blast2html: NCBI Blast reference example_files/results.js annotate

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.

author	Jan Kanis <jan.code@jankanis.nl>
date	Thu, 31 Jul 2014 16:14:36 +0200
parents	344cd76f6fd2
children

rev	line source
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1 // JScript source code
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	3 //Display Reformat page button only after the whole page is loaded
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	4
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	5 function ReformatPageEvent()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	6 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	7 var refPageLink = document.getElementById("refPage");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	8
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	9 //alert(refPageLink);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	10 //alert(refPageLink.getAttribute("submitForm"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	11 var submitForm = refPageLink.getAttribute("submitForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	12 alert(submitForm);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	13 if(refPageLink && submitForm) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	14 utils.addEvent(refPageLink,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	15 "click",
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	16 function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	17 document.getElementById(submitForm).submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	18 },
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	19 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	20 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	21 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	22
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	23
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	24 function SubmitEvent(linkID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	25 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	26
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	27 var link = document.getElementById(linkID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	28 //alert(link.getAttribute("submitForm"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	29 var submitForm = link.getAttribute("submitForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	30 if(link && submitForm) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	31 utils.addEvent(link,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	32 "click",
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	33 function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	34 document.getElementById(submitForm).submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	35 },
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	36 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	37 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	38 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	39
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	40
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	41 function SubmitEventSave(linkID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	42 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	43
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	44 var link = document.getElementById(linkID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	45 //alert(link.getAttribute("submitForm"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	46 var submitForm = link.getAttribute("submitForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	47 if(link && submitForm) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	48 utils.addEvent(link,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	49 "click",
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	50 function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	51 //$(submitForm).CMD.value = "GetSaved";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	52 document.getElementById(submitForm).submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	53 },
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	54 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	55 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	56 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	57
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	58
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	59
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	60
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	61 //This function creates submit form event on click
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	62 //form submitted is defined in submitForm attribute
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	63 //It also copies params from forms[0] (search paramateres) created by formatter
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	64 function SubmitEventNew(linkID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	65 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	66
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	67 var link = document.getElementById(linkID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	68 //alert(link.getAttribute("submitForm"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	69 if(!link) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	70 var submitForm = link.getAttribute("submitForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	71 if(link && submitForm) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	72 utils.addEvent(link,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	73 "click",
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	74 function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	75 document.forms[0].CMD.value = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	76 if(document.forms[0].PAGE_TYPE) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	77 document.forms[0].PAGE_TYPE.value = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	78 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	79 var s = document.forms[0].innerHTML;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	80 var form = $(submitForm);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	81 form.innerHTML = s + form.innerHTML;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	82 form.submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	83 },
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	84 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	85 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	86 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	87
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	88 function GetResults()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	89 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	90 form = $("results");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	91 form.QUERY_INDEX.value = $("queryList")[$("queryList").selectedIndex].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	92 form.submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	93 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	94
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	95 function isIdIn(id, idArray){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	96 var idSeen=false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	97
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	98 for(i=0; i<idArray.length; i++){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	99 if(id==idArray[i]){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	100 idSeen=true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	101 break;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	102 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	103 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	104 return idSeen;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	105 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	106
