# HG changeset patch # User Jan Kanis # Date 1399390570 -7200 # Node ID ffe82516a83cb1f1b9efc89e944a1247c43b0bba # Parent bad241dc701f2d24cec8113f7c1bb084e060d43e add trimmed down html example diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Blast output page example trimmed.html Tue May 06 17:36:10 2014 +0200 @@ -0,0 +1,1615 @@ + + + + + + + + + + + + + + + +NCBI Blast:Nucleotide Sequence (16 letters) + + + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + +
+ + + + + + + + + + + + + +
+ + + +
+ +
+
+

Nucleotide Sequence (16 letters)

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

+

+

+

+
+

+
+				

+				
+
+                 
+				
+				
+        

+
+		    	
+	
+   

+
+
+
+
+
+
+
+   
+
+
+
+
+
PreferencesTurn off
PreferencesTurn off

\ No newline at end of file
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/1.gif
Binary file Blast output page example trimmed_files/1.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/2.gif
Binary file Blast output page example trimmed_files/2.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/3.gif
Binary file Blast output page example trimmed_files/3.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/5.gif
Binary file Blast output page example trimmed_files/5.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/6.gif
Binary file Blast output page example trimmed_files/6.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/9.gif
Binary file Blast output page example trimmed_files/9.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/InstrumentPageStarterJS.js
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/InstrumentPageStarterJS.js	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,86 @@
+(function(){if(typeof ncbi==="undefined")ncbi={};if(ncbi.sg)typeof console!=="undefined"&&console.error&&console.error("The logging JavaScript was added twice in the document. Please include it one time.");else{ncbi.sg=function(){};ncbi.sg.getInstance=function(){if(!ncbi.sg._instance)ncbi.sg._instance=new ncbi.sg;return ncbi.sg._instance};ncbi.sg._instance=null;ncbi.sg._version="26";(function(){var a=navigator.cookieEnabled?true:false;if(typeof navigator.cookieEnabled==="undefined"&&!a){document.cookie=
+"testcookie";a=document.cookie.indexOf("testcookie")!==-1?true:false}ncbi.sg.isCookieEnabled=a})();ncbi.sg.appLogIgnore=["ncbi_sessionid","ncbi_clickdisabled"];ncbi.sg.prototype={init:function(){this.isProcessRunning=true;this._setUpMetaTagValues();this._setScrollingEnabled();if(this._cachedVals.ncbi_db&&this._cachedVals.ncbi_db.value.toLowerCase()=="pubmed"&&this._cachedVals.ncbi_report&&this._cachedVals.ncbi_report.value.toLowerCase()=="abstract"&&this._cachedVals.ncbi_resultcount&&this._cachedVals.ncbi_resultcount.value.toLowerCase()==
+"1"||this._cachedVals.ncbi_db&&this._cachedVals.ncbi_db.value.toLowerCase()=="pmc"&&this._cachedVals.ncbi_report&&this._cachedVals.ncbi_report.value.toLowerCase()=="record"&&this._cachedVals.ncbi_type&&this._cachedVals.ncbi_type.value.toLowerCase()=="fulltext")ncbi.sg.isHoverEnabled=true;this._setUpPathParts();this._setUpCustomProps();this._addOnScrollListeners();this._send("init");this._scheduleDOMReadyPing();this._sendPrev();this._addPrintPing();this._setBeforeScrollDetails()},_vals:{},_cachedVals:{},
+_hasInitRun:false,_readyPinged:false,_pathParts:{part1:"",part2:"",part3:"",part4:""},_scheduleDOMReadyPing:function(){var a=this,b=function(){return typeof jQuery!=="undefined"&&typeof jQuery.ui!=="undefined"&&typeof jQuery.ui.jig!=="undefined"?typeof jQuery.ui.jig.version!=="undefined"&&jQuery.ui.jig.version?jQuery.ui.jig.version:"unknown":"unknown"},d=function(){var k={},j=jQuery.ui.jig._foundWidgets;for(var t in j)k["jigWidget_"+t]=j[t];k.jigVersion=b();return k},c=function(){if(!a._readyPinged){var k=
+{};if(typeof jQuery!=="undefined"&&typeof jQuery.ui!=="undefined"&&typeof jQuery.ui.jig!=="undefined"&&typeof jQuery.ui.jig.scanned!=="undefined")if(jQuery.ui.jig.scanned){k=d();k.jsevent="domready";ncbi.sg._ping(k);a._readyPinged=true}else{if(typeof jQuery.ui.jig.scan!=="undefined"&&jQuery.ui.jig.scan){var j=jQuery.ui.jig.scan;jQuery.ui.jig.scan=function(){var t=j.apply(this,arguments);c();return t}}}else{k.jigVersion="nojig";k.jsevent="domready";ncbi.sg._ping(k);a._readyPinged=true}}};if(document.addEventListener){var e=
+function(){document.removeEventListener("DOMContentLoaded",e,false);c()};document.addEventListener("DOMContentLoaded",e)}else if(document.attachEvent){var g=function(){if(document.readyState==="complete"){document.detachEvent("onreadystatechange",g);c()}};document.attachEvent("onreadystatechange",g)}},_setScrollingEnabled:function(){try{ncbi.sg.isScrollingEnabled=false;var a=ncbi.sgAppsWithScrolling;if(typeof a!=="undefined")for(var b=0;b100&&this.ignoreLengthRestrictions.indexOf(a)===-1)b=b.substr(0,100);this._cachedVals[a]={sProp:a,value:b}}},getVal:function(a){return typeof this._cachedVals[a]!=="undefined"&&this._cachedVals[a]&&typeof this._cachedVals[a].value!=="undefined"?
