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<!DOCTYPE HTML>
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<title>Constant Field Values (biojava 7.1.4 API)</title>
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<h1 title="Constant Field Values" class="title">Constant Field Values</h1>
</div>
<section class="packages">
<h2 title="Contents">Contents</h2>
<ul class="contents-list">
<li><a href="#org.biojava">org.biojava.*</a></li>
</ul>
</section>
<section class="constants-summary" id="org.biojava">
<h2 title="org.biojava.*">org.biojava.*</h2>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.aaproperties.profeat.convertor.<a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convertor</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.group1">public static final char</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#group1">group1</a></code></div>
<div class="col-last even-row-color"><code>'1'</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.group2">public static final char</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#group2">group2</a></code></div>
<div class="col-last odd-row-color"><code>'2'</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.group3">public static final char</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#group3">group3</a></code></div>
<div class="col-last even-row-color"><code>'3'</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.unknownGroup">public static final char</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#unknownGroup">unknownGroup</a></code></div>
<div class="col-last odd-row-color"><code>'0'</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.alignment.io.<a href="org/biojava/nbio/alignment/io/StockholmFileParser.html" title="class in org.biojava.nbio.alignment.io">StockholmFileParser</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmFileParser.INFINITY">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmFileParser.html#INFINITY">INFINITY</a></code></div>
<div class="col-last even-row-color"><code>-1</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.alignment.io.<a href="org/biojava/nbio/alignment/io/StockholmStructure.html" title="class in org.biojava.nbio.alignment.io">StockholmStructure</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.PFAM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.html#PFAM">PFAM</a></code></div>
<div class="col-last even-row-color"><code>"PFAM"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.RFAM">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.html#RFAM">RFAM</a></code></div>
<div class="col-last odd-row-color"><code>"RFAM"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.alignment.io.<a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html" title="class in org.biojava.nbio.alignment.io">StockholmStructure.DatabaseReference</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.EXPERT">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#EXPERT">EXPERT</a></code></div>
<div class="col-last even-row-color"><code>"EXPERT"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.HOMSTRAD">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#HOMSTRAD">HOMSTRAD</a></code></div>
<div class="col-last odd-row-color"><code>"HOMSTRAD"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.INTERPRO">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#INTERPRO">INTERPRO</a></code></div>
<div class="col-last even-row-color"><code>"INTERPRO"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.LOAD">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#LOAD">LOAD</a></code></div>
<div class="col-last odd-row-color"><code>"LOAD"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.MIM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#MIM">MIM</a></code></div>
<div class="col-last even-row-color"><code>"MIM"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PDB">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PDB">PDB</a></code></div>
<div class="col-last odd-row-color"><code>"PDB"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PFAMB">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PFAMB">PFAMB</a></code></div>
<div class="col-last even-row-color"><code>"PFAMB"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PRINTS">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PRINTS">PRINTS</a></code></div>
<div class="col-last odd-row-color"><code>"PRINTS"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PROSITE">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PROSITE">PROSITE</a></code></div>
<div class="col-last even-row-color"><code>"PROSITE"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PROSITE_PROFILE">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PROSITE_PROFILE">PROSITE_PROFILE</a></code></div>
<div class="col-last odd-row-color"><code>"PROSITE_PROFILE"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.SCOP">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#SCOP">SCOP</a></code></div>
<div class="col-last even-row-color"><code>"SCOP"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.SMART">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#SMART">SMART</a></code></div>
<div class="col-last odd-row-color"><code>"SMART"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.URL">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#URL">URL</a></code></div>
<div class="col-last even-row-color"><code>"URL"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.exceptions.<a href="org/biojava/nbio/core/exceptions/Messages.html" title="class in org.biojava.nbio.core.exceptions">Messages</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.exceptions.Messages.ENDOFFILE">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/exceptions/Messages.html#ENDOFFILE">ENDOFFILE</a></code></div>
<div class="col-last even-row-color"><code>"end of file"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.exceptions.Messages.SECTIONKEYNULL">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/exceptions/Messages.html#SECTIONKEYNULL">SECTIONKEYNULL</a></code></div>
