleEvent($("ovrInfo"));        
+    InitToggleEvent($("queryInfo"));        
+    InitToggleEvent($("hitMatrixInfo"));            
+    InitToggleEvent($("bl2ovrInfo"));    
+    //Init only for PSI blastfse
+    if($("prevRID")) InitPsiBlast();    
+    InitSeqAlignLinks();
+    InitAllCustomButtons();        
+    if($("dnPSSMPar")) InitDownLoad(); 
+    InitHitMatrix();
+    if($("noRes")) {
+        if($("hitCvs")) utils.addClass($("hitCvs"),"hidden");
+        if($("hitText")) utils.addClass($("hitText"),"hidden");
+    }
+    InitIFrameLinks();
+    showDbDetails(); //fill behind the scene    
+    if ($("showDetails") && utils.hasClass($("showDetails"), "shown")) {
+        utils.addEvent($("showDetails"), "click", showDbDetails, false);
+    }
+    initContentWidth();    
+}
+
+function initContentWidth() {
+    var lineLengthElem = $("FormatForm").LINE_LENGTH;
+    if (lineLengthElem) {
+        var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
+        if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
+
+        var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
+        var minWidth = (lineLength + parseInt(17)) * charWidth;
+
+
+        var alignView = $("FormatForm").ALIGNMENT_VIEW;
+        var formatType = $("FormatForm").FORMAT_TYPE;
+        var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
+
+        var addWidth = ($("FormatForm").OLD_VIEW.checked || queryAnch) ? 250 : 350;
+
+        minWidth = minWidth + parseInt(addWidth) + "px";
+        jQuery($("content")).css("min-width", minWidth);
+    }
+    
+}
+
+
+
+
+
+function ShowHideAlnDeflines(alnID, checkbx) {
+    var dflTableID = "dln_" + alnID;
+    if ($(dflTableID)) {
+        var rmClass, addClass;
+        if (checkbx.checked) {
+            rmClass = "hidden";
+            addClass = "shown";
+        }
+        else {
+            rmClass = "shown";
+            addClass = "hidden";
+        }
+        var elems = $C(rmClass, "class", $(dflTableID), "tr");
+        if (elems) {
+            //alert(elems.length);
+            for (var i = 0; i < elems.length; i++) {
+                utils.removeClass(elems[i], rmClass);
+                utils.addClass(elems[i], addClass);
+            }
+        }
+    }
+}
+
+function SortAln(e, sortLink, sortItem) {
+    var p = utils.getParent(sortLink);
+    var p = utils.getParent(p);
+    p_TD = utils.getParent(p);
+    p_TR = utils.getParent(p_TD);
+    if (utils.hasClass(p_TR, "dflnAln")) {
+        p_TD.innerHTML = "Reading seqaligns...";
+        var gi = p_TD.id.substr(2);
+        var rid = p_TD.getAttribute("rid");
+        getAlignSort(rid, gi, p_TD, sortItem);
+        e = e || window.event;
+        utils.preventDefault(e);
+        return;
+    }
+    var links = document.getElementsByName("alnSort");
+    if (links.length >= sortItem) {
+        var href = links[sortItem].href.replace(new RegExp("selectAllTop.*(&|$)"), "");
+        var hrefLn = sortLink.href.replace(new RegExp(".*#"), "");
+        sortLink.href = href + hrefLn;
+    }
+}
+
+
+
+var fullArr;
+var numDbs;
+function showDbDetails(e,dbSetIndex) 
+{
+    if (!($("dbPlusSpecies"))) return; //No org display
+    if ($("dbPlusSpecies").getAttribute("init") == "on" && dbSetIndex == null) return;
+    $("dbPlusSpecies").setAttribute("init", "on");
+    
+    dbInfoUrl = "getDBInfo.cgi";
+    var rp = new RemoteDataProvider(dbInfoUrl);
+    rp.minArr = 10;
+
+    if (!fullArr) {
+        var arr = $("results").DATABASE.value.split(" ");
+        numDbs = arr.length;
+        if (arr.length > rp.minArr) {
+            fullArr = new Array();
+            while (arr.length > 1) {
+                var arrNew = arr.splice(0, rp.minArr); //does not include stopindex
+                fullArr.push(arrNew);
+            }
+            if (!dbSetIndex) dbSetIndex = 0;
+        }
+    }
+
+    rp.onSuccess = function(obj) {
+        var navDB = document.createElement("div");
+        if (fullArr) {
+            var prevLink, nextLink, firstLink, lastLink;
+            if (this.currDbSetIndex >= 1) {
+                var firstStart = 1;
+                var firstEnd = firstStart + fullArr[0].length - 1;
+                firstLink = document.createElement("a");
+                jQuery(firstLink).attr("href", "#");
+                jQuery(firstLink).attr("id", "firstDbSet");
+                jQuery(firstLink).attr("onclick", "showDbDetails(event,0);");
+                jQuery(firstLink).attr("title", "Databases " + firstStart + "-" + firstEnd);
