blast2html: NCBI Blast reference example_files/formatRes.js annotate

annotate NCBI Blast reference example_files/formatRes.js @ 73:67b1a319c6dc py2.6

First go at 2.6 compatibility The tests are running without errors, but they don't produce the same output as python3

author	Jan Kanis <jan.code@jankanis.nl>
date	Wed, 18 Jun 2014 16:21:45 +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 /***********************new code begin *****************************************************/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	3
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	4 function getHiddenFieldVal(elemName) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	5 var val;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	6 var elem = document.getElementsByName(elemName);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	7 if (elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	8 val = (elem.length > 1) ? elem[0].value : elem.value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	9 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	10 return val;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	11 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	12
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	13 function getHiddenFieldParamString(elemName) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	14 var ret = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	15 var val = getHiddenFieldVal(elemName);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	16 if (val) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	17 ret = "&" + elemName + "=" + val;
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 return ret;
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 function elementInViewport(el) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	23 if (!el) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	24 var rect = el.getBoundingClientRect();
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 var myWidth = 0, myHeight = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	27 if (typeof (window.innerWidth) == 'number') {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	28 //Non-IE
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	29 myWidth = window.innerWidth;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	30 myHeight = window.innerHeight;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	31 } else if (document.documentElement && (document.documentElement.clientWidth \|\| document.documentElement.clientHeight)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	32 //IE 6+ in 'standards compliant mode'
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	33 myWidth = document.documentElement.clientWidth;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	34 myHeight = document.documentElement.clientHeight;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	35 } else if (document.body && (document.body.clientWidth \|\| document.body.clientHeight)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	36 //IE 4 compatible
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	37 myWidth = document.body.clientWidth;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	38 myHeight = document.body.clientHeight;
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 //window.alert('Width = ' + myWidth);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	41 //window.alert('Height = ' + myHeight);
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 //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	45 //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	46 return (rect.top >= 0 && rect.bottom <= myHeight);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	47 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	48
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	49 function DisplayAlignFromDescription(elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	50 var alignView = $("FormatForm").ALIGNMENT_VIEW;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	51 if (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	52 DisplayDynamicAlign(elem);
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 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	55 location.href = "#" + elem.getAttribute("seqID");
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 //<a class="deflnDesc" hsp=<hsp_num> ind="<index>" gi="<gi>" id="deflnDesc_gi" href="#AlnHdrgi">desc</a>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	60 //<div class="alnHdr" gi="<gi>" id="alnHdr_<index>">
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	61 function DisplayDynamicAlign(elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	62 var currGi = elem.getAttribute("gi");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	63 var currInd = elem.getAttribute("ind");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	64 var stat = elem.getAttribute("stat");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	65 if (!currInd \|\| !currGi) return;
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 if (!stat \|\| stat == "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	68 //Get 4(5) aligns before currInd and 4(5) aligns after
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	69 ReadCurrentSeqAligns(currInd, 5);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	70 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	71 else if (stat == "read") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	72 var indexes = getCurrIndexRange(currInd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	73 if (indexes) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	74 var msgID = "alnShow_" + indexes[0];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	75 location.href = "#" + msgID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	76 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	77 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	78 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	79 //error status handling
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	80 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	81 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	82
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 function goToNextAlign(dtrID, next) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	85 var currInd = parseInt($(dtrID).getAttribute("ind"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	86 var rid = $("Rid").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	87 nextInd = (next) ? currInd + 1 : currInd - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	88
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	89 if ($("deflnDesc_" + nextInd)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	90 currGi = $("deflnDesc_" + nextInd).getAttribute("seqID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	91 scrollToGI = currGi;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	92 if (!$("deflnDesc_" + nextInd).getAttribute("stat") \|\| $("deflnDesc_" + nextInd).getAttribute("stat") == "") {
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 if (!next) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	95 ReadPrevSeqAligns(currInd, 5, scrollToGI);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	96 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	97 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	98 //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!!
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	99 ReadNextSeqAligns(currInd, 5, scrollToGI);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	100 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	101
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 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	104 location.href = "#" + scrollToGI;
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 }
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 function goToDefLine(dtrID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	110 if ($("psiInp")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	111 var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	112 togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	113 jQuery($(togglerID)).ncbitoggler("open");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	114 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	115 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	116
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	117 /*
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	118 readAln.rid = rid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	119 readAln.startIndex = parseInt(currInd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	120 readAln.numSeq = parseInt(maxNumAligns);
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 readAln.insertAfterID = insertAfterID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	123 readAln.seqList = giList;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	124 readAln.scrollToSeqID = scrollToGI;
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 ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	127 var lastDispIdx = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	128 var rid = $("Rid").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	129
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	130 var readAln = new Object();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	131 readAln.seqList = ""; //giList
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	132 readAln.rid = rid;
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 currInd = parseInt(currInd);
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 if (currInd != 0 && $("deflnDesc_" + currInd)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	137 var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_<ind>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	138 //alert(par.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	139 if (par) par = utils.getParent(par); //"alnShow_<ind>
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	140 //alert(par.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	141 if (par) readAln.insertAfterID = par.id;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	142 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	143 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	144 readAln.insertAfterID = "alnStart";
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
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	147
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	148
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	149 readAln.startIndex = currInd + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	150 readAln.numSeq = maxNumAligns;
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 checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next");
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 readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	155 readAln.hspSort = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	156 ReadSeqAlignByIndex(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	157 }
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 function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	160 var lastDispIdx = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	161 var rid = $("Rid").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	162
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	163 var readAln = new Object();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	164 readAln.seqList = ""; //giList