<div class="col-last odd-row-color"><code>"section key is null"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="class in org.biojava.nbio.core.sequence.io">GenbankSequenceParser<S,<wbr>C></a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.ACCESSION_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#ACCESSION_TAG">ACCESSION_TAG</a></code></div>
<div class="col-last even-row-color"><code>"ACCESSION"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.AUTHORS_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#AUTHORS_TAG">AUTHORS_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"AUTHORS"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.BASE_COUNT_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#BASE_COUNT_TAG">BASE_COUNT_TAG</a></code></div>
<div class="col-last even-row-color"><code>"BASE"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.BASE_COUNT_TAG_FULL">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#BASE_COUNT_TAG_FULL">BASE_COUNT_TAG_FULL</a></code></div>
<div class="col-last odd-row-color"><code>"BASE COUNT"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.COMMENT_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#COMMENT_TAG">COMMENT_TAG</a></code></div>
<div class="col-last even-row-color"><code>"COMMENT"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.CONSORTIUM_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"CONSRTM"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.DBLINK">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#DBLINK">DBLINK</a></code></div>
<div class="col-last even-row-color"><code>"DBLINK"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.DBSOURCE">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#DBSOURCE">DBSOURCE</a></code></div>
<div class="col-last odd-row-color"><code>"DBSOURCE"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.DEFINITION_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#DEFINITION_TAG">DEFINITION_TAG</a></code></div>
<div class="col-last even-row-color"><code>"DEFINITION"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.END_SEQUENCE_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"//"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.FEATURE_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#FEATURE_TAG">FEATURE_TAG</a></code></div>
<div class="col-last even-row-color"><code>"FEATURES"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.GENBANK_FORMAT">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#GENBANK_FORMAT">GENBANK_FORMAT</a></code></div>
<div class="col-last odd-row-color"><code>"GENBANK"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.JOURNAL_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#JOURNAL_TAG">JOURNAL_TAG</a></code></div>
<div class="col-last even-row-color"><code>"JOURNAL"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.KEYWORDS_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#KEYWORDS_TAG">KEYWORDS_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"KEYWORDS"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.LOCUS_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#LOCUS_TAG">LOCUS_TAG</a></code></div>
<div class="col-last even-row-color"><code>"LOCUS"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.MEDLINE_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#MEDLINE_TAG">MEDLINE_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"MEDLINE"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.ORGANISM_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#ORGANISM_TAG">ORGANISM_TAG</a></code></div>
<div class="col-last even-row-color"><code>"ORGANISM"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.PRIMARY">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#PRIMARY">PRIMARY</a></code></div>
<div class="col-last odd-row-color"><code>"PRIMARY"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.PUBMED_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#PUBMED_TAG">PUBMED_TAG</a></code></div>
<div class="col-last even-row-color"><code>"PUBMED"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.REFERENCE_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#REFERENCE_TAG">REFERENCE_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"REFERENCE"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.REMARK_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#REMARK_TAG">REMARK_TAG</a></code></div>
<div class="col-last even-row-color"><code>"REMARK"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.SOURCE_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#SOURCE_TAG">SOURCE_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"SOURCE"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.START_SEQUENCE_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></code></div>
<div class="col-last even-row-color"><code>"ORIGIN"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.TITLE_TAG">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#TITLE_TAG">TITLE_TAG</a></code></div>
<div class="col-last odd-row-color"><code>"TITLE"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.VERSION_TAG">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#VERSION_TAG">VERSION_TAG</a></code></div>
<div class="col-last even-row-color"><code>"VERSION"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html" title="class in org.biojava.nbio.core.sequence.io">GenbankWriterHelper</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankWriterHelper.CIRCULAR_DNA">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html#CIRCULAR_DNA">CIRCULAR_DNA</a></code></div>
<div class="col-last even-row-color"><code>"circular"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenbankWriterHelper.LINEAR_DNA">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html#LINEAR_DNA">LINEAR_DNA</a></code></div>
<div class="col-last odd-row-color"><code>"linear"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io">GenericInsdcHeaderFormat<S,<wbr>C></a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.MAX_WIDTH">protected static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#MAX_WIDTH">MAX_WIDTH</a></code></div>