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	107 function GetSelectedSeqString(formName)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	108 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	109 var selSeqs = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	110 var idArray=new Array();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	111 forms = document.getElementsByName(formName);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	112 for(var j=0; j < forms.length; j++){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	113 for(var i=0; i < forms[j].elements.length; i++){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	114 var theElem=forms[j].elements[i];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	115 if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"&&theElem.checked){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	116 if(!isIdIn(theElem.value, idArray)){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	117 idArray[idArray.length]=theElem.value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	118 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	119 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	120 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	121 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	122 selSeqs = idArray.join();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	123 return selSeqs;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	124 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	125
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	126 function ViewSelectedSeqs(e)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	127 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	128 var submitForm = $("submitterTop");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	129 var targetForm = submitForm.getAttribute("seqsForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	130 $("selSeqs").value = GetSelectedSeqString(targetForm);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	131 submitForm.submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	132 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	133 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	134
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	135
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	136 function ViewSelectedSeqTree()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	137 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	138 var submitForm = $("treesubmitterTop");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	139 var targetForm = submitForm.getAttribute("seqsForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	140 $("seqSet").value = GetSelectedSeqString(targetForm);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	141 $("scrWidth").value = screen.width;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	142 $("scrHeight").value = screen.height;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	143 submitForm.submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	144 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	145
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	146 function ViewTree(linkID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	147 link = document.getElementById(linkID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	148 var target = link.target;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	149 winRef = window.open(link.href + "&screenWidth=" + screen.width + "&screenHeight=" + screen.height, target);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	150 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	151
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	152 function ViewSelectedSeqMultiAlign()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	153 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	154 var submitForm = $("multisubmitterTop");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	155 var targetForm = submitForm.getAttribute("seqsForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	156 $("seqSetM").value = GetSelectedSeqString(targetForm);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	157 submitForm.submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	158 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	159
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	160
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	161
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	162 function selectAllSeqs()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	163 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	164 var formName = this.getAttribute("seqsForm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	165 forms = document.getElementsByName(formName);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	166 for(var j=0; j < forms.length; j++){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	167 for(var i=0; i < forms[j].elements.length; i++){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	168 //for(var i=0; i < document.forms[formName].elements.length; i++){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	169 var theElem=forms[j].elements[i];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	170 if(theElem.type=="checkbox"&&theElem.name=="getSeqGi"){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	171 theElem.checked=this.checked;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	172 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	173 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	174 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	175 links = document.getElementsByName("selectAll");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	176 for(var i=0; i < links.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	177 if(links[i] != this) links[i].checked = this.checked;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	178 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	179 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	180
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	181
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	182 function InitSeqAlignLinks()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	183 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	184 var links = document.getElementsByName("getSeqs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	185 for(var i=0; i < links.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	186 utils.addEvent(links[i],"click",ViewSelectedSeqs,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	187 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	188 links = document.getElementsByName("treeView");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	189 for(var i=0; i < links.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	190 utils.addEvent(links[i],"click",ViewSelectedSeqTree,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	191 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	192 links = document.getElementsByName("mltiAln");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	193 for(var i=0; i < links.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	194 utils.addEvent(links[i],"click",ViewSelectedSeqMultiAlign,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	195 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	196 links = document.getElementsByName("selectAll");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	197 for(var i=0; i < links.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	198 utils.addEvent(links[i],"click",selectAllSeqs,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	199 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	200
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	201 if($("showAlign"))
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	202 utils.addEvent($("showAlign"),"click",showHideLinks,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	203 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	204
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	205 function InitDownLoad()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	206 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	207 var deltaBlast = ($("diThresh") && $("diThresh").value != "") ? true : false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	208 if (!deltaBlast && ($("stepNumber").value == "" \|\| $("stepNumber").value < 2)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	209 utils.addClass($("dnPSSMPar"),"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	210 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	211 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	212 function Reformat()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	213 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	214 if(utils.hasClass($("FormatForm").FORMAT_ORGANISM,"orgHint")) $("FormatForm").FORMAT_ORGANISM.value = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	215
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	216 $("FormatForm").submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	217 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	218 function InitCustomButton(bn)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	219 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	220 utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	221 utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	222 utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	223 utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	224 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	225
