sequenceserver 2.0.0.beta4 → 2.0.0.rc1
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- checksums.yaml +4 -4
- data/.travis.yml +7 -4
- data/AppImage/sequenceserver.sh +5 -0
- data/lib/sequenceserver.rb +9 -5
- data/lib/sequenceserver/blast/job.rb +7 -24
- data/lib/sequenceserver/blast/report.rb +66 -33
- data/lib/sequenceserver/routes.rb +28 -2
- data/lib/sequenceserver/version.rb +1 -1
- data/public/SequenceServer_logo.png +0 -0
- data/public/css/grapher.css +8 -15
- data/public/css/sequenceserver.css +115 -55
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/circos.js +1 -1
- data/public/js/download_fasta.js +17 -0
- data/public/js/grapher.js +7 -9
- data/public/js/hit.js +217 -0
- data/public/js/hits_overview.js +12 -13
- data/public/js/hsp.js +104 -84
- data/public/js/{sequenceserver.js → jquery_world.js} +1 -18
- data/public/js/kablammo.js +337 -334
- data/public/js/length_distribution.js +1 -1
- data/public/js/query.js +147 -0
- data/public/js/report.js +203 -830
- data/public/js/search.js +176 -169
- data/public/js/sequence_modal.js +167 -0
- data/public/js/sidebar.js +210 -0
- data/public/js/utils.js +2 -19
- data/public/js/visualisation_helpers.js +2 -2
- data/public/sequenceserver-report.min.js +19 -19
- data/public/sequenceserver-search.min.js +11 -11
- data/public/vendor/github/twbs/bootstrap@3.3.5/js/bootstrap.js +2 -2
- data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +5 -5
- data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +5 -5
- data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +5 -5
- data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +5 -5
- data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +5 -5
- data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +5 -5
- data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +5 -5
- data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +5 -5
- data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +5 -5
- data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +2 -2
- data/spec/capybara_spec.rb +1 -1
- data/views/layout.erb +1 -1
- metadata +9 -3
data/public/js/search.js
CHANGED
@@ -1,6 +1,6 @@
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-
import
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2
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-
import _ from 'underscore';
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+
import './jquery_world';
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import React from 'react';
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import _ from 'underscore';
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/**
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* Load necessary polyfills.
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@@ -20,7 +20,7 @@ var Page = React.createClass({
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componentDidMount: function () {
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this.refs.dnd.setState({
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query: this.refs.form.refs.query
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})
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});
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}
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});
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@@ -31,14 +31,14 @@ var DnD = React.createClass({
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getInitialState: function () {
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return {
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query: null
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}
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};
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},
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render: function () {
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return (
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<div
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className="dnd-overlay"
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-
style={{display:
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+
style={{display: 'none'}}>
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<div
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className="container dnd-overlay-container">
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<div
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@@ -47,15 +47,15 @@ var DnD = React.createClass({
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className="col-md-offset-2 col-md-10">
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<p
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className="dnd-overlay-drop"
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-
style={{display:
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+
style={{display: 'none'}}>
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<i className="fa fa-2x fa-file-o"></i>
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Drop query sequence file here
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</p>
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<p
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className="dnd-overlay-overwrite"
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-
style={{display:
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+
style={{display: 'none'}}>
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<i className="fa fa-2x fa-file-o"></i>
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<span style={{color:
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<span style={{color: 'red'}}>Overwrite</span> query sequence file
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</p>
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<div
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@@ -63,7 +63,7 @@ var DnD = React.createClass({
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<div
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className="dnd-error row"
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id="dnd-multi-notification"
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-
style={{display:
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+
style={{display: 'none'}}>
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<div
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className="col-md-6 col-md-offset-3">
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One file at a time please.
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@@ -73,7 +73,7 @@ var DnD = React.createClass({
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<div
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className="dnd-error row"
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id="dnd-large-file-notification"
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-
style={{display:
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+
style={{display: 'none'}}>
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<div
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className="col-md-6 col-md-offset-3">
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Too big a file. Can only do less than 10 MB. >_<
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@@ -83,7 +83,7 @@ var DnD = React.createClass({
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<div
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className="dnd-error row"
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id="dnd-format-notification"
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-
style={{display:
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+
style={{display: 'none'}}>
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<div
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className="col-md-6 col-md-offset-3">
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Only FASTA files please.