<div class="col-last even-row-color"><code>80</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.QUALIFIER_INDENT">protected static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#QUALIFIER_INDENT">QUALIFIER_INDENT</a></code></div>
<div class="col-last odd-row-color"><code>21</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.QUALIFIER_INDENT_STR">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#QUALIFIER_INDENT_STR">QUALIFIER_INDENT_STR</a></code></div>
<div class="col-last even-row-color"><code>" "</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.QUALIFIER_INDENT_TMP">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#QUALIFIER_INDENT_TMP">QUALIFIER_INDENT_TMP</a></code></div>
<div class="col-last odd-row-color"><code>" %s "</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/IUPACParser.html" title="class in org.biojava.nbio.core.sequence.io">IUPACParser</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.IUPACParser.IUPAC_LOCATION">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/IUPACParser.html#IUPAC_LOCATION">IUPAC_LOCATION</a></code></div>
<div class="col-last even-row-color"><code>"org/biojava/nbio/core/sequence/iupac.txt"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.io.template.<a href="org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template">GenbankHeaderFormatInterface<S,<wbr>C></a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface.UNKNOWN_DNA">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html#UNKNOWN_DNA">UNKNOWN_DNA</a></code></div>
<div class="col-last even-row-color"><code>"UNK"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.loader.<a href="org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader">UniprotProxySequenceReader<C></a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader.DEFAULT_UNIPROT_BASE_URL">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.html#DEFAULT_UNIPROT_BASE_URL">DEFAULT_UNIPROT_BASE_URL</a></code></div>
<div class="col-last even-row-color"><code>"https://www.uniprot.org"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.location.<a href="org/biojava/nbio/core/sequence/location/InsdcParser.html" title="class in org.biojava.nbio.core.sequence.location">InsdcParser</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.location.InsdcParser.locationSplitPattern">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/location/InsdcParser.html#locationSplitPattern">locationSplitPattern</a></code></div>
<div class="col-last even-row-color"><code>",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.sequence.storage.<a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html" title="class in org.biojava.nbio.core.sequence.storage">BitSequenceReader.BitArrayWorker<C></a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker.BYTES_PER_INT">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html#BYTES_PER_INT">BYTES_PER_INT</a></code></div>
<div class="col-last even-row-color"><code>32</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.core.util.<a href="org/biojava/nbio/core/util/Hashcoder.html" title="class in org.biojava.nbio.core.util">Hashcoder</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.util.Hashcoder.PRIME">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/util/Hashcoder.html#PRIME">PRIME</a></code></div>
<div class="col-last even-row-color"><code>79</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.util.Hashcoder.SEED">public static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/util/Hashcoder.html#SEED">SEED</a></code></div>
<div class="col-last odd-row-color"><code>9</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.core.util.<a href="org/biojava/nbio/core/util/InputStreamProvider.html" title="class in org.biojava.nbio.core.util">InputStreamProvider</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.util.InputStreamProvider.CACHE_PROPERTY">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/util/InputStreamProvider.html#CACHE_PROPERTY">CACHE_PROPERTY</a></code></div>
<div class="col-last even-row-color"><code>"biojava.cache.files"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.core.util.InputStreamProvider.GZIP_MAGIC">public static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/core/util/InputStreamProvider.html#GZIP_MAGIC">GZIP_MAGIC</a></code></div>
<div class="col-last odd-row-color"><code>8075</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.core.util.<a href="org/biojava/nbio/core/util/SequenceTools.html" title="class in org.biojava.nbio.core.util">SequenceTools</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.util.SequenceTools.NUCLEOTIDE_LETTERS">protected static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/util/SequenceTools.html#NUCLEOTIDE_LETTERS">NUCLEOTIDE_LETTERS</a></code></div>
<div class="col-last even-row-color"><code>"GCTAUXN"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.core.util.<a href="org/biojava/nbio/core/util/SoftHashMap.html" title="class in org.biojava.nbio.core.util">SoftHashMap<K,<wbr>V></a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.core.util.SoftHashMap.DEFAULT_LIMIT">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/core/util/SoftHashMap.html#DEFAULT_LIMIT">DEFAULT_LIMIT</a></code></div>
<div class="col-last even-row-color"><code>1</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.genome.parsers.cytoband.<a href="org/biojava/nbio/genome/parsers/cytoband/CytobandParser.html" title="class in org.biojava.nbio.genome.parsers.cytoband">CytobandParser</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.genome.parsers.cytoband.CytobandParser.DEFAULT_LOCATION">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/genome/parsers/cytoband/CytobandParser.html#DEFAULT_LOCATION">DEFAULT_LOCATION</a></code></div>