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	165 readAln.rid = rid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	166
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	167 currInd = parseInt(currInd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	168
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	169
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	170 //sets readAln.insertAfterID and returns lastDispIdx;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	171 //Find the index of the previously displayed alignment
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	172 lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
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 readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	175 readAln.numSeq = currInd - readAln.startIndex; //stopIndex = currInd
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	176
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	177 checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev");
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 readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	180 readAln.hspSort = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	181 ReadSeqAlignByIndex(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	182 }
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 //When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	185 function ReadCurrentSeqAligns(currInd, maxNumAligns) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	186 var rid = $("Rid").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	187 var readAln = new Object();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	188 readAln.seqList = ""; //giList
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	189 readAln.rid = rid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	190
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	191 currInd = parseInt(currInd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	192
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	193
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	194 //sets readAln.insertAfterID and returns lastDispIdx;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	195 //Find the index of the previously displayed alignment
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	196 var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	197
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	198 //lastDispIdx = parseInt(lastDispIdx);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	199 readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	200 readAln.numSeq = parseInt(maxNumAligns * 2);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	201
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	202 checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr");
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 readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	205 readAln.hspSort = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	206 ReadSeqAlignByIndex(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	207 g_DisableAutoCheck = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	208 location.href = "#alnShow_" + readAln.startIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	209 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	210
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	211
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	212
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	213
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	214 function setupDynHSPParams(readAln)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	215 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	216 var currSeqInd = readAln.startIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	217 hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	218 alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	219 var maxDispLen = parseInt($("maxDispAlnLen").value);//20000
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	220 var minDispLen = parseInt($("minDispAlnLen").value);//2000
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	221 if (alnLen > maxDispLen) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	222 var lenPerMatch = alnLen / hspNum;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	223 readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	224 readAln.AlignDbPageNum = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	225 $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	226 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	227 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	228
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	229
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	230
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	231 function getCurrSeqsAlnLen(currSeqInd)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	232 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	233 var alnLen = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	234 if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") \|\| $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	235 alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	236 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	237 alnLen = (alnLen) ? parseInt(alnLen) : 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	238 return alnLen;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	239 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	240
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	241 function checkTotalAlignLen(startIndex,stopIndex)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	242 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	243 var dispAlnLen = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	244 var maxDispLen = parseInt($("maxDispAlnLen").value);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	245 for (var i = startIndex; i <= stopIndex; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	246 alnLen = getCurrSeqsAlnLen(i);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	247 if (alnLen == 0) break;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	248 dispAlnLen += alnLen;
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 return dispAlnLen;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	251 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	252 //Get total align length for seq currSeqInd and
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	253 //"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	254 function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	255 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	256 var startIndex = readAln.startIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	257 var stopIndex = readAln.startIndex + readAln.numSeq - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	258 if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	259 startIndex = Math.max(startIndex, currSeqInd - countSeqs);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	260 stopIndex = Math.min(stopIndex, currSeqInd + countSeqs);
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 else if(dispType == "prev") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	263 startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	264 stopIndex = currSeqInd - 1;
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 else {//next
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	267 stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1);
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 var totAlnLen = checkTotalAlignLen(startIndex,stopIndex);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	270 return totAlnLen;
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
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	273 function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	274 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	275 var maxDispLen = parseInt($("maxDispAlnLen").value);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	276 var totAlnLen = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	277 var exc = false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	278 for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	279 totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	280 if(totAlnLen > maxDispLen) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	281 break;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	282 }
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 if (totAlnLen > maxDispLen) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	285 if (numSeq != 0) numSeq--;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	286 if (dispType == "curr") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	287 readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	288 //prev + 1(curr) + next
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	289 readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	290 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	291 else if (dispType == "prev") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	292 readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	293 readAln.numSeq = numSeq + 1;
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 else { //"next" - readAln.startIndex stays
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	296 readAln.numSeq = numSeq + 1;
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
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	299 if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	300 setupDynHSPParams(readAln);
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 exc = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	304 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	305 return exc;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	306 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	307
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	308
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	309 //readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	310 function ReadSeqAlignByIndex(readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	311 var numAligns = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	312 for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	313
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	314 if (!$("deflnDesc_" + i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	315 break;
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 (!$("deflnDesc_" + i).getAttribute("stat") \|\| $("deflnDesc_" + i).getAttribute("stat") == "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	318 currGi = $("deflnDesc_" + i).getAttribute("seqFSTA");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	319 if (readAln.seqList != "") readAln.seqList += ",";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	320 readAln.seqList += currGi;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	321 numAligns++;
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 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	324 break;
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 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	327 if (readAln.seqList != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	328 readAln.numSeq = parseInt(numAligns);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	329 ReadSeqAlignForSeqList(readAln);
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 var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2...
