sequenceserver 0.8.5 → 0.8.6

data/public/css/beige.css~

@@ -1,226 +0,0 @@
-body {
-	background-color: #2B3E42;
-	/*background: #3f4555;*/
-	font-family: Tahoma, Arial, sans-serif;
-}
-
-.container {
-	width: 800px;  
-	margin: 50px auto;
-	background-color: white;
-	border: 2px solid white;
-	border-radius: 10px;
-	-moz-border-radius: 10px;
-}
-
-h1 {
-    margin: 0px;
-	padding: 0px;
-}
-
-.banner {
-	font-weight: bold;
-	background: #ebcd7b;
-	font-size: 300%;
-	font-family: Tahoma, Arial, sans-serif;
-	color: black;
-	padding: 2%;
-	margin-bottom: 2%;
-
-	border-bottom-left-radius: 0px;
-	border-bottom-right-radius: 0px;
-	border-top-left-radius: 10px;
-	border-top-right-radius: 10px;
-
-	-moz-border-radius-bottomleft: 0px;
-	-moz-border-radius-bottomright: 0px;
-	-moz-border-radius-topleft: 10px;
-	-moz-border-radius-topright: 10px;
-
-}
-
-.underbar { 
-	background-color: #ebcd7b; 
-	font-family:arial;
-	font-size: 12px;
-	text-align: center;
-	color: #333333;
-	padding: 1px 1px 1px 1px;
-	margin: 2% 0 0 0;
-	border-bottom-left-radius: 10px;
-	border-bottom-right-radius: 10px;
-}
-
-
-.entryfield {
-	padding:0;
-	margin:0;
-	float:left; /* otherwise each div is under the next. */
-	width:82%;
-}
-
-.entryfield textarea {
-	padding:0;
-	margin:0;
-	width:100%;
-	height: 168px;
-	border-color:black;
-}
-
-.blastmethods {
-	float					: right;
-	width 			        : 15%;
-	background				: #222222;
-	border					: none;
-	height                  :  150px;
-
-	border-top-right-radius	: 10px;
-	border-top-left-radius	: 0px;
-	border-bottom-right-radius: 10px;
-	border-bottom-left-radius	:  0px;
-
-	-moz-border-radius-topright: 10px;
-	-moz-border-radius-topleft: 0px;
-	-moz-border-radius-bottomright: 10px;
-	-moz-border-radius-bottomleft:  0px;
-
-
-	font-size					: 1.5em; 
-	font-family: Tahoma, Arial, sans-serif; 
-	color: black;
-	margin:0;
-	padding:0;
-}
-
-fieldset {
-	margin:0;
-	padding:0;
-}
-
-.horizontal {
-	margin: 2%;
-	padding-bottom:15px;
-	padding-top:15px;
-	width: 96%;
-	clear:both;
-}
-
-.rounded {
-	border-radius  :10px;
-	-moz-border-radius:10px;
-}
-
-.box {
-	background  : #D5E1DD;
-	/* background: -webkit-gradient(linear, left top, left bottom, from(#ccc), to(#000));   */
-
-	border      : none;
-
-	padding     : 10px;
-	margin: 0;
-	font-family : Tahoma, Arial, sans-serif;
-	color       : black;
-}
-
-.databases {
-	width       :46.5%;
-}
-.nucleotide {
-	float    :left;
-}
-.protein {
-	float    : right;
-}
-
-.radiobutton{
-	margin: 9px 5px 0px 0px;
-	padding: 0;
-	vertical-align: top;
-}
-.dbcheckbox {   /* within each "database box" */
-float:left;
-clear:both;
-margin: 5px 10px 0 0;
-padding: 0;
-}
-.dbdescription {
-	float:left;
-}
-
-.advanced {
-	float:left;
-	width: 78%;
-}
-
-.greytext {
-  color: #A9A9A9;
-}
-
-.pointer {
-	cursor:pointer;
-}
-
-.advanced pre {
-	display: none;
-}
-.advanced input {
-	float:right;
-	width: 60%;
-}
-
-.submit_button {
-	float:right;
-	width: 17.5%;
-}
-.submit_button input {
-	width: 100%;
-	background-color	: #323292;
-	background: -webkit-gradient(linear, left top, right bottom, from(#0066CC), to(#192D53));
-	background: -moz-linear-gradient(45deg,#0066CC,#192D53);
-
-	border			: 2px solid #192D53;
-	border-radius		: 10px;
-	-moz-border-radius: 10px;
-	color				: white;
-	padding			: 2.5px 10px 2.5px 10px;
-	cursor			: pointer;
-	font-size			: 1.8em;
-	font-family		: Tahoma, Arial, sans-serif;
-	margin: 0 0 0 0;
-
-}
-.submit_button input:active {
-	color: #1f2126;
-
-}
-.submit_button input:hover {
-	background: -webkit-gradient(linear, left top, right bottom, from(#009cff), to(#0261c2));
-	background: -moz-linear-gradient(45deg,#009cff,#0261c2);
-
-}
-
-h2, .bigtext{
-	font-family: Tahoma, Arial, serif;
-	font-weight: bold;
-	font-size: 20px;
-	color: black;
-	margin:0;
-	padding: 0px;
-	/*	margin: 8px 0 10px 0;*/
-}
-
-.smalltext{
-	font-size:10px;
-}
-
-
-#result{
-	clear:both;
-	background-color: white;
-	padding-left: 5%;
-	margin: 0 18px 0 18px;
-}
-
-a {
-    color: #b22222;
-}