<div class="col-last even-row-color"><code>"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.genome.parsers.genename.<a href="org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html" title="class in org.biojava.nbio.genome.parsers.genename">GeneChromosomePositionParser</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser.DEFAULT_MAPPING_URL">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html#DEFAULT_MAPPING_URL">DEFAULT_MAPPING_URL</a></code></div>
<div class="col-last even-row-color"><code>"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.genome.parsers.genename.<a href="org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html" title="class in org.biojava.nbio.genome.parsers.genename">GeneNamesParser</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.genome.parsers.genename.GeneNamesParser.DEFAULT_GENENAMES_URL">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html#DEFAULT_GENENAMES_URL">DEFAULT_GENENAMES_URL</a></code></div>
<div class="col-last even-row-color"><code>"https://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.genome.util.<a href="org/biojava/nbio/genome/util/ChromosomeMappingTools.html" title="class in org.biojava.nbio.genome.util">ChromosomeMappingTools</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.genome.util.ChromosomeMappingTools.CDS">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/genome/util/ChromosomeMappingTools.html#CDS">CDS</a></code></div>
<div class="col-last even-row-color"><code>"CDS"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.genome.util.ChromosomeMappingTools.CHROMOSOME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/genome/util/ChromosomeMappingTools.html#CHROMOSOME">CHROMOSOME</a></code></div>
<div class="col-last odd-row-color"><code>"CHROMOSOME"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.ontology.<a href="org/biojava/nbio/ontology/Synonym.html" title="class in org.biojava.nbio.ontology">Synonym</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.Synonym.BROAD_SYNONYM">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/Synonym.html#BROAD_SYNONYM">BROAD_SYNONYM</a></code></div>
<div class="col-last even-row-color"><code>3</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.Synonym.EXACT_SYNONYM">public static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/Synonym.html#EXACT_SYNONYM">EXACT_SYNONYM</a></code></div>
<div class="col-last odd-row-color"><code>1</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.Synonym.NARROW_SYNONYM">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/Synonym.html#NARROW_SYNONYM">NARROW_SYNONYM</a></code></div>
<div class="col-last even-row-color"><code>2</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.Synonym.RELATED_SYNONYM">public static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/Synonym.html#RELATED_SYNONYM">RELATED_SYNONYM</a></code></div>
<div class="col-last odd-row-color"><code>0</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.Synonym.UNKNOWN_SCOPE">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/Synonym.html#UNKNOWN_SCOPE">UNKNOWN_SCOPE</a></code></div>
<div class="col-last even-row-color"><code>-1</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.ontology.obo.<a href="org/biojava/nbio/ontology/obo/OboFileHandler.html" title="class in org.biojava.nbio.ontology.obo">OboFileHandler</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.ALT_ID">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#ALT_ID">ALT_ID</a></code></div>
<div class="col-last even-row-color"><code>"alt_id"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.BROAD_SYNONYM">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#BROAD_SYNONYM">BROAD_SYNONYM</a></code></div>
<div class="col-last odd-row-color"><code>"broad_synonym"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.COMMENT">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#COMMENT">COMMENT</a></code></div>
<div class="col-last even-row-color"><code>"comment"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.DEF">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#DEF">DEF</a></code></div>
<div class="col-last odd-row-color"><code>"def"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.DISJOINT_FROM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#DISJOINT_FROM">DISJOINT_FROM</a></code></div>
<div class="col-last even-row-color"><code>"disjoint_from"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.EXACT_SYNONYM">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#EXACT_SYNONYM">EXACT_SYNONYM</a></code></div>
<div class="col-last odd-row-color"><code>"exact_synonym"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.ID_KEY">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#ID_KEY">ID_KEY</a></code></div>
<div class="col-last even-row-color"><code>"id"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.INTERSECTION_OF">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#INTERSECTION_OF">INTERSECTION_OF</a></code></div>
<div class="col-last odd-row-color"><code>"intersection_of"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.IS_A">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#IS_A">IS_A</a></code></div>
<div class="col-last even-row-color"><code>"is_a"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.IS_OBSOLETE">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#IS_OBSOLETE">IS_OBSOLETE</a></code></div>
<div class="col-last odd-row-color"><code>"is_obsolete"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#NAME">NAME</a></code></div>
<div class="col-last even-row-color"><code>"name"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#NAMESPACE">NAMESPACE</a></code></div>
<div class="col-last odd-row-color"><code>"namespace"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.NARROW_SYNONYM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#NARROW_SYNONYM">NARROW_SYNONYM</a></code></div>
<div class="col-last even-row-color"><code>"narrow_synonym"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.ONTOLOGY">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#ONTOLOGY">ONTOLOGY</a></code></div>
