sequenceserver 0.8.9 → 1.0.0.pre.1

data/public/js/sequenceserver.blast.js

@@ -96,21 +96,21 @@ SS.blast = (function () {
         return true;
     }
 
-    /*
-        determine input sequence type, and trigger 'sequence_type_changed'
-        event if the input sequence type has changed
-    */
+    /**
+     * Determine input sequence type, and trigger 'sequence_type_changed' event
+     * if the input sequence type has changed, or cannot be determined.
+     */
     var signal_sequence_type_changed = function () {
-        var type, tmp;
+        var type, _type;
 
         $('#sequence').change(function () {
-            tmp = type_of_sequences();
+            _type = type_of_sequences();
 
-            if (tmp != type){
-              type = tmp;
+            if (!_type || _type !== type) {
+                type = _type;
 
-              //notify listeners
-              $(this).trigger('sequence_type_changed', type);
+                //notify listeners
+                $(this).trigger('sequence_type_changed', type);
             }
         });
     };
@@ -131,39 +131,36 @@ SS.blast = (function () {
         });
     }
 
-    /* */
+    /**
+     * Triggers 'blast_method_changed' event if BLAST algorithms that can be
+     * used for the user input have changed.
+     */
     var signal_blast_method_changed = function () {
-        var method, tmp;
+        var method, _method;
 
         $('#blast').on('sequence_type_changed database_type_changed',
             function (event) {
-                  tmp = determine_blast_method();
+                  _method = determine_blast_method();
 
-                  if (tmp != method) {
-                      method = tmp;
+                  if (!_.isEqual(_method, method)) {
+                      method = _method;
 
                       //notify listeners
-                      $(this).trigger('blast_method_changed', [method]);
+                      $(this).trigger('blast_method_changed', [method.slice()]);
                   }
             });
     }
 
-    /*
-        Return a BLAST method to use for the selected database and input
-        sequence type.
-
-             database       method
-            ------------------------
-             protein        blastx
-             protein        blastp
-            ------------------------
-             nucleotide     tblastx
-             nucleotide     tblastn
-             nucleotide     blastn
-    */
+    /**
+     * Returns name of BLAST algorithms that can be used for the input query
+     * and selected database combination.
+     *
+     * Returns empty array if no BLAST algorithm is appropriate for the user
+     * input.
+     */
     var determine_blast_method = function () {
         if (!required_params_present()) {
-            return
+            return [];
         }
 
         var database_type = type_of_databases();
@@ -190,6 +187,8 @@ SS.blast = (function () {
                         return ['blastn', 'tblastx'];
                 }
         }
+
+        return [];
     }
 
     /* public interface */

data/public/js/sequenceserver.js

@@ -2,31 +2,46 @@
 (function( $ ){
     //disable an element
     $.fn.disable = function() {
-        return this.attr('disabled', 'disabled');
+        return this.prop('disabled', true).addClass('disabled');
     };
 })( jQuery );
 
 (function( $ ){
     //enable an element
     $.fn.enable = function() {
-        return this.removeAttr('disabled');
+        return this.prop('disabled', false).removeClass('disabled');
     };
 })( jQuery );
 
 (function( $ ){
     //uncheck an element
     $.fn.uncheck = function() {
-        return this.removeAttr('checked');
+        return this.prop('checked', false);
     };
 })( jQuery );
 
 (function( $ ){
     //check an element
     $.fn.check = function() {
-        return this.attr('checked', 'checked');
+        return this.prop('checked', true);
     };
 })( jQuery );
 
+/**
+ * Wiggle an element.
+ *
+ * Used for wiggling BLAST button.
+ */
+(function ($) {
+    $.fn.wiggle = function() {
+        this.finish().effect("bounce", {
+            direction: 'left',
+            distance: 24,
+            times: 4,
+        }, 250);
+    };
+}(jQuery));
+
 (function( $ ){
     //(pre-)check the only active database checkbox
     $.onedb = function(selector) {
@@ -38,25 +53,12 @@
     };
 })( 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;
+        val  = that.val();
 
         (function ping () {
             tmp = that.val();
@@ -92,6 +94,9 @@ if (!SS) {
 //SS module
 (function () {
 