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@@ -99,6 +99,7 @@ var DnD = React.createClass({
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componentDidMount: function () {
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var self = this;
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+
var FASTA_FORMAT = /^>/;
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$(document).ready(function(){
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var tgtMarker = $('.dnd-overlay');
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@@ -110,80 +111,80 @@ var DnD = React.createClass({
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};
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$(document)
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-
|
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+
.on('dragenter', function (evt) {
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// Do not activate DnD if a modal is active.
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-
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+
if ($.modalActive()) return;
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-
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-
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-
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-
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+
// Based on http://stackoverflow.com/a/8494918/1205465.
|
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+
// Contrary to what the above link says, the snippet below can't
|
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+
// distinguish directories from files. We handle that on drop.
|
121
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+
var dt = evt.originalEvent.dataTransfer;
|
122
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+
var isFile = dt.types && ((dt.types.indexOf && // Chrome and Safari
|
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dt.types.indexOf('Files') != -1) ||
|
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(dt.types.contains && // Firefox
|
124
125
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dt.types.contains('application/x-moz-file')));
|
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-
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+
if (!isFile) { return; }
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-
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-
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-
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-
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+
$('.dnd-error').hide();
|
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+
tgtMarker.stop(true, true);
|
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+
tgtMarker.show();
|
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+
dt.effectAllowed = 'copy';
|
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+
if (self.state.query.isEmpty()) {
|
134
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+
$('.dnd-overlay-overwrite').hide();
|
135
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+
$('.dnd-overlay-drop').show('drop', {direction: 'down'}, 'fast');
|
136
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+
}
|
137
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+
else {
|
138
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+
$('.dnd-overlay-drop').hide();
|
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+
$('.dnd-overlay-overwrite').show('drop', {direction: 'down'}, 'fast');
|
140
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+
}
|
141
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+
})
|
142
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+
.on('dragleave', '.dnd-overlay', function (evt) {
|
143
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+
tgtMarker.hide();
|
137
144
|
$('.dnd-overlay-drop').hide();
|
138
|
-
$('.dnd-overlay-overwrite').
|
139
|
-
}
|
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-
|
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-
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-
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-
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-
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-
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155
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-
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156
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-
|
157
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-
var files = evt.originalEvent.dataTransfer.files;
|
158
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-
if (files.length > 1) {
|
159
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-
dndError('dnd-multi');
|
160
|
-
return;
|
161
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-
}
|
145
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+
$('.dnd-overlay-overwrite').hide();
|
146
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+
})
|
147
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+
.on('dragover', '.dnd-overlay', function (evt) {
|
148
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+
evt.originalEvent.dataTransfer.dropEffect = 'copy';
|
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+
evt.preventDefault();
|
150
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+
})
|
151
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+
.on('drop', '.dnd-overlay', function (evt) {
|
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+
evt.preventDefault();
|
153
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+
evt.stopPropagation();
|
154
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+
|
155
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+
var indicator = $('#sequence-file');
|
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+
self.state.query.focus();
|
157
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+
|
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+
var files = evt.originalEvent.dataTransfer.files;
|
159
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+
if (files.length > 1) {
|
160
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+
dndError('dnd-multi');
|
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+
return;
|
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}
|
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-
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-
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-
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166
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-
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-
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+
var file = files[0];
|
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+
if (file.size > 10 * 1048576) {
|
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+
dndError('dnd-large-file');
|
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+
return;
|
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+
}
|
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-
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-
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var reader = new FileReader();
|
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+
reader.onload = function (e) {
|
172
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+
var content = e.target.result;
|
173
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+
if (FASTA_FORMAT.test(content)) {
|
174
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+
indicator.text(file.name + ' ');
|
175
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+
self.state.query.value(content);
|
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+
tgtMarker.hide();
|
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} else {
|
177
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// apparently not FASTA
|
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-
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179
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-
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-
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-
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dndError('dnd-format');
|
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}
|
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};
|
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reader.onerror = function (e) {
|
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// Couldn't read. Means dropped stuff wasn't FASTA file.
