annotate NCBI Blast reference example_files/results.js @ 120:2729c2326235

Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.

// 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'/>");
}