data/public/js/sequenceserver.js~

@@ -1,250 +0,0 @@
-//helpers methods to disable, enable, and uncheck radio buttons and checkboxes
-(function( $ ){
-    //disable an element
-    $.fn.disable = function() {
-        return this.attr('disabled', 'disabled');
-    };
-})( jQuery );
-
-(function( $ ){
-    //enable an element
-    $.fn.enable = function() {
-        return this.removeAttr('disabled');
-    };
-})( jQuery );
-
-(function( $ ){
-    //uncheck an element
-    $.fn.uncheck = function() {
- return this.removeAttr('checked');
-        this.attr('checked') && this.removeAttr('checked');
-        return this;
-    };
-})( jQuery );
-
-(function( $ ){
-    //check an element
-    $.fn.check = function() {
-        return this.attr('checked', 'checked');
-    };
-})( jQuery );
-
-(function( $ ){
-    //(pre-)check the only active database checkbox
-    $.onedb = function(selector) {
-        active_dbs = $(".databases input[type=checkbox]").not(":disabled")
-        if (active_dbs.length == 1){
-            active_dbs.check()
-        }
-        return active_dbs;
-    };
-})( jQuery );
-
-(function( $ ){
-    //highlight an element
-    $.fn.highlight = function() {
-        return this.addClass('focussed');
-    };
-})( jQuery );
-
-(function( $ ){
-    //unhighlight an element
-    $.fn.unhighlight = function() {
-        return this.removeClass('focussed');
-    };
-})( jQuery );
-
-(function ($) {
-    $.fn.poll = function () {
-        var that, val, tmp;
-
-        that = this;
-
-        (function ping () {
-            tmp = that.val();
-
-            if (tmp != val){
-                val = tmp;
-                that.change();
-            }
-
-            setTimeout(ping, 100);
-        }());
-
-        return this;
-    };
-}(jQuery));
-
-/*
-    SS - SequenceServer's JavaScript module
-
-    Define a global SS (acronym for SequenceServer) object containing the
-    following methods:
-
-        main():
-            Initializes SequenceServer's various modules.
-*/
-
-//define global SS object
-var SS;
-if (!SS) {
-    SS = {};
-}
-
-//SS module
-(function () {
-
-    /*
-        ask each module to initialize itself
-    */
-    SS.main = function () {
-        SS.blast.init();
-    }
-}()); //end SS module
-
-$(document).ready(function(){
-    // poll the sequence textbox for a change in user input
-    $('#sequence').poll();
-
-    // start SequenceServer's event loop
-    SS.main();
-    $('input:submit').disable();
-
-    $('form').on('blast_valid', function () {
-        $('input:submit').enable();
-    });
-
-    $('form').on('blast_invalid', function () {
-        $('input:submit').disable();
-    });
-
-    $('#sequence').bind('sequence_type_changed', function(event, type){
-        if (type == "nucleotide"){
-            $("#blastn, #tblastx, #blastx").enable();
-            $("#blastp, #tblastn").uncheck().disable().first().change();
-        }
-        else if (type == "protein"){
-            $("#blastp, #tblastn").enable();
-            $("#blastn, #tblastx, #blastx").uncheck().disable().first().change();
-        }
-        else if (type == undefined){
-            //reset blast methods
-            $('.blastmethods input[type=radio]').enable().first().change();
-        }
-    });
-
-    $(".advanced label").click(function(event){
-        //toggle display of advanced options when "Advanced parameters" text is
-        //clicked
-        $(".advanced .help").toggle("fast");
-
-        //stop event propagation here; jQuery will call `click()` on input box