<div class="col-last odd-row-color"><code>"ontologys"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.REL_SYNONYM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#REL_SYNONYM">REL_SYNONYM</a></code></div>
<div class="col-last even-row-color"><code>"related_synonym"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.RELATIONSHIP">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#RELATIONSHIP">RELATIONSHIP</a></code></div>
<div class="col-last odd-row-color"><code>"relationship"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.REPLACED_BY">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#REPLACED_BY">REPLACED_BY</a></code></div>
<div class="col-last even-row-color"><code>"replaced_by"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.SUBSET">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#SUBSET">SUBSET</a></code></div>
<div class="col-last odd-row-color"><code>"subset"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.SYNONYM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#SYNONYM">SYNONYM</a></code></div>
<div class="col-last even-row-color"><code>"synonym"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.TERM">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#TERM">TERM</a></code></div>
<div class="col-last odd-row-color"><code>"Term"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.TYPEDEF">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#TYPEDEF">TYPEDEF</a></code></div>
<div class="col-last even-row-color"><code>"Typedef"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ontology.obo.OboFileHandler.XREF_ANALOG">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html#XREF_ANALOG">XREF_ANALOG</a></code></div>
<div class="col-last odd-row-color"><code>"xref_analog"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.phosphosite.<a href="org/biojava/nbio/phosphosite/Dataset.html" title="class in org.biojava.nbio.phosphosite">Dataset</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.ACETYLATION">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#ACETYLATION">ACETYLATION</a></code></div>
<div class="col-last even-row-color"><code>"https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.DISEASE_ASSOC">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#DISEASE_ASSOC">DISEASE_ASSOC</a></code></div>
<div class="col-last odd-row-color"><code>"https://www.phosphosite.org/downloads/Disease-associated_sites.gz"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.METHYLATION">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#METHYLATION">METHYLATION</a></code></div>
<div class="col-last even-row-color"><code>"https://www.phosphosite.org/downloads/Methylation_site_dataset.gz"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.PHOSPHORYLATION">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#PHOSPHORYLATION">PHOSPHORYLATION</a></code></div>
<div class="col-last odd-row-color"><code>"https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.REGULATORY">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#REGULATORY">REGULATORY</a></code></div>
<div class="col-last even-row-color"><code>"https://www.phosphosite.org/downloads/Regulatory_sites.gz"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.SUMOYLATION">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#SUMOYLATION">SUMOYLATION</a></code></div>
<div class="col-last odd-row-color"><code>"https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.phosphosite.Dataset.UBIQUITINATION">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/phosphosite/Dataset.html#UBIQUITINATION">UBIQUITINATION</a></code></div>
<div class="col-last even-row-color"><code>"https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.ronn.<a href="org/biojava/nbio/ronn/RonnConstraint.html" title="class in org.biojava.nbio.ronn">RonnConstraint</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ronn.RonnConstraint.DEFAULT_DISORDER">public static final float</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ronn/RonnConstraint.html#DEFAULT_DISORDER">DEFAULT_DISORDER</a></code></div>
<div class="col-last even-row-color"><code>0.5299999713897705f</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.ronn.RonnConstraint.DEFAULT_ORDER">public static final float</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/ronn/RonnConstraint.html#DEFAULT_ORDER">DEFAULT_ORDER</a></code></div>
<div class="col-last odd-row-color"><code>0.4699999988079071f</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.ronn.RonnConstraint.DEFAULT_RANGE_PROBABILITY_THRESHOLD">public static final float</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/ronn/RonnConstraint.html#DEFAULT_RANGE_PROBABILITY_THRESHOLD">DEFAULT_RANGE_PROBABILITY_THRESHOLD</a></code></div>
<div class="col-last even-row-color"><code>0.5f</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/AminoAcid.html" title="interface in org.biojava.nbio.structure">AminoAcid</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.AminoAcid.ATOMRECORD">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/AminoAcid.html#ATOMRECORD">ATOMRECORD</a></code></div>
<div class="col-last even-row-color"><code>"ATOM"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.AminoAcid.SEQRESRECORD">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/AminoAcid.html#SEQRESRECORD">SEQRESRECORD</a></code></div>
<div class="col-last odd-row-color"><code>"SEQRES"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/AtomImpl.html" title="class in org.biojava.nbio.structure">AtomImpl</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.AtomImpl.BONDS_INITIAL_CAPACITY">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/AtomImpl.html#BONDS_INITIAL_CAPACITY">BONDS_INITIAL_CAPACITY</a></code></div>
<div class="col-last even-row-color"><code>3</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/Group.html" title="interface in org.biojava.nbio.structure">Group</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.Group.SEC_STRUC">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/Group.html#SEC_STRUC">SEC_STRUC</a></code></div>
