# HG changeset patch # User Jan Kanis # Date 1400165584 -7200 # Node ID 2143f62809d06eeba56ec1b72dabb5dbce76df2a # Parent 420d0508dcd6128e28680de532ff24699ef4eb8d remove unneeded files diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed.html --- a/Blast output page example trimmed.html Thu May 15 16:50:38 2014 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1623 +0,0 @@ - - - - - - - - - - - - - - - -NCBI Blast:Nucleotide Sequence (16 letters) - - - - - - - - - - - - - - -
- - -
- - - - - - - - - - - - - - -
- - - - - - - - - - - - - -
- - - -
- -
- -

Nucleotide Sequence (16 letters)

- -
-
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RID
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-PHWP1JNZ014 (Expires on 05-07 22:33 pm) -
-
-
-
-
Query ID
- -
lcl|59987
-
Description
-
None
-
Molecule type
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nucleic acid
-
Query Length
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16
-
-
- -
-
-
-
Database Name
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pdb
-
Description
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PDB nucleotide database
-
Program
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BLASTN 2.2.29+
-
-
-
- - - - - - - -
-
- - - - - - -
- - - - - - - -
-

- -Alignments - - -

- -
-
-
-
-
- - - -GenBankGraphics - -
- -
- -Next -Previous -Descriptions - -
-
-
-
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit) -
pdb|3J5A|A29034
-
-
-
- -
-
GenBankGraphics - -Next Match -Previous Match - - -
- - - - - - - - - - - - -
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
- -
-
-
Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
- -
-
-
Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-
-
-
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GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-
-
-
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GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-
-
-
-
-
- - - -GenBankGraphics - -
- -
- -Next -Previous -Descriptions - -
-
-
-
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit) -
pdb|3J58|A29034
-
-
-
- -
-
GenBankGraphics - -Next Match -Previous Match - - -
- - - - - - - - - - - - -
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
- -
-
-
Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-
-
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GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
- -
-
-
Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-
-
-
-
-
- - - -GenBankGraphics - -
- -
- -Next -Previous -Descriptions - -
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-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit) -
pdb|3J56|A29034
-
-
-
- -
-
GenBankGraphics - -Next Match -Previous Match - - -
- - - - - - - - - - - - -
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
- -
-
-
Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
- -
-
-
Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-
-
-
-
-
- - - -GenBankGraphics - -
- -
- -Next -Previous -Descriptions - -
-
-
-
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit) -
pdb|3J54|A29034
-
-
-
- -
-
GenBankGraphics - -Next Match -Previous Match - - -
- - - - - - - - - - - - -
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
- -
-
-
Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
- -
-
-
Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-
-
-
-
-
- - - -GenBankGraphics - -
- -
- -Next -Previous -Descriptions - -
-
-
-
-Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit) -
pdb|3J52|A29034
-
-
-
- -
-
GenBankGraphics - -Next Match -Previous Match - - -
- - - - - - - - - - - - -
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
- -
-
-
Query  1    CGTCCGTCGTGAAGAG  16
-            ||||||||||||||||
-Sbjct  961  CGTCCGTCGTGAAGAG  976
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
- -
-
-
Query  5     CGTCGTGA  12
-             ||||||||
-Sbjct  2591  CGTCGTGA  2598
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  7    TCGTGAA  13
-            |||||||
-Sbjct  839  TCGTGAA  845
-
-
-
-
-
-
GenBankGraphics - -Next Match -Previous Match -First Match - -
- - - - - - - - - - - - -
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
- -
-
-
Query  9     GTGAAGA  15
-             |||||||
-Sbjct  2027  GTGAAGA  2033
-
-
-
-
-
-
-
- -
-

-

-

-

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\ No newline at end of file
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diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/9.gif
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diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/InstrumentPageStarterJS.js
--- a/Blast output page example trimmed_files/InstrumentPageStarterJS.js	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
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diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/black.gif
Binary file Blast output page example trimmed_files/black.gif has changed
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/blast.js
--- a/Blast output page example trimmed_files/blast.js	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,308 +0,0 @@
-
-function printfire()
-{
-    // Firefox
-    if (document.createEvent && window.dispatchEvent) {
-        printfire.args = arguments;
-        var ev = document.createEvent("Events");
-        ev.initEvent("printfire", false, true);
-        window.dispatchEvent(ev);
-    }
-}
-//This functions handle setting defaults for protein or nulcleotide suite  search page when
-//one of blast program radio buttons is clicked - not used now
-function AdjustMoreOptionsStyle()
-{
-	var optsEl = document.getElementById("moreopts");	
-	if(optsEl && optsEl.style.height != "0px") {
-		optsEl.style.height = optsEl.scrollHeight + "px";			
-	}
-}
-
-//Strip (taxid:XXX) from organism list selection
-//sgRunFunc="AdjustOrganism();" 
-function AdjustOrganism()
-{
-	var words = $("qorganism").value.split(" (taxid");
-	$("qorganism").value = words[0];		
-}
-
-
-/* JS Common to all BLAST pages */
-
-
-function setResultsTarget()
-{
-	//var newWin = $("newwin");	
-	var newWin = this;	
-	var searchFrm = $(newWin.getAttribute("form"));				
-	if(newWin && newWin.checked == true) {
-		if(newWin.getAttribute("winType") == "random") {		    
-			searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random());
-		}
-		else {
-			searchFrm.target = $("resPageTarget").value;		
-		}
-	}	
-	else {		
-		searchFrm.target = "";
-	}
-}
-
-function diffFromDefault(elem)
-{
-    var currentVal = "";
-    var ret = 0;
-
-    if (!(elem)) return;
-    var defVal = elem.getAttribute("defVal"); //Default value    
-    var elShowDiff = utils.getParent(elem);
-    if(!elem.type) {//div element for example
-        //Check if parent elem has "hide" class
-        if(utils.hasClass(utils.getParent(elem), "hide")) {
-            currentVal = "hide";
-        }
-        else {
-            currentVal = "show";
-        }   
-        elShowDiff = elem;
-    }
-    else if(elem.type == "select-one") {
-        if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value;
-        //If Default value is not specified - the first one in the selection list is the default          
-        if (!defVal && elem[0].value) defVal = elem[0].value;  
-    }
-    else if(elem.type == "select-multiple") {
-	    currentVal = "";//for now
-    }
-    else if(elem.type == "checkbox") {
-        //alert("defVal1=" + elem.id + " " + defVal);
-        //var defVal = elem.defVal; //Default value
-        //alert("defVal2=" + defVal);
-        if(elem.checked == true) currentVal = "checked"
-        else  currentVal = "unchecked";        
-    }
-    else {
-        currentVal = elem.value;
-    }
-    
-    
-    var numdiff = parseInt($("NUM_DIFFS").value,10);    
-    var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10);    
-    if(defVal != currentVal) {        
-        if(!utils.hasClass(elShowDiff, "nondef")) {        
-            utils.addClass(elShowDiff, "nondef");            
-            numdiff++;            
-            if(utils.hasClass(elem,"opts")) optsNumDiff++;        
-        }     
-        ret = 1;        
-    }
-    else {        
-        if(utils.hasClass(elShowDiff, "nondef")) {
-            utils.removeClass(elShowDiff, "nondef");        
-            //alert("noDiff-" + elem.id);
-            if(numdiff != 0) numdiff--;       
-            if(utils.hasClass(elem,"opts")) optsNumDiff--; 
-        }         
-        ret=0;
-    }
-    $("NUM_DIFFS").value = numdiff;       
-    $("NUM_OPTS_DIFFS").value = optsNumDiff;       
-    if(numdiff > 0) {    
-        $("diffMes").style.display = "inline";          
-    }
-    else {
-        $("diffMes").style.display = "none";           
-    }      
-    //alert(elem.id + " " + $("NUM_DIFFS").value);
-    return ret;    
-}
-
-function setDefalValue(elem)
-{
-    var currentVal;    
-    var defVal = elem.getAttribute("defVal"); //Default value    
-    if(elem.type == "select-one") {
-        //If Default value is not specified - the first one in the selection list is the default          
-        if(!defVal) defVal = elem[0].value;  
-        for(j=0; j < elem.options.length; j++) {
-		    if(elem.options[j].value == defVal) {
-		        elem.options[j].selected = true;
-		        break;
-		    }
-        }       
-    }
-    else if(elem.type == "checkbox" || elem.type == "radio") {        
-        if(!defVal) defVal = "checked";
-        if(defVal == "checked") elem.checked = true        
-        else elem.checked = false;
-    }
-    else {
-        if(!defVal) defVal = "";
-        elem.value = defVal;
-    }
-    
-    var elShowDiff = utils.getParent(elem);    
-    if(utils.hasClass(elShowDiff, "nondef")) {
-        utils.removeClass(elShowDiff, "nondef");        
-    }            
-    //alert(elem.id + " " + $("NUM_DIFFS").value);    
-}
-
-function newResultsWinInit() {
-    jQuery("[class='newwin']").each(function(index) {
-        utils.addEvent(this, "click", setResultsTarget, false);
-    });
-}
-
-function resetOrganismSuggest(orgEntryElem) 
-{
-    //suggestHint is in the hidden field used for SRA
-    var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested";
-    var suggestHint = $("qorganism").getAttribute("suggestHint");
-    if(suggestHint) defaultMessage = suggestHint;
-    if(orgEntryElem.value == "") {
-        orgEntryElem.value = defaultMessage;
-    }
-    if(orgEntryElem.value == defaultMessage) {            
-        utils.addClass(orgEntryElem,"orgHint");
-    }
-}  
-
-function setupOrganismSuggest(orgEntryElem)
-{
-    resetOrganismSuggest(orgEntryElem); 
-    utils.addEvent(orgEntryElem, "focus", function() {
-        clearOrgSuggest(orgEntryElem);        
-     }, false);     
-}
-
-function clearOrgSuggest(orgEntryElem)
-{
-    if(utils.hasClass(orgEntryElem,"orgHint")) {
-        orgEntryElem.value="";            
-        utils.removeClass(orgEntryElem,"orgHint");
-    }
-}    
-
-function InitCustomButton(bn)
-{
