sequenceserver 0.8.2 → 0.8.3

data/public/css/custom.css

@@ -190,31 +190,6 @@ span.highlight {
   border: 1px solid transparent;
 }
 
-ul.index {
-  list-style: none;
-  position: fixed;
-  margin-left: 710px;
-  padding: 15px;
-  width: 200px;
-  top: 5px;
-}
-
-ul.index li {
-  padding: 3%;
-}
-
-ul.index li.focussed {
-  background-color: #08C;
-}
-
-ul.index li.focussed a {
-  color: white;
-  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2);
-}
-
-ul.index li:visited {
-}
-
 div.focussed {
   border: 1px solid black;
 }

data/public/js/sequenceserver.js

@@ -244,21 +244,9 @@ $(document).ready(function(){
             $('#blast').addClass('detached-bottom');
             $('#underbar').addClass('detached-top');
 
-            //generate index
-            $('.resultn').index({container: '.results'});
-
             //jump to the results
             location.hash = hash;
 
-            $('#result').
-                scrollspy().
-                on('enter.scrollspy', function () {
-                    $('.index').removeAttr('style');
-                }).
-                on('leave.scrollspy', function () {
-                    $('.index').css({position: 'absolute', top: $(this).offset().top});
-                });
-
             $('.resultn').
                 scrollspy({
                     approach: screen.height / 4
@@ -295,17 +283,6 @@ $(document).ready(function(){
         return false;
     });
 
-    $('.results').
-        on('add.index', function (event, index) {
-            // make way for index
-            $('#result').css({width: '660px'});
-
-            $(index).addClass('box');
-        }).
-        on('remove.index', function () {
-            $('#result').removeAttr('style');
-        });
-
     (function (store) {
         try {
             var visits = store.get('visits') || 0;

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.8.2'
+  s.version     = '0.8.3'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'

data/views/search.erb

@@ -14,7 +14,6 @@
   <script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.scrollspy.js') %>"></script>
-  <script type="text/javascript" src="<%= uri('/js/jquery.index.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/bootstrap.transition.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/bootstrap.dropdown.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/bootstrap.modal.js') %>"></script>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 0.8.2
+  version: 0.8.3
   prerelease: 
 platform: ruby
 authors:
@@ -11,11 +11,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-01 00:00:00.000000000 Z
+date: 2013-03-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &20416580 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -23,10 +23,15 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *20416580
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.0
 - !ruby/object:Gem::Dependency
   name: sinatra
-  requirement: &20398120 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -34,10 +39,15 @@ dependencies:
         version: 1.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *20398120
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: ptools
-  requirement: &20396840 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -45,10 +55,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *20396840
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: minitest
-  requirement: &20383420 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -56,10 +71,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *20383420
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rack-test
-  requirement: &20376580 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -67,7 +87,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *20376580
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: ! 'SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
   user interface for use locally or over the web.
 
@@ -78,51 +103,48 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- lib/sequenceserver.rb
-- lib/sequenceserver/database_formatter.rb
-- lib/sequenceserver/sequencehelpers.rb
+- lib/sequenceserver/blast.rb
 - lib/sequenceserver/customisation.rb
+- lib/sequenceserver/database.rb
+- lib/sequenceserver/database_formatter.rb
 - lib/sequenceserver/helpers.rb
+- lib/sequenceserver/sequencehelpers.rb
 - lib/sequenceserver/sinatralikeloggerformatter.rb
-- lib/sequenceserver/blast.rb
-- lib/sequenceserver/web_blast/public/favicon.ico
-- lib/sequenceserver/web_blast/public/js/sequenceserver.sequence-viewer.js
 - lib/sequenceserver/version.rb
-- lib/sequenceserver/database.rb
-- views/search.erb
+- lib/sequenceserver.rb
 - views/500.erb
 - views/_options.erb
-- public/img/glyphicons-halflings-white.png
-- public/img/glyphicons-halflings.png
+- views/search.erb
+- public/css/bootstrap.dropdown.css
 - public/css/bootstrap.icons.css
-- public/css/bootstrap.modal.css
 - public/css/bootstrap.min.css
-- public/css/bootstrap.dropdown.css
+- public/css/bootstrap.modal.css
 - public/css/custom.css
-- public/js/jquery.js
-- public/js/jquery.enablePlaceholder.min.js
-- public/js/bootstrap.transition.js
-- public/js/jquery.ui.js
-- public/js/bootstrap.modal.js
+- public/img/glyphicons-halflings-white.png
+- public/img/glyphicons-halflings.png
 - public/js/bootstrap.dropdown.js
-- public/js/jquery.index.js
-- public/js/store.min.js
-- public/js/sequenceserver.js
+- public/js/bootstrap.modal.js
+- public/js/bootstrap.transition.js
 - public/js/jquery.activity.js
-- public/js/sequenceserver.blast.js
+- public/js/jquery.enablePlaceholder.min.js
+- public/js/jquery.js
 - public/js/jquery.scrollspy.js
-- tests/test_sequencehelpers.rb
-- tests/test_sequenceserver_blast.rb
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
+- public/js/jquery.ui.js
+- public/js/sequenceserver.blast.js
+- public/js/sequenceserver.js
+- public/js/store.min.js
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
-- tests/ui.specs.todo
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
 - tests/run
+- tests/test_sequencehelpers.rb
+- tests/test_sequenceserver_blast.rb
+- tests/ui.specs.todo
 - config.ru
 - example.config.yml
 - LICENSE.txt
@@ -130,8 +152,7 @@ files:
 - README.txt
 - Gemfile
 - sequenceserver.gemspec
-- !binary |-
-  YmluL3NlcXVlbmNlc2VydmVy
+- bin/sequenceserver
 homepage: http://sequenceserver.com
 licenses:
 - SequenceServer (custom)
@@ -156,7 +177,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: BLAST search made easy!

