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Add index.html
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‎src/main/java/org/biojava/http/ServerMain.java‎

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@@ -46,15 +46,17 @@ public class ServerMain {
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public static void main(String[] args) {
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port(8080);
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get("/", (r,r2) -> "BioJava HTTP");
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staticFileLocation("/static");
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// Document new routes in index.html
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get(BioJavaRoutes.PDB, new PDBRoute());
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get(BioJavaRoutes.MMCIF, new MMCIFRoute());
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get(BioJavaRoutes.NGL, new NGLRoute(), new HandlebarsTemplateEngine());
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get(BioJavaRoutes.CESYMM, new CeSymmRoute(), new HandlebarsTemplateEngine());
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get(BioJavaRoutes.CESYMM_JSON, new CeSymmResultRoute(),new JsonTransformer());
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get(BioJavaRoutes.CESYMM_PDB, new CeSymmResultRoute() {

‎src/main/resources/static/index.html‎

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<!DOCTYPE html>
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<html>
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<head>
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<meta charset='utf-8'>
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<title>BioJava Webservices</title>
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<style type="text/css">
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body {
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background: gray;
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}
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pre {
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margin: 0px auto;
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width: 100%;
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border: solid #ccc 1px;
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float: left;
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padding: 10px;
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position: relative;
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z-index: 10;
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}
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pre:after {
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background-color: #ccc;
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content: '';
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display: block;
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position: absolute;
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left: 0px;
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top: 0px;
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width: 10px;
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height: 100%;
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z-index: -1;
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}
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#main {
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max-width: 800px;
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background: white;
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margin: auto;
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padding: 25px;
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}
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.route {
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width: 100%;
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}
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.route td {
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width: 50%;
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padding-right: 25px;
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}
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.route td+td {
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padding-left: 25px;
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}
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</style>
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</head>
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<body>
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<div id="main">
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<h1>BioJava Webservices</h1>
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<p>
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<a href="http://biojava.org">BioJava</a> is a powerful library of
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bioinformatics tools, but leveraging BioJava from web interfaces is
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challenging. This provides a number of APIs and pre-build interfaces
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for accessing BioJava through the browser.
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</p>
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<h2>biojava-structure</h2>
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<p>
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BioJava understands and can automatically fetch a wide variety of
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structure formats. In the following examples,
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<tt>:id</tt>
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can be replaced by any of the following:
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<ul>
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<li><b>PDB</b> PDB identifier, optionally followed by chain
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and/or residue ranges. Examples: 4hhb, 4hhb.A, 4hhb.A:1-50.</li>
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<li><b>SCOP</b> SCOPe domain. Example: d1h6w.2</li>
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<li><b>PDP</b> Protein Domain Parser domain. Example: PDP:4HHBAa</li>
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<li><b>CATH</b> Cath domains. Example: 1qvrC03</li>
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<li><b>ECOD</b> ECOD domain. Example: e1lyw.1
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<li><b>BIO</b> Biological assembly. Example: BIO:2ehz:1</li>
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</ul>
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</p>
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<h3>Fetching structures</h3>
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<p>
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<table class="route">
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<tr>
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<td><pre>/pdb/:id</pre></td>
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<td>Example: <a href="/pdb/1itb.A">/pdb/1itb.A</a></td>
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</tr>
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<tr>
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<td><pre>/mmcif/:id</pre></td>
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<td>Example: <a href="/mmcif/1itb.A">/mmcif/1itb.A</a></td>
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</tr>
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</table>
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Returns the requested structure in PDB or mmCIF format.
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</p>
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<h3>Viewing structures</h3>
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<p>
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<table class="route">
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<tr>
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<td><pre>/ngl/:id</pre></td>
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<td>Example: <a href="/ngl/1itb.A">/ngl/1itb.A</a></td>
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</tr>
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</table>
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Views the requested structure using <a
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href="https://github.com/arose/ngl">NGL</a>.
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</p>
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<h3>CE-Symm</h3>
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<p>
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<table class="route">
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<tr>
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<td><pre>/cesymm/:id</pre></td>
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<td>Example: <a href="/cesymm/1itb.A">/cesymm/1itb.A</a></td>
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</tr>
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</table>
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Analyze the structure for internal symmetry using <a
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href="https://github.com/rcsb/symmetry">CE-Symm</a>.
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</p>
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<p>Information about the alignment is available in several
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formats:
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<table class="route">
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<tr>
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<td><pre>/cesymm/:id/pdb</pre></td>
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<td>Example: <a href="/cesymm/1itb.A">/cesymm/1itb.A/pdb</a></td>
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</tr>
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</table>
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PDB file with a superposition of the structure.
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<table class="route">
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<tr>
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<td><pre>/cesymm/:id/json</pre></td>
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<td>Example: <a href="/cesymm/1itb.A/json">/cesymm/1itb.A/json</a></td>
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</tr>
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</table>
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JSON describing the alignment.
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</p>
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</div>
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</body>
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</html>

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