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	335 //Find the range of indexes of displayed alignments for currAlnInd
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	336 //Returns array of 2 startIndex, stopIndex
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	337 function getCurrIndexRange(currAlinInd) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	338 var currRange;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	339 var ranges = g_DisplayeAlignsRanges.split(",");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	340 for (var i = 0; i < ranges.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	341 var indexes = ranges[i].split("-");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	342 if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	343 currRange = indexes;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	344 break;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	345 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	346 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	347 return currRange;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	348 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	349
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	350
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	351 //Find the index of the previous displayed alignment
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	352 function getPrevDisplyedAlignInfo(currInd, readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	353 readAln.insertAfterID = "alnStart";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	354 lastDispIdx = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	355 for (var i = currInd - 1; i >= 1; i--) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	356 indexes = getCurrIndexRange(i);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	357 if (indexes) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	358 lastDispIdx = indexes[1];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	359 readAln.insertAfterID = "alnShow_" + indexes[0];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	360 break;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	361 }
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 return parseInt(lastDispIdx);
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 //setReadStatus
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	368 function setSeqAlnReadStatus(readAln, status) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	369 for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	370 if ($("deflnDesc_" + i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	371 jQuery($($("deflnDesc_" + i))).attr("stat", status);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	372 if (status == "disp") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	373 g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	374 }
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 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	377 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	378
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	379 /*
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	380 readAln.rid = rid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	381 readAln.seqList = giList;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	382 readAln.startIndex = parseInt(idx);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	383 readAln.insertAfterID = insertAfterID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	384 readAln.numSeq = parseInt(numSeq);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	385 readAln.scrollToSeqID = scrollToGI;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	386 */
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	387 function SendReadSeqAlinRequest(readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	388 blastUrl = "t2g.cgi";
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 var rp = new RemoteDataProvider(blastUrl);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	391
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	392
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	393 rp.onSuccess = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	394 if ($("alignView")) utils.removeClass($("alignView"), "hidden");
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 if ($("alnShow_" + readAln.startIndex)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	397 var moreHspsLink = getNextHspsLink(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	398 jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	399 'widgets': ['ncbipopper', 'ncbitoggler'],
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	400 'configs': {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	401 'ncbipopper': { hasArrow: true, arrowDirection: 'top' }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	402 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	403 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	404 setSeqAlnReadStatus(readAln, "disp");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	405 jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	406 //Saves start and stop indexes of loaded alignments in global variables
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	407 saveIdxesForAutomaticLoad(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	408 jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	409 var seqID = this.getAttribute("seqID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	410 if(seqID) initAlignBatch(seqID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	411 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	412
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	413 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	414
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	415 if (readAln.scrollToSeqID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	416 location.href = "#" + readAln.scrollToSeqID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	417 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	418
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	419 };
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	420 rp.onError = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	421 if ($("alignView")) utils.removeClass($("alignView"), "hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	422 jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	423 $("alnShowReal_" + readAln.startIndex).innerHTML = "<div class=\"erm\" id=\"erm_" + readAln.startIndex + "\">Error loading alignment ...<span class=\"db\">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	424 "</span><a class=\"gbd\" href=\"#\" onclick=\"ReSubmitReadSeqAligns(event," + readAln.startIndex + ")\">Try again<\a></div>";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	425 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	426 var params = constructURLParams(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	427 if (readAln.numSeq == 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	428 params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	429 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	430 params += "&SEQ_LIST_START=" + readAln.startIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	431
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	432 var formatParams = constructFormatParams();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	433 params += formatParams;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	434
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	435 //alert(params);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	436 rp.Request(params);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	437 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	438
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	439
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	440 function constructURLParams(readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	441 var params;
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 if ($("useAlignDB") && $("useAlignDB").value == "true") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	444
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	445 var alignDbParams = "&USE_ALIGNDB=true";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	446 var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	447 if (batchID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	448 alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	449 alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	450 alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	451 alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH");
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 alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	454 alignDbParams += "&HSP_SORT=" + readAln.hspSort;
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 if (readAln.hasOwnProperty("AlignDbPageNum")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	457 alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	458 alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	459 alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum;
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 params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	463 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	464 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	465 params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	466 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	467 if ($("phiPtInd")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	468 params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	469 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	470 return params;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	471 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	472
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	473 /*
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	474 readAln.rid = rid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	475 readAln.seqList = giList;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	476 readAln.startIndex = parseInt(idx);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	477 readAln.insertAfterID = insertAfterID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	478 readAln.numSeq = parseInt(numSeq);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	479 readAln.scrollToSeqID = scrollToGI;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	480 */
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	481 /*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	482 2. Insert another div with id="alnShowReal_index and class="alnMsgR"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	483 3. For "alnShow_index" set atrr indexes="startInd-stopInd"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	484 4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	485 5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	486 6. Send read request
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	487 */
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	488
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	489 function ReadSeqAlignForSeqList(readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	490 var text = "<div id=\"alnShow_" + readAln.startIndex + "\" class=\"alnMsg\"><div class=\"alnMsgS\" id=\"alnMsg_" + readAln.startIndex + "\">Loading alignment...<span class=\"db\"> for sequences " + readAln.seqList;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	491 var stopIndex = readAln.startIndex + readAln.numSeq - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	492 var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	493 text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "</span></div>";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	494 text += "<div id=\"alnShowReal_" + readAln.startIndex + "\" class=\"alnMsgR\"></div></div>";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	495 var debugControl = "<div id=\"debug\"></div>";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	496 if (!$("debug")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	497 jQuery($($("descriptions"))).before(debugControl);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	498 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	499 if (!$("alnShow_" + readAln.startIndex)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	500 jQuery($($(readAln.insertAfterID))).after(text);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	501 jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	502 jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	503 g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	504 setSeqAlnReadStatus(readAln, "read");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	505 $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	506
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	507 if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ",";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	508 g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	509
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	510 SendReadSeqAlinRequest(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	511 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	512 else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	513 jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	514 jQuery($("erm_" + readAln.startIndex)).remove();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	515 SendReadSeqAlinRequest(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	516 }
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
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	519
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	520 function ReSubmitReadSeqAligns(e,currInd) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	521 var rid = $("Rid").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	522 if ($("alnShow_" + currInd)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	523 var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	524 var range = indexRange.split("-");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	525
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	526
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	527 var readAln = new Object();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	528 readAln.seqList = ""; //giList
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	529 readAln.rid = rid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	530 readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	531 readAln.startIndex = parseInt(range[0]);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	532 readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	533 readAln.hspSort = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	534 ReadSeqAlignForSeqList(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	535 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	536 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	537 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	538