-  utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false);
-  utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false);
-  utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false);
-  utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false);    
-}
-
-function showHideElem(id,hide)
-{
-  if($(id)) {
-    if(hide) {
-	    if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden");	    
-	}
-	else {
-	    if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden");	    
-	}	
-  }
-}
-
-function resetOrganismControls(orgEntryElem) {
-    resetOrganismSuggest(orgEntryElem);
-    if ($("orgExcl")) $("orgExcl").checked = false;
-    utils.replaceInHtml("", $("orgs"));
-    if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs"));
-    if ($("numOrg")) $("numOrg").value = 1;
-}
-
-function AddOrgRow(e,orgName,exclName) {
-    e = e || window.event;
-    utils.preventDefault(e);
-    var checkedExclude = new Array();
-    var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary");
-    orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict;
-    var len = $("qorganism").getAttribute("size");
-    
-    var newOrgFieldID = "qorganism" + $("numOrg").value;
-    var newOrgField = " 
";
-    if (exclName != "") {
-        newOrgField += "" +
-                       "" +
-                       "";
-    }
-    newOrgField += "
";
-    if (navigator.userAgent.match(/ie/i)) {
-        for (i = 1; i < $("numOrg").value; i++) {
-            if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked;
-        }
-    }
-    if (!navigator.userAgent.match(/firefox/i)) {    
-        jQuery($($(orgs))).append(newOrgField,true);
-    }
-    else {
-        utils.insertInHtml(newOrgField, $("orgs"));
-    }
-
-    if (navigator.userAgent.match(/ie/i)) {
-        for (i = 1; i < $("numOrg").value; i++) {
-            if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i];
-        }
-    }
-    setupOrganismSuggest($(newOrgFieldID));
-    jQuery($($(newOrgFieldID))).ncbiautocomplete();
-    $("numOrg").value++;    
-}
-
-function adjustOrgVal(orgEntryElem) 
-{
-    //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = "";
-    clearOrgSuggest(orgEntryElem);
-    if ($("numOrg")) {
-        for (i = 1; i < $("numOrg").value; i++) {
-            if ($("qorganism" + i)) {
-                clearOrgSuggest($("qorganism" + i));
-            }
-        }
-    }
-}
-
-function getUrlCompForEntryField(elem) {
-    var url = "";
-    if (elem && elem.value != "") {
-        url = "&" + elem.name + "=" + escape(elem.value);
-    }
-    return url;
-}
-
-
-function getUrlCompForCheckedField(elem) {
-    var url = "";
-    if (elem && elem.checked) {
-        url = "&" + elem.name + "=" + elem.value;
-    }
-    return url;
-
-}
-
-function getUrlCompForOptionsField(elem) {
-    var url = "";
-    if (elem) {
-        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
-    }
-    return url;
-}
-
-function getUrlCompForMultiOptionsField(elem) {
-    var url = "";
-    if (elem) {
-        for (i = 0; i < elem.options.length; i++) {
-            if (elem.options[i].selected) {
-                url += "&" + elem.name + "=" + elem.options[i].value;
-            }
-        }
-    }
-    return url;
-}
-
-  
-utils.addEvent(window, 'load', newResultsWinInit, false);
-
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/blastReq.css
--- a/Blast output page example trimmed_files/blastReq.css	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,332 +0,0 @@
-#msgR .info {
-background-color: #dfd;
-padding: 4px;
-border: solid 1px green;
-color: green;
-}
-
-dl.summary dt {
-float: left;
-width: 8em;
-clear:left;
-margin: 0;
-text-align: right;
-padding-right: 1em;
-color: #666;
-}
-
-dl.summary dd {
-padding-left: 0.5em;
-display: block;
-margin-left: 7em !important;
-margin: 0;
-}
-dl.summary dt, dl.summary dd {
-margin-bottom: 0.5em;
-}
-a.help 
-{
-float:right;	
-font-size: 110%;
-}
-
-dl.summary label {
-display: inline;
-}
-
-dl.summary tr th label {
-padding: 0;
-margin-right:0;
-}
-table.options {
-border: solid 1px #ccc;
-border-right: solid 1px #ccc;
-}
-
-table.options td,
-table.options td.frh {
-font-size: 90%;
-_font-size: 85%;
-}
-
-table.options label.rb {
-border-right: solid 1px #ccc;
-margin-right: 0.5em;
-padding-right: 2.0em;
-}
-
-table.options tr td {
-_font-size: 90%;
-padding-left: 0.5em;
-}
-
-table.options {
-/*border-collapse: collapse;*/
-margin-left: 0;
-padding-left: 0;
-width: 62em;
-}
-
-table.options td label {
-font-size: 90%;
-}
-
-table.options th label,
-table.options td label {
-margin-right: 0;
-_position: relative;
-_top: -0.1em;
-}
-
-table.options tr.hdr td,
-table.options tr.hdr th {
-padding: 2px;
-border: solid 1px #ccc;
-background-color: #ddd;
-}
-
-table.options td, table.options td.frh {
-padding: 0.25em 0;
-vertical-align: center;
-}
-
-table.options th {
-padding-right: 1em;
-text-align: right;
-padding-left: 1em;
-}
-
-/*
-*:focus{
-background-color: white !important;
-}
-*/
-
-table.options select,table.options input, #graphic input{
-border: solid 1px #888;
-padding: 1px;
-}
-
-select {
-font-size: 90%;
-}
-
-select option {
-padding-right: 0.5em;
-}
-
-input.cb, table.options input.cb {
-border: none;
-}
-
-select {
-margin-right:1em;
-}
-
-table.options tr {
-background-color: #eee;
-}
-
-table.options tr.odd {
-background-color: #e0e0e0;
-}
-
-table.options th {
-
-background-color: white;
-}
-
-table.options tr.paramSet td
-{
-	border-top: solid 2px white;		
-}
-
-
-
-
-.resetAll 
-{
-font-weight: normal;
-padding: 0.5em;
-font-size: 90%;
-margin-left:5em;
-}
-
-.button {
-background-color: #ccc;
-padding: 0.25em 0.25em;
-color: black;
-border: outset 3px #eee;
-_border: outset 3px #eee;
-font-size: 90%;
-_padding:0;
-font-weight: bold;
-height:25px;
-_height:22px;
-}
-
-.fbtn {
-margin-bottom: 0.5em;
-}
-
-.note {
-font-size: 80%;
-color: green;
-background-color: #ffc;
-margin-left: 2em;
-padding: 3px;
-}
-.instr {
-   margin-left: 1em;
-   color: #666;
-font-size: 90%;
-}
-.smaller {
-font-size: 90%;
-font-weight: normal;
-}
-
-/* Results Page styles */
-
-#ridRes 
-{
-	background-color: #FC9;	
-	padding:5px 5px;	
-}
-
-
-span dd.hidden,dt.hidden,dd.hidden span
-{
-	display:none;
-}
-
-dl.query .query,
-dl.title .title,
-dl.entrez .entrez,  
-dl.db .db  
-{
-	display:block;	
-}
-
-
-dl.entrez span.entrez
-{
-	display:inline;	
-}
-
-.hidden {
-display: none;
-}
-.hide {
-display: none;
-}
-.shown {
-display: block;
-}
-
-
-
-table.megaBlast tr.psiBlast,
-table.blastn tr.psiBlast,
-table.blastx tr.psiBlast,
-table.tblastn tr.psiBlast,
-table.tblastx tr.psiBlast,
-table.discoMegablast tr.psiBlast
-{
-display: none;
-}
-
-
-table.GlobalAln .xgl,
-body.GlobalAln div.xgl,
-body.GlobalAln dt.xgl,
-body.GlobalAln dd.xgl,
-body.GlobalAln span.xgl,
-body.GlobalAln table.xgl
-{
-display: none;
-}
-
-.dispType
-{
-	/*background-color:White;
-	border:solid 1px black;*/	
-	border-top:solid 2px gray;
-	border-left:solid 2px gray;	
-	font-size:90%;	
-	padding-left:2px;
-	
-}
-
-.newwin {
-border: none;
-}
-
-table.options .helplink
-{
-    font-weight:bold;
-    position:absolute;
-    right:0;
-}
-
-div#query label 
-{
-    display: inline;
-    font-weight:bold;
-    padding-right:1em;
-}
-#NEW_VIEW
-{
-    _margin-left:-2px;
-}
-
-
-table.blastp *.blastn,
-table.psiBlast *.blastn,
-table.phiBlast *.blastn,
-table.blastx *.blastn,
-table.tblastn *.blastn,
-table.tblastx *.blastn
-{
-display: none;
-}
-
-#formatTable th.col1 {
-width: 8em;
-vertical-align: top;
-}
-/*
-#formatTable .helplink span {
-position: relative;
-}
-*/
-#org
-{
-    margin-top:2em;      
-}
-#qorganism
-{
-    /*display:block;*/
-}    
-.fi
-{
-    position:relative;
-}
-
-a#organismHelp
-{
-    margin-top:-1.5em;
-}
-
-table.options tr.paramSet td.hd {
-padding-right: 1em;
-text-align: right;
-padding-left: 1em;
-background-color:White;
-font-weight:bold;
-border-top:none;
-}
-.oExcl
-{
-    margin-left:2px;
-}
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/blastRes.css
--- a/Blast output page example trimmed_files/blastRes.css	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,262 +0,0 @@
-a#refPage
-{
-	margin-left:3em;	
-}
-
-a.resLink
-{
-	margin-left:1em;
-	display:none;
-}
-
-a.resLinkhidden 
-{
-	display:none;
-}
-
-
-#cddResults
-{
-	float:right;
-	margin-top:-2em;
-	margin-right:1em;
-	color:#336699;
-    font-size:100%;
-}
-
-#cddResults.showing { 
-   background-image: url(images/down.gif);   
-}
-
-
-
-div.inlineDiv
-{
-	display:inline;
-}	
-
-span.reslink
-{
-	display:none;
-}
-
-div.statPage *.statPage,
-div.resPage *.resPage
-{
-	display:inline;
-}
-
-div.resHeader *.hidden 
-{
-	display:none;
-}
-
-#cddInfo 
-{
-    text-align:center;
-}
-#cddDesc 
-{
-    font-weight:bold;
-}
-div#desctbl 
-{
-border: solid 1px #018aac;
-/*min-width: 1000px;*/
-margin: none;
-width: 100%;
-background-color:White;
-/*line-height:0;
-_line-height:0;*/
-}
-
-table#descs 
-{
-font-family: Verdana, Sans-Serif;
-font-size: 90%;
-_font-size: 86%;
-border-collapse: collapse;
-/*min-width: 600px;*/
-width: 100%;
-}
-
-table#descs th a {
-text-decoration: none;
-color: #00c;
-}
-
-table#descs th a:visited {
-color: #00c;
-}
-
-table#descs th a:hover {position: relative;
-text-decoration: underline;
-}
-
-table#descs tr th.l,
-table#descs tr td.l {
-text-align: left;
-}
-
-table#descs tr th.sp {
-background-color: #def;
-}
-
-table#descs tr th,
-table#descs tr td {
-text-align: center;
-padding: 1px 4px;
-}
-
-table#descs tr.first th {
-padding-left:18px;
-border-left: solid 1px #A0ceff;
-border-top: solid 1px #A0ceff;
-border-bottom: solid 1px #018aac;
-border-right: solid 1px #018aac;
-padding-right: 8px;
-/*background-color: #01d5ff;*/
-background-color: #9cf;
-/*font-size: 92%;*/
-white-space:normal;
-line-height: 1.2em
-}
-
-
-table#descs td {
-border: solid 1px #ccc;
-border-width: 0px 1px;
-white-space:nowrap;
-overflow: hidden;
-}
-
-.slink {
-font-size: 90%;
-font-weight: normal;
-}
-
-table#descs tr.first th.sel {
-background: #9cf url(images/up.gif) no-repeat center left;
-padding-left: 18px;
-padding-right: 18px;
-}
-
-div.lim 
-{    
-/*overflow: hidden;-this used to work in Firefox 2- comment for now and set the width */
-width: 35em;
-display: inline-block;
-height: 1.3em;
-}
-
-table#descs tr:hover {
-background-color: #def;
-}
-
-pre 
-{
-	font-size:110%;
-	_font-size:100%;	
-	line-height:1;
-}
-
-#msg 
-{
-    white-space:normal;
-    border-color:#cccccc;
-    padding:0;
-    margin: 0;   
-    margin-top:2px; 
-}
-#msg li 
-{
-    display:none;
-    padding:0;
-    margin: 0;
-    text-indent: 0;
-}
-#msg li.warning, #msg li.error ,#msg li.info 
-{
-    display:block;
-} 
-
-#msg ul
-{
-    margin:0;    
-    padding:0;    
-} 
-
-table#statInfo
-{
-    border: solid 1px #ccc;
-    background-color: #eee;
-    width: 100%;    
-}
-
-table#statInfo tr.odd {
-background-color: #e0e0e0;
-}
-
-.READY, .UNKNOWN 
-{
-    display:none;
-}
-
-p.WAITING 
-{
-    margin-top:1em;
-}
-
-#frmPage
-{
-	margin-left:1em;
-}
-
