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<!DOCTYPE HTML>
<html lang>
<head>
<!-- Generated by javadoc (21) on Wed Jan 08 16:43:01 PST 2025 -->
<title>Deprecated List (biojava 7.1.4 API)</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta name="dc.created" content="2025-01-08">
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<h1 title="Deprecated API" class="title">Deprecated API</h1>
</div>
<h2 title="Contents">Contents</h2>
<ul class="contents-list">
<li id="contents-method"><a href="#method">Methods</a></li>
<li id="contents-constructor"><a href="#constructor">Constructors</a></li>
</ul>
<ul class="block-list">
<li>
<div id="method">
<div class="caption"><span>Deprecated Methods</span></div>
<div class="summary-table two-column-summary">
<div class="table-header col-first">Method</div>
<div class="table-header col-last">Description</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/genome/parsers/gff/LocIterator.html#main(java.lang.String%5B%5D)">org.biojava.nbio.genome.parsers.gff.LocIterator.main<wbr>(String[])</a></div>
<div class="col-last even-row-color"> </div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/align/client/PdbPair.html#getPDBCode1()">org.biojava.nbio.structure.align.client.PdbPair.getPDBCode1()</a></div>
<div class="col-last odd-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/align/client/PdbPair.html#getPDBCode1()"><code>PdbPair.getPDBCode1()</code></a> instead</div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/align/client/PdbPair.html#getPDBCode2()">org.biojava.nbio.structure.align.client.PdbPair.getPDBCode2()</a></div>
<div class="col-last even-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/align/client/PdbPair.html#getPDBCode2()"><code>PdbPair.getPDBCode2()</code></a> instead</div>
</div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html#showMultipleAligmentPanel(org.biojava.nbio.structure.align.multiple.MultipleAlignment,org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol)">org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay.showMultipleAligmentPanel<wbr>(MultipleAlignment, AbstractAlignmentJmol)</a></div>
<div class="col-last odd-row-color">
<div class="block">Replace with </div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/contact/Grid.html#getContacts()">org.biojava.nbio.structure.contact.Grid.getContacts()</a></div>
<div class="col-last even-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/contact/Grid.html#getAtomContacts()"><code>Grid.getAtomContacts()</code></a> instead</div>
</div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/PDBHeader.html#getDescription()">org.biojava.nbio.structure.PDBHeader.getDescription()</a></div>
<div class="col-last odd-row-color">
<div class="block">will be removed later. Use <a href="org/biojava/nbio/structure/PDBHeader.html#getKeywords()"><code>PDBHeader.getKeywords()</code></a> if you use
<code>description</code> to keep the keywords.</div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/PDBHeader.html#getIdCode()">org.biojava.nbio.structure.PDBHeader.getIdCode()</a></div>
<div class="col-last even-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/PDBHeader.html#getPdbId()"><code>PDBHeader.getPdbId()</code></a></div>
</div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/PDBHeader.html#setDescription(java.lang.String)">org.biojava.nbio.structure.PDBHeader.setDescription<wbr>(String)</a></div>
<div class="col-last odd-row-color">
<div class="block">will be removed later. Use <a href="org/biojava/nbio/structure/PDBHeader.html#getKeywords()"><code>PDBHeader.getKeywords()</code></a> if you use
<code>description</code> to keep the keywords.</div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/PDBHeader.html#setIdCode(java.lang.String)">org.biojava.nbio.structure.PDBHeader.setIdCode<wbr>(String)</a></div>
<div class="col-last even-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/PDBHeader.html#setPdbId(org.biojava.nbio.structure.PdbId)"><code>PDBHeader.setPdbId(PdbId)</code></a></div>
</div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/scop/ScopDomain.html#setPdbId(java.lang.String)">org.biojava.nbio.structure.scop.ScopDomain.setPdbId<wbr>(String)</a></div>
<div class="col-last odd-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/scop/ScopDomain.html#setPdbId(org.biojava.nbio.structure.PdbId)"><code>ScopDomain.setPdbId(PdbId)</code></a></div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/Structure.html#getPDBCode()">org.biojava.nbio.structure.Structure.getPDBCode()</a></div>
<div class="col-last even-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/Structure.html#getPdbId()"><code>Structure.getPdbId()</code></a> to get a <a href="org/biojava/nbio/structure/PdbId.html" title="class in org.biojava.nbio.structure"><code>PdbId</code></a> object or getPdbId().getId() to get a <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"><code>String</code></a></div>
</div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/Structure.html#setPDBCode(java.lang.String)">org.biojava.nbio.structure.Structure.setPDBCode<wbr>(String)</a></div>
<div class="col-last odd-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/Structure.html#setPdbId(org.biojava.nbio.structure.PdbId)"><code>Structure.setPdbId(PdbId)</code></a></div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/StructureImpl.html#getPDBCode()">org.biojava.nbio.structure.StructureImpl.getPDBCode()</a></div>
<div class="col-last even-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/StructureImpl.html#getPdbId()"><code>StructureImpl.getPdbId()</code></a> to get a <a href="org/biojava/nbio/structure/PdbId.html" title="class in org.biojava.nbio.structure"><code>PdbId</code></a> object or getPdbId().getId() to get a <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"><code>String</code></a></div>
</div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/structure/StructureImpl.html#setPDBCode(java.lang.String)">org.biojava.nbio.structure.StructureImpl.setPDBCode<wbr>(String)</a></div>
<div class="col-last odd-row-color">
<div class="block">use <a href="org/biojava/nbio/structure/StructureImpl.html#setPdbId(org.biojava.nbio.structure.PdbId)"><code>StructureImpl.setPdbId(PdbId)</code></a></div>
</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.html#setRefineResult(boolean)">org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult<wbr>(boolean)</a></div>
<div class="col-last even-row-color"></div>
</div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div id="constructor">
<div class="caption"><span>Deprecated Constructors</span></div>
<div class="summary-table two-column-summary">
<div class="table-header col-first">Constructor</div>
<div class="table-header col-last">Description</div>
<div class="col-summary-item-name even-row-color"><a href="org/biojava/nbio/core/sequence/GeneSequence.html#%3Cinit%3E(org.biojava.nbio.core.sequence.ChromosomeSequence,int,int,org.biojava.nbio.core.sequence.Strand)">org.biojava.nbio.core.sequence.GeneSequence<wbr>(ChromosomeSequence, int, int, Strand)</a></div>
<div class="col-last even-row-color"> </div>
<div class="col-summary-item-name odd-row-color"><a href="org/biojava/nbio/core/sequence/TranscriptSequence.html#%3Cinit%3E(org.biojava.nbio.core.sequence.GeneSequence,int,int)">org.biojava.nbio.core.sequence.TranscriptSequence<wbr>(GeneSequence, int, int)</a></div>
<div class="col-last odd-row-color"> </div>
</div>
</div>
</li>
</ul>
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