annotate NCBI Blast reference example_files/blast.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.

function printfire()
{
    // Firefox
    if (document.createEvent && window.dispatchEvent) {
        printfire.args = arguments;
        var ev = document.createEvent("Events");
        ev.initEvent("printfire", false, true);
        window.dispatchEvent(ev);
    }
}
//This functions handle setting defaults for protein or nulcleotide suite  search page when
//one of blast program radio buttons is clicked - not used now
function AdjustMoreOptionsStyle()
{
	var optsEl = document.getElementById("moreopts");	
	if(optsEl && optsEl.style.height != "0px") {
		optsEl.style.height = optsEl.scrollHeight + "px";			
	}
}

//Strip (taxid:XXX) from organism list selection
//sgRunFunc="AdjustOrganism();" 
function AdjustOrganism()
{
	var words = $("qorganism").value.split(" (taxid");
	$("qorganism").value = words[0];		
}


/* JS Common to all BLAST pages */


function setResultsTarget()
{
	//var newWin = $("newwin");	
	var newWin = this;	
	var searchFrm = $(newWin.getAttribute("form"));				
	if(newWin && newWin.checked == true) {
		if(newWin.getAttribute("winType") == "random") {		    
			searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random());
		}
		else {
			searchFrm.target = $("resPageTarget").value;		
		}
	}	
	else {		
		searchFrm.target = "";
	}
}

function diffFromDefault(elem)
{
    var currentVal = "";
    var ret = 0;

    if (!(elem)) return;
    var defVal = elem.getAttribute("defVal"); //Default value    
    var elShowDiff = utils.getParent(elem);
    if(!elem.type) {//div element for example
        //Check if parent elem has "hide" class
        if(utils.hasClass(utils.getParent(elem), "hide")) {
            currentVal = "hide";
        }
        else {
            currentVal = "show";
        }   
        elShowDiff = elem;
    }
    else if(elem.type == "select-one") {
        if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value;
        //If Default value is not specified - the first one in the selection list is the default          
        if (!defVal && elem[0].value) defVal = elem[0].value;  
    }
    else if(elem.type == "select-multiple") {
	    currentVal = "";//for now
    }
    else if(elem.type == "checkbox") {
        //alert("defVal1=" + elem.id + " " + defVal);
        //var defVal = elem.defVal; //Default value
        //alert("defVal2=" + defVal);
        if(elem.checked == true) currentVal = "checked"
        else  currentVal = "unchecked";        
    }
    else {
        currentVal = elem.value;
    }
    
    
    var numdiff = parseInt($("NUM_DIFFS").value,10);    
    var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10);    
    if(defVal != currentVal) {        
        if(!utils.hasClass(elShowDiff, "nondef")) {        
            utils.addClass(elShowDiff, "nondef");            
            numdiff++;            
            if(utils.hasClass(elem,"opts")) optsNumDiff++;        
        }     
        ret = 1;        
    }
    else {        
        if(utils.hasClass(elShowDiff, "nondef")) {
            utils.removeClass(elShowDiff, "nondef");        
            //alert("noDiff-" + elem.id);
            if(numdiff != 0) numdiff--;       
            if(utils.hasClass(elem,"opts")) optsNumDiff--; 
        }         
        ret=0;
    }
    $("NUM_DIFFS").value = numdiff;       
    $("NUM_OPTS_DIFFS").value = optsNumDiff;       
    if(numdiff > 0) {    
        $("diffMes").style.display = "inline";          
    }
    else {
        $("diffMes").style.display = "none";           
    }      
    //alert(elem.id + " " + $("NUM_DIFFS").value);
    return ret;    
}

function setDefalValue(elem)
{
    var currentVal;    
    var defVal = elem.getAttribute("defVal"); //Default value    
    if(elem.type == "select-one") {
        //If Default value is not specified - the first one in the selection list is the default          
        if(!defVal) defVal = elem[0].value;  
        for(j=0; j < elem.options.length; j++) {
		    if(elem.options[j].value == defVal) {
		        elem.options[j].selected = true;
		        break;
		    }
        }       
    }
    else if(elem.type == "checkbox" || elem.type == "radio") {        
        if(!defVal) defVal = "checked";
        if(defVal == "checked") elem.checked = true        
        else elem.checked = false;
    }
    else {
        if(!defVal) defVal = "";
        elem.value = defVal;
    }
    