-span.Gene_PubMedLinks
-{
-    color: Green; font-weight: bold;
-}
-
-ul.msg li p
-{
-    display:none;
-}
-
-.msg li p.warning, .msg li p.error, .msg li p.success,.msg li p.info  
-{
-    display:block;
-} 
-
-.mdlbox
-{
-    white-space:pre;
-    background-color:Transparent;
-    border:none;
-}
-
-#blastErr
-{
-    white-space:normal;
-}
-
-
-
-#RSIFrameNoRes,#RSIFrameDesc,#RSIFrameAln
-{
-    border:none;
-    width:519px;
-    height:35px;    
-    margin:0px auto;
-}
-
-
-a.ui-ncbitoggler.hidden, a.ui-ncbitoggler-open.hidden
-{
-    display:none;
-}
-
-.smn {
-  display: inline-block;
-  height: 16px;
-  width: 16px;
-}
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/dynFormatRes.css
--- a/Blast output page example trimmed_files/dynFormatRes.css	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,623 +0,0 @@
-/* style changes for redesign begin*/
-a.gbd
-{
-    text-decoration:none;
-}
-
-tr.dflLnk td span
-{ 
-    font-size:78%; 
-    display:none;
-    text-align:center;
-}
-a.dflSeq
-{
-    color:#369;
-    text-decoration:underline;
-    width:auto;    
-}
-table.defln tr.dflLnk a
-{
-	margin-right:auto;	
-	padding-left:0;
-}
-
-.alnParLinks
-{
-    float:right;    
-}
-
-.alnSeqLinks
-{
-    float:right;
-    margin-right:1em;    
-}
-
-
-.seqlinks select
-{
-    padding:0;
-}
-
-.dlfRow div
-{
-    font-size:90%;
-}
-
-.dlfRow
-{
-    display:inline;
-    font-size:110%;
-}
-
-.dlfRow.hidden
-{
-    display:none;    
-}
-.dlfRow label
-{
-    font-size:87%;
-    display:inline;
-    color:#606060;
-    font-weight:bold;
-}
-
-.dlfRow span.r label
-{
-    padding-left:0.8em;
-}
-
-
-div.relInf
-{
-    font-family: Verdana, Sans-Serif;
-    font-size: 80%;
-    float:right;    
-    width:21%;
-    border-top:solid 2px gray;
-    margin-top:-1em;
-    margin-right:3.5em;
-    left:3em;
-    max-width:25em;    
-    padding-left:1em;
-    position:relative;    
-    white-space:normal;    
-}
-
-div.relInf a
-{
-    padding-right:0.2em;
-}
-
-.rlLink
-{
-    padding-left:0.2em;
-}
-.relInf label
-{
-    font-size:110%;
-    color:brown;
-    font-weight:bold;    
-}
-div#content
-{
-    min-width:70em;
-}
-
-.dflLnk a
-{
-	font-size:90%;
-}
-a.dflSeq
-{
-    width:auto;
-    font-weight:normal;
-}
-
-
-#cntDesc,#cntDesc_psiw  
-{
-    margin-bottom:0.2em;
-    display:inline-block;
-    width:20em;
-}
-#cntDesc span,#cntDesc_psiw span
-{
-    margin-right:0.5em;
-}
-
-#cntDesc a,#cntDesc input,#cntDesc_psiw a,#cntDesc_psiw input
-{
-    margin-left:0.5em;
-}
-
-#cntSelNone,#cntShAll
-{
-    margin-left:0.2em;
-}
-
-.toolsCtr
-{
-    color:Blue;    
-}
-
-table.ui-ncbigrid th span.slink a 
-{
-  display:inline;  
-  padding-right: 0;  
-}
-table.ui-ncbigrid th.sp
-{
-    font-weight:bold;
-}
-
-table.ui-ncbigrid th span.slink
-{
-    margin-left:0.2em;
-}
-
-table.ui-ncbigrid td {
- white-space:nowrap;
-}
-table.ui-ncbigrid td.c3
-{
-    /*padding-left:0.8em;*/
-}
-table.ui-ncbigrid caption
-{
-    font-size:0;
-    line-height:0;
-}
-#content h3.cap,#content h3.cap a.ui-ncbitoggler.ui-widget, #content h3.cap a.ui-ncbitoggler-open
-{
-    color:#4d4d4d;
-    text-align:left;
-    margin:0 0 0.5em 0;
-}
-
-#content div.cap,#content div.cap a.ui-ncbitoggler.ui-widget, #content div.cap a.ui-ncbitoggler-open
-{
-    color:#4d4d4d;
-    text-align:left;
-    margin:0 0 0.5em 0;
-    letter-spacing:-1px;
-    font-size:110%;
-    font-weight:bold;
-}
-
-#descriptions div.caption-exists {
-  margin: 0;
-}
-
-/**********decrition toolbar styles *********/
-
-div.cnf {
-  -moz-border-bottom-colors: none;
-  -moz-border-image: none;
-  -moz-border-left-colors: none;
-  -moz-border-right-colors: none;
-  -moz-border-top-colors: none;  
-  background: url("images/cnf.png") repeat scroll 0 0 transparent; 
-  border-style: solid none none;
-  border-width: 1px medium medium;
-  /*clear: left;*/
-  height: 22px;
-  /*overflow: auto;*/
-  width: 100%;
-}
-
-ul.ui-ncbilocalnav li.has-child a.button_config {
-  background: url("/portal/portal3rc.fcgi/3493904/img/81796") no-repeat scroll right center transparent !important;
-  width: 22px;
-  height:22px;
-  margin-left:12em;
-}
-
-#li-config
-{
-    float:right;
-    width:17em;
-}
-div#descTblCtrl ul.ui-ncbilocalnav li
-{
-    border-right:none;
-}
-
-
-.cfg
-{
-    font-size:90%;
-}
-
-
-.oneSeqAln .hsp label
-{
-    color:#606060;
-    font-size:95%;
-    padding-right:0.5em;
-}
-
-.oneSeqAln pre
-{
-    margin-top:0.5em;
-}
-
-.aln_feat label
-{
-  color: #606060;
-  font-size: 95%;
-  padding-right: 0.5em;  
-}
-.oneSeqAln .dflLnk.aln_feat
-{
-    padding-bottom:1em;
-}
-div.oneSeqAln h4
-{
-    border:none;
-    font-size:100%; 
-    font-weight:normal;
-    letter-spacing:normal;
-    margin:0;
-}
-    
-.oneSeqAln .dflLnk
-{
-    width:56em;
-}
-.aln_feat a
-{
-    margin-left:1em;
-    display:block;
-}
-.dflLnk.aln_feat div
-{
-  /*display:inline-block;  */
-  margin-left:5em;
-  margin-top:-1em;
-}
-.aln_frame.shown
-{
-    display:block;
-}
-/*align params styles change */
-
-table.alnParams
-{
-    border-left:none;        
-    border-right:none;        
-    margin-top:0.5em;
-    width:49em;
-}
-
-table.alnParams th
-{
-    background-color:Transparent;    
-    border:none;    
-    text-align:left;
-}
-
-table.alnParams td
-{
-   border:none;      
-}
-
-
-.alnAll
-{
-    line-height:normal;
-    margin-top:1em;
-}
-
-.alnAll div
-{
-    width:70%;
-}
-
-/**new config staff begin**/
-.popDl
-{
-    display:none;
-}
-.popDl div
-{
-    margin-top:0.5em;
-}
-.popDl div.tl
-{
-    margin-top:0;
-    font-weight:bold;
-}
-a.button_config {  
-  background: url("images/cnfButn.png") no-repeat scroll right center transparent !important;
-  width: 22px;
-  height:22px;
-  margin-left:12em;
-  float:right;
-}
-
-a.toolsCtr,span.csLinks a
-{
-    margin-left:8px;
-    float:left;
-    cursor:pointer;
-}
-
-a.toolsCtr[disabled] {
-  cursor: default;
-}
-
-
-a.toolsCtr SPAN
-{
-	color: #14376c;
-	/*line-height: 22px;*/
-	padding-left: 15px;
-	background-repeat: no-repeat;
-	background-position:left center;		
-}
-
-a.toolsCtr[disabled] SPAN,a.toolsCtr[disabled]
-{
-    color:#C2C2C2;
-}
-
-a.dnld span
-{
-	background-image: url("images/dndl.png");
-}
-
-a.dnld[disabled] span
-{
-	background-image: url("images/dndl_dsb.png");
-}
-
-a.dialog
-{
-	padding-right: 18px;
-	background:transparent url(images/dialog.png) no-repeat scroll right center;	
-	text-decoration:none;
-}
-
-a.dialog[disabled] {
-    background-image: url("images/dialog_dsb.png");
-}
-
-
-a.alnNav span
-{
-	background-image: url("images/align_Normal.png");
-}
-
-a.alnNav
-{
-    text-decoration:none;
-}
-
-
-a.navNext span
-{
-	background-image: url("images/next_Normal.png");
-}
-
-
-a.navNext[disabled] span
-{	
-	background-image: url("images/next_Inactive.png");
-}
-
-
-a.navPrev span
-{
-	background-image: url("images/prev_Normal.png");
-}
-
-
-a.navPrev[disabled] span
-{
-	background-image: url("images/prev_Inactive.png");
-}
-
-
-a.navBack span
-{
-	background-image: url("images/table_Normal.png");
-}
-
-.alnRn
-{
-    float:left;
-}
-
-
-/* styles to change per discusssion with Mark begin*/
-.dflLnk a
-{
-	padding-left:0;	
-}
-
-
-table.ui-ncbigrid th {
-  padding-left:0.3em;
-  padding-right:0;
-  text-align:center;  
-}
-
-table.ui-ncbigrid td {
-  padding-left:0.4em;
-  padding-right:0.4em;
-  text-align:center;  
-}
-
-table.ui-ncbigrid td.c2,table.ui-ncbigrid td.c1 {  
-  text-align:left;  
-}
-
-table.ui-ncbigrid td.c3{
-  padding:0.363em 0.25em;
-}
-
-
-table.ui-ncbigrid th a {
-  padding-right: 5px;
-}
-table.ui-ncbigrid th.c0
-{
-    width:25px;
-    padding:0;
-}
-
-.dflnDth
-{
-    width:100%;
-}
-div.lim { 
-  width: 14em;
-}
-
-table.ui-ncbigrid th.c8,table.ui-ncbigrid th.c9 {  
-  padding-right: 0.3em;  
-}
-.c8,.c9
-{
-    font-size:80%;
-}
-
-
-td.lim.l.c2,td.lim.l.c1 
-{
-    overflow:hidden;
-}
-a.spr
-{ 
-    border-right:none; 
-}
-
-
-.psiInp 
-{
-    margin-left:1em;
-    margin-top:0.5em;
-}
-
-
-.c8 input
-{
-    border:none;
-}
-table.ui-ncbigrid td.c8
-{
-    padding-left:1.5em;
-}
-
-tr.psi_new td
-{
-    background-color:#FFFF99;
-    border-top:solid 4px white;
-    border-spacing:3px;
-    border-collapse:collapse;
-    line-height:normal;
-}
-/* accessibility setting */
-tr.dflLnk td span.psiNw,tr.first th span,a.button_config span, a span.accsb,.dflLnk label.accsb
-{
-    display:inline;
-    position:absolute;
-    left:-9999px;
-}
-
-div.tgl
-{
-    margin-top:-1em;
-}
-.shcl
-{
-    float:right;
-}
-
-/* styles to change per discusssion with Mark end*/
-
-.alnRn a
-{
-    padding-right:1em;
-}
-.alnAll .moreHsps
-{
-    font-family: Verdana, Sans-Serif;
-    font-size: 75%;        
-    margin-top:-2.5em;
-    width:58%;
-}
-.erm
-{
-    background-color:#FFFFCC;
-    padding:0.5em;    
-}
-
-#debug,.ind,.alnMsgS .db,.erm .db
-{
-    display:none;
-}
-
-.tmsAln label
-{
-    font-size:93%;
-    display:inline;
-    color:#606060;
-    font-weight:bold;
-}
-.alnAll .tmsAln, .tmsAln div
-{
-    width:100%;
-    margin-bottom:-1em;
-}
-.tmsAlnPar
-{
-    margin-top:-1em;
-}
-/*debug info styles begin */
-
-
-/* use those styles only in debug version 
-
-.alnMsg
-{
-    border:solid 1px black;
-}
-
-.alnMsgS.hidden,.alnMsgS .db
-{
-    display:block;
-}
-
-.oneSeqAln
-{
-    border:1px solid #C8C8C8;
-}
-
-#debug,tr.dflLnk td span.ind
-{
-    display:inline;
-}
-.c0
-{
-    width:30px;
-}
-/*debug info styles end */
-
-
-
-/**new config staff end**/
-/*
-ul.ui-ncbilocalnav li, ul.ui-ncbilocalnav {
-  background-color: #F4F4F4;
-  background-image: -moz-linear-gradient(center top , #FFFFFF, #F4F4F4);
-}
-ul.ui-ncbilocalnav li {
-  border-right: 1px solid #C4C4C4;
-}
-*/
-/**********decrition toolbar styles end*********/
-
-
-/* style chenges for redesign end*/
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/firefox-descriptions_002.css
--- a/Blast output page example trimmed_files/firefox-descriptions_002.css	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-table.dbInfo caption {    
- 
-}
\ No newline at end of file
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/format.js
--- a/Blast output page example trimmed_files/format.js	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,270 +0,0 @@
-
-function UpdateDisplayTypes(displayTypes) {	
-    dispMenu = displayTypes.options;		
-    for(i=0; i < dispMenu.length; i++) {
-	    //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") ||
-	    if($("stepNumber").value == "" || $("stepNumber").value < 2) {	    	    
-			if(dispMenu[i].value.indexOf("PSSM") != -1) {
-				dispMenu[i--] = null;
-				//break;
-			}			
-		}		
-	}	    
-}
-
-function GetIndexByValue(selectElem,val) {	
-    var idx = 0;
-    var opts = selectElem.options;		
-    for(i=0; i < opts.length; i++) {
-        if(opts[i].value == val) {
-            idx = i;
-            break;
-        }
-    }	
-    return idx;	    
-}
-
-function resetAdvView(show)
-{
-    var advView = $("advView");    
-    if(show) {
-        if(utils.hasClass(advView, "hidden")) {