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-
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-
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dndError('dnd-format');
|
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};
|
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reader.readAsText(file);
|
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});
|
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});
|
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}
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});
|
@@ -203,32 +204,39 @@ var Form = React.createClass({
|
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203
204
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componentDidMount: function () {
|
204
205
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/* Fetch data to initialise the search interface from the server. These
|
205
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* include list of databases to search against, advanced options to
|
206
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-
* apply when an algorithm is selected, and a query
|
207
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+
* apply when an algorithm is selected, and a query sequence that
|
207
208
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* the user may want to search in the databases.
|
208
209
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*/
|
209
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-
|
210
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+
var search = location.search.split(/\?|&/).filter(Boolean);
|
211
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+
var job_id = sessionStorage.getItem('job_id');
|
212
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+
if (job_id) {
|
213
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+
search.unshift(`job_id=${job_id}`);
|
214
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+
}
|
215
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+
$.getJSON(`searchdata.json?${search.join('&')}`, function(data) {
|
210
216
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/* Update form state (i.e., list of databases and predefined
|
211
217
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* advanced options.
|
212
218
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*/
|
213
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this.setState({
|
214
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-
databases: data[
|
220
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+
databases: data['database'],
|
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+
preSelectedDbs: data['preSelectedDbs'],
|
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+
preDefinedOpts: data['options']
|
215
223
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});
|
216
224
|
|
217
225
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/* Pre-populate the form with server sent query sequences
|
218
226
|
* (if any).
|
219
227
|
*/
|
220
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-
if (data[
|
221
|
-
this.refs.query.value(data[
|
228
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+
if (data['query']) {
|
229
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+
this.refs.query.value(data['query']);
|
222
230
|
}
|
223
231
|
}.bind(this));
|
224
232
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|
225
233
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/* Enable submitting form on Cmd+Enter */
|
226
|
-
|
227
|
-
|
234
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+
$(document).bind('keydown', _.bind(function (e) {
|
235
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+
if (e.ctrlKey && e.keyCode === 13 &&
|
228
236
|
!$('#method').is(':disabled')) {
|
229
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-
|
230
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-
|
231
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-
|
237
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+
$(this.getDOMNode()).trigger('submit');
|
238
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+
}
|
239
|
+
}, this));
|
232
240
|
},
|
233
241
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|
234
242
|
determineBlastMethod: function () {
|
@@ -241,26 +249,26 @@ var Form = React.createClass({
|
|
241
249
|
|
242
250
|
//database type is always known
|
243
251
|
switch (database_type) {
|
252
|
+
case 'protein':
|
253
|
+
switch (sequence_type) {
|
254
|
+
case undefined:
|
255
|
+
return ['blastp', 'blastx'];
|
244
256
|
case 'protein':
|
245
|
-
|
246
|
-
case undefined:
|
247
|
-
return ['blastp', 'blastx'];
|
248
|
-
case 'protein':
|
249
|
-
return ['blastp'];
|
250
|
-
case 'nucleotide':
|
251
|
-
return ['blastx'];
|
252
|
-
}
|
253
|
-
break;
|
257
|
+
return ['blastp'];
|
254
258
|
case 'nucleotide':
|
255
|
-
|
256
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-
|
257
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-
|
258
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-
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259
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-
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260
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-
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261
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-
|
262
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-
|
263
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-
|
259
|
+
return ['blastx'];
|
260
|
+
}
|
261
|
+
break;
|
262
|
+
case 'nucleotide':
|
263
|
+
switch (sequence_type) {
|
264
|
+
case undefined:
|
265
|
+
return ['tblastn', 'blastn', 'tblastx'];
|
266
|
+
case 'protein':
|
267
|
+
return ['tblastn'];
|
268
|
+
case 'nucleotide':
|
269
|
+
return ['blastn', 'tblastx'];
|
270
|
+
}
|
271
|
+
break;
|
264
272
|
}
|
265
273
|
|
266
274
|
return [];
|
@@ -285,35 +293,32 @@ var Form = React.createClass({
|
|
285
293
|
},
|
286
294
|
|
287
295
|
handleAlgoChanged: function (algo) {
|
288
|
-
|
289
|
-
|
290
|
-
|
291
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-
|
292
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-