<div class="col-last even-row-color"><code>"secstruc"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/PDBHeader.html" title="class in org.biojava.nbio.structure">PDBHeader</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.PDBHeader.DEFAULT_RESOLUTION">public static final float</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/PDBHeader.html#DEFAULT_RESOLUTION">DEFAULT_RESOLUTION</a></code></div>
<div class="col-last even-row-color"><code>99.0f</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.PDBHeader.DEFAULT_RFREE">public static final float</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/PDBHeader.html#DEFAULT_RFREE">DEFAULT_RFREE</a></code></div>
<div class="col-last odd-row-color"><code>1.0f</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/PDBStatus.html" title="class in org.biojava.nbio.structure">PDBStatus</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.PDBStatus.ALL_CURRENT_ENDPOINT">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/PDBStatus.html#ALL_CURRENT_ENDPOINT">ALL_CURRENT_ENDPOINT</a></code></div>
<div class="col-last even-row-color"><code>"https://%s/rest/v1/holdings/current/entry_ids"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.PDBStatus.DEFAULT_RCSB_DATA_API_SERVER">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/PDBStatus.html#DEFAULT_RCSB_DATA_API_SERVER">DEFAULT_RCSB_DATA_API_SERVER</a></code></div>
<div class="col-last odd-row-color"><code>"data.rcsb.org"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.PDBStatus.STATUS_ENDPOINT">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/PDBStatus.html#STATUS_ENDPOINT">STATUS_ENDPOINT</a></code></div>
<div class="col-last even-row-color"><code>"https://%s/rest/v1/holdings/status/%s"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.PDBStatus.STATUS_LIST_ENDPOINT">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/PDBStatus.html#STATUS_LIST_ENDPOINT">STATUS_LIST_ENDPOINT</a></code></div>
<div class="col-last odd-row-color"><code>"https://%s/rest/v1/holdings/status?ids=%s"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/StructureException.html" title="class in org.biojava.nbio.structure">StructureException</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureException.serialVersionUID">public static final long</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureException.html#serialVersionUID">serialVersionUID</a></code></div>
<div class="col-last even-row-color"><code>62946250941673093L</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/StructureTools.html" title="class in org.biojava.nbio.structure">StructureTools</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.C_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#C_ATOM_NAME">C_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"C"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.C1_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#C1_ATOM_NAME">C1_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"C1\'"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.C2_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#C2_ATOM_NAME">C2_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"C2\'"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.C3_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#C3_ATOM_NAME">C3_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"C3\'"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.C4_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#C4_ATOM_NAME">C4_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"C4\'"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.CA_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#CA_ATOM_NAME">CA_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"CA"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.CB_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#CB_ATOM_NAME">CB_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"CB"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.DEFAULT_LIGAND_PROXIMITY_CUTOFF">public static final double</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#DEFAULT_LIGAND_PROXIMITY_CUTOFF">DEFAULT_LIGAND_PROXIMITY_CUTOFF</a></code></div>
<div class="col-last odd-row-color"><code>5.0</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.N_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#N_ATOM_NAME">N_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"N"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.NUCLEOTIDE_REPRESENTATIVE">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#NUCLEOTIDE_REPRESENTATIVE">NUCLEOTIDE_REPRESENTATIVE</a></code></div>
<div class="col-last odd-row-color"><code>"P"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.O_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#O_ATOM_NAME">O_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"O"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.O2_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#O2_ATOM_NAME">O2_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"O2\'"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.O3_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#O3_ATOM_NAME">O3_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"O3\'"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.O4_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#O4_ATOM_NAME">O4_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"O4\'"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.O5_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#O5_ATOM_NAME">O5_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"O5\'"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.OP1_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#OP1_ATOM_NAME">OP1_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"OP1"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.OP2_ATOM_NAME">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#OP2_ATOM_NAME">OP2_ATOM_NAME</a></code></div>