+this._cachedVals[a].value:null},removeAllEntries:function(){for(var a={},b=this.cachedNames.length,d=0;d0?":"+this._pathParts.part2:"",d=this._pathParts.part3.length>0?":"+this._pathParts.part3:"",c=this._pathParts.part4.length>0?":"+this._pathParts.part4:"";a={pagename:a+b+
+d,server:window.location.hostname,sitesect2:a+b,subsect3:a+b+d,subsect4:a+b+d+c,heir1:(a+b+d+c).replace(/:/g,"|")};for(var e in a)this.addEntry(e,a[e]);this._sessionIdCheck();this._staticPageCheck();this._prevHitCheck();this._browserConfigurationSettings();this._hashCheck()},_staticPageCheck:function(){this._cachedVals.ncbi_app&&this._cachedVals.ncbi_app.value.length>0||this.addEntry("ncbi_app","static");this._cachedVals.ncbi_pdid&&this._cachedVals.ncbi_pdid.value.length>0||this.addEntry("ncbi_pdid",
+(document.title||"unknown").replace(/\s+/g,""))},_sessionIdCheck:function(){if(!(this._cachedVals.ncbi_sessionid&&this._cachedVals.ncbi_sessionid.value.length>0)){var a="";if(a.length===0){var b=this.getCookie("WebCubbyUser")||this.getCookie("WebEnv");if(b.length>0){b=unescape(b).split("@");if(b.length>1)a=b[b.length-1]}}if(a.length===0)a="NOSESSIONID";this.addEntry("ncbi_sessionid",a)}},getBrowserWidthHeight:function(){var a=this.getViewportWidth(),b=this.getViewportHeight();return{width:a,height:b}},
+_browserConfigurationSettings:function(){var a=this.getBrowserWidthHeight();this.addEntry("browserwidth",a.width);this.addEntry("browserheight",a.height);this.addEntry("screenwidth",screen.width);this.addEntry("screenheight",screen.height);this.addEntry("screenavailwidth",screen.availWidth);this.addEntry("screenavailheight",screen.availHeight);if(document&&document.body){var b=document.body.scrollWidth,d=document.body.scrollHeight,c=d>a.height?"true":"false";this.addEntry("canscroll_x",b>a.width?
+"true":"false");this.addEntry("canscroll_y",c);this.addEntry("scrollwidth",b);this.addEntry("scrollheight",d)}if(screen.colorDepth)this.addEntry("colorDepth",screen.colorDepth);else screen.pixelDepth&&this.addEntry("colorDepth",screen.pixelDepth)},_hashCheck:function(){var a=window.location.hash;if(a){a=a.replace("#","");this.addEntry("urlhash",a)}(a=window.location.search.match(/[?&]campaign=([^&]*)/))&&this.addEntry("campaign",a[1])},_createPHID:function(){var a=this._cachedVals.ncbi_sessionid.value,
+b=a.substr(0,15)+"9"+(new Date).getTime().toString(),d=a.length;b+=a.substr(d-(32-b.length),d);a={value:b};this.addEntry("ncbi_phid",b);return a},currentPageHitId:null,_prevHitCheck:function(){var a=this.getCookie("ncbi_prevPHID"),b=this._cachedVals.ncbi_phid;a.length>0&&this.addEntry("prev_phid",a);if(!b||!b.value||b.value.length===0)b=this._createPHID();this.currentPageHitId=b.value;var d=this;ncbi.sg._hasFocus&&d.setCookie("ncbi_prevPHID",b.value);var c=window.onfocus;window.onfocus=function(e){d.getCookie("ncbi_prevPHID")!==
+b.value&&d.setCookie("ncbi_prevPHID",b.value);typeof c==="function"&&c(e)}},_setUpPathParts:function(){var a=this._cachedVals.ncbi_app,b=this._cachedVals.ncbi_db,d=this._cachedVals.ncbi_pdid,c=this._cachedVals.ncbi_pcid;this._pathParts.part1=a!==undefined?a.value:"";this._pathParts.part2=b!==undefined?b.value:"";this._pathParts.part3=d!==undefined?d.value:"";this._pathParts.part4=c!==undefined?c.value:""},getPerfStats:function(){var a=window.performance;if(!a)return{};var b=a.timing;if(b)b={dns:b.domainLookupEnd-
+b.domainLookupStart,connect:b.connectEnd-b.connectStart,ttfb:b.responseStart-b.connectEnd,basePage:b.responseEnd-b.responseStart,frontEnd:b.loadEventStart-b.responseEnd};else return{};if(a=a.navigation){b.navType=a.type;b.redirectCount=a.redirectCount}return b},setPerfStats:function(a,b){var d=this.getPerfStats();for(var c in d){var e=d[c];if(e>=0){var g="jsperf_"+c;if(b)a[g]=e;else a.push(g+"="+e)}}},getExtraRenderStats:function(){var a={SELF_URL:encodeURIComponent(window.location.href)};if(typeof document!==
+"undefined"&&typeof document.referrer!=="undefined")a.HTTP_REFERER=encodeURIComponent(document.referrer);return a},setExtraRenderStats:function(a){var b=this.getExtraRenderStats();for(var d in b)a.push(d+"="+b[d])},_send:function(a,b,d){if(typeof d==="undefined"||d===null)d=true;var c=[];if(a==="init"){c.push("jsevent=render");ncbi.sg.renderTime=new Date;if(typeof ncbi_startTime!=="undefined"){c.push("jsrendertime="+(ncbi.sg.renderTime-ncbi_startTime));ncbi.sg.loadTime&&c.push("jsloadtime="+(ncbi.sg.loadTime-