-            utils.removeClass(advView, "hidden");
-        }    
-    }
-    else {
-        utils.addClass(advView, "hidden");
-    }
-}
-
-
-function ShowOrHide(hide,elem)
-{
-    if(hide) {
-        if(!utils.hasClass(elem, "hidden")) {
-            utils.addClass(elem, "hidden");
-        }    
-    }
-    else {
-        if(utils.hasClass(elem, "hidden")) {
-            utils.removeClass(elem, "hidden");
-        }    
-    }
-}    
-
-function UpdateFormatTypes(form) {    
-    var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value;
-    var hideAdvView = false;
-    bioseqFormatHide = true;
-    pssmFormatHide = true;
-    pssmScFormatHide = true;
-    formatTypeHide = true;
-	if (selectedObjType == "Alignment") {
-		formatObjectSelectedIndex = 0; //HTML		
-		formatTypeHide = false;		
-		hideAdvView = true;
-	}
-    if (selectedObjType == "PSSM") {		
-		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text");	
-		pssmFormatHide = false;		
-    }
-    if (selectedObjType == "PSSM_Scoremat") {		
-		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");		
-		pssmScFormatHide = false;		
-    }    
-    else if (selectedObjType == "Bioseq") {		
-		formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1");		
-		bioseqFormatHide = false;		
-    }
-    form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex;     
-	ShowOrHide(formatTypeHide,form.FORMAT_TYPE);
-	if ($("bioseqFormat")) {
-	    ShowOrHide(bioseqFormatHide,$("bioseqFormat"));
-	    $("bioseqFormat").readOnly=true;		
-	}
-	if ($("pssmFormat")) {
-	    ShowOrHide(pssmFormatHide,$("pssmFormat"));
-	    $("pssmFormat").readOnly=true;	
-	}
-	if ($("pssmScFormat")) {
-	    ShowOrHide(pssmScFormatHide,$("pssmScFormat"));
-	    $("pssmScFormat").readOnly=true;	
-	}	
-	resetAdvView(hideAdvView);
-}	
-
-function ResetForm()
-{
-    //var defValNodes = cssQuery(".reset");	
-    defValNodes = $("FormatForm").elements;
-	for(i=0; i < defValNodes.length; i++) {	  	  
-	  if(utils.hasClass(defValNodes[i],"reset"))
-	                 setDefalValue(defValNodes[i]); 	  
-	}
-	if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
-	    UpdateFormatTypes($("FormatForm"));
-	    UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);
-	}
-	if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH)
-	else $("FormatForm").I_THRESH.value="";
-	//resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
-	resetOrganismControls($("FormatForm").FORMAT_ORGANISM);
-	//TO DO: add threshold
-}
-
-function LimitByHitlistSize(list)
-{
-    var listBreak = false;
-    var optSel = false;
-    for(i=0; i < list.options.length; i++) {    
-        var optVal = parseInt(list.options[i].value ,10);
-        var hitListSize = parseInt($("maxNumSeq").value ,10);                
-        if(list.options[i].selected) optSel = true;
-        if(optVal >= hitListSize)  {
-            if(!optSel) {list.options[i].selected = true;}
-            list.options.length = i + 1; 
-            break;
-        }                
-    }             
-}
-
-function AddFormatOrgField(e) {
-    AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE");
-}
-
-function initSubmit() {
-
-
-}
-
-function adjustFormatOptions() 
-{
-    var alignView = $("FormatForm").ALIGNMENT_VIEW;
-    var formatType = $("FormatForm").FORMAT_TYPE;
-    var queryAnch =  formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities");
-    var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch;
-    dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities");    
-    
-    UpdateDescriptions(dynFormatPW);
-    if (dynFormatPW) {
-        jQuery("#frmAln").addClass("hidden");
-        if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
-        jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE
-        jQuery("#scf").removeClass("hidden");//show CDS_FEAT
-        $("FormatForm").SHOW_LINKOUT.checked = true;        
-    }
-    else {
-        if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex;
-        
-        jQuery("#frmAln").removeClass("hidden");
-        if (dynFormatQA) {
-            if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT
-        }
-        else {
-            jQuery("#shl").removeClass("hidden");
-        } 
-        if (queryAnch) {
-            jQuery("#scf").addClass("hidden"); //hide CDS_FEAT
-        }
-        else {//pairwise old_view=false
-            jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT
-        }
-        jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE
-    }
-    if ($("blastSpec").value == "VecScreen") {
-        adjustVecscreen(dynFormatPW);
-    }
-}
-
-function adjustVecscreen(dynFormatPW) 
-{
-    var dfltDescrInd = 0; //0
-    var dfltDynDescrInd = 5; //1000
-    var dfltAlnInd = 6; //1000
-    if (dynFormatPW) {
-        utils.addClass($("lr"), "hidden");
-        $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd;        
-    }
-    else {
-        utils.removeClass($("lr"), "hidden");
-        $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd;
-    }
-    $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd;
-}
-
-
-function UpdateDescriptions(removeZero) 
-{
-    if (removeZero) {        
-        dispMenu = $("FormatForm").DESCRIPTIONS;
-        dispMenu.remove(0);
-    }
-    else {
-        dispMenu = $("FormatForm").DESCRIPTIONS;        
-        if (dispMenu.options[0].value != "0") {            
-            if (navigator.userAgent.match(/ie/i)) {
-                dispMenu.add(new Option("0", "0"), 0);
-            }
-            else {
-                dispMenu.add(new Option("0", "0"), dispMenu[0]);
-            }
-        }
-	}
-}
-
-function InitDynFormatOptions() 
-{
-    if ($("OLD_VIEW")) {
-        utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false);
-        utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false);
-        utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false);
-        adjustFormatOptions();
-    }
-}
-
-function InitFormatPage()
-{
-    if ($("FormatForm").FORMAT_OBJECT.type == "select-one") {
-        UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT);    
-        UpdateFormatTypes($("FormatForm"));
-        list = $("FormatForm").FORMAT_OBJECT;
-        utils.addEvent(list, "change", function() {
-            UpdateFormatTypes($("FormatForm"));
-                               },
-	                           false);
-    }
-    utils.addEvent($("resetAll"), "click",  ResetForm, false);         
-    if($("maxNumSeq") != null) {
-    if($("maxNumSeq").value != "") {
-        LimitByHitlistSize($("FormatForm").DESCRIPTIONS);
-        LimitByHitlistSize($("FormatForm").ALIGNMENTS);
-        LimitByHitlistSize($("FormatForm").NUM_OVERVIEW);        
-    }
-    }    
-    setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM);
-    utils.addEvent($("FormatForm"), "submit", function() {
-                            adjustOrgVal($("FormatForm").FORMAT_ORGANISM);},
-                    false);
-                    
-    if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false);
-    InitDynFormatOptions();    
-	/* add this code if decide image for View Report
-	var imgButtons = jQuery("[class='viewReport']");
-    for (var i = 0; i < imgButtons.length; i++) {
-      var l = imgButtons[i];
-      utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false);          
-      utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false);
-      utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false);
-      utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false);
-      utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false);
-   }  
-   */ 
-}
-
-utils.addEvent(window, 'load', InitFormatPage, false);
-
-
-
-
-
-
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/formatRes.js
--- a/Blast output page example trimmed_files/formatRes.js	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1542 +0,0 @@
-// JScript source code
-/*************************new code begin *******************************************************/
-
-function getHiddenFieldVal(elemName) {
-    var val;
-    var elem = document.getElementsByName(elemName);
-    if (elem) {
-        val = (elem.length > 1) ? elem[0].value : elem.value;
-    }
-    return val;
-}
-
-function getHiddenFieldParamString(elemName) {
-    var ret = "";
-    var val = getHiddenFieldVal(elemName);
-    if (val) {
-        ret = "&" + elemName + "=" + val;
-    }
-    return ret;
-}
-
-function elementInViewport(el) {
-    if (!el) return;
-    var rect = el.getBoundingClientRect();
-
-    var myWidth = 0, myHeight = 0;
-    if (typeof (window.innerWidth) == 'number') {
-        //Non-IE
-        myWidth = window.innerWidth;
-        myHeight = window.innerHeight;
-    } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) {
-        //IE 6+ in 'standards compliant mode'
-        myWidth = document.documentElement.clientWidth;
-        myHeight = document.documentElement.clientHeight;
-    } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) {
-        //IE 4 compatible
-        myWidth = document.body.clientWidth;
-        myHeight = document.body.clientHeight;
-    }
-    //window.alert('Width = ' + myWidth);
-    //window.alert('Height = ' + myHeight);
-
-
-    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth)
-    //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth)
-    return (rect.top >= 0 && rect.bottom <= myHeight);
-}
-
-function DisplayAlignFromDescription(elem) {
-    var alignView = $("FormatForm").ALIGNMENT_VIEW;
-    if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") {
-        DisplayDynamicAlign(elem);
-    }
-    else {
-        location.href = "#" + elem.getAttribute("seqID");        
-    }
-}	
-
-// ind="" gi="" id="deflnDesc_gi" href="#AlnHdrgi">desc
-//

-function DisplayDynamicAlign(elem) {
-    var currGi = elem.getAttribute("gi");
-    var currInd = elem.getAttribute("ind");
-    var stat = elem.getAttribute("stat");
-    if (!currInd || !currGi) return;
-    
-    if (!stat || stat == "") {
-        //Get 4(5) aligns before currInd and 4(5) aligns after
-        ReadCurrentSeqAligns(currInd, 5);        
-    }
-    else if (stat == "read") {
-        var indexes = getCurrIndexRange(currInd);
-        if (indexes) {
-            var msgID = "alnShow_" + indexes[0];
-            location.href = "#" + msgID;
-        }
-    }
-    else {
-        //error status handling        
-    }
-}
-
-
-function goToNextAlign(dtrID, next) {
-    var currInd = parseInt($(dtrID).getAttribute("ind"));
-    var rid = $("Rid").value;
-    nextInd = (next) ? currInd + 1 : currInd - 1;
-
-    if ($("deflnDesc_" + nextInd)) {
-        currGi = $("deflnDesc_" + nextInd).getAttribute("seqID");
-        scrollToGI = currGi;
-        if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") {
-
-            if (!next) {
-                ReadPrevSeqAligns(currInd, 5, scrollToGI);
-            }
-            else {
-                //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!!
