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<!DOCTYPE HTML>
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (11.0.10) on Fri Mar 12 13:02:30 CST 2021 -->
<title>Deprecated List (biojava-legacy 1.9.5 API)</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="dc.created" content="2021-03-12">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<link rel="stylesheet" type="text/css" href="jquery/jquery-ui.css" title="Style">
<script type="text/javascript" src="script.js"></script>
<script type="text/javascript" src="jquery/jszip/dist/jszip.min.js"></script>
<script type="text/javascript" src="jquery/jszip-utils/dist/jszip-utils.min.js"></script>
<!--[if IE]>
<script type="text/javascript" src="jquery/jszip-utils/dist/jszip-utils-ie.min.js"></script>
<![endif]-->
<script type="text/javascript" src="jquery/jquery-3.5.1.js"></script>
<script type="text/javascript" src="jquery/jquery-ui.js"></script>
</head>
<body>
<script type="text/javascript"><!--
try {
if (location.href.indexOf('is-external=true') == -1) {
parent.document.title="Deprecated List (biojava-legacy 1.9.5 API)";
}
}
catch(err) {
}
//-->
var pathtoroot = "./";
var useModuleDirectories = true;
loadScripts(document, 'script');</script>
<noscript>
<div>JavaScript is disabled on your browser.</div>
</noscript>
<header role="banner">
<nav role="navigation">
<div class="fixedNav">
<!-- ========= START OF TOP NAVBAR ======= -->
<div class="topNav"><a id="navbar.top">
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</a>
<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
<a id="navbar.top.firstrow">
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</a>
<ul class="navList" title="Navigation">
<li><a href="index.html">Overview</a></li>
<li>Package</li>
<li>Class</li>
<li>Use</li>
<li><a href="overview-tree.html">Tree</a></li>
<li class="navBarCell1Rev">Deprecated</li>
<li><a href="index-all.html">Index</a></li>
<li><a href="help-doc.html">Help</a></li>
</ul>
</div>
<div class="subNav">
<ul class="navList" id="allclasses_navbar_top">
<li><a href="allclasses.html">All Classes</a></li>
</ul>
<ul class="navListSearch">
<li><label for="search">SEARCH:</label>
<input type="text" id="search" value="search" disabled="disabled">
<input type="reset" id="reset" value="reset" disabled="disabled">
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</script>
</nav>
</header>
<main role="main">
<div class="header">
<h1 title="Deprecated API" class="title">Deprecated API</h1>
<h2 title="Contents">Contents</h2>
<ul>
<li><a href="#interface">Interfaces</a></li>
<li><a href="#class">Classes</a></li>
<li><a href="#exception">Exceptions</a></li>
<li><a href="#field">Fields</a></li>
<li><a href="#method">Methods</a></li>
<li><a href="#constructor">Constructors</a></li>
</ul>
</div>
<div class="contentContainer"><a id="interface">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<table class="deprecatedSummary">
<caption><span>Interfaces</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Interface</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SeqFileFormer.html" title="interface in org.biojava.bio.seq.io">org.biojava.bio.seq.io.SeqFileFormer</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/SequenceFactory.html" title="interface in org.biojava.bio.seq">org.biojava.bio.seq.SequenceFactory</a></th>
<td class="colLast">
<div class="deprecationComment">use org.biojavax.bio.seq.io.RichSequenceBuilder or
use org.biojavax.bio.seq.io.SequenceBuilder</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">org.biojava.bio.taxa.Taxon</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/TaxonFactory.html" title="interface in org.biojava.bio.taxa">org.biojava.bio.taxa.TaxonFactory</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/TaxonParser.html" title="interface in org.biojava.bio.taxa">org.biojava.bio.taxa.TaxonParser</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
</tbody>
</table>
</li>
</ul>
<a id="class">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<table class="deprecatedSummary">
<caption><span>Classes</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Class</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/Annotatable.AnnotationForwarder.html" title="class in org.biojava.bio">org.biojava.bio.Annotatable.AnnotationForwarder</a></th>
<td class="colLast">
<div class="deprecationComment">use
<code>new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)</code>
instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dist/Distribution.NullModelForwarder.html" title="class in org.biojava.bio.dist">org.biojava.bio.dist.Distribution.NullModelForwarder</a></th>
<td class="colLast">
<div class="deprecationComment">use
<code>new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)</code>
instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dist/SimpleDistributionTrainer.html" title="class in org.biojava.bio.dist">org.biojava.bio.dist.SimpleDistributionTrainer</a></th>
<td class="colLast">