+ncbi_startTime))}this.setPerfStats(c);this.setExtraRenderStats(c);c.push("cookieenabled="+(ncbi.sg.isCookieEnabled?"true":"false"))}for(var e in this._cachedVals)ncbi.sg.appLogIgnore.indexOf(e)===-1&&c.push(e+"="+encodeURIComponent(this._cachedVals[e].value));this._sendAl(c.join("&"),b,true,d);this._hasInitRun=true;var g=this;setTimeout(function(){g.isProcessRunning=false;g.runSGProcess()},300)},send:function(a,b){this._send(a,b,false)},_sendPrev:function(){var a=ncbi.sg.getInstance(),b=a.getCookie("clicknext");
+if(b){ncbi.sg._ping(b);a.setCookie("clicknext","")}if(b=a.getCookie("prevsearch")){ncbi.sg._ping(b);a.setCookie("prevsearch","")}if(b=a.getCookie("unloadnext")){ncbi.sg._ping(b);a.setCookie("unloadnext","")}},_sendAl:function(a,b,d,c){if(typeof c==="undefined"||c===null)c=true;if(a.indexOf("jseventms")===-1)a+="&jseventms="+ncbi.sg.getInstance().getMillisecondsSinceSunday();a.match(/jsevent=search/i)&&this._storeNext("prevsearch",a.replace(/jsevent=search(next)?/i,"jsevent=searchnext"),null,c);a+=
+"&sgVersion="+ncbi.sg._version;if(a.indexOf("sgSource")===-1)a=this._setSgSource(a,c);c=window.location.port?":"+window.location.port:"";reqURL=typeof __ncbi_stat_url!=="undefined"?__ncbi_stat_url+"?"+a:window.location.protocol+"//"+window.location.hostname+c+"/stat?"+a;this.makeAjaxCall(reqURL,function(){typeof b==="function"&&b()},d)},sendAl:function(a,b,d){this._sendAl(a,b,d,false)},_processingQueue:[],isProcessRunning:false,addSGProcess:function(a){this._processingQueue.push(a)},getSGProcess:function(a){return this._processingQueue.shift(a)},
+runSGProcess:function(){if(this.isProcessRunning||this._processingQueue.length===0||!this._hasInitRun)return false;this.isProcessRunning=true;this.removeAllEntries();var a=this.getSGProcess();this._setUpCachedMetaTagValues(a.metadata);this.addEntry("jsevent",a.eventName);for(var b in a.props)this.addEntry(b,a.props[b]);this._send(a.eventName,a.callbackFnc);var d=this;setTimeout(function(){d.isProcessRunning=false;d.runSGProcess()},300)},noteEventData:function(a,b,d,c){this.addSGProcess({eventName:a,
+props:b,metadata:d,callback:c});this.runSGProcess()},setCookie:function(a,b,d){if(window.sessionStorage)try{sessionStorage.setItem(a,b)}catch(c){}var e=new Date;d!==null&&e.setDate(e.getDate()+d);document.cookie=a+"="+escape(b)+(d===null?"":"; expires="+e.toGMTString())+"; domain="+escape(".nih.gov")+"; path=/"},_setSgSource:function(a,b){a+="&sgSource="+(b?"native":"api");return a},_storeNext:function(a,b,d,c){if(typeof c==="undefined"||c===null)c=true;b=this._setSgSource(b,c);this.setCookie(a,b,
+d)},getCookie:function(a){var b;if(window.sessionStorage){try{b=sessionStorage.getItem(a)||""}catch(d){b=""}if(b.length>0)return b}if(document.cookie.length>0){b=document.cookie.indexOf(a+"=");if(b!==-1){b=b+a.length+1;a=document.cookie.indexOf(";",b);if(a===-1)a=document.cookie.length;return unescape(document.cookie.substring(b,a))}}return""},getTransport:function(){var a=null;if(window.XMLHttpRequest)try{a=new XMLHttpRequest;this.getTransport=function(){return new XMLHttpRequest}}catch(b){a=null}if(window.ActiveXObject&&
+a===null)try{a=new ActiveXObject("Msxml2.XMLHTTP");this.getTransport=function(){return new ActiveXObject("Msxml2.XMLHTTP")}}catch(d){try{a=new ActiveXObject("Microsoft.XMLHTTP");this.getTransport=function(){return new ActiveXObject("Microsoft.XMLHTTP")}}catch(c){a=false}}if(a===null)this.getTransport=function(){return null};return this.getTransport()},makeAjaxCall:function(a,b,d){var c=this.getTransport();c._ncbi_skipOverride=true;c.open("GET",a,d);if(d)c.onreadystatechange=function(){c.readyState===
+4&&b(c)};ncbi.sg.lastPing=c;c.send(null);return c},scrollDetails:{maxScroll_x:0,maxScroll_y:0,currScroll_x:0,currScroll_y:0,hasScrolled:false},scrollEventDetails:{xTenths:0,yTenths:0,xMax:0,yMax:0},_getScrollXYPx:function(){return[window.pageXOffset||document.documentElement.scrollLeft||document.body.scrollLeft||0,window.pageYOffset||document.documentElement.scrollTop||document.body.scrollTop||0]},_getScrollXY:function(){var a=this.getViewportHeight(),b=this.getViewportWidth(),d=document.body.scrollHeight,
+c=document.body.scrollWidth,e=this._getScrollXYPx(),g=Math.round(e[1]/a*10)/10;return{xRel:Math.round(e[0]/b*10)/10,yRel:g,viewportHeight:a,viewportWidth:b,pageHeight:d,pageWidth:c}},_addOnScrollListeners:function(){var a=window.onscroll,b=this;window.onscroll=function(){if(ncbi.sg.isScrollingEnabled){b._setScrollDetails();b.scrollDetails.hasScrolled=true;b._addScrollEvent()}else{b._setScrollDetails();b.scrollDetails.hasScrolled=true}if(typeof a==="function")return a()}},getViewportHeight:function(){return window.innerHeight?