-                ReadNextSeqAligns(currInd, 5, scrollToGI);
-            }
-
-        }
-        else {
-            location.href = "#" + scrollToGI;
-        }
-    }
-}
-
-function goToDefLine(dtrID) {
-    if ($("psiInp")) {
-        var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table
-        togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1";
-        jQuery($(togglerID)).ncbitoggler("open");
-    }
-}
-
-/*
-readAln.rid = rid;
-readAln.startIndex = parseInt(currInd);
-readAln.numSeq = parseInt(maxNumAligns);
-
-readAln.insertAfterID = insertAfterID;
-readAln.seqList = giList;
-readAln.scrollToSeqID = scrollToGI;
-*/
-function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) {
-    var lastDispIdx = 0;
-    var rid = $("Rid").value;
-
-    var readAln = new Object();
-    readAln.seqList = ""; //giList
-    readAln.rid = rid;
-
-    currInd = parseInt(currInd);
-
-    if (currInd != 0 && $("deflnDesc_" + currInd)) {
-        var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_
-        //alert(par.id);
-        if (par) par = utils.getParent(par); //"alnShow_
-        //alert(par.id);
-        if (par) readAln.insertAfterID = par.id;
-    }
-    else {
-        readAln.insertAfterID = "alnStart";
-    }
-
-
-
-    readAln.startIndex = currInd + 1;
-    readAln.numSeq = maxNumAligns;
-        
-    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next");
-        
-    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : "";
-    readAln.hspSort = 0;
-    ReadSeqAlignByIndex(readAln);
-}
-
-function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) {
-    var lastDispIdx = 0;
-    var rid = $("Rid").value;
-
-    var readAln = new Object();
-    readAln.seqList = ""; //giList
-    readAln.rid = rid;
-
-    currInd = parseInt(currInd);
-
-
-    //sets readAln.insertAfterID and returns lastDispIdx;
-    //Find the index of the previously displayed alignment
-    lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
-
-    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
-    readAln.numSeq = currInd - readAln.startIndex;    //stopIndex = currInd
-    
-    checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev");
-        
-    readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID");
-    readAln.hspSort = 0;
-    ReadSeqAlignByIndex(readAln);
-}
-
-//When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd
-function ReadCurrentSeqAligns(currInd, maxNumAligns) {
-    var rid = $("Rid").value;
-    var readAln = new Object();
-    readAln.seqList = ""; //giList
-    readAln.rid = rid;
-
-    currInd = parseInt(currInd);
-
-
-    //sets readAln.insertAfterID and returns lastDispIdx;
-    //Find the index of the previously displayed alignment
-    var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln);
-
-    //lastDispIdx = parseInt(lastDispIdx);
-    readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1;
-    readAln.numSeq = parseInt(maxNumAligns * 2);
-        
-    checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr");
-        
-    readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID");
-    readAln.hspSort = 0;
-    ReadSeqAlignByIndex(readAln);
-    g_DisableAutoCheck = true;
-    location.href = "#alnShow_" + readAln.startIndex;
-}
-
-
-
-
-function setupDynHSPParams(readAln) 
-{
-    var currSeqInd = readAln.startIndex;
-    hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp"));
-    alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len"));
-    var maxDispLen = parseInt($("maxDispAlnLen").value);//20000
-    var minDispLen = parseInt($("minDispAlnLen").value);//2000
-    if (alnLen > maxDispLen) {
-        var lenPerMatch = alnLen / hspNum;        
-        readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch);
-        readAln.AlignDbPageNum = 0;
-        $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize);
-    }
-}
-
-
-
-function getCurrSeqsAlnLen(currSeqInd) 
-{
-    var alnLen = 0;
-    if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) {
-        alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len");            
-    }
-    alnLen = (alnLen) ? parseInt(alnLen) : 0;
-    return alnLen;
-}
-
-function checkTotalAlignLen(startIndex,stopIndex)
-{
-    var dispAlnLen = 0;
-    var maxDispLen = parseInt($("maxDispAlnLen").value);    
-    for (var i = startIndex; i <= stopIndex; i++) {
-        alnLen = getCurrSeqsAlnLen(i);
-        if (alnLen == 0) break;
-        dispAlnLen += alnLen;        
-    }
-    return dispAlnLen;
-}
-//Get total align length for seq currSeqInd and
-//"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs
-function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType) 
-{
-    var startIndex = readAln.startIndex;
-    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
-    if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current                
-        startIndex = Math.max(startIndex, currSeqInd - countSeqs);        
-        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs);        
-    }
-    else if(dispType == "prev") {        
-        startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs);
-        stopIndex = currSeqInd - 1;        
-    }
-    else {//next                                
-        stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1);
-    }
-    var totAlnLen = checkTotalAlignLen(startIndex,stopIndex);
-    return totAlnLen;
-}
-
-function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType) 
-{
-    var maxDispLen = parseInt($("maxDispAlnLen").value);
-    var totAlnLen = 0;
-    var exc = false;
-    for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) {
-        totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType);
-        if(totAlnLen > maxDispLen) {
-            break;
-        }
-    }
-    if (totAlnLen > maxDispLen) {
-        if (numSeq != 0) numSeq--;      
-        if (dispType == "curr") {
-            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq);
-            //prev + 1(curr) + next            
-            readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq;
-        }
-        else if (dispType == "prev") {
-            readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq);
-            readAln.numSeq = numSeq + 1;
-        }
-        else { //"next" - readAln.startIndex stays
-            readAln.numSeq = numSeq + 1;
-        }
-        
-        if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") {
-            setupDynHSPParams(readAln);            
-        } 
-                   
-        exc = true;   
-    }
-    return exc;
-}
-
-
-//readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set
-function ReadSeqAlignByIndex(readAln) {
-    var numAligns = 0;
-    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
-
-        if (!$("deflnDesc_" + i)) {
-            break;
-        }
-        if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") {            
-            currGi = $("deflnDesc_" + i).getAttribute("seqFSTA");
-            if (readAln.seqList != "") readAln.seqList += ",";
-            readAln.seqList += currGi;
-            numAligns++;
-        }
-        else {
-            break;
-        }
-    }
-    if (readAln.seqList != "") {        
-        readAln.numSeq = parseInt(numAligns);
-        ReadSeqAlignForSeqList(readAln);
-    }
-}
-
-
-var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2...
-//Find the range of indexes of displayed alignments for currAlnInd
-//Returns array of 2 startIndex, stopIndex
-function getCurrIndexRange(currAlinInd) {
-    var currRange;
-    var ranges = g_DisplayeAlignsRanges.split(",");
-    for (var i = 0; i < ranges.length; i++) {
-        var indexes = ranges[i].split("-");
-        if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) {
-            currRange = indexes;
-            break;
-        }
-    }
-    return currRange;
-}
-
-
-//Find the index of the previous  displayed alignment
-function getPrevDisplyedAlignInfo(currInd, readAln) {
-    readAln.insertAfterID = "alnStart";
-    lastDispIdx = 0;
-    for (var i = currInd - 1; i >= 1; i--) {
-        indexes = getCurrIndexRange(i);
-        if (indexes) {
-            lastDispIdx = indexes[1];
-            readAln.insertAfterID = "alnShow_" + indexes[0];
-            break;
-        }
-    }
-    return parseInt(lastDispIdx);
-}
-
-
-//setReadStatus
-function setSeqAlnReadStatus(readAln, status) {
-    for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) {
-        if ($("deflnDesc_" + i)) {
-            jQuery($($("deflnDesc_" + i))).attr("stat", status);
-            if (status == "disp") {
-                g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex;
-            }
-        }
-    }
-}
-
-/*
-readAln.rid = rid;
-readAln.seqList = giList;
-readAln.startIndex = parseInt(idx);
-readAln.insertAfterID = insertAfterID;
-readAln.numSeq = parseInt(numSeq);
-readAln.scrollToSeqID = scrollToGI;
-*/
-function SendReadSeqAlinRequest(readAln) {        
-    blastUrl = "t2g.cgi";
-    
-    var rp = new RemoteDataProvider(blastUrl);
-
-
-    rp.onSuccess = function(obj) {
-        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
-
-        if ($("alnShow_" + readAln.startIndex)) {
-            var moreHspsLink = getNextHspsLink(readAln);            
-            jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, {
-                'widgets': ['ncbipopper', 'ncbitoggler'],
-                'configs': {
-                    'ncbipopper': { hasArrow: true, arrowDirection: 'top' }
-                }
-            }); 
-            setSeqAlnReadStatus(readAln, "disp");
-            jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");        
-            //Saves start and stop indexes of loaded alignments in global variables
-            saveIdxesForAutomaticLoad(readAln);
-            jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) {
-                var seqID = this.getAttribute("seqID");
-                if(seqID) initAlignBatch(seqID);
-            });
-
-        }
-
-        if (readAln.scrollToSeqID) {
-            location.href = "#" + readAln.scrollToSeqID;
-        }
-
-    };
-    rp.onError = function(obj) {        
-        if ($("alignView")) utils.removeClass($("alignView"), "hidden");
-        jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden");
-        $("alnShowReal_" + readAln.startIndex).innerHTML = "
Error loading alignment ...requests:" + this.iActiveRequests + " status:" + obj.status +
-                          "Try again<\a>
";
-    }
-    var params = constructURLParams(readAln);
-    if (readAln.numSeq == 1) {
-        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
-    }
-    params += "&SEQ_LIST_START=" + readAln.startIndex;    
-    
-    var formatParams = constructFormatParams();
-    params += formatParams;    
-    
-    //alert(params);
-    rp.Request(params);
-}
-
-
-function constructURLParams(readAln) {
-    var params;
-
-    if ($("useAlignDB") && $("useAlignDB").value == "true") {
-
-        var alignDbParams = "&USE_ALIGNDB=true";
-        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
-        if (batchID) {
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID");
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS");
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST");
-            alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH");
-        }
-        alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList;
-        alignDbParams += "&HSP_SORT=" + readAln.hspSort;
-
-        if (readAln.hasOwnProperty("AlignDbPageNum")) {
-            alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum;
-            alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize;
-            alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum;
-        }
-
-        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams;
-    }
-    else {
-        params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort;
-    }    
-    if ($("phiPtInd")) {
-        params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value;
-    }
-    return params;
-}
-
-/*
-readAln.rid = rid;
-readAln.seqList = giList;
-readAln.startIndex = parseInt(idx);
-readAln.insertAfterID = insertAfterID;
-readAln.numSeq = parseInt(numSeq);
-readAln.scrollToSeqID = scrollToGI;
-*/
-/*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes
-2. Insert another div with id="alnShowReal_index and class="alnMsgR"
-3. For "alnShow_index" set atrr indexes="startInd-stopInd"
-4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this 
-5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes
-6. Send read request
-*/
-
-function ReadSeqAlignForSeqList(readAln) {
-    var text = "
Loading alignment... for sequences " + readAln.seqList;
-    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