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293
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-
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294
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-
|
295
|
-
|
296
|
+
if (this.state.preDefinedOpts.hasOwnProperty(algo)) {
|
297
|
+
this.refs.opts.setState({
|
298
|
+
preOpts: this.state.preDefinedOpts[algo].join(' ')
|
299
|
+
});
|
300
|
+
}
|
301
|
+
else {
|
302
|
+
this.refs.opts.setState({preOpts: ''});
|
303
|
+
}
|
296
304
|
},
|
297
305
|
|
298
306
|
render: function () {
|
299
307
|
return (
|
300
|
-
<div
|
301
|
-
className="
|
302
|
-
|
303
|
-
id="blast" method="post" className="form-horizontal">
|
304
|
-
<div
|
305
|
-
className="form-group query-container">
|
308
|
+
<div className="container">
|
309
|
+
<form id="blast" method="post" className="form-horizontal">
|
310
|
+
<div className="form-group query-container">
|
306
311
|
<Query ref="query" onSequenceTypeChanged={this.handleSequenceTypeChanged}/>
|
307
312
|
</div>
|
308
|
-
<div
|
309
|
-
className="notifications" id="notifications">
|
313
|
+
<div className="notifications" id="notifications">
|
310
314
|
<NucleotideNotification/>
|
311
315
|
<ProteinNotification/>
|
312
316
|
<MixedNotification/>
|
313
317
|
</div>
|
314
|
-
<Databases ref="databases"
|
315
|
-
|
316
|
-
|
318
|
+
<Databases ref="databases" databases={this.state.databases}
|
319
|
+
preSelectedDbs={this.state.preSelectedDbs}
|
320
|
+
onDatabaseTypeChanged={this.handleDatabaseTypeChanaged} />
|
321
|
+
<div className="form-group">
|
317
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<Options ref="opts"/>
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<SearchButton ref="button" onAlgoChanged={this.handleAlgoChanged}/>
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</div>
|
@@ -346,7 +351,7 @@ var Query = React.createClass({
|
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351
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else {
|
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this.setState({
|
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value: val
|
349
|
-
})
|
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+
});
|
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return this;
|
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}
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},
|
@@ -451,12 +456,12 @@ var Query = React.createClass({
|
|
451
456
|
if (!tmp) { continue; }
|
452
457
|
|
453
458
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if (!type) {
|
454
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-
|
455
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-
|
459
|
+
// successfully guessed the type of atleast one sequence
|
460
|
+
type = tmp;
|
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461
|
}
|
457
462
|
else if (tmp !== type) {
|
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-
|
459
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-
|
463
|
+
// user has mixed different type of sequences
|
464
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+
return 'mixed';
|
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|
}
|
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466
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}
|
462
467
|
|
@@ -511,7 +516,7 @@ var Query = React.createClass({
|
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516
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// Lifecycle methods. //
|
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|
|
513
518
|
getInitialState: function () {
|
514
|
-
var input_sequence = $(
|
519
|
+
var input_sequence = $('input#input_sequence').val() || '';
|
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520
|
return {
|
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|
value: input_sequence
|
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};
|
@@ -619,10 +624,7 @@ var MixedNotification = React.createClass({
|
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619
624
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|
620
625
|
var Databases = React.createClass({
|
621
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|
getInitialState: function () {
|
622
|
-
return {
|
623
|
-
type: '',
|
624
|
-
databases: []
|
625
|
-
}
|
627
|
+
return { type: '' };
|
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|
},
|
627
629
|
|
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630
|
databases: function (category) {
|
@@ -631,9 +633,9 @@ var Databases = React.createClass({
|
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631
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|
}
|
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|
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|
return _.select(this.props.databases,
|
634
|
-
|
635
|
-
|
636
|
-
|
636
|
+
function (database) {
|
637
|
+
return database.type === category;
|
638
|
+
});
|
637
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|
},
|
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640
|
|
639
641
|
nselected: function () {
|
@@ -642,7 +644,7 @@ var Databases = React.createClass({
|
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642
644
|
|
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|
categories: function () {
|
644
646
|
return _.uniq(_.map(this.props.databases,
|
645
|
-
|
647
|
+
_.iteratee('type'))).sort();
|
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648
|
},
|
647
649
|
|
648
650
|
handleClick: function (database) {
|
@@ -652,12 +654,12 @@ var Databases = React.createClass({
|
|
652
654
|
|
653
655
|
handleToggle: function (toggleState, type) {
|
654
656
|
switch (toggleState) {
|
655
|
-
|
656
|
-
|
657
|
-
|
658
|
-
|
659
|
-
|
660
|
-
|
657
|
+
case '[Select all]':
|
658
|
+
$(`.${type} .database input:not(:checked)`).click();
|
659
|
+
break;
|
660
|
+
case '[Deselect all]':
|
661
|
+
$(`.${type} .database input:checked`).click();
|
662
|
+
break;
|
661
663
|
}
|
662
664
|
},
|
663
665
|
|
@@ -672,13 +674,13 @@ var Databases = React.createClass({
|
|
672
674
|
renderDatabases: function (category) {
|
673
675
|
// Panel name and column width.