+window.innerHeight:document.documentElement&&document.documentElement.clientHeight?document.documentElement.clientHeight:document.body!==null?document.body.clientHeight:"NA"},getViewportWidth:function(){return window.innerWidth?window.innerWidth:document.documentElement&&document.documentElement.clientWidth?document.documentElement.clientWidth:document.body!==null?document.body.clientWidth:"NA"},_setScrollDetails:function(){this.scrollDetails.currScroll_y=window.pageYOffset||document.documentElement.scrollTop||
+document.body.scrollTop||0;this.scrollDetails.currScroll_x=window.pageXOffset||document.documentElement.scrollLeft||document.body.scrollLeft||0;this.getViewportWidth();this.getViewportHeight();if(this.scrollDetails.maxScroll_y0){e-=parseInt(a.scrollTop);d=true}if(a.scrollLeft&&a.scrollLeft>0){c-=parseInt(a.scrollLeft);b=true}if(a.offsetParent){b=this.findElementPos(a.offsetParent,
+b,d);if(b==-1)return-1;c+=b[0];e+=b[1]}else if(a.ownerDocument){var g=a.ownerDocument.defaultView;if(!g&&a.ownerDocument.parentWindow)g=a.ownerDocument.parentWindow;if(g){var k=g.pageXOffset!==undefined?g.pageXOffset:(a.document.documentElement||a.document.body.parentNode||a.document.body).scrollLeft;a=g.pageYOffset!==undefined?g.pageYOffset:(a.document.documentElement||a.document.body.parentNode||a.document.body).scrollTop;if(!d&&a&&a>0)e-=parseInt(a);if(!b&&k&&k>0)c-=parseInt(k);if(g.frameElement){b=
+this.findElementPos(g.frameElement);if(b==-1)return-1;c+=b[0];e+=b[1]}}}return[c,e]},addObjData:function(a,b){for(var d in b)a[d]=b[d]},getJoinedData:function(a){var b=[];for(var d in a)b.push(d+"="+encodeURIComponent(a[d]));return b.join("&")},addScrollHeadingData:function(a,b){var d=this.scrollEventDetails.headings;if(d){a["numHeadings."+this._scrollOrder+".scrollInfo"]=d.length;for(var c=0;c=0&&g<=A&&j+y>=0&&j<=B)if(this.isVisible(e)){w.visible=true;a.push(w)}}}return a},_setBeforeScrollDetails:function(a){this._lastScroll=a?a:null;a=this._getScrollXY();var b=
+a.yRel;this.scrollEventDetails.xTenths=Math.round(a.xRel*10);this.scrollEventDetails.yTenths=Math.round(b*10);this.scrollEventDetails.xMax=Math.max(this.scrollEventDetails.xTenths,this.scrollEventDetails.xMax);this.scrollEventDetails.yMax=Math.max(this.scrollEventDetails.yTenths,this.scrollEventDetails.yMax);this.scrollEventDetails.headings=this.getVisibleHeadings()},getScrollDetails:function(a,b){if(!ncbi.sg.isScrollingEnabled){this._setScrollDetails();return this.scrollDetails}var d=this.scrollEventDetails;
+d.tstamp=(new Date).getTime();var c=this._getScrollXY(),e=null;if(b||!this._lastScroll||d.tstamp-this._lastScroll>1E3){this._scrollOrder=this._scrollOrder!=undefined?this._scrollOrder+1:0;b="yTenths."+this._scrollOrder+".scrollInfo";e="xTenths."+this._scrollOrder+".scrollInfo";var g="maxXTenths."+this._scrollOrder+".scrollInfo",k="maxYTenths."+this._scrollOrder+".scrollInfo",j={};j["duration."+this._scrollOrder+".scrollInfo"]=this._lastScroll?d.tstamp-this._lastScroll:new Date-ncbi.sg.loadTime;j[e]=
+this.scrollEventDetails.xTenths;j[b]=this.scrollEventDetails.yTenths;j[g]=this.scrollEventDetails.xMax;j[k]=this.scrollEventDetails.yMax;j["viewportHeight."+this._scrollOrder+".scrollInfo"]=c.viewportHeight;j["viewportWidth."+this._scrollOrder+".scrollInfo"]=c.viewportWidth;j["maxPossibleScrollTenthsY."+this._scrollOrder+".scrollInfo"]=Math.round((c.pageHeight/c.viewportHeight-1)*10);j["maxPossibleScrollTenthsX."+this._scrollOrder+".scrollInfo"]=Math.round((c.pageWidth/c.viewportWidth-1)*10);e=j=
+this.addScrollHeadingData(j,a)}this._setBeforeScrollDetails(d.tstamp);return e},getScrollDetailsAr:function(a,b){var d=[];a=this.getScrollDetails(a,b);for(var c in a)d.push(c+"="+encodeURIComponent(a[c]));return d},addScrollDetailsAr:function(a,b,d){b=this.getScrollDetailsAr(b,d);for(d=0;d0)for(;y.length>0;)d(y.pop());var f={jsevent:"unload",ncbi_pingaction:"unload"};if(typeof ncbi_startTime!=="undefined"){f.ncbi_timeonpage=new Date-ncbi_startTime;if(typeof ncbi_onloadTime!=="undefined"&&ncbi_onloadTime)f.ncbi_onloadTime=ncbi_onloadTime-ncbi_startTime}var i=ncbi.sg.getInstance();i.setPerfStats(f,true);i.addScrollDetails(f,
+1800-i.getJoinedData(f).length,true);if(!w){ncbi.sg._ping(f);var m="";for(var l in f)m+=l+"="+(l==="jsevent"?"unloadnext":f[l])+"&";m+="ncbi_phid="+i.currentPageHitId;i._storeNext("unloadnext",m,null)}w=true}function b(f){for(var i=y.length-1;i>=-1;i--)if(y[i]===f){y.slice(i,1);break}d(f)}function d(f,i){if(A.indexOf(f.tstamp)===-1){A.push(f.tstamp);B.push(f);c("click",f,i)}}function c(f,i,m,l){if(typeof l==="undefined"||l===null)l=true;var n=f==="click"?"link":"elem",h=i.link,o=i.evt,p=h.id||"",
+x=h.name||"",F=h.sid||"",G=h.href||"",C=h.innerText||h.textContent||"";if(C.length>50)C=C.substr(0,50);var H=h.getAttribute?h.getAttribute("ref")||h.ref||"":"",I=h.className?h.className.replace(/^\s?/,"").replace(/\s?$/,"").split(/\s/g).join(",")||"":"";i=[];var D=[],z=h.parentNode;if(z)for(var r=0;r<6&&z!==null;r++){(parId=z.id)&&i.push(parId);if(parClassName=z.className)D=D.concat(parClassName.split(/\s/));z=z.parentNode}z=ncbi.sg.getInstance();r=z.currentPageHitId||"";var q=[];p.length>0&&q.push(n+
+"_id="+encodeURIComponent(p));x.length>0&&q.push(n+"_name="+encodeURIComponent(x));F.length>0&&q.push(n+"_sid="+encodeURIComponent(F));G.length>0&&q.push(n+"_href="+encodeURIComponent(G));C.length>0&&q.push(n+"_text="+encodeURIComponent(C));I.length>0&&q.push(n+"_class="+encodeURIComponent(I));r=z.getBrowserWidthHeight();r.width!==null&&q.push("browserwidth="+encodeURIComponent(r.width));r.height!==null&&q.push("browserheight="+encodeURIComponent(r.height));for(var E in o){r=o[E];r!==undefined&&q.push(E.toLowerCase()+