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	226 function InitAllCustomButtons()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	227 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	228 if($("go")) InitCustomButton($("go"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	229 if($("dn")) InitCustomButton($("dn"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	230 if($("onPageReformat")) InitCustomButton($("onPageReformat"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	231 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	232 function showHideLinks()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	233 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	234 var links = document.getElementsByName("selectAll");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	235 for(var i=0; i < links.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	236 //This is done since IE does not recognize getElementsByName for span elem
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	237 var allLinks = utils.getParent(links[i]);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	238 var removeClass,addClass;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	239 if(utils.hasClass(allLinks,"shownInl")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	240 removeClass="shownInl";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	241 addClass="hidden";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	242 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	243 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	244 removeClass="hidden";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	245 addClass="shownInl";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	246 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	247 utils.removeClass(allLinks,removeClass);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	248 utils.addClass(allLinks,addClass);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	249 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	250 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	251 /remove this function /
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	252 function InitHelpLinks()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	253 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	254 for(var i=1; i <= 11;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	255 InitToggleEvent($("hlp" + i));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	256 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	257 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	258 //This function is used for collapsible deflines onmouseover="showInfo(this)"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	259 //Initialized in showdefline.cpp
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	260 function showInfo(elem)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	261 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	262 var targetElem = $("info_" + elem.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	263 if(!targetElem) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	264 if(elem.getAttribute("init") == "on") return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	265
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	266 Toggle.addTarget(elem, targetElem);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	267 elem.setAttribute("init","on");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	268 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	269
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	270 function InitPsiBlast()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	271 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	272 //utils.addEvent($("ttt"),"keyup",SetHitlistSize,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	273 var hts = document.getElementsByName("HITLIST_SIZE");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	274 for(var i=0; i < hts.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	275 utils.addEvent(hts[i],"keyup",SetHitlistSize,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	276 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	277 if($("psiInp")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	278 var numSubsets = $("psiInp").getAttribute("numSubsets");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	279 for(var i=1; i <= numSubsets;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	280 if ($("alnPos" + i)) InitToggleEvent($("alnPos" + i));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	281 if ($("deflnG" + i)) InitToggleEvent($("deflnG" + i));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	282 if ($("deflnB" + i)) InitToggleEvent($("deflnB" + i));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	283 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	284 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	285 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	286
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	287 function SetHitlistSize()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	288 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	289 var hts = document.getElementsByName("HITLIST_SIZE");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	290 for(var i=0; i < hts.length;i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	291 if(this != hts[i]) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	292 hts[i].value = this.value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	293 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	294 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	295 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	296 function InitToggleEvent(toggleNode)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	297 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	298 if(toggleNode) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	299 var srcid = toggleNode.getAttribute("toggle");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	300 if(srcid) Toggle.addTarget(srcid, toggleNode);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	301 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	302 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	303
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	304 function InitIFrameLinks()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	305 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	306 CheckIframe($("RSIFrameNoRes"),"prlink");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	307 CheckIframe($("RSIFrameDesc"),"prlink");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	308 CheckIframe($("RSIFrameAln"),"prlink");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	309 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	310
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	311 function CheckIframe(iframe,contentElemID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	312 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	313 if(!iframe) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	314
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	315 var iframeDoc;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	316
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	317 if(iframe.contentDocument) {//Firefox
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	318 iframeDoc = iframe.contentDocument;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	319 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	320 else if (iframe.contentWindow) {//IE
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	321 iframeDoc = iframe.contentWindow.document;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	322 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	323 else if(iframe.document) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	324 iframeDoc = iframe.document;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	325 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	326 if(iframeDoc){
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	327 if(iframeDoc.getElementById(contentElemID)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	328 utils.addClass(iframe,"shown");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	329 utils.removeClass(iframe,"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	330 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	331 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	332 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	333