<div class="col-last even-row-color"><code>"OP2"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.P_ATOM_NAME">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#P_ATOM_NAME">P_ATOM_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"P"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL">public static final double</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#RATIO_RESIDUES_TO_TOTAL">RATIO_RESIDUES_TO_TOTAL</a></code></div>
<div class="col-last even-row-color"><code>0.95</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.StructureTools.UNKNOWN_GROUP_LABEL">public static final char</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/StructureTools.html#UNKNOWN_GROUP_LABEL">UNKNOWN_GROUP_LABEL</a></code></div>
<div class="col-last odd-row-color"><code>'X'</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.<a href="org/biojava/nbio/structure/URLIdentifier.html" title="class in org.biojava.nbio.structure">URLIdentifier</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.URLIdentifier.CHAINID_PARAM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/URLIdentifier.html#CHAINID_PARAM">CHAINID_PARAM</a></code></div>
<div class="col-last even-row-color"><code>"chainid"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.URLIdentifier.FORMAT_PARAM">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/URLIdentifier.html#FORMAT_PARAM">FORMAT_PARAM</a></code></div>
<div class="col-last odd-row-color"><code>"format"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.URLIdentifier.PDBID_PARAM">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/URLIdentifier.html#PDBID_PARAM">PDBID_PARAM</a></code></div>
<div class="col-last even-row-color"><code>"pdbid"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.URLIdentifier.RESIDUES_PARAM">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/URLIdentifier.html#RESIDUES_PARAM">RESIDUES_PARAM</a></code></div>
<div class="col-last odd-row-color"><code>"residues"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.<a href="org/biojava/nbio/structure/align/BioJavaStructureAlignment.html" title="class in org.biojava.nbio.structure.align">BioJavaStructureAlignment</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.BioJavaStructureAlignment.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/BioJavaStructureAlignment.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"BioJava_structure"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.<a href="org/biojava/nbio/structure/align/ClusterAltAligs.html" title="class in org.biojava.nbio.structure.align">ClusterAltAligs</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ClusterAltAligs.DEFAULT_CLUSTER_CUTOFF">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ClusterAltAligs.html#DEFAULT_CLUSTER_CUTOFF">DEFAULT_CLUSTER_CUTOFF</a></code></div>
<div class="col-last even-row-color"><code>95</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CECalculator.html" title="class in org.biojava.nbio.structure.align.ce">CECalculator</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CECalculator.isPrint">protected static final boolean</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CECalculator.html#isPrint">isPrint</a></code></div>
<div class="col-last even-row-color"><code>false</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CECalculator.nIter">protected static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CECalculator.html#nIter">nIter</a></code></div>
<div class="col-last odd-row-color"><code>1</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CECalculator.zThr">protected static final double</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CECalculator.html#zThr">zThr</a></code></div>
<div class="col-last even-row-color"><code>-0.1</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html" title="class in org.biojava.nbio.structure.align.ce">CeCalculatorEnhanced</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced.GLOBAL_ALIGN1">public static final boolean</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html#GLOBAL_ALIGN1">GLOBAL_ALIGN1</a></code></div>
<div class="col-last even-row-color"><code>false</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced.GLOBAL_ALIGN2">public static final boolean</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html#GLOBAL_ALIGN2">GLOBAL_ALIGN2</a></code></div>
<div class="col-last odd-row-color"><code>false</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced.isPrint">protected static final boolean</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html#isPrint">isPrint</a></code></div>
<div class="col-last even-row-color"><code>true</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced.nIter">protected static final int</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html#nIter">nIter</a></code></div>
<div class="col-last odd-row-color"><code>1</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced.zThr">protected static final double</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html#zThr">zThr</a></code></div>
<div class="col-last even-row-color"><code>-0.1</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CeCPMain.html" title="class in org.biojava.nbio.structure.align.ce">CeCPMain</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCPMain.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCPMain.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jCE Circular Permutation"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CeCPMain.version">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeCPMain.html#version">version</a></code></div>
<div class="col-last odd-row-color"><code>"1.5"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CECPParameters.html" title="class in org.biojava.nbio.structure.align.ce">CECPParameters</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CECPParameters.DEFAULT_MIN_CP_LENGTH">public static final int</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CECPParameters.html#DEFAULT_MIN_CP_LENGTH">DEFAULT_MIN_CP_LENGTH</a></code></div>