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	539
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	540 var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	541 var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	542 var g_DisableAutoCheck = false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	543
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	544 var g_autoStartIdx = new Array();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	545 var g_autoStopIdx = new Array();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	546
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	547 function saveIdxesForAutomaticLoad(readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	548 var stopIndex = readAln.startIndex + readAln.numSeq - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	549 g_autoStartIdx.push(readAln.startIndex); //1,20,25
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	550 g_autoStopIdx.push(stopIndex); //4,24,29
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	551 $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	552 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	553
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	554 function getNextHspsLink(readAln)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	555 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	556 var moreHspsLink = ""
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	557 if (readAln.hasOwnProperty("AlignDbPageNum")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	558 var nextPageNum = readAln.AlignDbPageNum + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	559 var currHspInd = readAln.AlignDbPageSize * nextPageNum;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	560 var argstring = readAln.startIndex + "," + currHspInd;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	561 var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	562 var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	563 var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	564 var prevHspInd = readAln.AlignDbPageSize * nextPageNum;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	565 var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	566 var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	567
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	568 moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	569 moreHspsLink = moreHspsLink.replace(/@accs@/g, accs);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	570 moreHspsLink = moreHspsLink.replace("@argstring@", argstring);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	571 moreHspsLink = moreHspsLink.replace(/@segs@/g, segs);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	572 moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	573 moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	574 moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	575 moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	576 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	577 return moreHspsLink;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	578 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	579
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	580
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	581 function ReadNextHSPSet(currSeqInd, currHSPNum) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	582 var readAln = new Object();
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 readAln.rid = $("Rid").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	585 readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	586 readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	587 dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	588 readAln.startIndex = currSeqInd;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	589 readAln.numSeq = 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	590 if (dynHsps) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	591 readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	592 readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	593 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	594 if (currHSPNum != 0) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	595 readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	596 readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	597 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	598 var sortLink = $("sa_" + readAln.gi);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	599 readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	600 SendReadSeqAlinSortHSPRequest(readAln);
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 function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	604 ReadNextHSPSet(currSeqInd, currHSPNum);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	605 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	606 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	607
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	608
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	609
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	610 function checkAutoAlignArray() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	611 var stop = false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	612 var start = false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	613 var currAlignViewPos = $("alignView").getBoundingClientRect().top;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	614 if (currAlignViewPos < g_alignViewPos) {//scrolling down
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	615 g_alignViewPos = currAlignViewPos;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	616 if (g_DisableAutoCheck) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	617 g_DisableAutoCheck = false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	618 return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	619 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	620 for (i = 0; i < g_autoStopIdx.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	621 if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	622 //alert("Reading more aligns scrolling down!");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	623 var nextInd = parseInt(g_autoStopIdx[i] + 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	624 var currInd = g_autoStopIdx[i];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	625 if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") \|\| $("deflnDesc_" + nextInd).getAttribute("stat") == "")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	626 ReadNextSeqAligns(currInd, 5);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	627 stop = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	628 break;
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 if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	633 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	634 else if (currAlignViewPos > g_alignViewPos) {//scrolling up
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	635 g_alignViewPos = currAlignViewPos;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	636 //here maybe return if autoStop found!!!
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	637 /* commenting automic read when scroll up */
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	638 for (i = 0; i < g_autoStartIdx.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	639 if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	640 //alert("Reading more aligns scrolling up!");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	641 var currInd = g_autoStartIdx[i];
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	642 //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!!
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	643 if (currInd > 1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	644 ReadPrevSeqAligns(currInd, 5);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	645 start = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	646 break;
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 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	650 if (start) g_autoStartIdx.splice(i, 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	651 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	652 /end of comment/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	653 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	654
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	655 var g_alignViewPos = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	656
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	657 function checkAutoAlignLoad() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	658
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	659
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	660 checkAutoAlignArray();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	661
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	662 if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	663 //alert("bottom!");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	664
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	665 if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	666 //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	667 ReadNextSeqAligns(g_MaxDisplayedIndex, 5);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	668 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	669 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	670 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	671
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	672
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	673 function GetPatternLocResults()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	674 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	675 form = $("results");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	676 if (!form.PHI_PTTRN_INDEX) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	677 var el = document.createElement("input");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	678 el.name = "PHI_PTTRN_INDEX";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	679 el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	680 form.appendChild(el);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	681 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	682 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	683 form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	684 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	685 form.submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	686 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	687
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	688 function goToNextHSP(elem, next) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	689 var par = jQuery(elem).parent(); //parent span with class="alnParLinks"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	690 var parts = par[0].id.split("_"); //"hsp<seqid>_hspnum "hsp207524544_2"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	691 if (parts[0].indexOf("nxHsp") != -1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	692 parts[0] = parts[0].replace("nxHsp", "hsp");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	693 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	694 nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	695
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	696 gotoElem = jQuery($(nextID));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	697 if (gotoElem[0]) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	698 a = jQuery(gotoElem).offset();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	699 window.scroll(0, a.top);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	700 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	701
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	702 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	703 retrieveNextHSP(parts[0],parts[1]);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	704 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	705
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	706 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	707
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	708
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	709 //parts[0]//hsp<seqid>, parts[1] hspnum
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	710 function retrieveNextHSP(currLinkID, currHSPNum)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	711 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	712 var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	713 var currSeqInd, totalHsps;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	714 jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	715 currSeqInd = parseInt(this.getAttribute("ind"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	716 totalHsps = parseInt(this.getAttribute("hsp"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	717 dynHsps = this.getAttribute("dynHsps");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	718 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	719 currHSPNum = parseInt(currHSPNum);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	720 if (currHSPNum < totalHsps && dynHsps) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	721 ReadNextHSPSet(currSeqInd, currHSPNum);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	722 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	723 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	724 /******Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error******************************/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	725 function getUrlCompForEntryField(elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	726 var url = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	727 if (elem && elem.value != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	728 url = "&" + elem.name + "=" + escape(elem.value);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	729 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	730 return url;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	731 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	732
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	733
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	734 function getUrlCompForCheckedField(elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	735 var url = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	736 if (elem && elem.checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	737 url = "&" + elem.name + "=" + elem.value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	738 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	739 return url;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	740
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	741 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	742
