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<!DOCTYPE HTML>
<html lang="en">
<head>
<title>Source code</title>
<link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
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<body>
<main role="main">
<div class="sourceContainer">
<pre><span class="sourceLineNo">001</span><a id="line.1">/*</a>
<span class="sourceLineNo">002</span><a id="line.2"> * BioJava development code</a>
<span class="sourceLineNo">003</span><a id="line.3"> *</a>
<span class="sourceLineNo">004</span><a id="line.4"> * This code may be freely distributed and modified under the</a>
<span class="sourceLineNo">005</span><a id="line.5"> * terms of the GNU Lesser General Public Licence. This should</a>
<span class="sourceLineNo">006</span><a id="line.6"> * be distributed with the code. If you do not have a copy,</a>
<span class="sourceLineNo">007</span><a id="line.7"> * see:</a>
<span class="sourceLineNo">008</span><a id="line.8"> *</a>
<span class="sourceLineNo">009</span><a id="line.9"> * http://www.gnu.org/copyleft/lesser.html</a>
<span class="sourceLineNo">010</span><a id="line.10"> *</a>
<span class="sourceLineNo">011</span><a id="line.11"> * Copyright for this code is held jointly by the individual</a>
<span class="sourceLineNo">012</span><a id="line.12"> * authors. These should be listed in @author doc comments.</a>
<span class="sourceLineNo">013</span><a id="line.13"> *</a>
<span class="sourceLineNo">014</span><a id="line.14"> * For more information on the BioJava project and its aims,</a>
<span class="sourceLineNo">015</span><a id="line.15"> * or to join the biojava-l mailing list, visit the home page</a>
<span class="sourceLineNo">016</span><a id="line.16"> * at:</a>
<span class="sourceLineNo">017</span><a id="line.17"> *</a>
<span class="sourceLineNo">018</span><a id="line.18"> * http://www.biojava.org/</a>
<span class="sourceLineNo">019</span><a id="line.19"> *</a>
<span class="sourceLineNo">020</span><a id="line.20"> */</a>
<span class="sourceLineNo">021</span><a id="line.21">package demo;</a>
<span class="sourceLineNo">022</span><a id="line.22"></a>
<span class="sourceLineNo">023</span><a id="line.23">import org.biojava.nbio.core.sequence.ProteinSequence;</a>
<span class="sourceLineNo">024</span><a id="line.24">import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;</a>
<span class="sourceLineNo">025</span><a id="line.25">import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;</a>
<span class="sourceLineNo">026</span><a id="line.26">import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;</a>
<span class="sourceLineNo">027</span><a id="line.27">import org.biojava.nbio.ws.hmmer.HmmerDomain;</a>
<span class="sourceLineNo">028</span><a id="line.28">import org.biojava.nbio.ws.hmmer.HmmerResult;</a>
<span class="sourceLineNo">029</span><a id="line.29">import org.biojava.nbio.ws.hmmer.RemoteHmmerScan;</a>
<span class="sourceLineNo">030</span><a id="line.30"></a>
<span class="sourceLineNo">031</span><a id="line.31">import java.util.SortedSet;</a>
<span class="sourceLineNo">032</span><a id="line.32"></a>
<span class="sourceLineNo">033</span><a id="line.33">/**</a>
<span class="sourceLineNo">034</span><a id="line.34"> * The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service</a>
<span class="sourceLineNo">035</span><a id="line.35"> *</a>
<span class="sourceLineNo">036</span><a id="line.36"> * @author Andreas Prlic</a>
<span class="sourceLineNo">037</span><a id="line.37"> * @since 3.0.3</a>
<span class="sourceLineNo">038</span><a id="line.38"> */</a>
<span class="sourceLineNo">039</span><a id="line.39">public class HmmerDemo {</a>
<span class="sourceLineNo">040</span><a id="line.40"></a>
<span class="sourceLineNo">041</span><a id="line.41"> public static void main(String[] args) throws Exception {</a>
<span class="sourceLineNo">042</span><a id="line.42"></a>
<span class="sourceLineNo">043</span><a id="line.43"></a>
<span class="sourceLineNo">044</span><a id="line.44"> // first we get a UniProt sequence</a>
<span class="sourceLineNo">045</span><a id="line.45"> String uniProtID = "P08487";</a>