<div class="deprecationComment">Distribution impls should be providing custom trainers.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/gui/sequence/SequencePoster.html" title="class in org.biojava.bio.gui.sequence">org.biojava.bio.gui.sequence.SequencePoster</a></th>
<td class="colLast">
<div class="deprecationComment">This doesn't handle loads of stuff. Use SequencePoster.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search">org.biojava.bio.search.SequenceDBSearchHit</a></th>
<td class="colLast">
<div class="deprecationComment">SimpleSeqSimilaritySearchHit has been made Annotatable
and is now functionally identical.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search">org.biojava.bio.search.SequenceDBSearchResult</a></th>
<td class="colLast">
<div class="deprecationComment">SimpleSeqSimilaritySearchResult has been made
Annotatable and is now functionally identical.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search">org.biojava.bio.search.SequenceDBSearchSubHit</a></th>
<td class="colLast">
<div class="deprecationComment">SimpleSeqSimilaritySearchSubHit has been made
Annotatable and is now functionally identical.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.BioSQLSequenceDB</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.DBHelper</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.HypersonicDBHelper</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/MySQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.MySQLDBHelper</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.OracleDBHelper</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/TaxonSQL.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.TaxonSQL</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/db/biosql/UnknownDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">org.biojava.bio.seq.db.biosql.UnknownDBHelper</a></th>
<td class="colLast">
<div class="deprecationComment">Use hibernate and org.biojavax.bio.db.*</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.EmblFileFormer</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.EmblLikeFormat</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io.EMBLFormat instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/EmblLikeLocationParser.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.EmblLikeLocationParser</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.EmblProcessor</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/FastaDescriptionLineParser.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.FastaDescriptionLineParser</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io.FastaFormat</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.FastaFormat</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io.FastaFormat</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.FeatureTableParser</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenbankFileFormer</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenbankFormat</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io.GenbankFormat</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenbankProcessor</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenbankXmlFormat.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenbankXmlFormat</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io.INSDseqFormat</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenEmblFeatureComparator.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenEmblFeatureComparator</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenEmblPropertyComparator.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenEmblPropertyComparator</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenpeptFormat.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.GenpeptFormat</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.OrganismParser</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.taxa framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/ProteinRefSeqFileFormer.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.ProteinRefSeqFileFormer</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/ProteinRefSeqProcessor.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.ProteinRefSeqProcessor</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/ReferenceAnnotation.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.ReferenceAnnotation</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SeqIOEventEmitter.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.SeqIOEventEmitter</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SeqIOTools.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.SeqIOTools</a></th>
<td class="colLast">
<div class="deprecationComment">use org.biojavax.bio.seq.RichSequence.IOTools</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SwissprotFileFormer.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.SwissprotFileFormer</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SwissprotProcessor.html" title="class in org.biojava.bio.seq.io">org.biojava.bio.seq.io.SwissprotProcessor</a></th>