|
674
676
|
var panelTitle = category[0].toUpperCase() +
|
675
|
-
category.substring(1).toLowerCase() +
|
677
|
+
category.substring(1).toLowerCase() + ' databases';
|
676
678
|
var columnClass = this.categories().length === 1 ? 'col-md-12' :
|
677
679
|
'col-md-6';
|
678
680
|
|
679
681
|
// Toggle button.
|
680
682
|
var toggleState = '[Select all]';
|
681
|
-
var toggleClass = 'btn
|
683
|
+
var toggleClass = 'btn-link';
|
682
684
|
var toggleShown = this.databases(category).length > 1 ;
|
683
685
|
var toggleDisabled = this.state.type && this.state.type !== category;
|
684
686
|
if (toggleShown && toggleDisabled) toggleClass += ' disabled';
|
@@ -689,20 +691,20 @@ var Databases = React.createClass({
|
|
689
691
|
|
690
692
|
// JSX.
|
691
693
|
return (
|
692
|
-
<div className={columnClass} key={
|
694
|
+
<div className={columnClass} key={'DB_'+category}>
|
693
695
|
<div className="panel panel-default">
|
694
696
|
<div className="panel-heading">
|
695
|
-
<h4 style={{display:
|
697
|
+
<h4 style={{display: 'inline'}}>{panelTitle}</h4>
|
696
698
|
<button type="button" className={toggleClass} disabled={toggleDisabled}
|
697
|
-
onClick={ function () { this.handleToggle(toggleState, category) }.bind(this) }>
|
699
|
+
onClick={ function () { this.handleToggle(toggleState, category); }.bind(this) }>
|
698
700
|
{toggleState}
|
699
701
|
</button>
|
700
702
|
</div>
|
701
|
-
<ul className={
|
703
|
+
<ul className={'list-group databases ' + category}>
|
702
704
|
{
|
703
705
|
_.map(this.databases(category), _.bind(function (database,index) {
|
704
706
|
return (
|
705
|
-
<li className="list-group-item" key={
|
707
|
+
<li className="list-group-item" key={'DB_'+category+index}>
|
706
708
|
{ this.renderDatabase(database) }
|
707
709
|
</li>
|
708
710
|
);
|
@@ -724,18 +726,18 @@ var Databases = React.createClass({
|
|
724
726
|
type="checkbox" name="databases[]" value={database.id}
|
725
727
|
data-type={database.type} disabled={disabled}
|
726
728
|
onChange=
|
727
|
-
|
728
|
-
|
729
|
-
|
730
|
-
|
731
|
-
|
732
|
-
{
|
729
|
+
{
|
730
|
+
_.bind(function () {
|
731
|
+
this.handleClick(database);
|
732
|
+
}, this)
|
733
|
+
}/>
|
734
|
+
{' ' + (database.title || database.name)}
|
733
735
|
</label>
|
734
736
|
);
|
735
737
|
},
|
736
738
|
|
737
739
|
//shouldComponentUpdate: function (props, state) {
|
738
|
-
|
740
|
+
//return !(state.type && state.type === this.state.type);
|
739
741
|
//},
|
740
742
|
|
741
743
|
componentDidUpdate: function () {
|
@@ -744,6 +746,11 @@ var Databases = React.createClass({
|
|
744
746
|
this.handleClick(this.databases()[0]);
|
745
747
|
}
|
746
748
|
|
749
|
+
if (this.props.preSelectedDbs) {
|
750
|
+
var selectors = this.props.preSelectedDbs.map(db => `input[value=${db.id}]`);
|