-    var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : "";
-    text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "
";
-    text += "
";
-    var debugControl = "
";
-    if (!$("debug")) {
-        jQuery($($("descriptions"))).before(debugControl);
-    }
-    if (!$("alnShow_" + readAln.startIndex)) {        
-        jQuery($($(readAln.insertAfterID))).after(text);
-        jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex);
-        jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList);
-        g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex;
-        setSeqAlnReadStatus(readAln, "read");
-        $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex;
-
-        if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ",";
-        g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex;
-
-        SendReadSeqAlinRequest(readAln);
-    }
-    else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) {
-        jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden");
-        jQuery($("erm_" + readAln.startIndex)).remove();        
-        SendReadSeqAlinRequest(readAln);
-    }
-}
-
-
-function ReSubmitReadSeqAligns(e,currInd) {
-    var rid = $("Rid").value;
-    if ($("alnShow_" + currInd)) {
-        var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes");
-        var range = indexRange.split("-");
-
-
-        var readAln = new Object();
-        readAln.seqList = ""; //giList
-        readAln.rid = rid;
-        readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist");
-        readAln.startIndex = parseInt(range[0]);
-        readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1;
-        readAln.hspSort = 0;
-        ReadSeqAlignForSeqList(readAln);
-        utils.preventDefault(e);
-    }
-}
-
-
-var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read"
-var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N
-var g_DisableAutoCheck = false;
-
-var g_autoStartIdx = new Array();
-var g_autoStopIdx = new Array();
-
-function saveIdxesForAutomaticLoad(readAln) {
-    var stopIndex = readAln.startIndex + readAln.numSeq - 1;
-    g_autoStartIdx.push(readAln.startIndex); //1,20,25
-    g_autoStopIdx.push(stopIndex);  //4,24,29    
-    $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex;
-}
-
-function getNextHspsLink(readAln)
-{
-    var moreHspsLink = ""
-    if (readAln.hasOwnProperty("AlignDbPageNum")) {
-        var nextPageNum = readAln.AlignDbPageNum + 1;
-        var currHspInd = readAln.AlignDbPageSize * nextPageNum;
-        var argstring = readAln.startIndex + "," + currHspInd;                
-        var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId");
-        var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs");        
-        var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
-        var prevHspInd = readAln.AlignDbPageSize * nextPageNum;
-        var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize);        
-        var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1);
-
-        moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID);        
-        moreHspsLink = moreHspsLink.replace(/@accs@/g, accs);
-        moreHspsLink = moreHspsLink.replace("@argstring@", argstring);
-        moreHspsLink = moreHspsLink.replace(/@segs@/g, segs);
-        moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps);        
-        moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize);
-        moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd);
-        moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi);
-    }
-    return moreHspsLink;
-}
-
-
-function ReadNextHSPSet(currSeqInd, currHSPNum) {
-    var readAln = new Object();
-
-    readAln.rid = $("Rid").value;
-    readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA");
-    readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId");
-    dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps");
-    readAln.startIndex = currSeqInd;
-    readAln.numSeq = 1;
-    if (dynHsps) {
-        readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps);
-        readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve
-    }
-    if (currHSPNum != 0) {
-        readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1);
-        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum;
-    }
-    var sortLink = $("sa_" + readAln.gi);
-    readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0;
-    SendReadSeqAlinSortHSPRequest(readAln);
-}
-
-function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) {
-    ReadNextHSPSet(currSeqInd, currHSPNum);    
-    utils.preventDefault(e);
-}
-
-
-
-function checkAutoAlignArray() {
-    var stop = false;
-    var start = false;
-    var currAlignViewPos = $("alignView").getBoundingClientRect().top;
-    if (currAlignViewPos < g_alignViewPos) {//scrolling down
-        g_alignViewPos = currAlignViewPos;
-        if (g_DisableAutoCheck) {
-            g_DisableAutoCheck = false;
-            return;
-        }        
-        for (i = 0; i < g_autoStopIdx.length; i++) {
-            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) {
-                //alert("Reading more aligns scrolling down!");
-                var nextInd = parseInt(g_autoStopIdx[i] + 1);
-                var currInd = g_autoStopIdx[i];
-                if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) {
-                    ReadNextSeqAligns(currInd, 5);
-                    stop = true;
-                    break;
-                }
-            }
-        }
-        if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array
-    }
-    else if (currAlignViewPos > g_alignViewPos) {//scrolling up
-        g_alignViewPos = currAlignViewPos;
-        //here maybe return if autoStop found!!!
-        /* commenting automic read when scroll up */
-        for (i = 0; i < g_autoStartIdx.length; i++) {
-            if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) {
-                //alert("Reading more aligns scrolling up!");
-                var currInd = g_autoStartIdx[i];
-                //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!!
-                if (currInd > 1) {
-                    ReadPrevSeqAligns(currInd, 5);
-                    start = true;
-                    break;
-                }
-            }
-        }
-        if (start) g_autoStartIdx.splice(i, 1);
-    }
-    /*end of comment*/
-}
-
-var g_alignViewPos = 0;
-
-function checkAutoAlignLoad() {
-
-
-    checkAutoAlignArray();
-
-    if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) {
-        //alert("bottom!");       
-
-        if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") {
-            //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex
-            ReadNextSeqAligns(g_MaxDisplayedIndex, 5);
-        }
-    }
-}
-
-
-function GetPatternLocResults()
-{
-    form = $("results");
-    if (!form.PHI_PTTRN_INDEX) {
-        var el = document.createElement("input");
-        el.name = "PHI_PTTRN_INDEX";
-        el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
-        form.appendChild(el);
-    }
-    else {
-        form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value;
-    }
-    form.submit();
-}
-
-function goToNextHSP(elem, next) {    
-    var par = jQuery(elem).parent(); //parent span with class="alnParLinks"
-    var parts = par[0].id.split("_"); //"hsp_hspnum "hsp207524544_2"
-    if (parts[0].indexOf("nxHsp") != -1) {
-        parts[0] = parts[0].replace("nxHsp", "hsp");
-    }
-    nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1)
-    
-    gotoElem = jQuery($(nextID));
-    if (gotoElem[0]) {
-        a = jQuery(gotoElem).offset();
-        window.scroll(0, a.top);
-    }
-    
-    else {
-        retrieveNextHSP(parts[0],parts[1]);
-    }
-    
-}
-
-
-//parts[0]//hsp,    parts[1] hspnum
-function retrieveNextHSP(currLinkID, currHSPNum) 
-{
-    var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id
-    var currSeqInd, totalHsps;
-    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {
-        currSeqInd = parseInt(this.getAttribute("ind"));
-        totalHsps = parseInt(this.getAttribute("hsp"));
-        dynHsps = this.getAttribute("dynHsps");
-    });
-    currHSPNum = parseInt(currHSPNum);
-    if (currHSPNum < totalHsps && dynHsps) {        
-        ReadNextHSPSet(currSeqInd, currHSPNum);
-    }
-}
-/********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/
-function getUrlCompForEntryField(elem) {
-    var url = "";
-    if (elem && elem.value != "") {
-        url = "&" + elem.name + "=" + escape(elem.value);
-    }
-    return url;
-}
-
-
-function getUrlCompForCheckedField(elem) {
-    var url = "";
-    if (elem && elem.checked) {
-        url = "&" + elem.name + "=" + elem.value;
-    }
-    return url;
-
-}
-
-function getUrlCompForOptionsField(elem) {
-    var url = "";
-    if (elem) {
-        url = "&" + elem.name + "=" + elem[elem.selectedIndex].value;
-    }
-    return url;
-}
-/****************************************/
-
-function constructFormatParams() {
-    var formatParams = "";
-
-    if ($("queryList")) {
-        formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value;
-    }
-
-    
-    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT);
-    formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE);
-    formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI);
-    formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW);
-    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR);
-    formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR);    
-    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW);
-    formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH);
-    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW);
-    formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH);
-    formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH);
-    
-
-    formatParams += getHiddenFieldParamString("BUILD_NAME");
-    
-    var serviceType = "";
-    if ($("serviceType").value == "sra") {
-        serviceType = "sra";
-    }
-    else if ($("clientType").value == "TMSmart_restricted") {
-        serviceType = "restricted";
-    }
-    if (serviceType != "") {
-        formatParams += "&BOBJSRVC=" + serviceType;
-    }
-    if ($("currQuery").value != "") {
-        formatParams += "&CURR_QUERY_ID=" + $("currQuery").value;
-    }
-    
-    return formatParams;
-}
-
-//readAln.seqList contains one gi only for this
-function SendReadSeqAlinSortHSPRequest(readAln) {
-    blastUrl = "t2g.cgi";    
-    var rp = new RemoteDataProvider(blastUrl);
-
-
-    rp.onSuccess = function(obj) {
-        var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : "";        
-        var alnHtml = obj.responseText + moreHspsLink;
-        initHSPRequest(readAln, obj.responseText + moreHspsLink,false);        
-        if (readAln.scrollToSeqID) {
-            location.href = "#" + readAln.scrollToSeqID;
-        }                
-    };
-    rp.onError = function(obj) {        
-        var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;
-        var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
-        if (!$(msgID)) {
-            var msg = "";
-            initHSPRequest(readAln, msg, true);
-        }
-        else {
-            var attNum = parseInt($(msgID).getAttribute("att")) + 1;
-            $(msgID).setAttribute("att", attNum);
-            jQuery($(msgID)).find(".attmt").each(function(index) {
-                jQuery(this).html(", attempt " + attNum);
-            });
-        }
-    }
-    
-    var params = constructURLParams(readAln);
-    if (readAln.AlignDbPageSize) {    
-        params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp");
-    }    
-    params += "&SORT_ONE_ALN=on";
-    var formatParams = constructFormatParams();
-        
-    params += formatParams;
-    
-    //alert(params);
-    rp.Request(params);
-}
-function initHSPRequest(readAln, alnHtml, err) {
-    var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0;    
-    if (currHspInd != 0) {
-        readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd;
-        jQuery($(readAln.insertAfterID)).after(alnHtml);
-        moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1);
-        jQuery($(moreHspsID)).remove();
-        if (!err) {
-            errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1);
-            jQuery($(errMsgID)).remove();            
-        }
-    }
-    else {
-        jQuery($("alnAll_" + readAln.gi)).html(alnHtml);
-    }    
-}
-
-function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544"
-    var readAln = new Object();
-
-    
-    var desLineID = sortLink.id.replace("sa", "dtr"); //tr id
-    var seqInd;
-
-    jQuery($($(desLineID))).find(".deflnDesc").each(function(index) {        
