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commit 7ccf3fe Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Tue Jan 23 02:17:42 2018 -0600 fix tree layout not showing up commit d7aed99 Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Tue Jan 23 02:01:33 2018 -0600 allow drag and drop single file commit 85af19c Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Mon Jan 22 19:08:34 2018 -0600 disable color checking on label change (FIX LATER) commit 4b1a9e5 Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Mon Jan 22 19:03:20 2018 -0600 switch to colorpicker dependency commit c23857e Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Mon Jan 22 13:17:04 2018 -0600 refactor data parsing parser classes for different formats are instantiated in parse.js and returns arrays of words, links, and clusters commit 87bd8fd Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Fri Jan 19 16:47:20 2018 -0600 load external files commit a99db24 Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Tue Jan 16 14:21:31 2018 -0600 convert data[6-8].json to example[1-3].ann (standoff) -overlapping/nested TBMs not handled yet commit f18c5c0 Author: Kristine Lee <hmsklee@users.noreply.github.com> Date: Tue Jan 2 15:05:24 2018 -0600 add parser for ann
1 parent 0288d68 commit b5a9ca9

17 files changed

Lines changed: 960 additions & 463 deletions

File tree

‎css/style.css‎

Lines changed: 39 additions & 3 deletions
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#fill {
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/* ensure body takes up entire window */
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position:absolute;
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z-index:-1;
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top:0;
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left:0;
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width:100%;
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height:100%;
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}
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body {
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margin:0;
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-moz-osx-font-smoothing:grayscale;
@@ -63,6 +72,27 @@ header > button:hover {
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border-bottom:1px solid grey;
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}
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/* input */
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#input-modal {
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}
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#input-modal textarea {
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width:100%;
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height:300px;
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padding:5px;
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font-size:15px;
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}
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label[for="file-input"] {
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padding:10px 15px;
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cursor:pointer;
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background:steelblue;
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color:white;
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margin:10px 0;
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display:inline-block;
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border-radius:5px;
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}
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/* modal */
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.modal {
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color:#222;
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background:rgba(0,0,0,0.3);
@@ -159,9 +189,9 @@ header > button:hover {
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#taxonomy input[type="checkbox"] {
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margin-right: 0.5em;
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}
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#taxonomy input.jscolor {
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#taxonomy input.colorpicker {
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margin-left: 0.5em;
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width:4em;
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width:5em;
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text-align:center;
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display:inline-block;
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outline:none;
@@ -170,13 +200,19 @@ header > button:hover {
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border-radius: 3px;
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cursor: pointer;
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box-shadow: 0 0 8px rgba(0,0,0,0.2);
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text-transform:uppercase;
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-moz-osx-font-smoothing:initial;
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-webkit-font-smoothing:initial;
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}
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#taxonomy input.jscolor[disabled="true"] {
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#taxonomy input.colorpicker[disabled="true"] {
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border-color:#ccc;
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box-shadow: none;
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pointer-events:none;
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opacity:0.5;
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}
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.cp-app {
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z-index:1001;
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}
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body > #tree-svg {
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border-top: 1px solid #ccc;

‎data/example1.ann‎

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unlockable
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T1 BOUND 0 2 un
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T2 FREE 2 6 lock
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T3 BOUND 6 10 able
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R1 unlock controlled:T1 controller:T2
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R2 unlockable controller:R1 controlled:T3

‎data/example2.ann‎

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unlockable
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T1 BOUND 0 2 un
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T2 FREE 2 6 lock
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T3 BOUND 6 10 able
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R1 lockable controlled:T2 controller:T3
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R2 unlockable controller:T1 controlled:R1

‎data/example3.ann‎

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Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities.
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T1 Gene_or_gene_product 13 16 p21
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T2 Gene_or_gene_product 20 23 p53
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T3 BioProcess 34 44 DNA damage
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T4 Gene_or_gene_product 59 63 Cdk4
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T5 Gene_or_gene_product 68 72 Cdk2
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T6 Positive_activation 0 9 Induction
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T7 Negative_regulation 45 53 inhibits
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E1 Positive_activation:T6 Controller:T2 Controlled:T1
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E2 Negative_regulation::T7 Controller:E1 Controlled:T4
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E3 Negative_regulation::T7 Controller:E1 Controlled:T5

‎index.html‎

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<body>
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<div id="fill"></div>
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<header id="header">
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Examples:
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<select id="dataset">
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<option>-- select dataset --</option>
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<option>data1</option>
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<option>morpheme2</option>
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<option>event annotation</option>
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</select>
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<button id="custom-annotation">Custom annotation</button>
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<button id="taxonomy-toggle">Taxonomy</button>
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<button id="options-toggle">Options</button>
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</header>
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<div id="input-modal" class="modal">
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<div>
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<header>
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<span class="tab active">Custom annotation</span>
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</header>
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<div class="page active">
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<form id="form">
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<label for="file-input">Upload file(s)</label>
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<input type="file" id="file-input" style="display:none;" multiple>
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</form>
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<pre id="message"></pre>
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</div>
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</div>
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</div>
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<div id="main">
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<div id="tooltip">
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</div>
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<p><input type="checkbox" data-option="tree"> Open tree view in modal</p>
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</div>
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</div>
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</div>
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<script src="libs/svg.js"></script>
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<script src="libs/svg.draggable.js"></script>
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<script src="libs/jscolor.min.js"></script>
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<script src="libs/jsColorPicker.min.js"></script>
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<script src="libs/d3.min.js"></script>
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<script src="js/xhr.js"></script>
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<script src="js/ymljson.js"></script>
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<script src="js/parser.js"></script>
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<script src="js/parse/parse.js"></script>
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<script src="js/parse/ann.js"></script>
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<script src="js/parse/reach.js"></script>
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<script src="js/treelayout.js"></script>
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<script src="js/main.js"></script>
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<script src="js/managers/tooltip.js"></script>
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<script src="js/components/link.js"></script>
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<script type="text/javascript">
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// page setup
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// manage input
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// manage visualization
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Main.init();
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</script>
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‎js/components/link.js‎

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// helper function to return a path string for an arrowhead
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arrowhead(handle) {
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const s = 4;
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const s = 4, s2 = 6;
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return this.top ?
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'M' + [handle.x - s, handle.y - s] + 'l' + [s,s * 1.5] + 'l' + [s,-s * 1.5] :
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'M' + [handle.x - s, handle.y + s] + 'l' + [s, -s * 1.5] + 'l' + [s, s * 1.5];
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'M' + [handle.x - s, handle.y - s] + 'l' + [s, s2] + 'l' + [s, -s2] :
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'M' + [handle.x - s, handle.y + s] + 'l' + [s, -s2] + 'l' + [s, s2];
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}
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remove() {

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