751
|
+
$(...selectors).prop('checked',true);
|
752
|
+
setTimeout(() => this.handleClick(this.props.preSelectedDbs[0]));
|
753
|
+
}
|
747
754
|
this.props.onDatabaseTypeChanged(this.state.type);
|
748
755
|
}
|
749
756
|
});
|
@@ -751,15 +758,15 @@ var Databases = React.createClass({
|
|
751
758
|
var Options = React.createClass({
|
752
759
|
|
753
760
|
updateBox: function (evt) {
|
754
|
-
|
755
|
-
|
756
|
-
|
761
|
+
this.setState({
|
762
|
+
preOpts: evt.target.value
|
763
|
+
});
|
757
764
|
},
|
758
765
|
|
759
766
|
getInitialState: function () {
|
760
|
-
|
761
|
-
|
762
|
-
|
767
|
+
return {
|
768
|
+
preOpts: ''
|
769
|
+
};
|
763
770
|
},
|
764
771
|
|
765
772
|
render: function () {
|
@@ -784,7 +791,7 @@ var Options = React.createClass({
|
|
784
791
|
placeholder="eg: -evalue 1.0e-5 -num_alignments 100"
|
785
792
|
value={this.state.preOpts}
|
786
793
|
onChange={this.updateBox}
|
787
|
-
|
794
|
+
/>
|
788
795
|
<div
|
789
796
|
className="input-group-addon cursor-pointer"
|
790
797
|
data-toggle="modal" data-target="#help">
|
@@ -827,23 +834,23 @@ var SearchButton = React.createClass({
|
|
827
834
|
trigger: 'manual',
|
828
835
|
title: _.bind(function () {
|
829
836
|
if (!this.state.hasQuery && !this.state.hasDatabases) {
|
830
|
-
return
|
837
|
+
return 'You must enter a query sequence and select one or more databases above before you can run a search!';
|
831
838
|
}
|
832
839
|
else if (this.state.hasQuery && !this.state.hasDatabases) {
|
833
|
-
return
|
840
|
+
return 'You must select one or more databases above before you can run a search!';
|
834
841
|
}
|
835
842
|
else if (!this.state.hasQuery && this.state.hasDatabases) {
|
836
|
-
return
|
843
|
+
return 'You must enter a query sequence above before you can run a search!';
|
837
844
|
}
|
838
845
|
}, this)
|
839
846
|
});
|
840
847
|
|
841
848
|
this.submitButton().tooltip({
|
842
849
|
title: _.bind(function () {
|
843
|
-
var title =
|
850
|
+
var title = 'Click to BLAST or press Ctrl+Enter.';
|
844
851
|
if (this.state.methods.length > 1) {
|
845
|
-
title +=
|
846
|
-
|
852
|
+
title += ' Click dropdown button on the right for other' +
|
853
|
+
' BLAST algorithms that can be used.';
|
847
854
|
}
|
848
855
|
return title;
|
849
856
|
}, this)
|
@@ -902,7 +909,7 @@ var SearchButton = React.createClass({
|
|
902
909
|
methods: [],
|
903
910
|
hasQuery: false,
|
904
911
|
hasDatabases: false
|
905
|
-
}
|
912
|
+
};
|
906
913
|
},
|
907
914
|
|
908
915
|
render: function () {
|
@@ -970,7 +977,7 @@ var SearchButton = React.createClass({
|
|
970
977
|
this.props.onAlgoChanged(this.state.methods[0]);
|
971
978
|
}
|
972
979
|
else {
|
973
|
-
this.props.onAlgoChanged(
|
980
|
+
this.props.onAlgoChanged('');
|
974
981
|
}
|
975
982
|
}
|
976
983
|
});
|