-        //otherwise
-        return false;
-    });
-
-    $(".advanced input").click(function(event){
-        //but for input box toggling might get annoying
-        $(".advanced .help").show("fast");
-    });
-
-    $("input#advanced").enablePlaceholder({"withPlaceholderClass": "greytext"});
-    $("textarea#sequence").enablePlaceholder({"withPlaceholderClass": "greytext"});
-
-    //when a blast method is selected
-    $('#blastp, #blastx, #blastn, #tblastx, #tblastn').change(function(event){
-        //then find the selected blast method
-        var method = $('.blastmethods input[type=radio]').filter(':checked').val();
-
-        //and accordingly disable incompatible databases
-        if (method == 'blastx' || method == 'blastp'){
-            $('.databases.nucleotide input[type=checkbox]').uncheck().disable();
-            $('.databases.protein input[type=checkbox]').enable();
-        }
-        else if (method == 'blastn' || method == 'tblastx' || method == 'tblastn'){
-            $('.databases.protein input[type=checkbox]').uncheck().disable();
-            $('.databases.nucleotide input[type=checkbox]').enable();
-        }
-        else{
-            $('.databases input[type=checkbox]').enable();
-        }
-
-        $.onedb();
-    });
-
-    $('#blast').submit(function(){
-        //parse AJAX URL
-        var action = $(this).attr('action');
-        var index  = action.indexOf('#');
-        var url    = action.slice(0, index);
-        var hash   = action.slice(index, action.length);
-
-        var button = $(this).find('input:submit');
-
-        //prevent submitting another query while this one is being processed
-        button.disable();
-
-        //overlay div will contain the spinner
-        $('body').append('<div id="overlay"></div>')
-
-        //activate spinner to indicate query in progress
-        $('#overlay').css({
-           top:              '0px',
-           left:             '0px',
-           width:            '100%',
-           height:           '100%',
-           position:         'fixed',
-           'z-index':        1000,
-           'pointer-events': 'none',
-        }).activity({
-           segments: 8,
-           length:   40,
-           width:    16,
-           speed:    1.8
-        });
-
-        // BLAST now
-        $.post(url, $('form').serialize()).
-          done(function (data) {
-            // BLASTed successfully
-
-            // display the result
-            $('#result').html(data);
-            location.hash = hash;
-        }).
-          fail(function (jqXHR, status, error) {
-            // BLAST failed
-
-            //alert user
-            alert('BLAST failed: ' + error);
-        }).
-          always(function () {
-            // BLAST complete (succefully or otherwise)
-
-            // remove progress notification
-            $('#overlay').activity(false).remove();
-
-            // allow submitting a new query
-            button.enable();
-        });
-
-        return false;
-    });
-
-    $(window).scroll(function() {
-      var areaHeight = $(this).height();
-
-      $('.resultn').each(function() {
-        var scrolled = $(window).scrollTop();
-        var start    = $(this).offset().top   - screen.height/2;
-        var end      = start + $(this).height();
-
-        if (scrolled > start && scrolled < end){
-          $(this).highlight();
-        }
-        else {
-          $(this).unhighlight();
-        }
-      });
-    });
-});