+    // Starts with >.
+    SS.FASTA_FORMAT = /^>/;
+
     SS.decorate = function (name) {
       return name.match(/(.?)(blast)(.?)/).slice(1).map(function (token, _) {
         if (token) {
@@ -103,28 +108,437 @@ if (!SS) {
             }
         }
       }).join('');
-    }
+    };
+
+    SS.generateGraphicalOverview = function () {
+        $("[data-graphit='overview']").each(function () {
+            var $this = $(this);
+            var $graphDiv = $('<div/>').addClass('graphical-overview');
+            $this.children().eq(1).children().eq(0).before($graphDiv);
+
+            $.graphIt($this, $graphDiv, 0, 20);
+        });
+    };
+
+    SS.updateDownloadFastaOfAllLink = function () {
+        var num_hits = $('.hitn').length;
+
+        var $a = $('.download-fasta-of-all');
+        if (num_hits >= 1 && num_hits <= 30) {
+            var sequence_ids = $('.hitn :checkbox').map(function() {
+                return this.value;
+            }).get();
+            $a
+            .enable()
+            .attr('href', SS.generateURI(sequence_ids, $a.data().databases))
+            .tooltip('destroy')
+            .tooltip({
+                placement: 'left',
+                title: num_hits + " hit(s)."
+            });
+            return;
+        }
+
+        if (num_hits == 0) {
+            $a
+            .tooltip('destroy')
+            .tooltip({
+                placement: 'left',
+                title: "No hit to download."
+            });
+        }
+
+        if (num_hits > 30) {
+            $a
+            .tooltip('destroy')
+            .tooltip({
+                placement: 'left',
+                title: "Can't download more than 30 hits."
+            });
+        }
+        $a.disable();
+    };
+
+    /* Update the FASTA downloader button's state appropriately.
+     *
+     * When more than 30 hits are obtained, the link is disabled.
+     * When no hits are obtained, the link is not present at all.
+     */
+    SS.updateDownloadFastaOfSelectedLink = function () {
+        var num_checked  = $('.hitn :checkbox:checked').length;
+
+        var $a = $('.download-fasta-of-selected');
+        var $n = $a.find('span');
+
+        if (num_checked >= 1 && num_checked <= 30) {
+            var sequence_ids = $('.hitn :checkbox:checked').map(function () {
+                return this.value;
+            }).get();
+
+            $a
+            .enable()
+            .attr('href', SS.generateURI(sequence_ids, $a.data().databases))
+            .tooltip('destroy')
+            .tooltip({
+                placement: 'left',
+                title: num_checked + " hit(s) selected."
+            })
+            .find('span').html(num_checked);
+            return;
+        }
+
+        if (num_checked == 0) {
+            $n.empty();
+            $a
+            .tooltip('destroy')
+            .tooltip({
+                placement: 'left',
+                title: "No hit selected."
+            });
+        }
+
+        if (num_checked > 30) {
+            $a
+            .tooltip('destroy')
+            .tooltip({
+                placement: 'left',
+                title: "Can't download more than 30 hits."
+            });
+        }
+
+        $a
+        .disable()
+        .removeAttr('href');
+    };
+
+    SS.updateSequenceViewerLinks = function () {
+        var MAX_LENGTH = 10000;
+
+        $('.view-sequence').each(function () {
+            var $this = $(this);
+            var $hitn = $this.closest('.hitn');
+            if ($hitn.data().hitLen > MAX_LENGTH) {
+                $this
+                .disable()
+                .removeAttr('href')
+                .tooltip({
+                    title: 'Sequence too long to show. Please view it ' +
+                           'locally after download.'
+                });
+            }
+        });
+    };
+
+    SS.setupTooltipsForPosLabels = function () {
+        $('.pos-label').each(function () {
+            $(this).tooltip({
+                container: 'body',
+                placement: 'right',
+            });
+        });
+    };
+
+    SS.generateURI = function (sequence_ids, database_ids) {
+        // Encode URIs against strange characters in sequence ids.
+        sequence_ids = encodeURIComponent(sequence_ids.join(' '));
+        database_ids = encodeURIComponent(database_ids);
+
+        var url = "get_sequence/?sequence_ids=" + sequence_ids +
+            "&database_ids=" + database_ids + '&download=fasta';
+
+        return url;
+    },
+
+    SS.showErrorModal = function (jqXHR, beforeShow) {
+        setTimeout(function () {
+            beforeShow();
+            if (jqXHR.responseText) {
+                $("#error").html(jqXHR.responseText).modal();
+            }
+            else {
+                $("#error-no-response").modal();
+            }
+        }, 500);
+    },
+
+    SS.init = function () {
+        this.$sequence = $('#sequence');
+        this.$sequenceFile = $('#sequence-file');
+        this.$sequenceControls = $('.sequence-controls');
+
+        this.$sequence.poll();
 
