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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<title>Class Hierarchy (biojava-legacy 1.9.2 API)</title>
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<div class="header">
<h1 class="title">Hierarchy For All Packages</h1>
<span class="packageHierarchyLabel">Package Hierarchies:</span>
<ul class="horizontal">
<li><a href="org/biojava/package-tree.html">org.biojava</a>, </li>
<li><a href="org/biojava/bibliography/package-tree.html">org.biojava.bibliography</a>, </li>
<li><a href="org/biojava/bio/package-tree.html">org.biojava.bio</a>, </li>
<li><a href="org/biojava/bio/alignment/package-tree.html">org.biojava.bio.alignment</a>, </li>
<li><a href="org/biojava/bio/annodb/package-tree.html">org.biojava.bio.annodb</a>, </li>
<li><a href="org/biojava/bio/chromatogram/package-tree.html">org.biojava.bio.chromatogram</a>, </li>
<li><a href="org/biojava/bio/chromatogram/graphic/package-tree.html">org.biojava.bio.chromatogram.graphic</a>, </li>
<li><a href="org/biojava/bio/dist/package-tree.html">org.biojava.bio.dist</a>, </li>
<li><a href="org/biojava/bio/dp/package-tree.html">org.biojava.bio.dp</a>, </li>
<li><a href="org/biojava/bio/dp/onehead/package-tree.html">org.biojava.bio.dp.onehead</a>, </li>
<li><a href="org/biojava/bio/dp/twohead/package-tree.html">org.biojava.bio.dp.twohead</a>, </li>
<li><a href="org/biojava/bio/gui/package-tree.html">org.biojava.bio.gui</a>, </li>
<li><a href="org/biojava/bio/gui/glyph/package-tree.html">org.biojava.bio.gui.glyph</a>, </li>
<li><a href="org/biojava/bio/gui/sequence/package-tree.html">org.biojava.bio.gui.sequence</a>, </li>
<li><a href="org/biojava/bio/gui/sequence/tracklayout/package-tree.html">org.biojava.bio.gui.sequence.tracklayout</a>, </li>
<li><a href="org/biojava/bio/molbio/package-tree.html">org.biojava.bio.molbio</a>, </li>
<li><a href="org/biojava/bio/program/package-tree.html">org.biojava.bio.program</a>, </li>
<li><a href="org/biojava/bio/program/abi/package-tree.html">org.biojava.bio.program.abi</a>, </li>
<li><a href="org/biojava/bio/program/blast2html/package-tree.html">org.biojava.bio.program.blast2html</a>, </li>
<li><a href="org/biojava/bio/program/fastq/package-tree.html">org.biojava.bio.program.fastq</a>, </li>
<li><a href="org/biojava/bio/program/formats/package-tree.html">org.biojava.bio.program.formats</a>, </li>
<li><a href="org/biojava/bio/program/gff/package-tree.html">org.biojava.bio.program.gff</a>, </li>
<li><a href="org/biojava/bio/program/gff3/package-tree.html">org.biojava.bio.program.gff3</a>, </li>
<li><a href="org/biojava/bio/program/hmmer/package-tree.html">org.biojava.bio.program.hmmer</a>, </li>
<li><a href="org/biojava/bio/program/homologene/package-tree.html">org.biojava.bio.program.homologene</a>, </li>
<li><a href="org/biojava/bio/program/indexdb/package-tree.html">org.biojava.bio.program.indexdb</a>, </li>
<li><a href="org/biojava/bio/program/phred/package-tree.html">org.biojava.bio.program.phred</a>, </li>
<li><a href="org/biojava/bio/program/sax/package-tree.html">org.biojava.bio.program.sax</a>, </li>