<td class="colLast">
<div class="deprecationComment">Use org.biojavax.bio.seq.io framework instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.AbstractTaxon</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.EbiFormat</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.SimpleTaxon</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/SimpleTaxonFactory.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.SimpleTaxonFactory</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.WeakTaxon</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/WeakTaxonFactory.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.WeakTaxonFactory</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/stats/svm/LinearKernel.html" title="class in org.biojava.stats.svm">org.biojava.stats.svm.LinearKernel</a></th>
<td class="colLast">
<div class="deprecationComment">Just use SparseVector.kernel instead...</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils">org.biojava.utils.ProcessTools</a></th>
<td class="colLast">
<div class="deprecationComment">preferable to use org.biojava.utils.ExecRunner
or the org.biojava.utils.process package.</div>
</td>
</tr>
</tbody>
</table>
</li>
</ul>
<a id="exception">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<table class="deprecatedSummary">
<caption><span>Exceptions</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Exceptions</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa">org.biojava.bio.taxa.CircularReferenceException</a></th>
<td class="colLast">
<div class="deprecationComment">replaced by classes in <a href="org/biojavax/bio/taxa/package-summary.html"><code>org.biojavax.bio.taxa</code></a></div>
</td>
</tr>
</tbody>
</table>
</li>
</ul>
<a id="field">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<table class="deprecatedSummary">
<caption><span>Fields</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Field</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/gff/GFFRecord.html#NO_FRAME">org.biojava.bio.program.gff.GFFRecord.NO_FRAME</a></th>
<td class="colLast">
<div class="deprecationComment">Use GFFTools.NO_FRAME instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/gff/GFFRecord.html#NO_SCORE">org.biojava.bio.program.gff.GFFRecord.NO_SCORE</a></th>
<td class="colLast">
<div class="deprecationComment">Use GFFTools.NO_SCORE instead</div>
</td>
</tr>
</tbody>
</table>
</li>
</ul>
<a id="method">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<table class="deprecatedSummary">
<caption><span>Methods</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Method</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dist/DistributionTools.html#generateOrderNSequence(java.lang.String,org.biojava.bio.dist.OrderNDistribution,int)">org.biojava.bio.dist.DistributionTools.generateOrderNSequence​(String, OrderNDistribution, int)</a></th>
<td class="colLast">
<div class="deprecationComment">use generateSequence() or generateSymbolList() instead.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dp/MarkovModel.html#heads()">org.biojava.bio.dp.MarkovModel.heads()</a></th>
<td class="colLast">
<div class="deprecationComment">use <code>advance().length</code></div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/gff/GFFTools.html#readGFF(java.lang.String)">org.biojava.bio.program.gff.GFFTools.readGFF​(String)</a></th>
<td class="colLast">
<div class="deprecationComment">use: readGff(File)</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/phred/PhredFormat.html#getDefaultFormat()">org.biojava.bio.program.phred.PhredFormat.getDefaultFormat()</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/phred/PhredFormat.html#writeSequence(org.biojava.bio.seq.Sequence,java.lang.String,java.io.PrintStream)">org.biojava.bio.program.phred.PhredFormat.writeSequence​(Sequence, String, PrintStream)</a></th>
<td class="colLast">
<div class="deprecationComment">use writeSequence(Sequence seq, PrintStream os)</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/sax/FastaSearchSAXParser.html#setQuerySeq(java.lang.String)">org.biojava.bio.program.sax.FastaSearchSAXParser.setQuerySeq​(String)</a></th>
<td class="colLast">
<div class="deprecationComment">use <code>setQueryID</code> instead.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/program/sax/FastaSearchSAXParser.html#setSubjectDB(java.lang.String)">org.biojava.bio.program.sax.FastaSearchSAXParser.setSubjectDB​(String)</a></th>
<td class="colLast">
<div class="deprecationComment">use <code>setDatabaseID</code> instead.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/impl/SimpleSequence.html#createFeature(org.biojava.bio.seq.FeatureHolder,org.biojava.bio.seq.Feature.Template)">org.biojava.bio.seq.impl.SimpleSequence.createFeature​(FeatureHolder, Feature.Template)</a></th>
<td class="colLast">
