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Commit f137f24

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sblivensbliven
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Add MSAViewer to other CE-Symm page
Also switches to NGL master, since the alpha stopped working.
1 parent 9cb199a commit f137f24

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4 files changed

+51
-29
lines changed

4 files changed

+51
-29
lines changed

‎src/main/java/org/biojava/http/models/NGLParams.java‎

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@@ -31,6 +31,7 @@ public class NGLParams {
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public NGLParams(String structUrl) {
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url = "https://cdn.rawgit.com/arose/ngl/v0.7.1a/js/build/ngl.embedded.min.js";
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url = "https://rawgit.com/arose/ngl/master/dist/ngl.js";
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this.structUrl = structUrl;
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this.setSize(500);
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}

‎src/main/resources/static/js/ngl_ui.js‎

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@@ -49,4 +49,19 @@ function screenshot(stage,factor) {
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function defaultNGLRepr(stage) {
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stage.addRepresentation("cartoon", {sele:""});
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stage.addRepresentation("ball+stick",{sele:"hetero and not ( water or ion )"});
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}
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/**
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* Returns a dynamic color scheme function that colors letters by their row
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*/
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function repeatScheme(numrows){
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var colors = palette('cb-Dark2', numrows);
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return function(letter,opts) {
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if(/[A-Z]/.exec(letter) && /[^a-z]/.exec(m.g.seqs.models[opts.y].attributes.seq[opts.pos]) ){
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return "#"+colors[opts.y];
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//return "#0f0";
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} else {
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return "#fff";
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}
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}
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}

‎src/main/resources/templates/cesymm.html.hbs‎

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@@ -3,17 +3,18 @@
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<head>
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<meta charset='utf-8'>
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<title>{{structureId}} CE-Symm Analysis</title>
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<script src='//code.jquery.com/jquery-1.11.0.min.js'></script>
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<script src="{{url}}"></script>
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</head>
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<body>
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<h1>CE-Symm Analysis of {{structureId}}</h1>
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<script src='//code.jquery.com/jquery-1.11.0.min.js'></script>
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<script src="{{url}}"></script>
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<div id="viewport" style="width: 100vw; height: 500px; display:block;"></div>
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<div id="messages"></div>
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<p><a href="/cesymm/{{structureId}}/multi">Multiple Superposition</a></p>
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<div id="msa">Loading Multiple Alignment...</div>
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<script src="https://cdn.rawgit.com/google/palette.js/master/palette.js"></script>
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<!--script src="{{pallete_url}}"></script-->
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<script src="/js/ngl_ui.js"></script>
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<script>
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NGL.mainScriptFilePath = "{{url}}";
@@ -70,11 +71,28 @@ document.addEventListener( "DOMContentLoaded", function() {
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});
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} );
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</script>
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<script src="https://cdn.bio.sh/msa/latest/msa.min.gz.js"></script>
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<script src="https://cdn.rawgit.com/google/palette.js/master/palette.js"></script>
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<!--script src="{{pallete_url}}"></script-->
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<script>
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var opts = {
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el: document.getElementById("msa"),
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vis: {
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conserv: false,
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overviewbox: false
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}
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};
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var m = new msa.msa(opts);
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m.u.file.importURL("/cesymm/{{structureId}}/fasta", function(){
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var numrows = m.g.seqs.length;
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m.g.colorscheme.addDynScheme("Repeats", repeatScheme(numrows) );
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m.g.colorscheme.set("scheme", "Repeats");
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m.render();
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});
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</script>
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<div id="viewport" style="width: 100vw; height: 100vh; display:block;"></div>
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<div id="messages"></div>
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<p><a href="/cesymm/{{structureId}}/multi">Multiple Superposition</a>
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</p>
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</body>
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</html>

‎src/main/resources/templates/cesymm_multi.html.hbs‎

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@@ -10,6 +10,12 @@
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<h1>CE-Symm Analysis of {{structureId}}: Multiple Superposition</h1>
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<div id="viewport" style="width: 100vw; height: 500px; display:block;"></div>
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<div id="messages"></div>
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<p><a href="/cesymm/{{structureId}}">CE-Symm Alignment</a></p>
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<div id="msa">Loading Multiple Alignment...</div>
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<script src="/js/ngl_ui.js"></script>
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<script>
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NGL.mainScriptFilePath = "{{url}}";
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var stage;
@@ -69,13 +75,11 @@ document.addEventListener( "DOMContentLoaded", function() {
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</script>
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<div id="viewport" style="width: 100vw; height: 100vh; display:block;"></div>
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<div id="messages"></div>
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<p><a href="/cesymm/{{structureId}}">CE-Symm Alignment</a></p>
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<script src="https://cdn.bio.sh/msa/latest/msa.min.gz.js"></script>
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<div id="msa">Loading Multiple Alignment...</div>
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<script src="https://cdn.rawgit.com/google/palette.js/master/palette.js"></script>
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<!--script src="{{pallete_url}}"></script-->
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<script>
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var opts = {
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el: document.getElementById("msa"),
@@ -87,28 +91,12 @@ var opts = {
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var m = new msa.msa(opts);
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m.u.file.importURL("/cesymm/{{structureId}}/fasta", function(){
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/* Returns a dynamic color scheme function that colors letters by their row
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*/
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function repeatScheme(numrows){
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var colors = palette('cb-Dark2', numrows);
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return function(letter,opts) {
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if(/[A-Z]/.exec(letter) && /[^a-z]/.exec(m.g.seqs.models[opts.y].attributes.seq[opts.pos]) ){
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return "#"+colors[opts.y];
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//return "#0f0";
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} else {
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return "#fff";
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}
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}
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}
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var numrows = m.g.seqs.length;
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m.g.colorscheme.addDynScheme("Repeats", repeatScheme(numrows) );
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m.g.colorscheme.set("scheme", "Repeats");
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m.render();
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});
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</script>
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<script src="https://cdn.rawgit.com/google/palette.js/master/palette.js"></script>
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<!--script src="{{pallete_url}}"></script-->
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<script src="/js/ngl_ui.js"></script>
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</body>

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