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	334
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	335 function InitHitMatrix()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	336 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	337 if($("bl2seImg")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	338
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	339 utils.addEvent($("hitmtImg"),"load",
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	340 function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	341 utils.addClass($("bl2seImg"),"shown");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	342 utils.removeClass($("bl2seImg"),"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	343
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	344 },
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	345 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	346 utils.addEvent($("showHitMatrix"),"click",
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	347 function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	348 $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	349 if(utils.hasClass($("htmb"),"shown")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	350 utils.addClass($("htmb"),"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	351 utils.removeClass($("htmb"),"shown");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	352 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	353 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	354 utils.addClass($("htmb"),"shown");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	355 utils.removeClass($("htmb"),"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	356 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	357 },
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	358 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	359
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	360 if($("blastSpec") && $("blastSpec").value=="GlobalAln") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	361 $("hitmtImg").src= $("hitmtImg").getAttribute("imgsrc");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	362 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	363 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	364 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	365
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	366
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	367
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	368
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	369
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	370 function SetFormSubmitEvent()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	371 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	372 var el = $("refPage");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	373 if(el) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	374 SubmitEventNew("refPage");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	375 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	376 SubmitEventNew("frmPage");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	377 el = $("searchOptions");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	378 if(el) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	379 SubmitEventNew("searchOptions");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	380 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	381 el = $("saveSearchOptions");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	382 if(el) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	383 SubmitEventNew("saveSearchOptions");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	384 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	385 //SubmitEventNew("breadCrSearchOptions");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	386 list = $("queryList");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	387 if(list) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	388 utils.addEvent(list,"change",GetResults,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	389 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	390
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	391 list = $("go");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	392 if(list) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	393 utils.addEvent(list,"click",GetResults,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	394 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	395
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	396
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	397 list= $("onPageReformat");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	398 if(list) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	399 utils.addEvent(list,"click",Reformat,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	400 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	401
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	402 if ($("cddResults") && $("statInfo")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	403 jQuery($("cddResults")).ncbitoggler('toggle');
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	404 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	405 //New design still uses toggle
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	406 if ($("showCDD")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	407 InitToggleEvent($("cddInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	408 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	409 InitToggleEvent($("refInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	410 InitToggleEvent($("resStat"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	411 InitToggleEvent($("dbDetails"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	412 InitToggleEvent($("graphicInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	413 InitToggleEvent($("descrInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	414 InitToggleEvent($("alignInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	415 InitToggleEvent($("ovrInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	416 InitToggleEvent($("queryInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	417 InitToggleEvent($("hitMatrixInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	418 InitToggleEvent($("bl2ovrInfo"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	419 //Init only for PSI blastfse
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	420 if($("prevRID")) InitPsiBlast();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	421 InitSeqAlignLinks();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	422 InitAllCustomButtons();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	423 if($("dnPSSMPar")) InitDownLoad();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	424 InitHitMatrix();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	425 if($("noRes")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	426 if($("hitCvs")) utils.addClass($("hitCvs"),"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	427 if($("hitText")) utils.addClass($("hitText"),"hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	428 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	429 InitIFrameLinks();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	430 showDbDetails(); //fill behind the scene
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	431 if ($("showDetails") && utils.hasClass($("showDetails"), "shown")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	432 utils.addEvent($("showDetails"), "click", showDbDetails, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	433 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	434 initContentWidth();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	435 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	436
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	437 function initContentWidth() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	438 var lineLengthElem = $("FormatForm").LINE_LENGTH;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	439 if (lineLengthElem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	440 var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	441 if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	442
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	443 var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	444 var minWidth = (lineLength + parseInt(17)) * charWidth;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	445
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	446