-    /*
-        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();
+/**
+ * Highlight hit div corresponding to given checkbox and update bulk download
+ * link.
+ */
+SS.selectHit = function (checkbox) {
+    if (!checkbox || !checkbox.value) return;
+
+    var $hitn = $('.hitn[data-hit-def="' + checkbox.value + '"]');
+
+    // Highlight selected hit and sync checkboxes if sequence viewer is open.
+    if(checkbox.checked) {
+        $hitn
+        .addClass('glow')
+        .find(":checkbox").not(checkbox).check();
+    } else {
+        $hitn
+        .removeClass('glow')
+        .find(":checkbox").not(checkbox).uncheck();
+    }
+
+    this.updateDownloadFastaOfSelectedLink();
+};
 
-    // start SequenceServer's event loop
-    SS.main();
+SS.showSequenceViewer = (function () {
+
+    var $viewer = $('#sequence-viewer');
+    var $spinner = $('.spinner', $viewer);
+    var $viewerBody = $('.modal-body', $viewer);
+    var $viewerFooter = $('.modal-footer', $viewer);
+
+    var widgetClass = 'biojs-vis-sequence';
+
+    var initViewer = function ($clicked) {
+        $viewerBody.empty();
+        $viewerFooter.empty();
+
+        initFooter($clicked);
+        $spinner.show();
+        $viewer.modal('show');
+    };
+
+    var initFooter = function ($clicked) {
+        // Generate links in the footer.
+        var links = $clicked.parent().clone();
+        var viewSequenceLink = links.find('.view-sequence');
+        var nextSeparator = $(viewSequenceLink[0].nextSibling);
+        viewSequenceLink.remove();
+        nextSeparator.remove();
+        $viewerFooter.empty().append(links);
+    };
+
+    var showSequences = function (sequence_ids, sequences, databases) {
+        // Inform user if number of sequences retrieved is more or less than requested for.
+        if (sequence_ids.length != sequences.length) {
+            showLessOrMoreSequencesRetrievedMessage(sequence_ids, sequences, databases);
+        }
+
+        // Render sequence.
+        sequences.forEach(showSequence);
+    };
+
+    var showSequence = function (sequence) {
+        // generate html template
+        var header = sequence.id + "<small>&nbsp;" + sequence.title + "</small>";
+        var widgetId = widgetClass + (new Date().getUTCMilliseconds());
+
+        $viewerBody
+        .append(
+            $('<div/>')
+            .addClass('fastan')
+            .append(
+                $('<div/>')
+                .addClass('page-header')
+                .append(
+                    $('<h4>')
+                    .html(header)
+                ),
+                $('<div>')
+                .attr('id', widgetId)
+                .addClass(widgetClass)
+                .addClass('page-content')
+            )
+        );
+
+        // attach BioJS sequence viewer
+        var widget = new Sequence({
+            sequence: sequence.value,
+            target: widgetId,
+            format: 'CODATA',
+            columns: {
+                size: 35
+            },
+            formatOptions: {
+                title: false,
+                footer: false
+            }
+        });
+        widget.hideFormatSelector();
+    };
+
+    var showLessOrMoreSequencesRetrievedMessage = function (sequence_ids, sequences, databases) {
+        $viewerBody
+        .append(
+            $('<h4/>')
+            .html("ERROR: incorrect number of sequences found."),
+            $('<p/>')
+            .html('You requested ' + sequence_ids.length +
+                  ' sequence(s) with the following identifiers: <br>' +
+                  '<code>' + sequence_ids.join(', ') + '</code> <br>' +
+                  'from the following databases: <br>' +
+                  '<code>' + databases.join(', ') + '</code> <br>' +
+                  'but we found ' + sequences.length + ' sequence(s).'),
+            $('<p/>')
+            .html('This is likley due to a problem with how databases ' +
+                  'are formatted.<strong> Please share this text with ' +
+                  'the person managing this website so that the issue ' +
+                  'can be resolved.'),
+            $('<p/>')
+            .html('If any sequences were retrieved, you ' +
+                  'can find them below (but some may be incorrect, so ' +
+                  'be careful!)')
+        );
+    };
+
+    return function (clicked) {
+        var $clicked = $(clicked);
+        initViewer($clicked);
+
+        var url = $clicked.attr('href');
+        $.getJSON(url)
+        .done(function (response) {
+            showSequences(response.sequence_ids, response.sequences, response.databases);
+            $spinner.hide();
+        })
+        .fail(function (jqXHR, status, error) {
+            SS.showErrorModal(jqXHR, function () {
+                $viewer.modal('hide');
+            });
+        });
+    };
+}());
+
+$(document).ready(function(){
+    SS.init();
 
     var notification_timeout;
 