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	743 function getUrlCompForOptionsField(elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	744 var url = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	745 if (elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	746 url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	747 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	748 return url;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	749 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	750 /****************************************/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	751
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	752 function constructFormatParams() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	753 var formatParams = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	754
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	755 if ($("queryList")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	756 formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	757 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	758
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	759
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	760 formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	761 formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	762 formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	763 formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	764 formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	765 formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	766 formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	767 formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	768 formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	769 formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	770 formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	771
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	772
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	773 formatParams += getHiddenFieldParamString("BUILD_NAME");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	774
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	775 var serviceType = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	776 if ($("serviceType").value == "sra") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	777 serviceType = "sra";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	778 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	779 else if ($("clientType").value == "TMSmart_restricted") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	780 serviceType = "restricted";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	781 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	782 if (serviceType != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	783 formatParams += "&BOBJSRVC=" + serviceType;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	784 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	785 if ($("currQuery").value != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	786 formatParams += "&CURR_QUERY_ID=" + $("currQuery").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	787 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	788
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	789 return formatParams;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	790 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	791
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	792 //readAln.seqList contains one gi only for this
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	793 function SendReadSeqAlinSortHSPRequest(readAln) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	794 blastUrl = "t2g.cgi";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	795 var rp = new RemoteDataProvider(blastUrl);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	796
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	797
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	798 rp.onSuccess = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	799 var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	800 var alnHtml = obj.responseText + moreHspsLink;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	801 initHSPRequest(readAln, obj.responseText + moreHspsLink,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	802 if (readAln.scrollToSeqID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	803 location.href = "#" + readAln.scrollToSeqID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	804 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	805 };
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	806 rp.onError = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	807 var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	808 var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	809 if (!$(msgID)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	810 var msg = "<div class=\"erm\" att=\"1\" id=\"" + msgID + "\">Error loading alignment ...<span class=\"db\">status:" + obj.status +
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	811 "</span><a class=\"gbd\" href=\"#\" onclick=\"ReadNextHSPSetEvt(event," + readAln.startIndex + "," + currHspInd +
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	812 ")\">Try again <span class=\"attmt\"></span> <\a></div>";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	813 initHSPRequest(readAln, msg, true);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	814 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	815 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	816 var attNum = parseInt($(msgID).getAttribute("att")) + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	817 $(msgID).setAttribute("att", attNum);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	818 jQuery($(msgID)).find(".attmt").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	819 jQuery(this).html(", attempt " + attNum);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	820 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	821 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	822 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	823
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	824 var params = constructURLParams(readAln);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	825 if (readAln.AlignDbPageSize) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	826 params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	827 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	828 params += "&SORT_ONE_ALN=on";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	829 var formatParams = constructFormatParams();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	830
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	831 params += formatParams;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	832
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	833 //alert(params);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	834 rp.Request(params);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	835 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	836 function initHSPRequest(readAln, alnHtml, err) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	837 var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	838 if (currHspInd != 0) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	839 readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	840 jQuery($(readAln.insertAfterID)).after(alnHtml);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	841 moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	842 jQuery($(moreHspsID)).remove();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	843 if (!err) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	844 errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	845 jQuery($(errMsgID)).remove();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	846 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	847 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	848 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	849 jQuery($("alnAll_" + readAln.gi)).html(alnHtml);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	850 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	851 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	852
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	853 function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	854 var readAln = new Object();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	855
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	856
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	857 var desLineID = sortLink.id.replace("sa", "dtr"); //tr id
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	858 var seqInd;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	859
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	860 jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	861 seqInd = this.getAttribute("ind");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	862 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	863
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	864 ReadNextHSPSet(parseInt(seqInd), 0);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	865 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	866
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	867
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	868 function configDescriptions(e,btn,dlgId)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	869 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	870 var suffix = PsiBelowThresh(dlgId);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	871 var colmnsInfId = "cfcDsInf" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	872 var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	873 var showAllColId = "shcl" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	874 var chkBoxes = $C("checkbox", "type", $(dlgId), "input");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	875 if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	876 for (i = 0; i < chkBoxes.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	877 var check;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	878 if (utils.hasClass(btn, "cnc")) {//cancel
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	879 if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	880 check = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	881 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	882 else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	883 check = false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	884 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	885 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	886 else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	887 check = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	888 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	889 if (typeof (check) != 'undefined') {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	890 chkBoxes[i].checked = check;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	891 showHideCol(tblID,parseInt(chkBoxes[i].value), !check);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	892 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	893 if (!utils.hasClass(btn, "cnc")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	894 if (chkBoxes[i].checked) { //OK
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	895 if ($(colmnsInfId).value != "") $(colmnsInfId).value += ",";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	896 $(colmnsInfId).value += chkBoxes[i].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	897 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	898 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	899 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	900 if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	901 jQuery($(showAllColId)).removeClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	902 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	903 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	904 jQuery($(showAllColId)).addClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	905 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	906
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	907 var chConfig = $("cfcDsSave").value != $(colmnsInfId).value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	908
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	909 var cfds = document.getElementsByName("CONFIG_DESCR");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	910 if (cfds) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	911 for (i = 0; i < cfds.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	912 cfds[i].value = $(colmnsInfId).value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	913 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	914 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	915 $("cfcDsSave").value = $(colmnsInfId).value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	916 if (chConfig) SaveConfigTable();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	917 jQuery(document.body).click();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	918 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	919 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	920
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	921
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	922
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	923 function initDescConfig()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	924 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	925 initConfigColumns("dsConfig");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	926 if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	927 initConfigColumns("dsConfig_psiw");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	928 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	929 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	930
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	931
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	932 function initConfigColumns(cnfDlgID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	933 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	934 var suffix = PsiBelowThresh(cnfDlgID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	935 //cnfDlgID is "dsConfig[_psiw]"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	936 var colmnsInfId = "cfcDsInf" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	937 var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	938 var showAllColId = "shcl" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	939
