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<!DOCTYPE HTML>
<html lang>
<head>
<!-- Generated by javadoc (21) -->
<title>Source code</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="source: package: demo, class: ParseGO">
<meta name="generator" content="javadoc/SourceToHTMLConverter">
<link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
</head>
<body class="source-page">
<main role="main">
<div class="source-container">
<pre><span class="source-line-no">001</span><span id="line-1">/*</span>
<span class="source-line-no">002</span><span id="line-2"> * BioJava development code</span>
<span class="source-line-no">003</span><span id="line-3"> *</span>
<span class="source-line-no">004</span><span id="line-4"> * This code may be freely distributed and modified under the</span>
<span class="source-line-no">005</span><span id="line-5"> * terms of the GNU Lesser General Public Licence. This should</span>
<span class="source-line-no">006</span><span id="line-6"> * be distributed with the code. If you do not have a copy,</span>
<span class="source-line-no">007</span><span id="line-7"> * see:</span>
<span class="source-line-no">008</span><span id="line-8"> *</span>
<span class="source-line-no">009</span><span id="line-9"> * http://www.gnu.org/copyleft/lesser.html</span>
<span class="source-line-no">010</span><span id="line-10"> *</span>
<span class="source-line-no">011</span><span id="line-11"> * Copyright for this code is held jointly by the individual</span>
<span class="source-line-no">012</span><span id="line-12"> * authors. These should be listed in @author doc comments.</span>
<span class="source-line-no">013</span><span id="line-13"> *</span>
<span class="source-line-no">014</span><span id="line-14"> * For more information on the BioJava project and its aims,</span>
<span class="source-line-no">015</span><span id="line-15"> * or to join the biojava-l mailing list, visit the home page</span>
<span class="source-line-no">016</span><span id="line-16"> * at:</span>
<span class="source-line-no">017</span><span id="line-17"> *</span>
<span class="source-line-no">018</span><span id="line-18"> * http://www.biojava.org/</span>
<span class="source-line-no">019</span><span id="line-19"> *</span>
<span class="source-line-no">020</span><span id="line-20"> * Created on Mar 19, 2014</span>
<span class="source-line-no">021</span><span id="line-21"> * Author: andreas</span>
<span class="source-line-no">022</span><span id="line-22"> *</span>
<span class="source-line-no">023</span><span id="line-23"> */</span>
<span class="source-line-no">024</span><span id="line-24"></span>
<span class="source-line-no">025</span><span id="line-25">package demo;</span>
<span class="source-line-no">026</span><span id="line-26"></span>
<span class="source-line-no">027</span><span id="line-27">import org.biojava.nbio.ontology.Ontology;</span>
<span class="source-line-no">028</span><span id="line-28">import org.biojava.nbio.ontology.Term;</span>
<span class="source-line-no">029</span><span id="line-29">import org.biojava.nbio.ontology.io.OboParser;</span>
<span class="source-line-no">030</span><span id="line-30">import org.slf4j.Logger;</span>
<span class="source-line-no">031</span><span id="line-31">import org.slf4j.LoggerFactory;</span>
<span class="source-line-no">032</span><span id="line-32"></span>
<span class="source-line-no">033</span><span id="line-33">import java.io.BufferedReader;</span>
<span class="source-line-no">034</span><span id="line-34">import java.io.InputStream;</span>
<span class="source-line-no">035</span><span id="line-35">import java.io.InputStreamReader;</span>
<span class="source-line-no">036</span><span id="line-36"></span>
<span class="source-line-no">037</span><span id="line-37">import java.util.Iterator;</span>
<span class="source-line-no">038</span><span id="line-38">import java.util.Set;</span>
<span class="source-line-no">039</span><span id="line-39"></span>
<span class="source-line-no">040</span><span id="line-40">public class ParseGO {</span>
<span class="source-line-no">041</span><span id="line-41"></span>
<span class="source-line-no">042</span><span id="line-42"> static final Logger logger = LoggerFactory.getLogger(ParseGO.class);</span>
<span class="source-line-no">043</span><span id="line-43"></span>
<span class="source-line-no">044</span><span id="line-44"> /**</span>
<span class="source-line-no">045</span><span id="line-45"> * Parses Biosapiens OBO file and logs name/description at INFO level</span>
<span class="source-line-no">046</span><span id="line-46"> * </span>
<span class="source-line-no">047</span><span id="line-47"> * @param args</span>
<span class="source-line-no">048</span><span id="line-48"> */</span>
<span class="source-line-no">049</span><span id="line-49"> public static void main(String[] args) {</span>
<span class="source-line-no">050</span><span id="line-50"></span>
<span class="source-line-no">051</span><span id="line-51"> OboParser parser = new OboParser();</span>
<span class="source-line-no">052</span><span id="line-52"> try (InputStream inStream = OboParser.class.getResourceAsStream("/ontology/biosapiens.obo");</span>
<span class="source-line-no">053</span><span id="line-53"> BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream))) {</span>
<span class="source-line-no">054</span><span id="line-54"> Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");</span>
<span class="source-line-no">055</span><span id="line-55"> Set<Term> keys = ontology.getTerms();</span>
<span class="source-line-no">056</span><span id="line-56"> Iterator<Term> iter = keys.iterator();</span>
<span class="source-line-no">057</span><span id="line-57"> while (iter.hasNext()) {</span>
<span class="source-line-no">058</span><span id="line-58"> Term t = iter.next();</span>
<span class="source-line-no">059</span><span id="line-59"> logger.info("{} [{}]", t.getName(), t.getDescription());</span>
<span class="source-line-no">060</span><span id="line-60"> }</span>
<span class="source-line-no">061</span><span id="line-61"></span>
<span class="source-line-no">062</span><span id="line-62"> } catch (Exception e) {</span>
<span class="source-line-no">063</span><span id="line-63"> logger.error("Exception: " + e);</span>
<span class="source-line-no">064</span><span id="line-64"> System.exit(1);</span>
<span class="source-line-no">065</span><span id="line-65"> }</span>
<span class="source-line-no">066</span><span id="line-66"> }</span>
<span class="source-line-no">067</span><span id="line-67">}</span>
</pre>
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</main>
</body>
</html>