sequenceserver 2.0.0.rc8 → 2.0.0
Sign up to get free protection for your applications and to get access to all the features.
Potentially problematic release.
This version of sequenceserver might be problematic. Click here for more details.
- checksums.yaml +4 -4
- data/bin/sequenceserver +22 -30
- data/lib/sequenceserver/api_errors.rb +5 -1
- data/lib/sequenceserver/blast/constants.rb +1 -1
- data/lib/sequenceserver/blast/hit.rb +5 -16
- data/lib/sequenceserver/blast/job.rb +9 -18
- data/lib/sequenceserver/blast/report.rb +5 -3
- data/lib/sequenceserver/config.rb +4 -1
- data/lib/sequenceserver/database.rb +69 -9
- data/lib/sequenceserver/job.rb +1 -1
- data/lib/sequenceserver/makeblastdb.rb +40 -45
- data/lib/sequenceserver/routes.rb +4 -0
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver.rb +15 -11
- data/public/config.js +143 -142
- data/public/css/fonts.css +23 -22
- data/public/css/grapher.css +598 -594
- data/public/css/sequenceserver.css +86 -24
- data/public/css/sequenceserver.min.css +2 -2
- data/public/js/alignment_exporter.js +14 -14
- data/public/js/databases_tree.js +215 -0
- data/public/js/download_fasta.js +1 -1
- data/public/js/hit.js +6 -2
- data/public/js/hits_overview.js +1 -1
- data/public/js/length_distribution.js +5 -5
- data/public/js/query.js +4 -7
- data/public/js/report.js +12 -24
- data/public/js/search.js +21 -2
- data/public/js/sidebar.js +4 -4
- data/public/js/svgExporter.js +12 -12
- data/public/js/visualisation_helpers.js +4 -5
- data/public/sequenceserver-report.min.js +11 -11
- data/public/sequenceserver-search.min.js +15 -11
- data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
- data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
- data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
- data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
- data/public/vendor/system-csp-production.js +3 -3
- data/public/vendor/system-csp-production.js.map +1 -1
- data/public/vendor/system-csp-production.src.js +146 -140
- data/public/vendor/system-polyfills.js.map +1 -1
- data/public/vendor/system-polyfills.src.js +1 -0
- data/public/vendor/system.js +3 -3
- data/public/vendor/system.js.map +1 -1
- data/public/vendor/system.src.js +4771 -2383
- data/views/_options.erb +21 -0
- data/views/layout.erb +17 -18
- metadata +102 -43
- data/bin/chromedriver +0 -0
- data/bin/geckodriver +0 -0
- data/public/shims/form-core.js +0 -3
- data/public/shims/form-validation.js +0 -3
- data/public/shims/plugins/jquery.ui.position.js +0 -13
- data/public/shims/styles/shim.css +0 -1
@@ -0,0 +1,122 @@
|
|
1
|
+
/**
|
2
|
+
* ### Wholerow plugin
|
3
|
+
*
|
4
|
+
* Makes each node appear block level. Making selection easier. May cause slow down for large trees in old browsers.
|
5
|
+
*/
|
6
|
+
/*globals jQuery, define, exports, require */
|
7
|
+
(function (factory) {
|
8
|
+
"use strict";
|
9
|
+
if (typeof define === 'function' && define.amd) {
|
10
|
+
define('jstree.wholerow', ['jquery','jstree'], factory);
|
11
|
+
}
|
12
|
+
else if(typeof exports === 'object') {
|
13
|
+
factory(require('jquery'), require('jstree'));
|
14
|
+
}
|
15
|
+
else {
|
16
|
+
factory(jQuery, jQuery.jstree);
|
17
|
+
}
|
18
|
+
}(function ($, jstree, undefined) {
|
19
|
+
"use strict";
|
20
|
+
|
21
|
+
if($.jstree.plugins.wholerow) { return; }
|
22
|
+
|
23
|
+
var div = document.createElement('DIV');
|
24
|
+
div.setAttribute('unselectable','on');
|
25
|
+
div.setAttribute('role','presentation');
|
26
|
+
div.className = 'jstree-wholerow';
|
27
|
+
div.innerHTML = ' ';
|
28
|
+
$.jstree.plugins.wholerow = function (options, parent) {
|
29
|
+
this.bind = function () {
|
30
|
+
parent.bind.call(this);
|
31
|
+
|
32
|
+
this.element
|
33
|
+
.on('ready.jstree set_state.jstree', $.proxy(function () {
|
34
|
+
this.hide_dots();
|
35
|
+
}, this))
|
36
|
+
.on("init.jstree loading.jstree ready.jstree", $.proxy(function () {
|
37
|
+
//div.style.height = this._data.core.li_height + 'px';
|
38
|
+
this.get_container_ul().addClass('jstree-wholerow-ul');
|
39
|
+
}, this))
|
40
|
+
.on("deselect_all.jstree", $.proxy(function (e, data) {
|
41