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	940 if (navigator.userAgent.match(/ie/i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	941 if ($("FormatForm").NCBI_GI.checked \|\| $("serviceType").value == "sra") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	942 jQuery($(tblID)).find("th.c1").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	943 db = getHiddenFieldVal("DATABASE");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	944 var width = (db.match(/WGS/i) \|\| db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	945 jQuery(this).css("width", width);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	946 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	947 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	948 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	949
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	950 jQuery($(tblID)).find("tr.first").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	951 jQuery(this).find("a.dcs").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	952 jQuery(this).bind("click", function(e) { checkConfig(this); });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	953 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	954 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	955
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	956 jQuery($(cnfDlgID)).find("button").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	957 jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	958 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	959
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	960
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	961 jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	962
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	963 $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	964 if ($(colmnsInfId).value == "" \|\| $(colmnsInfId).value == "undefined") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	965 $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	966 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	967 if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	968 jQuery($(showAllColId)).removeClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	969 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	970 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	971 jQuery($(showAllColId)).addClass("hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	972 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	973 var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input")
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	974 for (i = 0; i < chkBoxes.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	975 jQuery(chkBoxes[i]).bind("click", configColumn);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	976 if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	977 chkBoxes[i].checked = true;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	978 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	979 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	980 //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	981 showHideCol($(tblID), chkBoxes[i].value, true);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	982 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	983 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	984 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	985 function showAllCol(e,elem)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	986 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	987 var suffix = PsiBelowThresh(elem.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	988 var rdf = "dscRsDf" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	989 jQuery($(rdf)).click();//click "restore defaults'
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	990 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	991 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	992
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	993
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	994 function configColumn() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	995 var suffix = PsiBelowThresh(this.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	996 var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	997
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	998 cCls = "c" + this.value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	999 if (this.checked) {//show
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1000 showHideCol(tblID,parseInt(this.value), false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1001 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1002 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1003 showHideCol(tblID,parseInt(this.value), true);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1004 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1005 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1006
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1007 function showHideCol(tblID, columnIndex, hide) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1008
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1009 if ($("Transcr")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1010 colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1011 hide = hide && !colHidden;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1012 show = !hide && colHidden;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1013 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1014 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1015 show = !hide;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1016 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1017 if (hide) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1018 jQuery($(tblID)).ncbigrid("hideColumn", columnIndex);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1019 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1020 else if (show) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1021 jQuery($(tblID)).ncbigrid("showColumn", columnIndex);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1022 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1023 if ($("Transcr") && (hide \|\| show) ) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1024 var colsp = parseInt($("Transcr").getAttribute("colspan"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1025 colsp = (hide) ? colsp - 1 : colsp + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1026 $("Transcr").setAttribute("colSpan", colsp);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1027 if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1028 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1029 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1030
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1031 function checkConfig(lnk) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1032 var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1033 lnk.href = lnk.href + cnfCol + "#sort_mark";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1034 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1035
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1036 function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1037 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1038 var dflLineLinks = $C(seqID, "gi", document, "a");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1039 for (i = 0; i < dflLineLinks.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1040 jQuery(dflLineLinks[i]).click();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1041 break;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1042 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1043 location.href = dflLineLinks[i].href;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1044 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1045
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1046
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1047
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1048 function initDescSelect()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1049 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1050
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1051 jQuery("#cntDesc").find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1052 jQuery(this).bind("click", configDescrSelect);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1053 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1054 jQuery("#cntSelN").click();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1055 jQuery("#descTblCtrl").find("a[view]").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1056 jQuery(this).bind("click", DisplaySelectedView);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1057 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1058 if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1059 jQuery("#cntDesc_psiw").find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1060 jQuery(this).bind("click", configDescrSelect);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1061 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1062 jQuery("#cntSelN_psiw").click();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1063 jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1064 jQuery(this).bind("click", DisplaySelectedView);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1065 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1066 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1067
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1068
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1069 //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });??
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1070
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1071 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1072
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1073 function DisplaySelectedView(e) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1074 if (this.getAttribute("view") == "graph") { //seqviewer
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1075 ViewSelectedSeqViewer(e,this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1076 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1077 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1078 if (this.getAttribute("view") == "tree") { //seqviewer
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1079 $("scrWidth").value = screen.width;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1080 $("scrHeight").value = screen.height;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1081 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1082 ViewSelectedSeqsEx(e, this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1083 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1084 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1085
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1086 function PsiBelowThresh(elemID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1087 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1088 var suffix = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1089 if (elemID.indexOf("_psiw") != -1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1090 suffix = "_psiw";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1091 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1092 return suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1093 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1094
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1095 function ViewSelectedSeqsEx(e,elem) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1096 var sbmForm = elem.getAttribute("frm");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1097 var seqList = elem.getAttribute("seqList");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1098
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1099 var cnfElem = utils.getParent(elem); //.cnf div
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1100 var suffix = PsiBelowThresh(cnfElem.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1101 var tblID = "dscTable" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1102
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1103 $(seqList).value = createSelseqString(tblID,true);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1104 $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1105 if ($(seqList).value.indexOf("dbSNP") != -1) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1106 $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1107 elem.href = $(sbmForm).action + $(seqList).value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1108 elem.target = "new";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1109 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1110 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1111 $(sbmForm).submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1112 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1113 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1114 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1115
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1116 function ViewSelectedSeqsTree(e) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1117 $("scrWidth").value = screen.width;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1118 $("scrHeight").value = screen.height;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1119 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1120
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1121 function initSeqViewerGet(seqList) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1122 if (seqList.length >= 2000) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1123 seqList = seqList.substr(0,2000);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1124 lastComma = seqList.lastIndexOf(",");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1125 seqList = seqList.substr(0,lastComma);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1126 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1127 $("seqViewParams").name = "RID";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1128 $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1129 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1130
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1131 function ViewSelectedSeqViewer(e, elem)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1132 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1133 var cnfElem = utils.getParent(elem); //.cnf div
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1134 var suffix = PsiBelowThresh(cnfElem.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1135 var tblID = "dscTable" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1136
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1137 //change to false when new verison of seqVier is installed in production
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1138 var seqList = createSelseqString(tblID, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1139 $("sbmtGraphics").action = $("seqViewUrl").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1140