+"="+r.toString())}q.push("jsevent="+f);H.length>0&&q.push(H);if(typeof jQuery!=="undefined")if(h=jQuery(h).attr("sg")){h=h.split(/\}\s*,\s*\{/);for(r=0;r0)for(;m.length>0;)q.push(m.shift());i.length>0&&q.push("ancestorId="+i.join(","));D.length>0&&q.push("ancestorClassName="+D.join(",").replace(/\s+/g," ").replace(/(^\s|\s$)/g,
+""));z.addScrollDetailsAr(q,1800-q.join("&").length,true);if(f==="click"){f=q.join("&").replace("jsevent=click","jsevent=clicknext");r=ncbi.sg.getInstance().currentPageHitId||"";f+="&ncbi_phid="+r;z._storeNext("clicknext",f,null,l)}ncbi.sg._ping(q,true,null,null,l)}function e(f){var i={};if(f){if(f.clientX||f.clientY){var m=ncbi.sg.getInstance()._getScrollXYPx();i.evt_coor_x=f.clientX+m[0];i.evt_coor_y=f.clientY+m[1]}else if(f.pageX||f.pageY){i.evt_coor_x=f.pageX;i.evt_coor_y=f.pageY}i.jseventms=
+ncbi.sg.getInstance().getMillisecondsSinceSunday()}return i}function g(f,i,m,l,n){var h={},o=null,p=null;if(typeof i==="string"){o=i;p=m}else{h=e(i);o=m;p=l}if(p){i=typeof p;if(i==="string")p=[p];else if(i==="object"&&!(p instanceof Array)){i=[];for(var x in p)i.push(x+"="+p[x]);p=i}}c(o,{link:f,evt:h},p,n)}function k(f,i,m){var l=[];if(typeof i==="undefined")i=true;if(typeof f==="object"&&!(f instanceof Array))for(var n in f)l.push(n+"="+encodeURIComponent(f[n]));else if(typeof f==="string")l.push(f);
+else l=f;f=ncbi.sg.getInstance().currentPageHitId||"";n=null;if(typeof ncbi.sg.loadTime!=="undefined")n=new Date-ncbi.sg.loadTime;var h=l.join("&");if(h.indexOf("jsevent=clicknext")!==-1||h.indexOf("jsevent=searchnext")!==-1||h.indexOf("jsevent=unloadnext")!==-1){f.length>0&&l.push("next_phid="+encodeURIComponent(f));n!==null&&l.push("next_ncbi_timesinceload="+n)}else{f.length>0&&l.push("ncbi_phid="+encodeURIComponent(f));n!==null&&l.push("ncbi_timesinceload="+n)}ncbi.sg.getInstance()._sendAl(l.join("&"),
+null,i,m)}var j=window.onerror;window.onerror=function(f,i,m){if(!ncbi.sg.hasNotedErrorEvent){ncbi.sg.getInstance().noteEventData("jserror",{jserror:f,jserrorlocation:i,jserrorline:m,SELF_URL:window.location.href},["ncbi_sessionid","ncbi_phid"]);ncbi.sg.hasNotedErrorEvent=true;if(typeof j==="function")return j(f,i,m)}};var t=window.onbeforeunload;window.onbeforeunload=function(f){a();if(typeof t==="function")return t(f)};var y=[],A=[],B=[],w=false;ncbi.sg.sendElementEvent=function(f,i,m){c(f,i,m,
+false)};ncbi.sg.clickTimers=[];if(typeof ncbi.sg.isClickEnabled==="undefined"){for(var v=document.getElementsByTagName("meta"),u=v.length-1,s=true;u>=0;){if(v[u].name.toLowerCase()==="ncbi_clickdisabled"){s=v[u].content.toLowerCase()==="false";break}u--}ncbi.sg.isClickEnabled=s}setClickEvent=function(){var f=function(h){return(h=typeof h.parentNode!=="undefined"?h.parentNode:null)?m(h)?h:f(h):false},i=function(h){h=h.target||h.srcElement;if(typeof h=="undefined"||h==null)return null;if(h.nodeType==
+3)h=target.parentNode;m(h)||(h=f(h));return h},m=function(h){var o=typeof h.tagName!=="undefined"?h.tagName.toLowerCase():null,p=false,x=false;if(typeof jQuery!=="undefined")p=jQuery(h).is("button, input[type=button], input[type=submit], input[type=reset]");else if(o==="input"){h=inp.type;p=h=="button"||h=="submit"||h=="reset"}else p=o==="button"?true:false;p||(x=o=="a"||o=="area");return x?"link":p?"button":null},l=function(h,o,p,x){if(!(x&&x=="click"&&h.which&&h.which==3))if(!(!o||m(o)==null)){ncbi.sg.getInstance().setCookie("ncbi_prevPHID",
+ncbi.sg.getInstance().currentPageHitId);h=e(h);h.iscontextmenu=x=="contextmenu"?"true":"false";o={evt:h,link:o,tstamp:(new Date).getTime(),floodTstamp:(new Date).getTime()};b(o);ncbi.sg.clickTimers&&window.clearTimeout(ncbi.sg.clickTimers);ncbi.sg.clickTimers=window.setTimeout(function(){ncbi.sg.clickTimers=null},300)}};if(window.addEventListener){window.addEventListener("click",function(h){l(h,i(h),[],"click")});window.addEventListener("contextmenu",function(h){l(h,i(h),[],"contextmenu")},false)}else if(window.attachEvent){document.attachEvent("onclick",
+function(h){l(h,i(h),[],"click")});document.attachEvent("oncontextmenu",function(h){l(h,i(h),[],"contextmenu")},false)}if(Event.prototype.stopPropagation){var n=Event.prototype.stopPropagation;Event.prototype.stopPropagation=function(){var h=i(this);if(m(h)!=null)if(this.type=="click")l(this,h,[],"click");else this.type=="contextmenu"&&l(this,h,[],"contextmenu");return n.apply(this,arguments)}}};setClickEvent();ncbi.sg.scanLinks=function(){};ncbi.sg._ping=function(f,i,m,l,n){if(typeof n==="undefined"||
+n===null)n=true;typeof f==="undefined"||f===null||(typeof f==="object"&&f.nodeName!==undefined?g(f,i,m,l,n):k(f,i,n))};ncbi.sg.ping=function(f,i,m,l){ncbi.sg._ping(f,i,m,l,false)};ncbi.sg.loadTime=new Date})();if(!Array.prototype.indexOf)Array.prototype.indexOf=function(a,b){var d=this.length>>>0;b=Number(b)||0;b=b<0?Math.ceil(b):Math.floor(b);if(b<0)b+=d;for(;b0&&k.push("next_phid="+encodeURIComponent(c));j!==null&&k.push("next_ncbi_timesinceload="+
+j);ncbi.sg.getInstance()._sendAl(k.join("&"),null,e,g)},b=ncbi.sg.getInstance().getCookie("hovernext");if(b){a(b);ncbi.sg.getInstance().setCookie("hovernext","")}var d=function(c){var e={};if(c){if(c.clientX||c.clientY){var g=ncbi.sg.getInstance()._getScrollXYPx();e.evt_coor_x=c.clientX+g[0];e.evt_coor_y=c.clientY+g[1]}else if(c.pageX||c.pageY){e.evt_coor_x=c.pageX;e.evt_coor_y=c.pageY}e.jseventms=ncbi.sg.getInstance().getMillisecondsSinceSunday()}return e};jQuery(document).on("mousedown","a[ref*='itool=Abstract-nondef'], #disc_col a",