<div class="deprecationComment">Please use new 1-arg createFeature instead.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/EmblLikeFormat.html#getDefaultFormat()">org.biojava.bio.seq.io.EmblLikeFormat.getDefaultFormat()</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/EmblLikeFormat.html#writeSequence(org.biojava.bio.seq.Sequence,java.lang.String,java.io.PrintStream)">org.biojava.bio.seq.io.EmblLikeFormat.writeSequence​(Sequence, String, PrintStream)</a></th>
<td class="colLast">
<div class="deprecationComment">use writeSequence(Sequence seq, PrintStream os)</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/FastaFormat.html#getDefaultFormat()">org.biojava.bio.seq.io.FastaFormat.getDefaultFormat()</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/FastaFormat.html#writeSequence(org.biojava.bio.seq.Sequence,java.lang.String,java.io.PrintStream)">org.biojava.bio.seq.io.FastaFormat.writeSequence​(Sequence, String, PrintStream)</a></th>
<td class="colLast">
<div class="deprecationComment">use writeSequence(Sequence seq, PrintStream os)</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GAMEFormat.html#getDefaultFormat()">org.biojava.bio.seq.io.GAMEFormat.getDefaultFormat()</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenbankFormat.html#getDefaultFormat()">org.biojava.bio.seq.io.GenbankFormat.getDefaultFormat()</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/GenbankFormat.html#writeSequence(org.biojava.bio.seq.Sequence,java.lang.String,java.io.PrintStream)">org.biojava.bio.seq.io.GenbankFormat.writeSequence​(Sequence, String, PrintStream)</a></th>
<td class="colLast">
<div class="deprecationComment">use writeSequence(Sequence seq, PrintStream os)</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SeqIOTools.html#formatToFactory(org.biojava.bio.seq.io.SequenceFormat,org.biojava.bio.symbol.Alphabet)">org.biojava.bio.seq.io.SeqIOTools.formatToFactory​(SequenceFormat, Alphabet)</a></th>
<td class="colLast">
<div class="deprecationComment">as this essentially duplicates the operation
available in the method <code>identifyBuilderFactory</code>.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SeqIOTools.html#guessFileType(java.io.File)">org.biojava.bio.seq.io.SeqIOTools.guessFileType​(File)</a></th>
<td class="colLast">
<div class="deprecationComment">because there is no standard file naming convention
and guessing by file name is inherantly error prone and bad.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SequenceFormat.html#getDefaultFormat()">org.biojava.bio.seq.io.SequenceFormat.getDefaultFormat()</a></th>
<td class="colLast">
<div class="deprecationComment">new implementations should only write a single
format.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/io/SequenceFormat.html#writeSequence(org.biojava.bio.seq.Sequence,java.lang.String,java.io.PrintStream)">org.biojava.bio.seq.io.SequenceFormat.writeSequence​(Sequence, String, PrintStream)</a></th>
<td class="colLast">
<div class="deprecationComment">use writeSequence(Sequence seq, PrintStream os)</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/seq/RNATools.html#transcribe(org.biojava.bio.symbol.SymbolList)">org.biojava.bio.seq.RNATools.transcribe​(SymbolList)</a></th>
<td class="colLast">
<div class="deprecationComment">The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or
DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/symbol/AlphabetManager.html#createSymbol(char,java.lang.String,org.biojava.bio.Annotation)">org.biojava.bio.symbol.AlphabetManager.createSymbol​(char, String, Annotation)</a></th>
<td class="colLast">
<div class="deprecationComment">Use the two-arg version of this method instead.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/symbol/AlphabetManager.html#instance()">org.biojava.bio.symbol.AlphabetManager.instance()</a></th>
<td class="colLast">
<div class="deprecationComment">all AlphabetManager methods have become static</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/symbol/AlphabetManager.html#symbolForName(java.lang.String)">org.biojava.bio.symbol.AlphabetManager.symbolForName​(String)</a></th>
<td class="colLast">
<div class="deprecationComment">use symbolForLifeScienceID() instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/utils/Changeable.html#addChangeListener(org.biojava.utils.ChangeListener)">org.biojava.utils.Changeable.addChangeListener​(ChangeListener)</a></th>
<td class="colLast">
<div class="deprecationComment">use addChangeListener(cl, ChangeType.UNKNOWN)</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/utils/Changeable.html#removeChangeListener(org.biojava.utils.ChangeListener)">org.biojava.utils.Changeable.removeChangeListener​(ChangeListener)</a></th>
<td class="colLast">
<div class="deprecationComment">use removeChangeListener(cl, ChangeType.UNKNOWN)</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/bio/phylo/io/nexus/TreesBlock.html#addTree(java.lang.String,org.jgrapht.WeightedGraph)">org.biojavax.bio.phylo.io.nexus.TreesBlock.addTree​(String, WeightedGraph<String, DefaultWeightedEdge>)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/bio/seq/io/RichSeqIOListener.html#setURI(java.lang.String)">org.biojavax.bio.seq.io.RichSeqIOListener.setURI​(String)</a></th>
