biojava.github.io/docs/api5.0.0/src-html/demo/ParseGO.html at master · biojava/biojava.github.io

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">

<head>

<title>Source code</title>

</head>

<body>

002 * BioJava development code<a name="line.2"></a>

003 *<a name="line.3"></a>

004 * This code may be freely distributed and modified under the<a name="line.4"></a>

005 * terms of the GNU Lesser General Public Licence. This should<a name="line.5"></a>

006 * be distributed with the code. If you do not have a copy,<a name="line.6"></a>

007 * see:<a name="line.7"></a>

008 *<a name="line.8"></a>

009 * http://www.gnu.org/copyleft/lesser.html<a name="line.9"></a>

010 *<a name="line.10"></a>

011 * Copyright for this code is held jointly by the individual<a name="line.11"></a>

012 * authors. These should be listed in @author doc comments.<a name="line.12"></a>

013 *<a name="line.13"></a>

014 * For more information on the BioJava project and its aims,<a name="line.14"></a>

015 * or to join the biojava-l mailing list, visit the home page<a name="line.15"></a>

016 * at:<a name="line.16"></a>

017 *<a name="line.17"></a>

018 * http://www.biojava.org/<a name="line.18"></a>

019 *<a name="line.19"></a>

020 * Created on Mar 19, 2014<a name="line.20"></a>

021 * Author: andreas<a name="line.21"></a>

022 *<a name="line.22"></a>

023 */<a name="line.23"></a>

024<a name="line.24"></a>

025package demo;<a name="line.25"></a>

026<a name="line.26"></a>

027import org.biojava.nbio.ontology.Ontology;<a name="line.27"></a>

028import org.biojava.nbio.ontology.Term;<a name="line.28"></a>

029import org.biojava.nbio.ontology.io.OboParser;<a name="line.29"></a>

030import org.slf4j.Logger;<a name="line.30"></a>

031import org.slf4j.LoggerFactory;<a name="line.31"></a>

032<a name="line.32"></a>

033import java.io.BufferedReader;<a name="line.33"></a>

034import java.io.InputStream;<a name="line.34"></a>

035import java.io.InputStreamReader;<a name="line.35"></a>

036import java.net.URL;<a name="line.36"></a>

037import java.util.Iterator;<a name="line.37"></a>

038import java.util.Set;<a name="line.38"></a>

039<a name="line.39"></a>

040public class ParseGO {<a name="line.40"></a>

041<a name="line.41"></a>

042 private static final Logger logger = LoggerFactory.getLogger(ParseGO.class);<a name="line.42"></a>

043<a name="line.43"></a>

044 public static void main(String[] args){<a name="line.44"></a>

045<a name="line.45"></a>

046 String u = "http://sourceforge.net/p/song/svn/HEAD/tree/trunk/subsets/biosapiens.obo?format=raw";<a name="line.46"></a>

047<a name="line.47"></a>

048 try {<a name="line.48"></a>

049 URL url = new URL(u);<a name="line.49"></a>

050<a name="line.50"></a>

051 OboParser parser = new OboParser();<a name="line.51"></a>

052 InputStream inStream = url.openStream();<a name="line.52"></a>

053<a name="line.53"></a>

054 BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );<a name="line.54"></a>

055<a name="line.55"></a>

056 Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");<a name="line.56"></a>

057<a name="line.57"></a>

058 Set<Term> keys = ontology.getTerms();<a name="line.58"></a>

059 Iterator<Term> iter = keys.iterator();<a name="line.59"></a>

060 while (iter.hasNext()){<a name="line.60"></a>

061 Term t = iter.next();<a name="line.61"></a>

062 logger.info("{} [{}]", t.getName(), t.getDescription());<a name="line.62"></a>

063 }<a name="line.63"></a>

064 } catch (Exception e){<a name="line.64"></a>

065 logger.error("Exception: ", e);<a name="line.65"></a>

066 }<a name="line.66"></a>

067 }<a name="line.67"></a>

068}<a name="line.68"></a>

</pre>

</div>

</body>

</html>

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