+function(c){c=c.originalEvent;var e=d(c);jQuery(c.target);(new Date).getTime();(new Date).getTime();var g=jQuery(c.target),k=g.id||"",j=g.name||"",t=g.sid||"",y=g.href||"",A=g.innerText||g.textContent||"";if(A.length>50)A=A.substr(0,50);var B=g.getAttribute?g.getAttribute("ref")||g.ref||"":"",w=g.className?g.className.replace(/^\s?/,"").replace(/\s?$/,"").split(/\s/g).join(",")||"":"";c=[];var v=[],u=g.parentNode;if(u)for(var s=0;s<6&&u!==null;s++){(parId=u.id)&&c.push(parId);if(parClassName=u.className)v=
+v.concat(parClassName.split(/\s/));u=u.parentNode}u=ncbi.sg.getInstance();var f=u.currentPageHitId||"";f=[];k.length>0&&f.push("link_id="+encodeURIComponent(k));j.length>0&&f.push("link_name="+encodeURIComponent(j));t.length>0&&f.push("link_sid="+encodeURIComponent(t));y.length>0&&f.push("link_href="+encodeURIComponent(y));A.length>0&&f.push("link_text="+encodeURIComponent(A));w.length>0&&f.push("link_class="+encodeURIComponent(w));s=u.getBrowserWidthHeight();s.width!==null&&f.push("browserwidth="+
+encodeURIComponent(s.width));s.height!==null&&f.push("browserheight="+encodeURIComponent(s.height));for(var i in e){s=e[i];s!==undefined&&f.push(i.toLowerCase()+"="+s.toString())}f.push("jsevent=hovernext");B.length>0&&f.push(B);if(typeof jQuery!=="undefined")if(e=jQuery(g).attr("sg")){e=e.split(/\}\s*,\s*\{/);for(s=0;s0&&f.push("ancestorId="+
+c.join(","));v.length>0&&f.push("ancestorClassName="+v.join(",").replace(/\s+/g," ").replace(/(^\s|\s$)/g,""));u.addScrollDetailsAr(f,1800-f.join("&").length,true);c=f.join("&");f=ncbi.sg.getInstance().currentPageHitId||"";c+="&ncbi_phid="+f;ncbi.sg.getInstance()._storeNext("hovernext",c,null)});jQuery(document).on("mouseup mousedown",function(c){!jQuery(c.target).is("a[ref*='itool=Abstract-nondef']")&&jQuery(c.target).parents("a[ref*='itool=Abstract-nondef']").length==0&&!jQuery(c.target).is("#disc_col a")&&
+jQuery(c.target).parents("#disc_col a").length==0&&ncbi.sg.getInstance().setCookie("hovernext","")})}});
+
+;
+// This code creates window.console if it doesn't exist.
+// It also creates stub functions for those functions that are missing in window.console.
+// (Safari implements some but not all of the firebug window.console methods--this implements the rest.)
+(function() {
+    var names = [ "log", "debug", "info", "warn", "error", "assert", "dir", "dirxml", "group",
+                  "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd" ];
+
+    if (typeof(console) === 'undefined' || typeof console === "function" ) {
+      //"typeof function" is needed see PP-769 
+      console = {};
+    }
+
+    for (var i = 0; i < names.length; ++i) {
+       if (typeof(console[names[i]]) === 'undefined') {
+          console[names[i]] = function() { return false; };
+       }
+    }
+    ncbi.sg.getInstance().init();                          
+})();
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/black.gif
Binary file Blast output page example trimmed_files/black.gif has changed
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/blast.js
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/blast.js	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,308 @@
+
+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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/blastReq.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/blastReq.css	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,332 @@
+#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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/blastRes.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/blastRes.css	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,262 @@
+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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/dynFormatRes.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/dynFormatRes.css	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,623 @@
+/* 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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/firefox-descriptions_002.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/firefox-descriptions_002.css	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,3 @@
+table.dbInfo caption {    
+ 
+}
\ No newline at end of file
diff -r bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/format.js
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/format.js	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,270 @@
+
+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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/formatRes.js
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/formatRes.js	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,1542 @@
+// 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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/jig.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/jig.css	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,1 @@
