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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: PredictDisorder">
<meta name="generator" content="javadoc/SourceToHTMLConverter">
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<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"> */</span>
<span class="source-line-no">021</span><span id="line-21">package demo;</span>
<span class="source-line-no">022</span><span id="line-22"></span>
<span class="source-line-no">023</span><span id="line-23">import org.biojava.nbio.core.sequence.ProteinSequence;</span>
<span class="source-line-no">024</span><span id="line-24">import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;</span>
<span class="source-line-no">025</span><span id="line-25">import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;</span>
<span class="source-line-no">026</span><span id="line-26">import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;</span>
<span class="source-line-no">027</span><span id="line-27">import org.biojava.nbio.ronn.Jronn;</span>
<span class="source-line-no">028</span><span id="line-28"></span>
<span class="source-line-no">029</span><span id="line-29">import java.util.Arrays;</span>
<span class="source-line-no">030</span><span id="line-30"></span>
<span class="source-line-no">031</span><span id="line-31">public class PredictDisorder {</span>
<span class="source-line-no">032</span><span id="line-32"></span>
<span class="source-line-no">033</span><span id="line-33"> public static void main(String[] args) throws Exception{</span>
<span class="source-line-no">034</span><span id="line-34"></span>
<span class="source-line-no">035</span><span id="line-35"> String uniprotID = "O30642";</span>
<span class="source-line-no">036</span><span id="line-36"></span>
<span class="source-line-no">037</span><span id="line-37"> ProteinSequence seq = getUniprot(uniprotID);</span>
<span class="source-line-no">038</span><span id="line-38"> System.out.println("Protein Sequence: "+ seq.toString());</span>
<span class="source-line-no">039</span><span id="line-39"> AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();</span>
<span class="source-line-no">040</span><span id="line-40"></span>
<span class="source-line-no">041</span><span id="line-41"> if (!compoundSet.isValidSequence(seq) ) {</span>
<span class="source-line-no">042</span><span id="line-42"> System.err.println("Invalid sequence, exiting");</span>
<span class="source-line-no">043</span><span id="line-43"> System.exit(1);</span>
<span class="source-line-no">044</span><span id="line-44"> }</span>
<span class="source-line-no">045</span><span id="line-45"></span>
<span class="source-line-no">046</span><span id="line-46"> float[] values = Jronn.getDisorderScores(seq);</span>
<span class="source-line-no">047</span><span id="line-47"></span>
<span class="source-line-no">048</span><span id="line-48"> System.out.println("Disorder Scores: "+ Arrays.toString(values));</span>
<span class="source-line-no">049</span><span id="line-49"></span>
<span class="source-line-no">050</span><span id="line-50"></span>
<span class="source-line-no">051</span><span id="line-51"> }</span>
<span class="source-line-no">052</span><span id="line-52"></span>
<span class="source-line-no">053</span><span id="line-53"> /** Fetch a protein sequence from the UniProt web site</span>
<span class="source-line-no">054</span><span id="line-54"> *</span>
<span class="source-line-no">055</span><span id="line-55"> * @param uniProtID</span>
<span class="source-line-no">056</span><span id="line-56"> * @return a Protein Sequence</span>
<span class="source-line-no">057</span><span id="line-57"> * @throws Exception</span>
<span class="source-line-no">058</span><span id="line-58"> */</span>
<span class="source-line-no">059</span><span id="line-59"> private static ProteinSequence getUniprot(String uniProtID) throws Exception {</span>
<span class="source-line-no">060</span><span id="line-60"></span>
<span class="source-line-no">061</span><span id="line-61"> AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();</span>
<span class="source-line-no">062</span><span id="line-62"> UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniProtID,set);</span>
<span class="source-line-no">063</span><span id="line-63"></span>
<span class="source-line-no">064</span><span id="line-64"> ProteinSequence seq = new ProteinSequence(uniprotSequence);</span>
<span class="source-line-no">065</span><span id="line-65"></span>
<span class="source-line-no">066</span><span id="line-66"> return seq;</span>
<span class="source-line-no">067</span><span id="line-67"> }</span>
<span class="source-line-no">068</span><span id="line-68">}</span>
</pre>
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