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Apidocs for 7.1.4 (fixing biojava/biojava#1102)
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‎docs/api

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api6.1.0/
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<!DOCTYPE HTML>
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<html lang>
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<head>
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<!-- Generated by javadoc (21) on Wed Jan 08 16:43:01 PST 2025 -->
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<title>AFPFromFasta (biojava 7.1.4 API)</title>
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<meta name="dc.created" content="2025-01-08">
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<meta name="description" content="declaration: package: demo, class: AFPFromFasta">
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<meta name="generator" content="javadoc/ClassWriterImpl">
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<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
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<!-- ========= START OF TOP NAVBAR ======= -->
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<p>Summary:</p>
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<ul>
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<li>Nested</li>
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<li>Field</li>
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<li><a href="#constructor-summary">Constr</a></li>
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<li><a href="#method-summary">Method</a></li>
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</ul>
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<p>Detail:</p>
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<li>Field</li>
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<li><a href="#constructor-detail">Constr</a></li>
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<main role="main">
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<!-- ======== START OF CLASS DATA ======== -->
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<div class="header">
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<div class="sub-title"><span class="package-label-in-type">Package</span>&nbsp;<a href="package-summary.html">demo</a></div>
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<h1 title="Class AFPFromFasta" class="title">Class AFPFromFasta</h1>
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</div>
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<div class="inheritance" title="Inheritance Tree"><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">java.lang.Object</a>
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<div class="inheritance">demo.AFPFromFasta</div>
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</div>
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<section class="class-description" id="class-description">
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<hr>
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<div class="type-signature"><span class="modifiers">public class </span><span class="element-name"><a href="../src-html/demo/AFPFromFasta.html#line-48">AFPFromFasta</a></span>
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<span class="extends-implements">extends <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a></span></div>
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<div class="block">Demo displaying a structural alignment from a FASTA file using <a href="../org/biojava/nbio/structure/io/FastaAFPChainConverter.html" title="class in org.biojava.nbio.structure.io"><code>FastaAFPChainConverter</code></a>.
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See <a href="DemoAlignmentFromFasta.html" title="class in demo"><code>DemoAlignmentFromFasta</code></a> Also demonstrates the display of <a href="../org/biojava/nbio/structure/align/StructureAlignment.html" title="interface in org.biojava.nbio.structure.align"><code>StructureAlignments</code></a> from FASTA sequences, but does so using the more general
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<a href="../org/biojava/nbio/structure/io/FastaStructureParser.html" title="class in org.biojava.nbio.structure.io"><code>FastaStructureParser</code></a></div>
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<dl class="notes">
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<dt>Author:</dt>
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<dd>dmyerstu</dd>
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</dl>
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</section>
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<section class="summary">
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<ul class="summary-list">
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<!-- ======== CONSTRUCTOR SUMMARY ======== -->
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<li>
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<section class="constructor-summary" id="constructor-summary">
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<h2>Constructor Summary</h2>
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<div class="caption"><span>Constructors</span></div>
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<div class="summary-table two-column-summary">
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<div class="table-header col-first">Constructor</div>
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<div class="table-header col-last">Description</div>
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<div class="col-constructor-name even-row-color"><code><a href="#%3Cinit%3E()" class="member-name-link">AFPFromFasta</a>()</code></div>
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<div class="col-last even-row-color">&nbsp;</div>
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</div>
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</section>
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</li>
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<!-- ========== METHOD SUMMARY =========== -->
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<li>
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<section class="method-summary" id="method-summary">
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<h2>Method Summary</h2>
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<div id="method-summary-table">
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<div class="table-tabs" role="tablist" aria-orientation="horizontal"><button id="method-summary-table-tab0" role="tab" aria-selected="true" aria-controls="method-summary-table.tabpanel" tabindex="0" onkeydown="switchTab(event)" onclick="show('method-summary-table', 'method-summary-table', 3)" class="active-table-tab">All Methods</button><button id="method-summary-table-tab1" role="tab" aria-selected="false" aria-controls="method-summary-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('method-summary-table', 'method-summary-table-tab1', 3)" class="table-tab">Static Methods</button><button id="method-summary-table-tab4" role="tab" aria-selected="false" aria-controls="method-summary-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('method-summary-table', 'method-summary-table-tab4', 3)" class="table-tab">Concrete Methods</button></div>
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<div id="method-summary-table.tabpanel" role="tabpanel" aria-labelledby="method-summary-table-tab0">
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<div class="summary-table three-column-summary">
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<div class="table-header col-first">Modifier and Type</div>
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<div class="table-header col-second">Method</div>
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<div class="table-header col-last">Description</div>
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<div class="col-first even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code>static void</code></div>
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<div class="col-second even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code><a href="#main(java.lang.String%5B%5D)" class="member-name-link">main</a><wbr>(<a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a>[]&nbsp;args)</code></div>
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<div class="col-last even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4">&nbsp;</div>
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</div>
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</div>
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</div>
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<div class="inherited-list">
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<h3 id="methods-inherited-from-class-java.lang.Object">Methods inherited from class&nbsp;java.lang.<a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a></h3>
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<code><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#clone()" title="class or interface in java.lang" class="external-link">clone</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#equals(java.lang.Object)" title="class or interface in java.lang" class="external-link">equals</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#finalize()" title="class or interface in java.lang" class="external-link">finalize</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#getClass()" title="class or interface in java.lang" class="external-link">getClass</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#hashCode()" title="class or interface in java.lang" class="external-link">hashCode</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#notify()" title="class or interface in java.lang" class="external-link">notify</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#notifyAll()" title="class or interface in java.lang" class="external-link">notifyAll</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#toString()" title="class or interface in java.lang" class="external-link">toString</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#wait()" title="class or interface in java.lang" class="external-link">wait</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#wait(long)" title="class or interface in java.lang" class="external-link">wait</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#wait(long,int)" title="class or interface in java.lang" class="external-link">wait</a></code></div>
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</section>
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</li>
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</ul>
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</section>
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<section class="details">
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<ul class="details-list">
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<!-- ========= CONSTRUCTOR DETAIL ======== -->
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<li>
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<section class="constructor-details" id="constructor-detail">
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<h2>Constructor Details</h2>
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<ul class="member-list">
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<li>
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<section class="detail" id="&lt;init&gt;()">
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<h3>AFPFromFasta</h3>
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<div class="member-signature"><span class="modifiers">public</span>&nbsp;<span class="element-name"><a href="../src-html/demo/AFPFromFasta.html#line-48">AFPFromFasta</a></span>()</div>
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</section>
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</li>
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</ul>
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</section>
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</li>
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<!-- ============ METHOD DETAIL ========== -->
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<li>
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<section class="method-details" id="method-detail">
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<h2>Method Details</h2>
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<ul class="member-list">
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<li>
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<section class="detail" id="main(java.lang.String[])">
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<h3>main</h3>
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<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type">void</span>&nbsp;<span class="element-name"><a href="../src-html/demo/AFPFromFasta.html#line-50">main</a></span><wbr><span class="parameters">(<a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a>[]&nbsp;args)</span>
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throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Exception.html" title="class or interface in java.lang" class="external-link">Exception</a></span></div>
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<dl class="notes">
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<dt>Throws:</dt>
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<dd><code><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Exception.html" title="class or interface in java.lang" class="external-link">Exception</a></code></dd>
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