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	447 var alignView = $("FormatForm").ALIGNMENT_VIEW;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	448 var formatType = $("FormatForm").FORMAT_TYPE;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	449 var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	450
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	451 var addWidth = ($("FormatForm").OLD_VIEW.checked \|\| queryAnch) ? 250 : 350;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	452
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	453 minWidth = minWidth + parseInt(addWidth) + "px";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	454 jQuery($("content")).css("min-width", minWidth);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	455 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	456
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	457 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	458
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	459
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	460
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	461
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	462
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	463 function ShowHideAlnDeflines(alnID, checkbx) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	464 var dflTableID = "dln_" + alnID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	465 if ($(dflTableID)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	466 var rmClass, addClass;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	467 if (checkbx.checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	468 rmClass = "hidden";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	469 addClass = "shown";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	470 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	471 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	472 rmClass = "shown";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	473 addClass = "hidden";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	474 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	475 var elems = $C(rmClass, "class", $(dflTableID), "tr");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	476 if (elems) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	477 //alert(elems.length);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	478 for (var i = 0; i < elems.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	479 utils.removeClass(elems[i], rmClass);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	480 utils.addClass(elems[i], addClass);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	481 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	482 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	483 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	484 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	485
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	486 function SortAln(e, sortLink, sortItem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	487 var p = utils.getParent(sortLink);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	488 var p = utils.getParent(p);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	489 p_TD = utils.getParent(p);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	490 p_TR = utils.getParent(p_TD);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	491 if (utils.hasClass(p_TR, "dflnAln")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	492 p_TD.innerHTML = "Reading seqaligns...";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	493 var gi = p_TD.id.substr(2);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	494 var rid = p_TD.getAttribute("rid");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	495 getAlignSort(rid, gi, p_TD, sortItem);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	496 e = e \|\| window.event;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	497 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	498 return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	499 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	500 var links = document.getElementsByName("alnSort");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	501 if (links.length >= sortItem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	502 var href = links[sortItem].href.replace(new RegExp("selectAllTop.*(&\|$)"), "");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	503 var hrefLn = sortLink.href.replace(new RegExp(".*#"), "");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	504 sortLink.href = href + hrefLn;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	505 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	506 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	507
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	508
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	509
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	510 var fullArr;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	511 var numDbs;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	512 function showDbDetails(e,dbSetIndex)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	513 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	514 if (!($("dbPlusSpecies"))) return; //No org display
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	515 if ($("dbPlusSpecies").getAttribute("init") == "on" && dbSetIndex == null) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	516 $("dbPlusSpecies").setAttribute("init", "on");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	517
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	518 dbInfoUrl = "getDBInfo.cgi";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	519 var rp = new RemoteDataProvider(dbInfoUrl);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	520 rp.minArr = 10;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	521
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	522 if (!fullArr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	523 var arr = $("results").DATABASE.value.split(" ");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	524 numDbs = arr.length;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	525 if (arr.length > rp.minArr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	526 fullArr = new Array();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	527 while (arr.length > 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	528 var arrNew = arr.splice(0, rp.minArr); //does not include stopindex
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	529 fullArr.push(arrNew);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	530 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	531 if (!dbSetIndex) dbSetIndex = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	532 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	533 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	534
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	535 rp.onSuccess = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	536 var navDB = document.createElement("div");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	537 if (fullArr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	538 var prevLink, nextLink, firstLink, lastLink;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	539 if (this.currDbSetIndex >= 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	540 var firstStart = 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	541 var firstEnd = firstStart + fullArr[0].length - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	542 firstLink = document.createElement("a");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	543 jQuery(firstLink).attr("href", "#");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	544 jQuery(firstLink).attr("id", "firstDbSet");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	545 jQuery(firstLink).attr("onclick", "showDbDetails(event,0);");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	546 jQuery(firstLink).attr("title", "Databases " + firstStart + "-" + firstEnd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	547 jQuery(firstLink).html("First " + this.minArr + " dbs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	548