+    // drag-and-drop code
+    var tgtMarker = $('.dnd-overlay');
+    var $sequence = $('#sequence');
+
+    var dndError = function (id) {
+        $('.dnd-error').hide();
+        $('#' + id + '-notification').show();
+        tgtMarker.effect('fade', 2500);
+    };
+
+    $(document)
+    .on('dragenter', function (evt) {
+        // Based on http://stackoverflow.com/a/8494918/1205465.
+        // Contrary to what the above link says, the snippet below can't
+        // distinguish directories from files. We handle that on drop.
+        var dt = evt.originalEvent.dataTransfer;
+        var isFile = dt.types && ((dt.types.indexOf &&  // Chrome and Safari
+                                  dt.types.indexOf('Files') != -1) ||
+                                  (dt.types.contains && // Firefox
+                                   dt.types.contains('application/x-moz-file')));
+
+        if (!isFile) { return; }
+
+        $('.dnd-error').hide();
+        tgtMarker.stop(true, true);
+        tgtMarker.show();
+        dt.effectAllowed = 'copy';
+        if ($sequence.val() === '') {
+            $('.dnd-overlay-overwrite').hide();
+            $('.dnd-overlay-drop').show('drop', {direction: 'down'}, 'fast');
+        }
+        else {
+            $('.dnd-overlay-drop').hide();
+            $('.dnd-overlay-overwrite').show('drop', {direction: 'down'}, 'fast');
+        }
+    })
+    .on('dragleave', '.dnd-overlay', function (evt) {
+        tgtMarker.hide();
+        $('.dnd-overlay-drop').hide();
+        $('.dnd-overlay-overwrite').hide();
+    })
+    .on('dragover', '.dnd-overlay', function (evt) {
+        evt.originalEvent.dataTransfer.dropEffect = 'copy';
+        evt.preventDefault();
+    })
+    .on('drop', '.dnd-overlay', function (evt) {
+        evt.preventDefault();
+        evt.stopPropagation();
+
+        var textarea  = $('#sequence');
+        var indicator = $('#sequence-file');
+        textarea.focus();
+
+        var files = evt.originalEvent.dataTransfer.files;
+        if (files.length > 1) {
+            dndError('dnd-multi');
+            return;
+        }
+
+        var file = files[0];
+        if (file.size > 10 * 1048576) {
+            dndError('dnd-large-file');
+            return;
+        }
+
+        var reader = new FileReader();
+        reader.onload = function (e) {
+            var content = e.target.result;
+            if (SS.FASTA_FORMAT.test(content)) {
+                textarea.val(content);
+                indicator.text(file.name);
+                tgtMarker.hide();
+            } else {
+                // apparently not FASTA
+                dndError('dnd-format');
+            }
+        };
+        reader.onerror = function (e) {
+            // Couldn't read. Means dropped stuff wasn't FASTA file.
+            dndError('dnd-format');
+        }
+        reader.readAsText(file);
+    });
+    // end drag-and-drop
+
+    SS.$sequence.change(function () {
+        if (SS.$sequence.val()) {
+            // Calculation below is based on -
+            // http://chris-spittles.co.uk/jquery-calculate-scrollbar-width/
+            var sequenceControlsRight = SS.$sequence[0].offsetWidth -
+                SS.$sequence[0].clientWidth;
+            SS.$sequenceControls.css('right', sequenceControlsRight + 17);
+            SS.$sequenceControls.removeClass('hidden');
+        }
+        else {
+            SS.$sequenceFile.empty();
+            SS.$sequenceControls.addClass('hidden');
+            SS.$sequence.parent().removeClass('has-error');
+        }
+    });
+
+    // Handle clearing query sequences(s) when x button is pressed.
+    $('#btn-sequence-clear').click(function (e) {
+        $('#sequence').val("").focus();
+    })
+
+    // pre-select if only on db
+    $.onedb();
+
+    // Handles the form submission when Ctrl+Enter is pressed anywhere on page
+    $(document).bind("keydown", function (e) {
+        if (e.ctrlKey && e.keyCode === 13 && !$('#method').is(':disabled')) {
+            $('#method').trigger('submit');
+        }
+    });
+
     $('#sequence').on('sequence_type_changed', function (event, type) {
         clearTimeout(notification_timeout);
-        $(this).parent('.control-group').removeClass('error');
+        $(this).parent().removeClass('has-error');
         $('.notifications .active').hide().removeClass('active');
 