-        seqInd = this.getAttribute("ind");
-    });    
-    
-    ReadNextHSPSet(parseInt(seqInd), 0);
-}
-
-
-function configDescriptions(e,btn,dlgId) 
-{
-    var suffix = PsiBelowThresh(dlgId);    
-    var colmnsInfId = "cfcDsInf" + suffix;
-    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
-    var showAllColId = "shcl" + suffix;    
-    var chkBoxes = $C("checkbox", "type", $(dlgId), "input");
-    if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = "";    
-    for (i = 0; i < chkBoxes.length; i++) {
-        var check;
-        if (utils.hasClass(btn, "cnc")) {//cancel
-            if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) {
-                check = true;
-            }
-            else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) {
-                check = false;
-            }
-        }
-        else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) {
-            check = true;
-        }
-        if (typeof (check) != 'undefined') {
-            chkBoxes[i].checked = check;
-            showHideCol(tblID,parseInt(chkBoxes[i].value), !check);
-        }
-        if (!utils.hasClass(btn, "cnc")) {
-            if (chkBoxes[i].checked) { //OK
-                if ($(colmnsInfId).value != "") $(colmnsInfId).value += ",";
-                $(colmnsInfId).value += chkBoxes[i].value;
-            }
-        }
-    }
-    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
-        jQuery($(showAllColId)).removeClass("hidden");
-    }
-    else {
-        jQuery($(showAllColId)).addClass("hidden");
-    }
-
-    var chConfig = $("cfcDsSave").value != $(colmnsInfId).value;
-    
-    var cfds = document.getElementsByName("CONFIG_DESCR");        
-    if (cfds) {
-        for (i = 0; i < cfds.length; i++) {
-            cfds[i].value = $(colmnsInfId).value;
-        }
-    }    
-    $("cfcDsSave").value = $(colmnsInfId).value;
-    if (chConfig) SaveConfigTable();
-    jQuery(document.body).click();
-    utils.preventDefault(e);
-}
-
-
-
-function initDescConfig() 
-{
-    initConfigColumns("dsConfig");
-    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
-        initConfigColumns("dsConfig_psiw");
-    }        
-}
-
-
-function initConfigColumns(cnfDlgID) 
-{
-    var suffix = PsiBelowThresh(cnfDlgID);
-    //cnfDlgID is "dsConfig[_psiw]"
-    var colmnsInfId = "cfcDsInf" + suffix;
-    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
-    var showAllColId = "shcl" + suffix;
-    
-    if (navigator.userAgent.match(/ie/i)) {
-        if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") {        
-            jQuery($(tblID)).find("th.c1").each(function(index) {            
-                db = getHiddenFieldVal("DATABASE");
-                var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em";
-                jQuery(this).css("width", width);
-            });        
-        }
-    }
-
-    jQuery($(tblID)).find("tr.first").each(function(index) {
-        jQuery(this).find("a.dcs").each(function(index) {        
-           jQuery(this).bind("click", function(e) { checkConfig(this); });           
-        });
-    });
-
-    jQuery($(cnfDlgID)).find("button").each(function(index) {
-        jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); });
-    });
-
-        
-    jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); });
-
-    $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR");
-    if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") {
-        $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval");
-    }
-    if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8"
-        jQuery($(showAllColId)).removeClass("hidden");
-    }    
-    else {
-        jQuery($(showAllColId)).addClass("hidden");
-    }
-    var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input")
-    for (i = 0; i < chkBoxes.length; i++) {
-        jQuery(chkBoxes[i]).bind("click", configColumn);
-        if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) {
-            chkBoxes[i].checked = true;
-        }
-        else {
-            //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value);
-            showHideCol($(tblID), chkBoxes[i].value, true); 
-        }
-    }
-}
-function showAllCol(e,elem) 
-{
-    var suffix = PsiBelowThresh(elem.id);
-    var rdf = "dscRsDf" + suffix;
-    jQuery($(rdf)).click();//click "restore defaults'
-    utils.preventDefault(e);
-}
-
-
-function configColumn() {
-    var suffix = PsiBelowThresh(this.id);
-    var tblID = "dscTable" + suffix; //"dscTable[_psiw]"
-    
-    cCls = "c" + this.value;
-    if (this.checked) {//show        
-        showHideCol(tblID,parseInt(this.value), false);        
-    }
-    else {
-        showHideCol(tblID,parseInt(this.value), true);        
-    }
-}
-
-function showHideCol(tblID, columnIndex, hide) {
-
-    if ($("Transcr")) {
-        colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden");
-        hide = hide && !colHidden;
-        show = !hide && colHidden;
-    }
-    else {
-        show = !hide;
-    }    
-    if (hide) {
-        jQuery($(tblID)).ncbigrid("hideColumn", columnIndex);        
-    }
-    else if (show) {
-        jQuery($(tblID)).ncbigrid("showColumn", columnIndex);    
-    }
-    if ($("Transcr") && (hide || show) ) {
-        var colsp = parseInt($("Transcr").getAttribute("colspan"));
-        colsp = (hide) ? colsp - 1 : colsp + 1;
-        $("Transcr").setAttribute("colSpan", colsp);
-        if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp);
-    }
-}
-
-function checkConfig(lnk) {
-    var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value;
-    lnk.href = lnk.href + cnfCol + "#sort_mark";    
-}
-
-function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists
-{
-    var dflLineLinks = $C(seqID, "gi", document, "a");    
-    for (i = 0; i < dflLineLinks.length; i++) {
-        jQuery(dflLineLinks[i]).click();
-        break;
-    }    
-    location.href = dflLineLinks[i].href;
-}
-
-
-
-function initDescSelect() 
-{
-
-    jQuery("#cntDesc").find("a").each(function(index) {
-        jQuery(this).bind("click", configDescrSelect);
-    });
-    jQuery("#cntSelN").click();
-    jQuery("#descTblCtrl").find("a[view]").each(function(index) {
-        jQuery(this).bind("click", DisplaySelectedView);
-    });
-    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
-        jQuery("#cntDesc_psiw").find("a").each(function(index) {
-            jQuery(this).bind("click", configDescrSelect);
-        });
-        jQuery("#cntSelN_psiw").click();
-        jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) {
-            jQuery(this).bind("click", DisplaySelectedView);
-        });
-    }
-    
-    
-    //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });??
-
-}
-
-function DisplaySelectedView(e) {
-    if (this.getAttribute("view") == "graph") {    //seqviewer
-        ViewSelectedSeqViewer(e,this);
-    }
-    else {
-        if (this.getAttribute("view") == "tree") {    //seqviewer
-            $("scrWidth").value = screen.width;
-            $("scrHeight").value = screen.height;
-        }
-        ViewSelectedSeqsEx(e, this);
-    }
-}
-
-function PsiBelowThresh(elemID) 
-{
-    var suffix = "";
-    if (elemID.indexOf("_psiw") != -1) {
-        suffix = "_psiw";
-    }
-    return suffix;
-}
-
-function ViewSelectedSeqsEx(e,elem) {
-    var sbmForm = elem.getAttribute("frm");
-    var seqList = elem.getAttribute("seqList");
-
-    var cnfElem = utils.getParent(elem); //.cnf div    
-    var suffix = PsiBelowThresh(cnfElem.id);
-    var tblID = "dscTable" + suffix;
-
-    $(seqList).value = createSelseqString(tblID,true);
-    $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces
-    if ($(seqList).value.indexOf("dbSNP") != -1) {
-        $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp
-        elem.href = $(sbmForm).action + $(seqList).value;
-        elem.target = "new";
-    }
-    else {
-        $(sbmForm).submit();
-        utils.preventDefault(e);
-    }    
-}
-
-function ViewSelectedSeqsTree(e) {
-    $("scrWidth").value = screen.width;
-    $("scrHeight").value = screen.height;
-}
-
-function initSeqViewerGet(seqList) {
-    if (seqList.length >= 2000) {    
-        seqList = seqList.substr(0,2000);
-        lastComma = seqList.lastIndexOf(",");
-        seqList = seqList.substr(0,lastComma);             
-    }
-    $("seqViewParams").name = "RID";
-    $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]";
-}
-
-function ViewSelectedSeqViewer(e, elem) 
-{
-    var cnfElem = utils.getParent(elem); //.cnf div    
-    var suffix = PsiBelowThresh(cnfElem.id);
-    var tblID = "dscTable" + suffix;
-
-    //change to false when new verison of seqVier is installed in production
-    var seqList = createSelseqString(tblID, false);
-    $("sbmtGraphics").action = $("seqViewUrl").value;
-    
-    var rp = new RemoteDataProvider("url2nc.cgi");
-    rp.onSuccess = function(obj) {
-        var jsnResp = JSON.parse(obj.responseText);
-        ncid = jsnResp.ncid;
-
-        if (ncid != "") {
-            $("seqViewParams").name = "rkey";
-            $("seqViewParams").value = ncid;
-        }
-        else {
-            initSeqViewerGet(seqList);
-        }
-        $("sbmtGraphics").submit();        
-    };
-    rp.onError = function(obj) {
-        initSeqViewerGet(seqList);
-        $("sbmtGraphics").submit();
-        utils.preventDefault(e);   
-    }
-    var params = $("ridParam").value + "[" + seqList + "]";    
-    rp.Request(params, "POST");
-    utils.preventDefault(e);   
-}
-
-function configDescrSelect(e) {    
-    var sel = this.getAttribute("sel");    
-    if (sel) {
-        var selNum = 0;
-        var check = (sel == "all") ? true : false;
-
-        var suffix = PsiBelowThresh(this.id);
-        var tblID = "dscTable" + suffix;
-        var toolbarID = "descTblCtrl" + suffix;
-        var selElID = "slcNum" + suffix;
-
-        jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
-            jQuery(this)[0].checked = check;
-            if (check) selNum++;
-        });
-        enableDescrLinks(selNum, toolbarID, selElID);        
-    }     
-    utils.preventDefault(e);
-}
-
-
-
-function enableDescrLinks(selNum, toolbarID, selElID) {
-    jQuery($(toolbarID)).find("a[minSlct]").each(function(index) {
-        var minSelected = this.getAttribute("minSlct");
-        minSelected = parseInt(minSelected);
-        if (selNum >= minSelected) {
-            this.removeAttribute("disabled");
-        }
-        else {
-            this.setAttribute("disabled", "disabled");
-        }
-    });    
-    $(selElID).innerHTML = selNum;
-}
-
-
-
-function configDescrLinks(e, elem) 
-{
-
-    ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false");     
-    var par = jQuery(elem).parents(".jig-ncbigrid");//parent table
-    if (par) {
-        var suffix = PsiBelowThresh(par[0].id);
-        var tblID = "dscTable" + suffix;
-        var toolbarID = "descTblCtrl" + suffix;
-        var selElID = "slcNum" + suffix;
-        
-        var currSelNum = parseInt($(selElID).innerHTML);
-        var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1;
-        enableDescrLinks(selNum, toolbarID, selElID);
-    }
-}
-/***Download code begin****/
-
-function initDownLoadPopup(dwnDialog) {
-
-    jQuery(dwnDialog).find("button").each(function(index) {        
-        jQuery(this).bind("click", execDownLoad);        
-    });
-
-    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });
-}
-
-function initDescDownLoad() {
-    initDownLoadPopup($("dsDownload"));
-
-    if ($("psiw") && utils.hasClass($("psiw"), "shown")) {
-        initDownLoadPopup($("dsDownload_psiw"));        
-    }
-}
-
-function initAlignDownLoad(navObj) 
-{
-    var seqID = navObj.seqID;
-    var dwnDialog = $("dlgDwnl_" + seqID);
-    jQuery(dwnDialog).find("button").each(function(index) {        
-        jQuery(this).bind("click", execDownLoad);        
-    });
-
-    var dwnFSTW = $("dwFST_" + seqID);//whole seq
-    var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions
-    
-    if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID); 
-    if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID); 
-    
-    jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); });    
-}
-
-    
-function execDownLoad(e) {
-    if (!utils.hasClass(this, "cnc")) {
-        par = utils.getParent(this);
-        dwnDialog = utils.getParent(par); //parent dialog with popDl class
-        var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false;
-        jQuery(dwnDialog).find("input").each(function(index) {
-            if (this.checked) {
-                submitDownLoad(this, descr);
-            }
-        });
-    }
-    jQuery(document.body).click();
-    utils.preventDefault(e);      