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	549 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	550 if (this.currDbSetIndex >= 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	551 var prevStart = (this.currDbSetIndex - 1) * this.minArr + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	552 var prevEnd = prevStart + fullArr[this.currDbSetIndex - 1].length - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	553 prevLink = document.createElement("a");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	554 jQuery(prevLink).attr("href", "#");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	555 jQuery(prevLink).attr("id", "prevDbSet");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	556 jQuery(prevLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex - 1) + ");");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	557 jQuery(prevLink).attr("title", "Databases " + prevStart + "-" + prevEnd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	558 jQuery(prevLink).html("Prev " + this.minArr + " dbs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	559 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	560
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	561 if (this.currDbSetIndex < fullArr.length - 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	562 var nextStart = (this.currDbSetIndex + 1) * this.minArr + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	563 var nextEnd = nextStart + fullArr[this.currDbSetIndex + 1].length - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	564 nextLink = document.createElement("a");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	565 jQuery(nextLink).attr("href", "#");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	566 jQuery(nextLink).attr("id", "nextDbSet");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	567 jQuery(nextLink).attr("onclick", "showDbDetails(event," + (this.currDbSetIndex + 1) + ");");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	568 jQuery(nextLink).attr("title", "Databases " + nextStart + "-" + nextEnd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	569 jQuery(nextLink).html("Next " + this.minArr + " dbs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	570 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	571 if (this.currDbSetIndex < fullArr.length - 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	572 var lastInd = fullArr.length - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	573 var lastStart = numDbs - fullArr[lastInd].length;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	574 var lastEnd = numDbs;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	575 lastLink = document.createElement("a");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	576 jQuery(lastLink).attr("href", "#");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	577 jQuery(lastLink).attr("id", "lastDbSet");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	578 jQuery(lastLink).attr("onclick", "showDbDetails(event," + lastInd + ");");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	579 jQuery(lastLink).attr("title", "Databases " + lastStart + "-" + lastEnd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	580 jQuery(lastLink).html("Last " + this.minArr + " dbs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	581 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	582
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	583
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	584 jQuery(navDB).attr("id", "addDbSet");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	585 if (firstLink) jQuery(navDB).append(firstLink);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	586 if (prevLink) jQuery(navDB).append(prevLink);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	587 if (lastLink) jQuery(navDB).append(lastLink);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	588 if (nextLink) jQuery(navDB).append(nextLink);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	589 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	590
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	591 jQuery($("dbPlusSpecies")).html(navDB);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	592 jQuery(navDB).after(obj.responseText);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	593 if (fullArr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	594 var cap = jQuery($("dbSpecies")).find("caption");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	595 if (cap) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	596 var currStart = (this.currDbSetIndex) * this.minArr + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	597 var currEnd = currStart + fullArr[this.currDbSetIndex].length - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	598 var capText = cap.html() + "<div class=\"cpAdd\"> Databases " + currStart + "-" + currEnd;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	599 cap.html(capText);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	600 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	601 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	602 };
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	603 rp.onError = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	604 $("dbPlusSpecies").innerHTML += "error, requests:" + this.iActiveRequests + " status:" + obj.status;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	605 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	606 var dbs;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	607 if (fullArr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	608 rp.currDbSetIndex = dbSetIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	609 var currArr = fullArr[dbSetIndex];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	610 dbs = currArr.join(",");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	611 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	612 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	613 dbs = $("results").DATABASE.value.replace(/ /g, ",");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	614 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	615
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	616 rp.Request("CMD=getDBOrg&DATABASE=" + dbs, "POST");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	617 if(e) utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	618 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	619
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	620 function synchronizeCheck(id, formName, inputName, isChecked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	621
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	622 for (var i = 0; i < document.forms[formName].elements.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	623 var theElem = document.forms[formName].elements[i];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	624 if (theElem.type == "checkbox" && theElem.name == inputName && id == theElem.value) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	625 theElem.checked = isChecked;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	626
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	627 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	628 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	629
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	630 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	631
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	632 utils.addEvent(window,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	633 "load", SetFormSubmitEvent,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	634 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	635
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	636
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	637 /* If user agent has "safari" in it, include safari-specific stylesheet. */
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	638 if (navigator.userAgent.match(/safari/i) \|\| navigator.userAgent.match(/opera/i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	639 document.write("<link rel='stylesheet' type='text/css' href='css/safari-descriptions.css' media='screen'/>");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	640 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	641 if (navigator.userAgent.match(/opera/i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	642 document.write("<link rel='stylesheet' type='text/css' href='css/opera-descriptions.css' media='screen'/>");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	643 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	644 if (navigator.userAgent.match(/firefox/i) \|\| navigator.userAgent.match(/safari/i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	645 document.write("<link rel='stylesheet' type='text/css' href='css/firefox-descriptions.css' media='screen'/>");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	646 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	647
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	648
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	649