         if (type) {
@@ -135,7 +549,7 @@ $(document).ready(function(){
             }, 5000);
 
             if (type === 'mixed') {
-                $(this).parent('.control-group').addClass('error');
+                $(this).parent().addClass('has-error');
             }
         }
     });
@@ -148,70 +562,113 @@ $(document).ready(function(){
         switch (type) {
             case 'protein':
                 $('.databases.nucleotide input:checkbox').uncheck().disable();
+                $('.databases.nucleotide .checkbox').addClass('disabled');
                 break;
             case 'nucleotide':
                 $('.databases.protein input:checkbox').uncheck().disable();
+                $('.databases.protein .checkbox').addClass('disabled');
                 break;
             default:
                 $('.databases input:checkbox').enable();
+                $('.databases .checkbox').removeClass('disabled');
                 break;
         }
     });
 
-    $('form').on('blast_method_changed', function (event, methods){
+    $('form').on('blast_method_changed', function (event, methods) {
         // reset
-        $('#methods .dropdown-menu').html('');
-        $('#method').disable().val('').html('blast');
-        $('#methods').removeClass('btn-group').children('.dropdown-toggle').hide();
+        $('#method')
+        .disable().val('').html('blast')
+        .removeClass('col-md-11').addClass('col-md-12');
 
-        if (methods) {
+        $('#methods')
+        .children().not('#method').remove();
+
+        // set
+        if (methods.length > 0) {
             var method = methods.shift();
 
-            $('#method').enable().val(method).html(SS.decorate(method));
+            $('#method')
+            .enable().val(method).html(SS.decorate(method));
 
             if (methods.length >=1) {
-                $('#methods').addClass('btn-group').
-                    children('.dropdown-toggle').show();
-
-                var methods_list = $.map(methods, function (method, _) {
-                    return "<li>" + SS.decorate(method) + "</li>";
-                }).join('');
-
-                $('#methods .dropdown-menu').html(methods_list);
+                $('#methods')
+                .append
+                (
+                    $('<button/>')
+                    .attr('type', 'button')
+                    .addClass("btn btn-primary dropdown-toggle col-md-1")
+                    .attr('data-toggle', 'dropdown')
+                    .append
+                    (
+                        $('<span/>')
+                        .addClass('caret')
+                    ),
+                    $('<ul/>')
+                    .addClass('dropdown-menu')
+                    .append
+                    (
+                        $.map(methods, function (method) {
+                            return $('<li/>').html(SS.decorate(method));
+                        })
+                    )
+                );
+
+                $('#method')
+                .removeClass('col-md-12').addClass('col-md-11');
             }
 
             // jiggle
-            $("#methods").effect("bounce", { times:5, direction: 'left', distance: 12 }, 120);
+            $("#methods").wiggle();
         }
     });
 
-    $('#methods .dropdown-menu').click(function (event) {
-        // The list of possible blast methods is dynamically generated.  So we
-        // leverage event bubbling to trap 'click' event on the list items.
-        var clicked = $(event.target);
+    // The list of possible blast methods is dynamically generated.  So we
+    // leverage event bubbling and delegation to trap 'click' event on the list items.
+    // Please see : http://api.jquery.com/on/#direct-and-delegated-events
+    $(document).on("click", "#methods .dropdown-menu li", function(event) {
+        var clicked = $(this);
         var mbutton = $('#method');
-
         var old_method = mbutton.text();
         var new_method = clicked.text();
 
-        //swap
+        // swap
         clicked.html(SS.decorate(old_method));
         mbutton.val(new_method).html(SS.decorate(new_method));
 
         // jiggle
-        $("#methods").effect("bounce", { times:5, direction: 'left', distance: 12 }, 120);
+        $("#methods").wiggle();
     });
 