<li><a href="org/biojava/bio/program/sax/blastxml/package-tree.html">org.biojava.bio.program.sax.blastxml</a>, </li>
<li><a href="org/biojava/bio/program/scf/package-tree.html">org.biojava.bio.program.scf</a>, </li>
<li><a href="org/biojava/bio/program/ssaha/package-tree.html">org.biojava.bio.program.ssaha</a>, </li>
<li><a href="org/biojava/bio/program/ssbind/package-tree.html">org.biojava.bio.program.ssbind</a>, </li>
<li><a href="org/biojava/bio/program/tagvalue/package-tree.html">org.biojava.bio.program.tagvalue</a>, </li>
<li><a href="org/biojava/bio/program/unigene/package-tree.html">org.biojava.bio.program.unigene</a>, </li>
<li><a href="org/biojava/bio/program/xff/package-tree.html">org.biojava.bio.program.xff</a>, </li>
<li><a href="org/biojava/bio/program/xml/package-tree.html">org.biojava.bio.program.xml</a>, </li>
<li><a href="org/biojava/bio/proteomics/package-tree.html">org.biojava.bio.proteomics</a>, </li>
<li><a href="org/biojava/bio/proteomics/aaindex/package-tree.html">org.biojava.bio.proteomics.aaindex</a>, </li>
<li><a href="org/biojava/bio/search/package-tree.html">org.biojava.bio.search</a>, </li>
<li><a href="org/biojava/bio/seq/package-tree.html">org.biojava.bio.seq</a>, </li>
<li><a href="org/biojava/bio/seq/db/package-tree.html">org.biojava.bio.seq.db</a>, </li>
<li><a href="org/biojava/bio/seq/db/biofetch/package-tree.html">org.biojava.bio.seq.db.biofetch</a>, </li>
<li><a href="org/biojava/bio/seq/db/biosql/package-tree.html">org.biojava.bio.seq.db.biosql</a>, </li>
<li><a href="org/biojava/bio/seq/db/emblcd/package-tree.html">org.biojava.bio.seq.db.emblcd</a>, </li>
<li><a href="org/biojava/bio/seq/db/flat/package-tree.html">org.biojava.bio.seq.db.flat</a>, </li>
<li><a href="org/biojava/bio/seq/distributed/package-tree.html">org.biojava.bio.seq.distributed</a>, </li>
<li><a href="org/biojava/bio/seq/filter/package-tree.html">org.biojava.bio.seq.filter</a>, </li>
<li><a href="org/biojava/bio/seq/homol/package-tree.html">org.biojava.bio.seq.homol</a>, </li>
<li><a href="org/biojava/bio/seq/impl/package-tree.html">org.biojava.bio.seq.impl</a>, </li>
<li><a href="org/biojava/bio/seq/io/package-tree.html">org.biojava.bio.seq.io</a>, </li>
<li><a href="org/biojava/bio/seq/io/agave/package-tree.html">org.biojava.bio.seq.io.agave</a>, </li>
<li><a href="org/biojava/bio/seq/io/filterxml/package-tree.html">org.biojava.bio.seq.io.filterxml</a>, </li>
<li><a href="org/biojava/bio/seq/io/game/package-tree.html">org.biojava.bio.seq.io.game</a>, </li>
<li><a href="org/biojava/bio/seq/io/game12/package-tree.html">org.biojava.bio.seq.io.game12</a>, </li>
<li><a href="org/biojava/bio/seq/projection/package-tree.html">org.biojava.bio.seq.projection</a>, </li>
<li><a href="org/biojava/bio/symbol/package-tree.html">org.biojava.bio.symbol</a>, </li>
<li><a href="org/biojava/bio/taxa/package-tree.html">org.biojava.bio.taxa</a>, </li>
<li><a href="org/biojava/directory/package-tree.html">org.biojava.directory</a>, </li>
<li><a href="org/biojava/naming/package-tree.html">org.biojava.naming</a>, </li>
<li><a href="org/biojava/ontology/package-tree.html">org.biojava.ontology</a>, </li>
<li><a href="org/biojava/ontology/io/package-tree.html">org.biojava.ontology.io</a>, </li>
