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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: DemoLoadSubstMax">
<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"> */</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.alignment.matrices.SubstitutionMatrixHelper;</span>
<span class="source-line-no">024</span><span id="line-24">import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;</span>
<span class="source-line-no">025</span><span id="line-25">import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;</span>
<span class="source-line-no">026</span><span id="line-26"></span>
<span class="source-line-no">027</span><span id="line-27">public class DemoLoadSubstMax {</span>
<span class="source-line-no">028</span><span id="line-28"></span>
<span class="source-line-no">029</span><span id="line-29"></span>
<span class="source-line-no">030</span><span id="line-30"> public static void main (String[] args){</span>
<span class="source-line-no">031</span><span id="line-31"> // that's the PAM250 matrix (named a bit unclear in AAindex...)</span>
<span class="source-line-no">032</span><span id="line-32"> String max2="DAYM780301";</span>
<span class="source-line-no">033</span><span id="line-33"> SubstitutionMatrix<AminoAcidCompound> substMax2 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(max2);</span>
<span class="source-line-no">034</span><span id="line-34"> System.out.println("PAM250 matrix: "+ substMax2);</span>
<span class="source-line-no">035</span><span id="line-35"></span>
<span class="source-line-no">036</span><span id="line-36"> // and here BLOSUM62...</span>
<span class="source-line-no">037</span><span id="line-37"> String max3="HENS920102";</span>
<span class="source-line-no">038</span><span id="line-38"> SubstitutionMatrix<AminoAcidCompound> substMax3 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(max3);</span>
<span class="source-line-no">039</span><span id="line-39"> System.out.printf("%s matrix: %s", max3, substMax3);</span>
<span class="source-line-no">040</span><span id="line-40"> System.out.println();</span>
<span class="source-line-no">041</span><span id="line-41"></span>
<span class="source-line-no">042</span><span id="line-42"> // This one I developed a while ago to be optimised for the alignment of distantly related sequences</span>
<span class="source-line-no">043</span><span id="line-43"> String matrixName4 = "PRLA000101";</span>
<span class="source-line-no">044</span><span id="line-44"> SubstitutionMatrix<AminoAcidCompound> substMax4 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(matrixName4);</span>
<span class="source-line-no">045</span><span id="line-45"> System.out.printf("%s matrix: %s", matrixName4, substMax4);</span>
<span class="source-line-no">046</span><span id="line-46"> System.out.println();</span>
<span class="source-line-no">047</span><span id="line-47"> }</span>
<span class="source-line-no">048</span><span id="line-48">}</span>
</pre>
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