data/tests/chromedriver.log

@@ -1,98 +0,0 @@
-[0.000][INFO]:      ChromeDriver 26.0.1383.0 /usr/local/bin/chromedriver
-[0.246][FINE]:      Initializing session with capabilities {
-   "browserName": "chrome",
-   "chrome.detach": true,
-   "chromeOptions": {
-      "detach": true
-   },
-   "cssSelectorsEnabled": true,
-   "javascriptEnabled": true,
-   "nativeEvents": false,
-   "platform": "ANY",
-   "rotatable": false,
-   "takesScreenshot": false,
-   "version": ""
-}
-
-[0.248][INFO]:      Using named testing interface
-[1.014][INFO]:      Connected to Chrome successfully. Version: 25.0.1364.160
-[1.062][FINE]:      Command received (/session/02d813cd7f3704d0df88e423b982bb02)
-[1.062][FINE]:      Command finished (/session/02d813cd7f3704d0df88e423b982bb02) with response {
-   "sessionId": "02d813cd7f3704d0df88e423b982bb02",
-   "status": 0,
-   "value": {
-      "acceptSslCerts": false,
-      "applicationCacheEnabled": false,
-      "browserConnectionEnabled": false,
-      "browserName": "chrome",
-      "chrome.chromedriverVersion": "26.0.1383.0",
-      "cssSelectorsEnabled": true,
-      "databaseEnabled": false,
-      "handlesAlerts": true,
-      "javascriptEnabled": true,
-      "locationContextEnabled": false,
-      "nativeEvents": true,
-      "platform": "linux",
-      "rotatable": false,
-      "takesScreenshot": true,
-      "version": "25.0.1364.160",
-      "webStorageEnabled": true
-   }
-}
-
-[1.065][FINE]:      Command received (/session/02d813cd7f3704d0df88e423b982bb02/url) with params {
-   "url": "http://localhost:4567"
-}
-
-[1.065][FINER]:     Waiting for all views to stop loading...
-[1.142][FINER]:     Done waiting for all views to stop loading
-[6.740][FINER]:     Waiting for all views to stop loading...
-[6.750][FINER]:     Done waiting for all views to stop loading
-[6.750][FINE]:      Command finished (/session/02d813cd7f3704d0df88e423b982bb02/url) with response {
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-   "status": 0,
-   "value": {
-
-   }
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-[6.752][FINE]:      Command received (/session/02d813cd7f3704d0df88e423b982bb02/url)
-[6.752][FINER]:     Waiting for all views to stop loading...
-[6.752][FINER]:     Done waiting for all views to stop loading
-[6.772][FINER]:     Waiting for all views to stop loading...
-[6.772][FINER]:     Done waiting for all views to stop loading
-[6.772][FINE]:      Command finished (/session/02d813cd7f3704d0df88e423b982bb02/url) with response {
-   "sessionId": "02d813cd7f3704d0df88e423b982bb02",
-   "status": 0,
-   "value": "http://localhost:4567/"
-}
-
-[6.774][FINE]:      Command received (/session/02d813cd7f3704d0df88e423b982bb02/url)
-[6.774][FINER]:     Waiting for all views to stop loading...
-[6.774][FINER]:     Done waiting for all views to stop loading
-[6.777][FINER]:     Waiting for all views to stop loading...
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-   "status": 0,
-   "value": "http://localhost:4567/"
-}
-
-[6.779][FINE]:      Command received (/session/02d813cd7f3704d0df88e423b982bb02/execute) with params {
-   "args": [  ],
-   "script": "return document.readyState"
-}
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-[6.779][FINER]:     Waiting for all views to stop loading...
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-}
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-[6.788][FINE]:      Command received (/session/02d813cd7f3704d0df88e423b982bb02)
-[17.881][WARNING]:  Chrome still running, terminating...
-[17.881][INFO]:     Chrome shutdown

data/tests/database/nucleotide/head.fa

@@ -1,10 +0,0 @@
->SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2
-ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG
-GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT
-CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG
-ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT
-TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA
-TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT
-ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG
-TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT
-TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG

data/tests/database/nucleotide/head.faVno_parse.html

@@ -1,96 +0,0 @@
-<HTML>
-<TITLE>BLAST Search Results</TITLE>
-<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
-<PRE>
-
-<b>BLASTN 2.2.25+</b>
-
-
-<b><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10890397&dopt=Citation">Reference</a>:</b>
-Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
-"A greedy algorithm for aligning DNA sequences", J Comput Biol 2000;
-7(1-2):203-14.
-
-
-
-Database: no_parse.fa
-           473 sequences; 287,752 total letters
-
-
-
-<b>Query=</b> SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2
-
-Length=540
-                                                                      Score     E
-Sequences producing significant alignments:                          (Bits)  Value
-
-  SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2          <a href=#BL_ORD_ID:0> 998</a>    0.0  
-
-
-<script src="blastResult.js"></script>><a name=BL_ORD_ID:0></a> SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2
-Length=597
-
- Score =  998 bits (540),  Expect = 0.0
- Identities = 540/540 (100%), Gaps = 0/540 (0%)
- Strand=Plus/Plus
-
-Query  1    ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG  60
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  1    ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG  60
-
-Query  61   GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT  120
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  61   GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT  120
-
-Query  121  CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG  180
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  121  CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG  180
-
-Query  181  ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT  240
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  181  ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT  240
-
-Query  241  TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA  300
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  241  TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA  300
-
-Query  301  TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT  360
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  301  TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT  360
-
-Query  361  ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG  420
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  361  ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG  420
-
-Query  421  TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT  480
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  421  TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT  480
-
-Query  481  TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG  540
-            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct  481  TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG  540
-
-
-
-Lambda     K      H
-    1.33    0.621     1.12 
-
-Gapped
-Lambda     K      H
-    1.28    0.460    0.850 
-
-Effective search space used: 145236565
-
-
-  Database: no_parse.fa
-    Posted date:  Sep 25, 2011  10:05 AM
-  Number of letters in database: 287,752
-  Number of sequences in database:  473
-
-
-
-Matrix: blastn matrix 1 -2
-Gap Penalties: Existence: 0, Extension: 2.5
-</PRE>
-</BODY>
-</HTML>