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1141 var rp = new RemoteDataProvider("url2nc.cgi");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1142 rp.onSuccess = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1143 var jsnResp = JSON.parse(obj.responseText);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1144 ncid = jsnResp.ncid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1145
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1146 if (ncid != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1147 $("seqViewParams").name = "rkey";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1148 $("seqViewParams").value = ncid;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1149 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1150 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1151 initSeqViewerGet(seqList);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1152 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1153 $("sbmtGraphics").submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1154 };
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1155 rp.onError = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1156 initSeqViewerGet(seqList);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1157 $("sbmtGraphics").submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1158 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1159 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1160 var params = $("ridParam").value + "[" + seqList + "]";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1161 rp.Request(params, "POST");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1162 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1163 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1164
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1165 function configDescrSelect(e) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1166 var sel = this.getAttribute("sel");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1167 if (sel) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1168 var selNum = 0;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1169 var check = (sel == "all") ? true : false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1170
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1171 var suffix = PsiBelowThresh(this.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1172 var tblID = "dscTable" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1173 var toolbarID = "descTblCtrl" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1174 var selElID = "slcNum" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1175
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1176 jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1177 jQuery(this)[0].checked = check;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1178 if (check) selNum++;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1179 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1180 enableDescrLinks(selNum, toolbarID, selElID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1181 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1182 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1183 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1184
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1185
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1186
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1187 function enableDescrLinks(selNum, toolbarID, selElID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1188 jQuery($(toolbarID)).find("a[minSlct]").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1189 var minSelected = this.getAttribute("minSlct");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1190 minSelected = parseInt(minSelected);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1191 if (selNum >= minSelected) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1192 this.removeAttribute("disabled");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1193 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1194 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1195 this.setAttribute("disabled", "disabled");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1196 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1197 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1198 $(selElID).innerHTML = selNum;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1199 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1200
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1201
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1202
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1203 function configDescrLinks(e, elem)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1204 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1205
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1206 ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1207 var par = jQuery(elem).parents(".jig-ncbigrid");//parent table
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1208 if (par) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1209 var suffix = PsiBelowThresh(par[0].id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1210 var tblID = "dscTable" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1211 var toolbarID = "descTblCtrl" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1212 var selElID = "slcNum" + suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1213
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1214 var currSelNum = parseInt($(selElID).innerHTML);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1215 var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1216 enableDescrLinks(selNum, toolbarID, selElID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1217 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1218 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1219 /*Download code begin**/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1220
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1221 function initDownLoadPopup(dwnDialog) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1222
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1223 jQuery(dwnDialog).find("button").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1224 jQuery(this).bind("click", execDownLoad);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1225 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1226
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1227 jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1228 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1229
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1230 function initDescDownLoad() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1231 initDownLoadPopup($("dsDownload"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1232
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1233 if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1234 initDownLoadPopup($("dsDownload_psiw"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1235 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1236 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1237
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1238 function initAlignDownLoad(navObj)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1239 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1240 var seqID = navObj.seqID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1241 var dwnDialog = $("dlgDwnl_" + seqID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1242 jQuery(dwnDialog).find("button").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1243 jQuery(this).bind("click", execDownLoad);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1244 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1245
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1246 var dwnFSTW = $("dwFST_" + seqID);//whole seq
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1247 var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1248
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1249 if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1250 if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1251
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1252 jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1253 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1254
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1255
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1256 function execDownLoad(e) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1257 if (!utils.hasClass(this, "cnc")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1258 par = utils.getParent(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1259 dwnDialog = utils.getParent(par); //parent dialog with popDl class
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1260 var descr = (this.id == "dw_cont" \|\| this.id == "dw_cont_psiw") ? true : false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1261 jQuery(dwnDialog).find("input").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1262 if (this.checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1263 submitDownLoad(this, descr);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1264 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1265 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1266 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1267 jQuery(document.body).click();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1268 utils.preventDefault(e);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1269 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1270
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1271 function submitDownLoad(radioElem, descr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1272 var toolURL = radioElem.getAttribute("url");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1273 if (toolURL) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1274 if (descr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1275 var getGi = radioElem.getAttribute("getGi");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1276 getGi = (getGi) ? true : false;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1277
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1278 var tblID = "dscTable";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1279 var suffix = PsiBelowThresh(radioElem.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1280 tblID += suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1281
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1282 $("selDnSeqs").value = createSelseqString(tblID,getGi);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1283 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1284 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1285 var seqfsta = radioElem.getAttribute("seqfsta");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1286 $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1287 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1288 var addParams = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1289 if (radioElem.getAttribute("addParam")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1290 addParams = addDwnlParams();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1291 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1292 var submitName = radioElem.getAttribute("sbName")
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1293 $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1294 $("dwdlSubmit").action = toolURL + addParams;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1295 $("dwdlSubmit").submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1296 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1297 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1298 var sbFunction = radioElem.getAttribute("sbFunc");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1299 if (sbFunction) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1300 eval(sbFunction + "(radioElem, descr)");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1301 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1302 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1303 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1304
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1305
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1306 function initDownLoadFSTA(radioElem, descr)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1307 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1308 if (descr) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1309
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1310 var tblID = "dscTable";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1311 var suffix = PsiBelowThresh(radioElem.id);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1312 tblID += suffix;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1313
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1314 $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1315 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1316 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1317 $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1318 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1319 $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1320
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1321 $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1322 if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1323 var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1324 if (batchID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1325 $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1326 $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1327 $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1328 $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1329 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1330 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1331 $("sbmtFASTA").submit();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1332 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1333
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1334 function createSelseqString(tblID,getGi) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1335 var selSeqs = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1336 jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1337 if (jQuery(this)[0].checked) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1338 if (selSeqs != "") selSeqs += ",";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1339 if (getGi) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1340 selSeqs += jQuery(this)[0].value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1341 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1342 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1343 var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1344 selSeqs += $(linkID).getAttribute("seqFSTA");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1345 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1346 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1347 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1348 return selSeqs;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1349 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1350
