blast2html: NCBI Blast reference example_files/formatRes.js annotate

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

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

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

rev	line source
0 bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1 // JScript source code
bad241dc701f add example input blast xml and output html page Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2 /***********************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*******************************************************************/