-    $("input#advanced").enablePlaceholder({"withPlaceholderClass": "greytext"});
-    $("textarea#sequence").enablePlaceholder({"withPlaceholderClass": "greytext"});
+    // HACK to allow users to select names from hit headers
+    $('.result').on('mousedown', ".hitn > .page-header > h4", function (event) {
+        var $this = $(this);
+        $this.on('mouseup mousemove', function handler(event) {
+            if (event.type === 'mouseup') {
+                // user wants to toggle
+                $this.attr('data-toggle', 'collapse');
+                $this.find('.fa-chevron-down').toggleClass('fa-rotate-270');
+            } else {
+                // user wants to select
+                $this.attr('data-toggle', '');
+            }
+            $this.off('mouseup mousemove', handler);
+        });
+    });
 
-    $('.advanced pre').hover(function () {
-        $(this).addClass('hover-focus');
-    },
-    function () {
-        $(this).removeClass('hover-focus');
+    $('.result').on('click', '.view-sequence', function (event) {
+        event.preventDefault();
+        event.stopPropagation();
+        if (!event.target.disabled)
+            SS.showSequenceViewer(event.target);
+    });
+
+    $(document).on('change', '.hit-links :checkbox', function (event) {
+        event.stopPropagation();
+        SS.selectHit(this);
     });
 
+
     $('#blast').submit(function(){
         //parse AJAX URL
         var action = $(this).attr('action');
@@ -222,14 +679,8 @@ $(document).ready(function(){
         // reset hash so we can always _jump_ back to result
         location.hash = '';
 
-        // display a modal window and attach an activity spinner to it
+        // show activity spinner
         $('#spinner').modal();
-        $('#spinner > div').activity({
-           segments: 8,
-           length:   40,
-           width:    16,
-           speed:    1.8
-        });
 
         // BLAST now
         var data = ($(this).serialize() + '&method=' + $('#method').val());
@@ -238,67 +689,40 @@ $(document).ready(function(){
             // BLASTed successfully
 
             // display the result
-            $('.results').show();
-            $('#result').html(data);
-
-            $('#blast').addClass('detached-bottom');
-            $('#underbar').addClass('detached-top');
+            $('.result').html(data).show();
+
+            // affix sidebar
+            var $sidebar = $('.sidebar');
+            if ($sidebar.length !== 0) {
+                $sidebar.affix({
+                    offset: {
+                        top: $sidebar.offset().top
+                    }
+                })
+                .width($sidebar.width());
+            }
 
             //jump to the results
             location.hash = hash;
 
-            $('.resultn').
-                scrollspy({
-                    approach: screen.height / 4
-                }).
-                on('enter.scrollspy', function () {
-                    var id = $(this).attr('id');
-                    $(this).highlight();
-                    $('.index').find('a[href="#' + id + '"]').parent().highlight();
-
-                    return false;
-                }).
-                on('leave.scrollspy', function () {
-                    var id = $(this).attr('id');
-                    $(this).unhighlight();
-                    $('.index').find('a[href="#' + id + '"]').parent().unhighlight();
-
-                    return false;
-                });
-        }).
-          fail(function (jqXHR, status, error) {
-            //alert user
-            $("#error-type").text(error);
-            if(jqXHR.responseText == ''){
-              $("#error-message").text('Is the SequenceServer running? The JQuery status was \''+status+'\', and the JQuery error was \''+error+'\'.');
-            } else {
-              $("#error-message").text(jqXHR.responseText);
-            }
-            $("#error").modal();
-        }).
-          always(function () {
-            // BLAST complete (succefully or otherwise)
+            SS.generateGraphicalOverview();
+
+            SS.updateDownloadFastaOfAllLink();
+            SS.updateDownloadFastaOfSelectedLink();
+            SS.updateSequenceViewerLinks();
+            SS.setupTooltipsForPosLabels();
+
+            $('body').scrollspy({target: '.sidebar'});
 
-            // remove progress notification
-            $('#spinner > div').activity(false);
             $('#spinner').modal('hide');
+
+        }).
+          fail(function (jqXHR, status, error) {
+            SS.showErrorModal(jqXHR, function () {
+                $('#spinner').modal('hide');
+            });
         });
 
         return false;
     });
-
-    (function (store) {
-        try {
-            var visits = store.get('visits') || 0;
-            visits = visits + 1;
-            if (visits <= 10) {
-                store.set('visits', visits);
-
-                if (visits === 10) {
-                    $('#social').modal();
-                }
-            }
-        }
-        catch (e) {};
-    }(store));
 });