-}
-
-function submitDownLoad(radioElem, descr) {    
-    var toolURL = radioElem.getAttribute("url");
-    if (toolURL) {
-        if (descr) {
-            var getGi = radioElem.getAttribute("getGi");
-            getGi = (getGi) ? true : false;
-            
-            var tblID = "dscTable";
-            var suffix = PsiBelowThresh(radioElem.id);
-            tblID += suffix;
-
-            $("selDnSeqs").value = createSelseqString(tblID,getGi);
-        }
-        else {
-            var seqfsta = radioElem.getAttribute("seqfsta");
-            $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi");
-        }
-        var addParams = "";
-        if (radioElem.getAttribute("addParam")) {
-            addParams = addDwnlParams();
-        }
-        var submitName = radioElem.getAttribute("sbName")
-        $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST";
-        $("dwdlSubmit").action = toolURL + addParams;
-        $("dwdlSubmit").submit();
-    }       
-    else {
-        var sbFunction = radioElem.getAttribute("sbFunc");        
-        if (sbFunction) {
-            eval(sbFunction + "(radioElem, descr)");
-        }        
-    }
-}
-
-
-function initDownLoadFSTA(radioElem, descr) 
-{
-    if (descr) {
-    
-        var tblID = "dscTable";
-        var suffix = PsiBelowThresh(radioElem.id);
-        tblID += suffix;
-
-        $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false);
-    }
-    else {        
-        $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta");
-    }
-    $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType");
-    
-    $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE");
-    if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox    
-        var batchID = document.getElementsByName("ALIGNDB_BATCH_ID");
-        if (batchID) {
-            $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID");
-            $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS");
-            $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST");
-            $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH");
-        }
-    }
-    $("sbmtFASTA").submit();    
-}
-
-function createSelseqString(tblID,getGi) {    
-    var selSeqs = "";
-    jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) {
-        if (jQuery(this)[0].checked) {
-            if (selSeqs != "") selSeqs += ",";
-            if (getGi) {
-                selSeqs += jQuery(this)[0].value;
-            }
-            else {
-                var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc");
-                selSeqs += $(linkID).getAttribute("seqFSTA");
-            }
-        }
-    });
-    return selSeqs;
-}
-
-/***Download code end****/
-
-/***Init navigation code begin **/
-
-function initNavigation(navObj) {    
-    initNextAlnLink(navObj, true);
-    initNextAlnLink(navObj, false);        
-}
-
-
-function initNavInfo(navObj) {
-    var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind"));
-    nextInd = currInd + 1;
-    prevInd = currInd - 1;
-    
-    navObj.currSeqID = "";
-    navObj.nextSeqID = "";
-    navObj.prevSeqID = "";
-        
-    if ($("deflnDesc_" + nextInd)) {
-        navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs");
-        if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA");
-    }
-    if ($("deflnDesc_" + prevInd)) {
-        navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs");
-        if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA");
-    }
-    if ($("deflnDesc_" + currInd)) {
-        navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA");        
-    }
-}
-
-
-function initNextAlnLink(navObj, next) {
-
-    var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID);
-    var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID;
-    
-    if (nextLinkEl) {
-        if (nextSeqid != "") {
-            var text = (next) ? "next" : "previous";
-            nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid);
-        }
-        else {
-            nextLinkEl.setAttribute("disabled", "disabled");
-        }
-    }
-}
-function scan(link) {
-    var init = link.getAttribute("init");
-    if (!init) {
-        ncbi.sg.scanLinks(link);
-        link.setAttribute("init","on");
-    }
-}
-
-function initWidth(seqID) {
-    var lineLengthElem = $("FormatForm").LINE_LENGTH;
-    var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value);
-    if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return;
-    
-    var relWidth = (lineLength > 90) ? "12%" : "15%";
-    var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7;
-    lineLength = (lineLength + parseInt(17)) * charWidth;
-    var width = lineLength + "px";
-    jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) {
-        jQuery(this).css("width", width);
-    });
-    jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) {
-        jQuery(this).css("width", width);
-    });    
-    jQuery($("relInf_" + seqID)).css("width", relWidth);
-}
-
-
-/***Init navigation code end **/
-function initAlignBatch(seqID)
-{
-    var navObj = new Object();
-    navObj.seqID = seqID;
-    initNavInfo(navObj);
-
-    initAlignDownLoad(navObj);
-    initNavigation(navObj);
-    ncbi.sg.scanLinks($("alnNxt_" + seqID));
-    ncbi.sg.scanLinks($("alnPrv_" + seqID));
-    if ($("serviceType").value == "vecscreen") {
-        utils.addClass($("alnDsc_" + seqID), "hidden");
-    }
-    ncbi.sg.scanLinks($("alnDwnld_" + seqID));
-    jQuery($("csLinks_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("relInf_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("rng_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("dln_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    initWidth(seqID); 
-/*        
-    jQuery($("alnHdr_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-    jQuery($("aln_" + seqID)).find("a").each(function(index) {
-        ncbi.sg.scanLinks(this);
-    });
-*/    
-}
-
-function SaveConfigTable() {
-    blastUrl = "fmtsave.cgi";
-    
-
-    var rp = new RemoteDataProvider(blastUrl);
-
-
-    rp.onSuccess = function(obj) {
-        //alert("success");
-    };
-    rp.onError = function(obj) {
-        //alert("error");
-    }    
-
-    var program = getHiddenFieldVal("PROGRAM");
-    var rid = getHiddenFieldVal("RID");
-    var blastSpec = getHiddenFieldVal("BLAST_SPEC");
-    var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value;
-    if(blastSpec) {
-        params += "&BLAST_SPEC=" + blastSpec;
-    }     
-    rp.Request(params,"POST");
-}
-
-function removeRID() {
-    var rid = document.getElementsByName("RID");
-    for (var i = 0; i <= rid.length; i++) {
-        jQuery(rid[i]).remove();        
-    }
-}
-
-function initAdvancedView()
-{
-    if ($("dsConfig")) {
-    
-        var alnView = getHiddenFieldVal("ALIGNMENT_VIEW");
-        if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") {
-            var rid = getHiddenFieldVal("RID");        
-            ReadNextSeqAligns(0, 5);            
-            g_alignViewPos = $("alignView").getBoundingClientRect().top;
-            utils.addEvent(window, "scroll", checkAutoAlignLoad, false);
-        }
-        list = $("phiPtInd");
-        if (list) {
-            utils.addEvent(list, "change", GetPatternLocResults, false);
-        }                
-        initDescConfig();
-        initDescSelect();
-        initDescDownLoad();
-        if ($("psiInp")) {
-            var nextIter = document.getElementsByName("NEXT_I");
-            for (var i = 0; i < nextIter.length; i++) {
-                utils.addEvent(nextIter[i], "click", removeRID, false);
-            }
-        }
-    }
-}
-
-//takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4"
-function initjQry() 
-{
-    var oldCreate = jQuery.ui.ncbipopper.prototype._create;
-    jQuery.ui.ncbipopper.prototype._create = function() {
-        var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash");
-        this.options.destSelector = destSelector.replace(/\./g, "\\.");
-        oldCreate.apply(this, arguments);
-    }
-}
-utils.addEvent(window,
-				"load", initAdvancedView,
-				false);
-
-initjQry()
-
-/* If user agent has "safari" in it, include safari-specific stylesheet. */
-if (navigator.userAgent.match(/ie/i)) {
-    document.write("");
-}
-/*****************************new code end*********************************************************************/
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/jig.css
--- a/Blast output page example trimmed_files/jig.css	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-.ui-helper-hidden{display:none;}.ui-helper-hidden-accessible{position:absolute;left:-99999999px;}.ui-helper-reset{margin:0;padding:0;border:0;outline:0;line-height:1.3;text-decoration:none;font-size:100%;list-style:none;}.ui-helper-clearfix:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-helper-clearfix{display:inline-block;}/* required comment for clearfix to work in Opera \*/ * html .ui-helper-clearfix{height:1%;}.ui-helper-clearfix{display:block;}/* end clearfix */ .ui-helper-zfix{width:100%;height:100%;top:0;left:0;position:absolute;opacity:0;filter:Alpha(Opacity=0);}.ui-state-disabled{cursor:default!important;}.ui-icon{display:block;text-indent:-99999px;overflow:hidden;background-repeat:no-repeat;}.ui-widget-overlay{position:absolute;top:0;left:0;width:100%;height:100%;}.ui-widget{font-size:1.1em;}.ui-widget-content{border:1px solid #aaa;background:#fff url(images/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x;color:#222;}.ui-widget-content a{color:#222;}.ui-widget-header{border:1px solid #aaa;background:#ccc url(images/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x;color:#222;font-weight:bold;}.ui-widget-header a{color:#222;}.ui-state-default,.ui-widget-content .ui-state-default{border:1px solid #d3d3d3;background:#e6e6e6 url(images/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#555;}.ui-state-default a,.ui-state-default a:link,.ui-state-default a:visited{color:#555;text-decoration:none;}.ui-state-hover,.ui-widget-content .ui-state-hover,.ui-state-focus,.ui-widget-content .ui-state-focus{border:1px solid #999;background:#dadada url(images/ui-bg_glass_75_dadada_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#212121;}.ui-state-hover a,.ui-state-hover a:hover{color:#212121;text-decoration:none;}.ui-state-active,.ui-widget-content .ui-state-active{border:1px solid #aaa;background:#fff url(images/ui-bg_glass_65_ffffff_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#212121;}.ui-state-active a,.ui-state-active a:link,.ui-state-active a:visited{color:#212121;text-decoration:none;}.ui-state-highlight,.ui-widget-content .ui-state-highlight{border:1px solid #fcefa1;background:#fbf9ee url(images/ui-bg_glass_55_fbf9ee_1x400.png) 50% 50% repeat-x;color:#363636;}.ui-state-highlight a,.ui-widget-content .ui-state-highlight a{color:#363636;}.ui-state-error,.ui-widget-content .ui-state-error{border:1px solid #cd0a0a;background:#fef1ec url(images/ui-bg_glass_95_fef1ec_1x400.png) 50% 50% repeat-x;color:#cd0a0a;}.ui-state-error a,.ui-widget-content .ui-state-error a{color:#cd0a0a;}.ui-state-error-text,.ui-widget-content .ui-state-error-text{color:#cd0a0a;}.ui-priority-primary,.ui-widget-content .ui-priority-primary{font-weight:bold;}.ui-priority-secondary,.ui-widget-content .ui-priority-secondary{opacity:.7;filter:Alpha(Opacity=70);font-weight:normal;}.ui-state-disabled,.ui-widget-content 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url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x;opacity:.30;filter:Alpha(Opacity=30);}.ui-widget-shadow{margin:-8px 0 0 -8px;padding:8px;background:#aaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x;opacity:.30;filter:Alpha(Opacity=30);-moz-border-radius:8px;-webkit-border-radius:8px;border-radius:8px;}.ui-widget{font-family:arial,"sans-serif"!important;font-size:100%;}.ui-helper-reset{font-size:100%!important;}iframe.ui-ncbi-iframe-fix{position:absolute;top:0;left:0;height:200px;z-index:3000;display:block;filter:alpha(opacity=1);}#ui-datepicker-div{display:none;}.ui-widget-content a{color:#2F4A8B;}.ui-helper-hidden-accessible{left:-10000000px!important;}#jig-ncbi_requires_login iframe{border:none;}
\ No newline at end of file
diff -r 420d0508dcd6 -r 2143f62809d0 Blast output page example trimmed_files/jig.js
--- a/Blast output page example trimmed_files/jig.js	Thu May 15 16:50:38 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,265 +0,0 @@
-(function(){function Ka(){var g=null,j=jQuery.cookie("WebCubbyUser");if(j)if(j.indexOf("logged-in=true")>-1)if(j=j.match(/my-name=([^;]+)/i))g=j[1];return g}function W(g){this.name=this.selector="";this.onPage=false;this.dependsOn=[];this.interactions=[];this.overrideDefaults={};this.addCss=function(){document.write('')};this.addJs=function(){document.write('