<td class="colLast">
<div class="deprecationComment">There is no clear mapping between URI and BioSQL. This
method is no longer used or supported in biojavax. Don't use it. Calling
it may result in exceptions. Use instead setName(String name),
setAccession(String accession), setVersion(int version) etc as
appropriate.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/SimpleRichAnnotation.html#containsProperty(java.lang.Object)">org.biojavax.SimpleRichAnnotation.containsProperty​(Object)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/SimpleRichAnnotation.html#getProperties(java.lang.Object)">org.biojavax.SimpleRichAnnotation.getProperties​(Object)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/SimpleRichAnnotation.html#getProperty(java.lang.Object)">org.biojavax.SimpleRichAnnotation.getProperty​(Object)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/SimpleRichAnnotation.html#removeProperty(java.lang.Object)">org.biojavax.SimpleRichAnnotation.removeProperty​(Object)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojavax/SimpleRichAnnotation.html#setProperty(java.lang.Object,java.lang.Object)">org.biojavax.SimpleRichAnnotation.setProperty​(Object, Object)</a></th>
<td class="colLast"> </td>
</tr>
</tbody>
</table>
</li>
</ul>
<a id="constructor">
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<ul class="blockList">
<li class="blockList">
<table class="deprecatedSummary">
<caption><span>Constructors</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Constructor</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/BioError.html#%3Cinit%3E(java.lang.Throwable,java.lang.String)">org.biojava.bio.BioError​(Throwable, String)</a></th>
<td class="colLast">
<div class="deprecationComment">Use BioError(message, ex) instead.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/BioException.html#%3Cinit%3E(java.lang.Throwable,java.lang.String)">org.biojava.bio.BioException​(Throwable, String)</a></th>
<td class="colLast">
<div class="deprecationComment">use new BioException(message, ex) instead</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/BioRuntimeException.html#%3Cinit%3E(java.lang.Throwable,java.lang.String)">org.biojava.bio.BioRuntimeException​(Throwable, String)</a></th>
<td class="colLast">
<div class="deprecationComment">use new BioRuntimeException(message, ex) instead</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dp/ProfileHMM.html#%3Cinit%3E(org.biojava.bio.symbol.Alphabet,int,org.biojava.bio.dist.DistributionFactory,org.biojava.bio.dist.DistributionFactory)">org.biojava.bio.dp.ProfileHMM​(Alphabet, int, DistributionFactory, DistributionFactory)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dp/SimpleDotState.html#%3Cinit%3E(char,java.lang.String,org.biojava.bio.Annotation)">org.biojava.bio.dp.SimpleDotState​(char, String, Annotation)</a></th>
<td class="colLast">
<div class="deprecationComment">token is ignored since 1.2. Use the 2-arg constructor instead.</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/dp/SimpleMarkovModel.html#%3Cinit%3E(int,org.biojava.bio.symbol.Alphabet)">org.biojava.bio.dp.SimpleMarkovModel​(int, Alphabet)</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/proteomics/Protease.html#%3Cinit%3E(org.biojava.bio.symbol.SymbolList,boolean,org.biojava.bio.symbol.SymbolList)">org.biojava.bio.proteomics.Protease​(SymbolList, boolean, SymbolList)</a></th>
<td class="colLast">
<div class="deprecationComment">Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/bio/symbol/PackedSymbolListFactory.html#%3Cinit%3E(boolean)">org.biojava.bio.symbol.PackedSymbolListFactory​(boolean)</a></th>
<td class="colLast">
<div class="deprecationComment">the argumentless constructor creates a SymbolListFactory
that will autoselect the packing appropriately.</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/directory/RegistryException.html#%3Cinit%3E(java.lang.Throwable,java.lang.String)">org.biojava.directory.RegistryException​(Throwable, String)</a></th>
<td class="colLast">
<div class="deprecationComment">use new RegistryException(message, cause)</div>
</td>
</tr>
<tr class="rowColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/utils/ChangeVetoException.html#%3Cinit%3E(java.lang.Throwable,java.lang.String)">org.biojava.utils.ChangeVetoException​(Throwable, String)</a></th>
<td class="colLast">
<div class="deprecationComment">use new ChangeVetoException(reason, ex);</div>
</td>
</tr>
<tr class="altColor">
<th class="colDeprecatedItemName" scope="row"><a href="org/biojava/utils/ParserException.html#%3Cinit%3E(java.lang.Throwable,java.lang.String)">org.biojava.utils.ParserException​(Throwable, String)</a></th>
<td class="colLast">
<div class="deprecationComment">use new ParserException(detail, t)</div>
</td>
</tr>
</tbody>
</table>
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