+                jQuery(firstLink).html("First " + this.minArr + " dbs");
+
+            }
+            if (this.currDbSetIndex >= 1) {
+                var prevStart = (this.currDbSetIndex - 1) * this.minArr + 1;
+                var prevEnd = prevStart + fullArr[this.currDbSetIndex - 1].length - 1;
+                prevLink = document.createElement("a");
+                jQuery(prevLink).attr("href", "#");
+                jQuery(prevLink).attr("id", "prevDbSet");
+                jQuery(prevLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex - 1) + ");");
+                jQuery(prevLink).attr("title", "Databases " + prevStart + "-" + prevEnd);
+                jQuery(prevLink).html("Prev " + this.minArr + " dbs");
+            }
+
+            if (this.currDbSetIndex < fullArr.length - 1) {
+                var nextStart = (this.currDbSetIndex + 1) * this.minArr + 1;
+                var nextEnd = nextStart + fullArr[this.currDbSetIndex + 1].length - 1;
+                nextLink = document.createElement("a");
+                jQuery(nextLink).attr("href", "#");
+                jQuery(nextLink).attr("id", "nextDbSet");
+                jQuery(nextLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex + 1) + ");");
+                jQuery(nextLink).attr("title", "Databases " + nextStart + "-" + nextEnd);
+                jQuery(nextLink).html("Next " + this.minArr + " dbs");
+            }
+            if (this.currDbSetIndex < fullArr.length - 1) {
+                var lastInd = fullArr.length - 1;
+                var lastStart = numDbs - fullArr[lastInd].length;
+                var lastEnd = numDbs;
+                lastLink = document.createElement("a");
+                jQuery(lastLink).attr("href", "#");
+                jQuery(lastLink).attr("id", "lastDbSet");
+                jQuery(lastLink).attr("onclick", "showDbDetails(event," + lastInd + ");");
+                jQuery(lastLink).attr("title", "Databases " + lastStart + "-" + lastEnd);
+                jQuery(lastLink).html("Last " + this.minArr + " dbs");
+            }
+
+
+            jQuery(navDB).attr("id", "addDbSet");
+            if (firstLink) jQuery(navDB).append(firstLink);
+            if (prevLink) jQuery(navDB).append(prevLink);
+            if (lastLink) jQuery(navDB).append(lastLink);
+            if (nextLink) jQuery(navDB).append(nextLink);
+        }
+
+        jQuery($("dbPlusSpecies")).html(navDB);
+        jQuery(navDB).after(obj.responseText);
+        if (fullArr) {
+            var cap = jQuery($("dbSpecies")).find("caption");
+            if (cap) {
+                var currStart = (this.currDbSetIndex) * this.minArr + 1;
+                var currEnd = currStart + fullArr[this.currDbSetIndex].length - 1;
+                var capText = cap.html() + "<div class=\"cpAdd\"> Databases " + currStart + "-" + currEnd;
+                cap.html(capText);
+            }
+        }
+    };
+    rp.onError = function(obj) {
+        $("dbPlusSpecies").innerHTML += "error, requests:" + this.iActiveRequests + " status:" + obj.status;
+    }
+    var dbs;
+    if (fullArr) {
+        rp.currDbSetIndex = dbSetIndex;        
+        var currArr = fullArr[dbSetIndex];
+        dbs = currArr.join(",");
+    }
+    else {
+        dbs = $("results").DATABASE.value.replace(/ /g, ",");
+    }
+
+    rp.Request("CMD=getDBOrg&DATABASE=" + dbs, "POST");
+    if(e) utils.preventDefault(e);
+}
+
+function synchronizeCheck(id, formName, inputName, isChecked) {
+
+    for (var i = 0; i < document.forms[formName].elements.length; i++) {
+        var theElem = document.forms[formName].elements[i];
+        if (theElem.type == "checkbox" && theElem.name == inputName && id == theElem.value) {
+            theElem.checked = isChecked;
+
+        }
+    }
+
+}
+
+utils.addEvent(window,
+				"load", SetFormSubmitEvent,				
+				false);
+
+
+/* If user agent has "safari" in it, include safari-specific stylesheet. */ 
+if (navigator.userAgent.match(/safari/i) || navigator.userAgent.match(/opera/i)) {
+document.write("<link rel='stylesheet' type='text/css' href='css/safari-descriptions.css'  media='screen'/>");
+}
+if (navigator.userAgent.match(/opera/i)) {    
+document.write("<link rel='stylesheet' type='text/css' href='css/opera-descriptions.css'  media='screen'/>");
+}
+if (navigator.userAgent.match(/firefox/i) || navigator.userAgent.match(/safari/i)) {
+document.write("<link rel='stylesheet' type='text/css' href='css/firefox-descriptions.css'  media='screen'/>");
+}
+
+
+