+.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 .ui-state-disabled{opacity:.35;filter:Alpha(Opacity=35);background-image:none;}.ui-icon{width:16px;height:16px;background-image:url(images/ui-icons_222222_256x240.png);}.ui-widget-content .ui-icon{background-image:url(images/ui-icons_222222_256x240.png);}.ui-widget-header .ui-icon{background-image:url(images/ui-icons_222222_256x240.png);}.ui-state-default .ui-icon{background-image:url(images/ui-icons_888888_256x240.png);}.ui-state-hover .ui-icon,.ui-state-focus .ui-icon{background-image:url(images/ui-icons_454545_256x240.png);}.ui-state-active .ui-icon{background-image:url(images/ui-icons_454545_256x240.png);}.ui-state-highlight .ui-icon{background-image:url(images/ui-icons_2e83ff_256x240.png);}.ui-state-error .ui-icon,.ui-state-error-text .ui-icon{background-image:url(images/ui-icons_cd0a0a_256x240.png);}.ui-icon-carat-1-n{background-position:0 0;}.ui-icon-carat-1-ne{background-position:-16px 0;}.ui-icon-carat-1-e{background-position:-32px 0;}.ui-icon-carat-1-se{background-position:-48px 0;}.ui-icon-carat-1-s{background-position:-64px 0;}.ui-icon-carat-1-sw{background-position:-80px 0;}.ui-icon-carat-1-w{background-position:-96px 0;}.ui-icon-carat-1-nw{background-position:-112px 0;}.ui-icon-carat-2-n-s{background-position:-128px 0;}.ui-icon-carat-2-e-w{background-position:-144px 0;}.ui-icon-triangle-1-n{background-position:0 -16px;}.ui-icon-triangle-1-ne{background-position:-16px -16px;}.ui-icon-triangle-1-e{background-position:-32px -16px;}.ui-icon-triangle-1-se{background-position:-48px -16px;}.ui-icon-triangle-1-s{background-position:-64px -16px;}.ui-icon-triangle-1-sw{background-position:-80px -16px;}.ui-icon-triangle-1-w{background-position:-96px -16px;}.ui-icon-triangle-1-nw{background-position:-112px -16px;}.ui-icon-triangle-2-n-s{background-position:-128px -16px;}.ui-icon-triangle-2-e-w{background-position:-144px -16px;}.ui-icon-arrow-1-n{background-position:0 -32px;}.ui-icon-arrow-1-ne{background-position:-16px -32px;}.ui-icon-arrow-1-e{background-position:-32px -32px;}.ui-icon-arrow-1-se{background-position:-48px -32px;}.ui-icon-arrow-1-s{background-position:-64px -32px;}.ui-icon-arrow-1-sw{background-position:-80px -32px;}.ui-icon-arrow-1-w{background-position:-96px -32px;}.ui-icon-arrow-1-nw{background-position:-112px -32px;}.ui-icon-arrow-2-n-s{background-position:-128px -32px;}.ui-icon-arrow-2-ne-sw{background-position:-144px -32px;}.ui-icon-arrow-2-e-w{background-position:-160px -32px;}.ui-icon-arrow-2-se-nw{background-position:-176px -32px;}.ui-icon-arrowstop-1-n{background-position:-192px -32px;}.ui-icon-arrowstop-1-e{background-position:-208px -32px;}.ui-icon-arrowstop-1-s{background-position:-224px -32px;}.ui-icon-arrowstop-1-w{background-position:-240px -32px;}.ui-icon-arrowthick-1-n{background-position:0 -48px;}.ui-icon-arrowthick-1-ne{background-position:-16px -48px;}.ui-icon-arrowthick-1-e{background-position:-32px -48px;}.ui-icon-arrowthick-1-se{background-position:-48px -48px;}.ui-icon-arrowthick-1-s{background-position:-64px -48px;}.ui-icon-arrowthick-1-sw{background-position:-80px -48px;}.ui-icon-arrowthick-1-w{background-position:-96px -48px;}.ui-icon-arrowthick-1-nw{background-position:-112px -48px;}.ui-icon-arrowthick-2-n-s{background-position:-128px -48px;}.ui-icon-arrowthick-2-ne-sw{background-position:-144px -48px;}.ui-icon-arrowthick-2-e-w{background-position:-160px -48px;}.ui-icon-arrowthick-2-se-nw{background-position:-176px -48px;}.ui-icon-arrowthickstop-1-n{background-position:-192px -48px;}.ui-icon-arrowthickstop-1-e{background-position:-208px -48px;}.ui-icon-arrowthickstop-1-s{background-position:-224px -48px;}.ui-icon-arrowthickstop-1-w{background-position:-240px -48px;}.ui-icon-arrowreturnthick-1-w{background-position:0 -64px;}.ui-icon-arrowreturnthick-1-n{background-position:-16px -64px;}.ui-icon-arrowreturnthick-1-e{background-position:-32px -64px;}.ui-icon-arrowreturnthick-1-s{background-position:-48px -64px;}.ui-icon-arrowreturn-1-w{background-position:-64px -64px;}.ui-icon-arrowreturn-1-n{background-position:-80px -64px;}.ui-icon-arrowreturn-1-e{background-position:-96px -64px;}.ui-icon-arrowreturn-1-s{background-position:-112px -64px;}.ui-icon-arrowrefresh-1-w{background-position:-128px -64px;}.ui-icon-arrowrefresh-1-n{background-position:-144px -64px;}.ui-icon-arrowrefresh-1-e{background-position:-160px -64px;}.ui-icon-arrowrefresh-1-s{background-position:-176px -64px;}.ui-icon-arrow-4{background-position:0 -80px;}.ui-icon-arrow-4-diag{background-position:-16px -80px;}.ui-icon-extlink{background-position:-32px -80px;}.ui-icon-newwin{background-position:-48px -80px;}.ui-icon-refresh{background-position:-64px -80px;}.ui-icon-shuffle{background-position:-80px -80px;}.ui-icon-transfer-e-w{background-position:-96px -80px;}.ui-icon-transferthick-e-w{background-position:-112px -80px;}.ui-icon-folder-collapsed{background-position:0 -96px;}.ui-icon-folder-open{background-position:-16px -96px;}.ui-icon-document{background-position:-32px -96px;}.ui-icon-document-b{background-position:-48px -96px;}.ui-icon-note{background-position:-64px -96px;}.ui-icon-mail-closed{background-position:-80px -96px;}.ui-icon-mail-open{background-position:-96px -96px;}.ui-icon-suitcase{background-position:-112px -96px;}.ui-icon-comment{background-position:-128px -96px;}.ui-icon-person{background-position:-144px -96px;}.ui-icon-print{background-position:-160px -96px;}.ui-icon-trash{background-position:-176px -96px;}.ui-icon-locked{background-position:-192px -96px;}.ui-icon-unlocked{background-position:-208px -96px;}.ui-icon-bookmark{background-position:-224px -96px;}.ui-icon-tag{background-position:-240px -96px;}.ui-icon-home{background-position:0 -112px;}.ui-icon-flag{background-position:-16px -112px;}.ui-icon-calendar{background-position:-32px -112px;}.ui-icon-cart{background-position:-48px -112px;}.ui-icon-pencil{background-position:-64px -112px;}.ui-icon-clock{background-position:-80px -112px;}.ui-icon-disk{background-position:-96px -112px;}.ui-icon-calculator{background-position:-112px -112px;}.ui-icon-zoomin{background-position:-128px -112px;}.ui-icon-zoomout{background-position:-144px -112px;}.ui-icon-search{background-position:-160px -112px;}.ui-icon-wrench{background-position:-176px -112px;}.ui-icon-gear{background-position:-192px -112px;}.ui-icon-heart{background-position:-208px -112px;}.ui-icon-star{background-position:-224px -112px;}.ui-icon-link{background-position:-240px -112px;}.ui-icon-cancel{background-position:0 -128px;}.ui-icon-plus{background-position:-16px -128px;}.ui-icon-plusthick{background-position:-32px -128px;}.ui-icon-minus{background-position:-48px -128px;}.ui-icon-minusthick{background-position:-64px -128px;}.ui-icon-close{background-position:-80px -128px;}.ui-icon-closethick{background-position:-96px -128px;}.ui-icon-key{background-position:-112px -128px;}.ui-icon-lightbulb{background-position:-128px -128px;}.ui-icon-scissors{background-position:-144px -128px;}.ui-icon-clipboard{background-position:-160px -128px;}.ui-icon-copy{background-position:-176px -128px;}.ui-icon-contact{background-position:-192px -128px;}.ui-icon-image{background-position:-208px -128px;}.ui-icon-video{background-position:-224px -128px;}.ui-icon-script{background-position:-240px -128px;}.ui-icon-alert{background-position:0 -144px;}.ui-icon-info{background-position:-16px -144px;}.ui-icon-notice{background-position:-32px -144px;}.ui-icon-help{background-position:-48px -144px;}.ui-icon-check{background-position:-64px -144px;}.ui-icon-bullet{background-position:-80px -144px;}.ui-icon-radio-off{background-position:-96px -144px;}.ui-icon-radio-on{background-position:-112px -144px;}.ui-icon-pin-w{background-position:-128px -144px;}.ui-icon-pin-s{background-position:-144px -144px;}.ui-icon-play{background-position:0 -160px;}.ui-icon-pause{background-position:-16px -160px;}.ui-icon-seek-next{background-position:-32px -160px;}.ui-icon-seek-prev{background-position:-48px -160px;}.ui-icon-seek-end{background-position:-64px -160px;}.ui-icon-seek-start{background-position:-80px -160px;}.ui-icon-seek-first{background-position:-80px -160px;}.ui-icon-stop{background-position:-96px -160px;}.ui-icon-eject{background-position:-112px -160px;}.ui-icon-volume-off{background-position:-128px -160px;}.ui-icon-volume-on{background-position:-144px -160px;}.ui-icon-power{background-position:0 -176px;}.ui-icon-signal-diag{background-position:-16px -176px;}.ui-icon-signal{background-position:-32px -176px;}.ui-icon-battery-0{background-position:-48px -176px;}.ui-icon-battery-1{background-position:-64px -176px;}.ui-icon-battery-2{background-position:-80px -176px;}.ui-icon-battery-3{background-position:-96px -176px;}.ui-icon-circle-plus{background-position:0 -192px;}.ui-icon-circle-minus{background-position:-16px -192px;}.ui-icon-circle-close{background-position:-32px -192px;}.ui-icon-circle-triangle-e{background-position:-48px -192px;}.ui-icon-circle-triangle-s{background-position:-64px -192px;}.ui-icon-circle-triangle-w{background-position:-80px -192px;}.ui-icon-circle-triangle-n{background-position:-96px -192px;}.ui-icon-circle-arrow-e{background-position:-112px -192px;}.ui-icon-circle-arrow-s{background-position:-128px -192px;}.ui-icon-circle-arrow-w{background-position:-144px -192px;}.ui-icon-circle-arrow-n{background-position:-160px -192px;}.ui-icon-circle-zoomin{background-position:-176px -192px;}.ui-icon-circle-zoomout{background-position:-192px -192px;}.ui-icon-circle-check{background-position:-208px -192px;}.ui-icon-circlesmall-plus{background-position:0 -208px;}.ui-icon-circlesmall-minus{background-position:-16px -208px;}.ui-icon-circlesmall-close{background-position:-32px -208px;}.ui-icon-squaresmall-plus{background-position:-48px -208px;}.ui-icon-squaresmall-minus{background-position:-64px -208px;}.ui-icon-squaresmall-close{background-position:-80px -208px;}.ui-icon-grip-dotted-vertical{background-position:0 -224px;}.ui-icon-grip-dotted-horizontal{background-position:-16px -224px;}.ui-icon-grip-solid-vertical{background-position:-32px -224px;}.ui-icon-grip-solid-horizontal{background-position:-48px -224px;}.ui-icon-gripsmall-diagonal-se{background-position:-64px -224px;}.ui-icon-grip-diagonal-se{background-position:-80px -224px;}.ui-corner-tl{-moz-border-radius-topleft:4px;-webkit-border-top-left-radius:4px;border-top-left-radius:4px;}.ui-corner-tr{-moz-border-radius-topright:4px;-webkit-border-top-right-radius:4px;border-top-right-radius:4px;}.ui-corner-bl{-moz-border-radius-bottomleft:4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;}.ui-corner-br{-moz-border-radius-bottomright:4px;-webkit-border-bottom-right-radius:4px;border-bottom-right-radius:4px;}.ui-corner-top{-moz-border-radius-topleft:4px;-webkit-border-top-left-radius:4px;border-top-left-radius:4px;-moz-border-radius-topright:4px;-webkit-border-top-right-radius:4px;border-top-right-radius:4px;}.ui-corner-bottom{-moz-border-radius-bottomleft:4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;-moz-border-radius-bottomright:4px;-webkit-border-bottom-right-radius:4px;border-bottom-right-radius:4px;}.ui-corner-right{-moz-border-radius-topright:4px;-webkit-border-top-right-radius:4px;border-top-right-radius:4px;-moz-border-radius-bottomright:4px;-webkit-border-bottom-right-radius:4px;border-bottom-right-radius:4px;}.ui-corner-left{-moz-border-radius-topleft:4px;-webkit-border-top-left-radius:4px;border-top-left-radius:4px;-moz-border-radius-bottomleft:4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;}.ui-corner-all{-moz-border-radius:4px;-webkit-border-radius:4px;border-radius:4px;}.ui-widget-overlay{background:#aaa 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 bad241dc701f -r ffe82516a83c Blast output page example trimmed_files/jig.js
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Blast output page example trimmed_files/jig.js	Tue May 06 17:36:10 2014 +0200
@@ -0,0 +1,265 @@
+(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('