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1351 /*Download code end**/
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1352
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1353 /*Init navigation code begin /
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1354
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1355 function initNavigation(navObj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1356 initNextAlnLink(navObj, true);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1357 initNextAlnLink(navObj, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1358 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1359
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1360
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1361 function initNavInfo(navObj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1362 var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind"));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1363 nextInd = currInd + 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1364 prevInd = currInd - 1;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1365
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1366 navObj.currSeqID = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1367 navObj.nextSeqID = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1368 navObj.prevSeqID = "";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1369
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1370 if ($("deflnDesc_" + nextInd)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1371 navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1372 if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1373 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1374 if ($("deflnDesc_" + prevInd)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1375 navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1376 if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1377 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1378 if ($("deflnDesc_" + currInd)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1379 navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1380 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1381 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1382
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1383
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1384 function initNextAlnLink(navObj, next) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1385
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1386 var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1387 var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1388
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1389 if (nextLinkEl) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1390 if (nextSeqid != "") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1391 var text = (next) ? "next" : "previous";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1392 nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1393 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1394 else {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1395 nextLinkEl.setAttribute("disabled", "disabled");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1396 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1397 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1398 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1399 function scan(link) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1400 var init = link.getAttribute("init");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1401 if (!init) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1402 ncbi.sg.scanLinks(link);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1403 link.setAttribute("init","on");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1404 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1405 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1406
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1407 function initWidth(seqID) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1408 var lineLengthElem = $("FormatForm").LINE_LENGTH;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1409 var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1410 if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1411
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1412 var relWidth = (lineLength > 90) ? "12%" : "15%";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1413 var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1414 lineLength = (lineLength + parseInt(17)) * charWidth;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1415 var width = lineLength + "px";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1416 jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1417 jQuery(this).css("width", width);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1418 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1419 jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1420 jQuery(this).css("width", width);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1421 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1422 jQuery($("relInf_" + seqID)).css("width", relWidth);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1423 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1424
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1425
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1426 /*Init navigation code end /
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1427 function initAlignBatch(seqID)
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1428 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1429 var navObj = new Object();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1430 navObj.seqID = seqID;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1431 initNavInfo(navObj);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1432
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1433 initAlignDownLoad(navObj);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1434 initNavigation(navObj);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1435 ncbi.sg.scanLinks($("alnNxt_" + seqID));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1436 ncbi.sg.scanLinks($("alnPrv_" + seqID));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1437 if ($("serviceType").value == "vecscreen") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1438 utils.addClass($("alnDsc_" + seqID), "hidden");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1439 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1440 ncbi.sg.scanLinks($("alnDwnld_" + seqID));
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1441 jQuery($("csLinks_" + seqID)).find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1442 ncbi.sg.scanLinks(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1443 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1444 jQuery($("relInf_" + seqID)).find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1445 ncbi.sg.scanLinks(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1446 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1447 jQuery($("rng_" + seqID)).find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1448 ncbi.sg.scanLinks(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1449 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1450 jQuery($("dln_" + seqID)).find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1451 ncbi.sg.scanLinks(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1452 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1453 initWidth(seqID);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1454 /*
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1455 jQuery($("alnHdr_" + seqID)).find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1456 ncbi.sg.scanLinks(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1457 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1458 jQuery($("aln_" + seqID)).find("a").each(function(index) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1459 ncbi.sg.scanLinks(this);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1460 });
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1461 */
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1462 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1463
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1464 function SaveConfigTable() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1465 blastUrl = "fmtsave.cgi";
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1466
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1467
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1468 var rp = new RemoteDataProvider(blastUrl);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1469
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1470
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1471 rp.onSuccess = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1472 //alert("success");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1473 };
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1474 rp.onError = function(obj) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1475 //alert("error");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1476 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1477
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1478 var program = getHiddenFieldVal("PROGRAM");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1479 var rid = getHiddenFieldVal("RID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1480 var blastSpec = getHiddenFieldVal("BLAST_SPEC");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1481 var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1482 if(blastSpec) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1483 params += "&BLAST_SPEC=" + blastSpec;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1484 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1485 rp.Request(params,"POST");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1486 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1487
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1488 function removeRID() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1489 var rid = document.getElementsByName("RID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1490 for (var i = 0; i <= rid.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1491 jQuery(rid[i]).remove();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1492 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1493 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1494
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1495 function initAdvancedView()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1496 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1497 if ($("dsConfig")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1498
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1499 var alnView = getHiddenFieldVal("ALIGNMENT_VIEW");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1500 if (alnView == "Pairwise" \|\| alnView == "PairwiseWithIdentities") {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1501 var rid = getHiddenFieldVal("RID");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1502 ReadNextSeqAligns(0, 5);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1503 g_alignViewPos = $("alignView").getBoundingClientRect().top;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1504 utils.addEvent(window, "scroll", checkAutoAlignLoad, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1505 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1506 list = $("phiPtInd");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1507 if (list) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1508 utils.addEvent(list, "change", GetPatternLocResults, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1509 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1510 initDescConfig();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1511 initDescSelect();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1512 initDescDownLoad();
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1513 if ($("psiInp")) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1514 var nextIter = document.getElementsByName("NEXT_I");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1515 for (var i = 0; i < nextIter.length; i++) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1516 utils.addEvent(nextIter[i], "click", removeRID, false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1517 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1518 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1519 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1520 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1521
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1522 //takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4"
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1523 function initjQry()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1524 {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1525 var oldCreate = jQuery.ui.ncbipopper.prototype._create;
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1526 jQuery.ui.ncbipopper.prototype._create = function() {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1527 var destSelector = this.options.destSelector \|\| this.options.sourceSelector \|\| this.element.prop("hash");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1528 this.options.destSelector = destSelector.replace(/\./g, "\\.");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1529 oldCreate.apply(this, arguments);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1530 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1531 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1532 utils.addEvent(window,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1533 "load", initAdvancedView,
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1534 false);
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1535
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1536 initjQry()
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1537
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1538 /* 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	1539 if (navigator.userAgent.match(/ie/i)) {
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1540 document.write("<link rel='stylesheet' type='text/css' href='css/ie-descriptions.css' media='screen'/>");
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1541 }
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1542 /***************************new code end*******************************************************************/