|
+
this.element.find('.jstree-wholerow-clicked').removeClass('jstree-wholerow-clicked');
|
42
|
+
}, this))
|
43
|
+
.on("changed.jstree", $.proxy(function (e, data) {
|
44
|
+
this.element.find('.jstree-wholerow-clicked').removeClass('jstree-wholerow-clicked');
|
45
|
+
var tmp = false, i, j;
|
46
|
+
for(i = 0, j = data.selected.length; i < j; i++) {
|
47
|
+
tmp = this.get_node(data.selected[i], true);
|
48
|
+
if(tmp && tmp.length) {
|
49
|
+
tmp.children('.jstree-wholerow').addClass('jstree-wholerow-clicked');
|
50
|
+
}
|
51
|
+
}
|
52
|
+
}, this))
|
53
|
+
.on("open_node.jstree", $.proxy(function (e, data) {
|
54
|
+
this.get_node(data.node, true).find('.jstree-clicked').parent().children('.jstree-wholerow').addClass('jstree-wholerow-clicked');
|
55
|
+
}, this))
|
56
|
+
.on("hover_node.jstree dehover_node.jstree", $.proxy(function (e, data) {
|
57
|
+
if(e.type === "hover_node" && this.is_disabled(data.node)) { return; }
|
58
|
+
this.get_node(data.node, true).children('.jstree-wholerow')[e.type === "hover_node"?"addClass":"removeClass"]('jstree-wholerow-hovered');
|
59
|
+
}, this))
|
60
|
+
.on("contextmenu.jstree", ".jstree-wholerow", $.proxy(function (e) {
|
61
|
+
if (this._data.contextmenu) {
|
62
|
+
e.preventDefault();
|
63
|
+
var tmp = $.Event('contextmenu', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey, pageX : e.pageX, pageY : e.pageY });
|
64
|
+
$(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp);
|
65
|
+
}
|
66
|
+
}, this))
|
67
|
+
/*!
|
68
|
+
.on("mousedown.jstree touchstart.jstree", ".jstree-wholerow", function (e) {
|
69
|
+
if(e.target === e.currentTarget) {
|
70
|
+
var a = $(e.currentTarget).closest(".jstree-node").children(".jstree-anchor");
|
71
|
+
e.target = a[0];
|
72
|
+
a.trigger(e);
|
73
|
+
}
|
74
|
+
})
|
75
|
+
*/
|
76
|
+
.on("click.jstree", ".jstree-wholerow", function (e) {
|
77
|
+
e.stopImmediatePropagation();
|
78
|
+
var tmp = $.Event('click', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey });
|
79
|
+
$(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp).focus();
|
80
|
+
})
|
81
|
+
.on("dblclick.jstree", ".jstree-wholerow", function (e) {
|
82
|
+
e.stopImmediatePropagation();
|
83
|
+
var tmp = $.Event('dblclick', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey });
|
84
|
+
$(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp).focus();
|
85
|
+
})
|
86
|
+
.on("click.jstree", ".jstree-leaf > .jstree-ocl", $.proxy(function (e) {
|
87
|
+
e.stopImmediatePropagation();
|
88
|
+
var tmp = $.Event('click', { metaKey : e.metaKey, ctrlKey : e.ctrlKey, altKey : e.altKey, shiftKey : e.shiftKey });
|
89
|
+
$(e.currentTarget).closest(".jstree-node").children(".jstree-anchor").first().trigger(tmp).focus();
|
90
|
+
}, this))
|
91
|
+
.on("mouseover.jstree", ".jstree-wholerow, .jstree-icon", $.proxy(function (e) {
|
92
|
+
e.stopImmediatePropagation();
|
93
|
+
if(!this.is_disabled(e.currentTarget)) {
|
94
|
+
this.hover_node(e.currentTarget);
|
95
|
+
}
|
96
|
+
return false;
|
97
|
+
}, this))
|
98
|
+
.on("mouseleave.jstree", ".jstree-node", $.proxy(function (e) {
|
99
|
+
this.dehover_node(e.currentTarget);
|
100
|
+
}, this));
|
101
|
+
};
|
102
|
+
this.teardown = function () {
|
103
|
+
if(this.settings.wholerow) {
|
104
|
+
this.element.find(".jstree-wholerow").remove();
|
105
|
+
}
|
106
|
+
parent.teardown.call(this);
|
107
|
+
};
|
108
|
+
this.redraw_node = function(obj, deep, callback, force_render) {
|
109
|
+
obj = parent.redraw_node.apply(this, arguments);
|
110
|
+
if(obj) {
|
111
|
+
var tmp = div.cloneNode(true);
|
112
|
+
//tmp.style.height = this._data.core.li_height + 'px';
|
113
|
+
if($.inArray(obj.id, this._data.core.selected) !== -1) { tmp.className += ' jstree-wholerow-clicked'; }
|
114
|
+
if(this._data.core.focused && this._data.core.focused === obj.id) { tmp.className += ' jstree-wholerow-hovered'; }
|
115
|
+
obj.insertBefore(tmp, obj.childNodes[0]);
|
116
|
+
}
|
117
|
+
return obj;
|
118
|
+
};
|
119
|
+
};
|
120
|
+
// include the wholerow plugin by default
|
121
|
+
// $.jstree.defaults.plugins.push("wholerow");
|
122
|
+
}));
|