<div class="col-last even-row-color"><code>5</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CeMain.html" title="class in org.biojava.nbio.structure.align.ce">CeMain</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeMain.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeMain.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jCE"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CeMain.version">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeMain.html#version">version</a></code></div>
<div class="col-last odd-row-color"><code>"1.2"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CeParameters.html" title="class in org.biojava.nbio.structure.align.ce">CeParameters</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeParameters.DEFAULT_GAP_EXTENSION">protected static final double</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeParameters.html#DEFAULT_GAP_EXTENSION">DEFAULT_GAP_EXTENSION</a></code></div>
<div class="col-last even-row-color"><code>0.5</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CeParameters.DEFAULT_GAP_OPEN">protected static final double</code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeParameters.html#DEFAULT_GAP_OPEN">DEFAULT_GAP_OPEN</a></code></div>
<div class="col-last odd-row-color"><code>5.0</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeParameters.DEFAULT_oRmsdThr">protected static final double</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeParameters.html#DEFAULT_oRmsdThr">DEFAULT_oRmsdThr</a></code></div>
<div class="col-last even-row-color"><code>2.0</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.CeParameters.DEFAULT_SUBSTITUTION_MATRIX">protected static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeParameters.html#DEFAULT_SUBSTITUTION_MATRIX">DEFAULT_SUBSTITUTION_MATRIX</a></code></div>
<div class="col-last odd-row-color"><code>"PRLA000101"</code></div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeParameters.DISTANCE_INCREMENT">protected static final double</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeParameters.html#DISTANCE_INCREMENT">DISTANCE_INCREMENT</a></code></div>
<div class="col-last even-row-color"><code>0.5</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/CeSideChainMain.html" title="class in org.biojava.nbio.structure.align.ce">CeSideChainMain</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.CeSideChainMain.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/CeSideChainMain.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jCE-sidechain"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.ce.<a href="org/biojava/nbio/structure/align/ce/OptimalCECPMain.html" title="class in org.biojava.nbio.structure.align.ce">OptimalCECPMain</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.ce.OptimalCECPMain.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/ce/OptimalCECPMain.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jCE Optimal Circular Permutation"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.ce.OptimalCECPMain.version">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/ce/OptimalCECPMain.html#version">version</a></code></div>
<div class="col-last odd-row-color"><code>"1.0"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.fatcat.<a href="org/biojava/nbio/structure/align/fatcat/FatCat.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCat</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.fatcat.FatCat.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/fatcat/FatCat.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jFatCat"</code></div>
<div class="col-first odd-row-color"><code id="org.biojava.nbio.structure.align.fatcat.FatCat.VERSION">public static final <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></code></div>
<div class="col-second odd-row-color"><code><a href="org/biojava/nbio/structure/align/fatcat/FatCat.html#VERSION">VERSION</a></code></div>
<div class="col-last odd-row-color"><code>"1.1"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.fatcat.<a href="org/biojava/nbio/structure/align/fatcat/FatCatFlexible.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCatFlexible</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.fatcat.FatCatFlexible.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/fatcat/FatCatFlexible.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jFatCat_flexible"</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.fatcat.<a href="org/biojava/nbio/structure/align/fatcat/FatCatRigid.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCatRigid</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.fatcat.FatCatRigid.algorithmName">public static final <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></code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/fatcat/FatCatRigid.html#algorithmName">algorithmName</a></code></div>
<div class="col-last even-row-color"><code>"jFatCat_rigid"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.fatcat.calc.<a href="org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPCalculator</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator.debug">public static final boolean</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html#debug">debug</a></code></div>
<div class="col-last even-row-color"><code>false</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.fatcat.calc.<a href="org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPChainer</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="org.biojava.nbio.structure.align.fatcat.calc.AFPChainer.debug">public static final boolean</code></div>
<div class="col-second even-row-color"><code><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html#debug">debug</a></code></div>
<div class="col-last even-row-color"><code>false</code></div>
</div>
</li>
<li>
<div class="caption"><span>org.biojava.nbio.structure.align.fatcat.calc.<a href="org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPOptimizer</a></span></div>
<div class="summary-table three-column-summary">
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