<span class="sourceLineNo">046</span><a id="line.46"> ProteinSequence seq = getUniprot(uniProtID);</a>
<span class="sourceLineNo">047</span><a id="line.47"></a>
<span class="sourceLineNo">048</span><a id="line.48"></a>
<span class="sourceLineNo">049</span><a id="line.49"> // now we submit this sequence to the Hmmer web site</a>
<span class="sourceLineNo">050</span><a id="line.50"> RemoteHmmerScan hmmer = new RemoteHmmerScan();</a>
<span class="sourceLineNo">051</span><a id="line.51"></a>
<span class="sourceLineNo">052</span><a id="line.52"> SortedSet<HmmerResult> results = hmmer.scan(seq);</a>
<span class="sourceLineNo">053</span><a id="line.53"></a>
<span class="sourceLineNo">054</span><a id="line.54"> // and now let's print out the obtained annotations</a>
<span class="sourceLineNo">055</span><a id="line.55"></a>
<span class="sourceLineNo">056</span><a id="line.56"> System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",</a>
<span class="sourceLineNo">057</span><a id="line.57"> "Domain","ACC", "Start","End","eValue","Description"));</a>
<span class="sourceLineNo">058</span><a id="line.58"></a>
<span class="sourceLineNo">059</span><a id="line.59"> int counter = 0;</a>
<span class="sourceLineNo">060</span><a id="line.60"> for (HmmerResult hmmerResult : results) {</a>
<span class="sourceLineNo">061</span><a id="line.61"> //System.out.println(hmmerResult);</a>
<span class="sourceLineNo">062</span><a id="line.62"></a>
<span class="sourceLineNo">063</span><a id="line.63"> for ( HmmerDomain domain : hmmerResult.getDomains()) {</a>
<span class="sourceLineNo">064</span><a id="line.64"> counter++;</a>
<span class="sourceLineNo">065</span><a id="line.65"> System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",</a>
<span class="sourceLineNo">066</span><a id="line.66"> counter,</a>
<span class="sourceLineNo">067</span><a id="line.67"> hmmerResult.getName(), domain.getHmmAcc(),</a>
<span class="sourceLineNo">068</span><a id="line.68"> domain.getSqFrom(),domain.getSqTo(),</a>
<span class="sourceLineNo">069</span><a id="line.69"> domain.getEvalue(), hmmerResult.getDesc()</a>
<span class="sourceLineNo">070</span><a id="line.70"> ));</a>
<span class="sourceLineNo">071</span><a id="line.71"></a>
<span class="sourceLineNo">072</span><a id="line.72"> }</a>
<span class="sourceLineNo">073</span><a id="line.73"></a>
<span class="sourceLineNo">074</span><a id="line.74"> }</a>
<span class="sourceLineNo">075</span><a id="line.75"></a>
<span class="sourceLineNo">076</span><a id="line.76"></a>
<span class="sourceLineNo">077</span><a id="line.77"> }</a>
<span class="sourceLineNo">078</span><a id="line.78"></a>
<span class="sourceLineNo">079</span><a id="line.79"> /**</a>
<span class="sourceLineNo">080</span><a id="line.80"> * Fetch a protein sequence from the UniProt web site</a>
<span class="sourceLineNo">081</span><a id="line.81"> *</a>
<span class="sourceLineNo">082</span><a id="line.82"> * @param uniProtID</a>
<span class="sourceLineNo">083</span><a id="line.83"> * @return a Protein Sequence</a>
<span class="sourceLineNo">084</span><a id="line.84"> * @throws Exception</a>
<span class="sourceLineNo">085</span><a id="line.85"> */</a>
<span class="sourceLineNo">086</span><a id="line.86"> private static ProteinSequence getUniprot(String uniProtID) throws Exception {</a>
<span class="sourceLineNo">087</span><a id="line.87"></a>
<span class="sourceLineNo">088</span><a id="line.88"> AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();</a>
<span class="sourceLineNo">089</span><a id="line.89"> UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);</a>
<span class="sourceLineNo">090</span><a id="line.90"></a>
<span class="sourceLineNo">091</span><a id="line.91"> ProteinSequence seq = new ProteinSequence(uniprotSequence);</a>
<span class="sourceLineNo">092</span><a id="line.92"></a>
<span class="sourceLineNo">093</span><a id="line.93"> return seq;</a>
<span class="sourceLineNo">094</span><a id="line.94"> }</a>
<span class="sourceLineNo">095</span><a id="line.95">}</a>
</pre>
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