    var elShowDiff = utils.getParent(elem);    
    if(utils.hasClass(elShowDiff, "nondef")) {
        utils.removeClass(elShowDiff, "nondef");        
    }            
    //alert(elem.id + " " + $("NUM_DIFFS").value);    
}

function newResultsWinInit() {
    jQuery("[class='newwin']").each(function(index) {
        utils.addEvent(this, "click", setResultsTarget, false);
    });
}

function resetOrganismSuggest(orgEntryElem) 
{
    //suggestHint is in the hidden field used for SRA
    var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested";
    var suggestHint = $("qorganism").getAttribute("suggestHint");
    if(suggestHint) defaultMessage = suggestHint;
    if(orgEntryElem.value == "") {
        orgEntryElem.value = defaultMessage;
    }
    if(orgEntryElem.value == defaultMessage) {            
        utils.addClass(orgEntryElem,"orgHint");
    }
}  

function setupOrganismSuggest(orgEntryElem)
{
    resetOrganismSuggest(orgEntryElem); 
    utils.addEvent(orgEntryElem, "focus", function() {
        clearOrgSuggest(orgEntryElem);        
     }, false);     
}

function clearOrgSuggest(orgEntryElem)
{
    if(utils.hasClass(orgEntryElem,"orgHint")) {
        orgEntryElem.value="";            
        utils.removeClass(orgEntryElem,"orgHint");
    }
}    

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 showHideElem(id,hide)
{
  if($(id)) {
    if(hide) {
	    if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden");	    
	}
	else {
	    if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden");	    
	}	
  }
}

function resetOrganismControls(orgEntryElem) {
    resetOrganismSuggest(orgEntryElem);
    if ($("orgExcl")) $("orgExcl").checked = false;
    utils.replaceInHtml("", $("orgs"));
    if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs"));
    if ($("numOrg")) $("numOrg").value = 1;
}

function AddOrgRow(e,orgName,exclName) {
    e = e || window.event;
    utils.preventDefault(e);
    var checkedExclude = new Array();
    var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary");
    orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict;
    var len = $("qorganism").getAttribute("size");
    
    var newOrgFieldID = "qorganism" + $("numOrg").value;
    var newOrgField = " <div><input name=\"" + orgName + $("numOrg").value + "\" size=\"" + len + "\" id=\"" + newOrgFieldID +
                       "\" type=\"text\" data-jigconfig=\"dictionary:'" + orgDict + "'\" autocomplete=\"off\" class=\"jig-ncbiautocomplete multiOrg\" />";
    if (exclName != "") {
        newOrgField += "<span class=\"orgExcl\">" +
                       "<input type=\"checkbox\" name=\"" + exclName + $("numOrg").value + "\" class=\"oExcl cb\" id=\"orgExcl" + $("numOrg").value + "\" />" +
                       "<label for=\"orgExcl" + $("numOrg").value + "\" class=\"right oExclRl\">Exclude</label></span>";
    }
    newOrgField += "</div>";
    if (navigator.userAgent.match(/ie/i)) {
        for (i = 1; i < $("numOrg").value; i++) {
            if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked;
        }
    }
    if (!navigator.userAgent.match(/firefox/i)) {    
        jQuery($($(orgs))).append(newOrgField,true);
    }
    else {
        utils.insertInHtml(newOrgField, $("orgs"));
    }

    if (navigator.userAgent.match(/ie/i)) {
        for (i = 1; i < $("numOrg").value; i++) {
            if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i];
        }
    }
    setupOrganismSuggest($(newOrgFieldID));
    jQuery($($(newOrgFieldID))).ncbiautocomplete();
    $("numOrg").value++;    
}

function adjustOrgVal(orgEntryElem) 
{
    //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = "";
    clearOrgSuggest(orgEntryElem);
    if ($("numOrg")) {
        for (i = 1; i < $("numOrg").value; i++) {
            if ($("qorganism" + i)) {
                clearOrgSuggest($("qorganism" + i));
            }
        }
    }
}

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 getUrlCompForMultiOptionsField(elem) {
    var url = "";
    if (elem) {
        for (i = 0; i < elem.options.length; i++) {
            if (elem.options[i].selected) {
                url += "&" + elem.name + "=" + elem.options[i].value;
            }
        }
    }
    return url;
}

  
utils.addEvent(window, 'load', newResultsWinInit, false);