data/lib/sequenceserver/web_blast/public/js/sequenceserver.sequence-viewer.js

@@ -1,83 +0,0 @@
-/*global SS*/
-
-/*
-    Sequence viewer:  given URL of a sequence, use Bootstrap Modal to load that
-    sequence from the server and present it to the users.
-*/
-SS.sequence_viewer = (function () {
-
-    var sequence_viewer = $('#sequence-viewer').modal({ show: false });
-
-    var _object = {};
-
-    _object.download_link = function (value) {
-
-        var element = sequence_viewer.find('#download_link');
-
-        if (value) {
-            element.attr('href', value);
-            return this;
-        }
-        else {
-            return element;
-        }
-    };
-
-    _object.sequences = function (value) {
-
-        var element = sequence_viewer.find('#sequences');
-
-        if (value) {
-            element.html(value);
-            return this;
-        }
-        else {
-            return element;
-        }
-    };
-
-    _object.show = function () {
-
-        sequence_viewer.modal('show');
-    };
-
-    _object.dismiss = function () {
-
-        sequence_viewer.modal('hide');
-    };
-
-    _object.render = function (sequence, download_link) {
-
-        this.sequence(sequence);
-        this.download_link(download_link);
-        this.show();
-    };
-
-    _object.load = function (sequence) {
-        var url  = sequence.attr('href');
-        var ddl  = sequence.attr('data-download');
-
-        var render  = $.proxy(_object, render);
-        $.get(url)
-        .done(function (sequence) {
-            render(sequence, ddl);
-        })
-        .failure(function (jqXHR) {
-            if (!jqXHR.responseText) {
-                $("#error-no-response").modal();
-            }
-        });
-    };
-
-    return function () {
-        function F() {}
-        F.protoype = _object;
-        return new F();
-    };
-}());
-
-//sequence_viewer.download_link().on('click', function (event) {
-    //this.dismiss();
-    //return true;
-//});
-

data/public/js/jquery.index.js

@@ -1,67 +0,0 @@
-;(function ($) {
-    var defaults = {
-        threshold: 1
-    };
-
-    /*
-        Generate an index from the selected elements and add to or replace it
-        in the given container element.
-
-        Events:
-
-            add.index:
-
-                After the index has been created and added to the container.
-
-            remove.index:
-
-                When an index on the selected element is removed.
-
-        Options:
-
-            threshold:
-
-                Maximum number of elements selected with 'map' for which no
-                index is to be created.  Or the index should be deleted if
-                already exists.
-
-            container:
-
-                A jQuery selector.  The index is appended to or deleted from
-                the container.
-
-        Usage:
-
-            $('.resultn').index({container: '.results'})
-
-    */
-    $.fn.index = function (options) {
-        var options   = $.extend({}, defaults, options);
-        var container = $(options.container);
-
-        if (this.length > options.threshold) {
-            var entries = this.map(function () {
-                var id  = $(this).attr('id');
-                var sid = (id.length > 25) ? (id.slice(0, 22) + ' ...') : id // sid => short/display id :P
-                return '<li><a href="#' + id + '" title="' + id + '">' + sid + '</a></li>';
-            });
-
-            var index = $('<ul class="index">' + entries.get().join('') + '</ul>');
-
-            // remove previous index if any
-            container.find('.index').remove();
-            container.trigger('remove.index');
-
-            // add the new one
-            container.append(index);
-            container.trigger('add.index', index);
-        }
-        else {
-            // remove previous index if any
-            container.find('.index').remove();
-            container.trigger('remove.index');
-        }
-
-        return this;
-    }
-})(jQuery);