<li><a href="org/biojava/ontology/obo/package-tree.html">org.biojava.ontology.obo</a>, </li>
<li><a href="org/biojava/stats/svm/package-tree.html">org.biojava.stats.svm</a>, </li>
<li><a href="org/biojava/stats/svm/tools/package-tree.html">org.biojava.stats.svm.tools</a>, </li>
<li><a href="org/biojava/utils/package-tree.html">org.biojava.utils</a>, </li>
<li><a href="org/biojava/utils/automata/package-tree.html">org.biojava.utils.automata</a>, </li>
<li><a href="org/biojava/utils/bytecode/package-tree.html">org.biojava.utils.bytecode</a>, </li>
<li><a href="org/biojava/utils/cache/package-tree.html">org.biojava.utils.cache</a>, </li>
<li><a href="org/biojava/utils/candy/package-tree.html">org.biojava.utils.candy</a>, </li>
<li><a href="org/biojava/utils/io/package-tree.html">org.biojava.utils.io</a>, </li>
<li><a href="org/biojava/utils/lsid/package-tree.html">org.biojava.utils.lsid</a>, </li>
<li><a href="org/biojava/utils/math/package-tree.html">org.biojava.utils.math</a>, </li>
<li><a href="org/biojava/utils/net/package-tree.html">org.biojava.utils.net</a>, </li>
<li><a href="org/biojava/utils/process/package-tree.html">org.biojava.utils.process</a>, </li>
<li><a href="org/biojava/utils/regex/package-tree.html">org.biojava.utils.regex</a>, </li>
<li><a href="org/biojava/utils/stax/package-tree.html">org.biojava.utils.stax</a>, </li>
<li><a href="org/biojava/utils/walker/package-tree.html">org.biojava.utils.walker</a>, </li>
<li><a href="org/biojava/utils/xml/package-tree.html">org.biojava.utils.xml</a>, </li>
<li><a href="org/biojavax/package-tree.html">org.biojavax</a>, </li>
<li><a href="org/biojavax/bio/package-tree.html">org.biojavax.bio</a>, </li>
<li><a href="org/biojavax/bio/alignment/package-tree.html">org.biojavax.bio.alignment</a>, </li>
<li><a href="org/biojavax/bio/alignment/blast/package-tree.html">org.biojavax.bio.alignment.blast</a>, </li>
<li><a href="org/biojavax/bio/db/package-tree.html">org.biojavax.bio.db</a>, </li>
<li><a href="org/biojavax/bio/db/biosql/package-tree.html">org.biojavax.bio.db.biosql</a>, </li>
<li><a href="org/biojavax/bio/db/ncbi/package-tree.html">org.biojavax.bio.db.ncbi</a>, </li>
<li><a href="org/biojavax/bio/phylo/package-tree.html">org.biojavax.bio.phylo</a>, </li>
<li><a href="org/biojavax/bio/phylo/io/nexus/package-tree.html">org.biojavax.bio.phylo.io.nexus</a>, </li>
<li><a href="org/biojavax/bio/phylo/io/phylip/package-tree.html">org.biojavax.bio.phylo.io.phylip</a>, </li>
<li><a href="org/biojavax/bio/seq/package-tree.html">org.biojavax.bio.seq</a>, </li>
<li><a href="org/biojavax/bio/seq/io/package-tree.html">org.biojavax.bio.seq.io</a>, </li>
<li><a href="org/biojavax/bio/taxa/package-tree.html">org.biojavax.bio.taxa</a>, </li>
<li><a href="org/biojavax/bio/taxa/io/package-tree.html">org.biojavax.bio.taxa.io</a>, </li>
<li><a href="org/biojavax/ga/package-tree.html">org.biojavax.ga</a>, </li>
<li><a href="org/biojavax/ga/exception/package-tree.html">org.biojavax.ga.exception</a>, </li>
<li><a href="org/biojavax/ga/functions/package-tree.html">org.biojavax.ga.functions</a>, </li>
<li><a href="org/biojavax/ga/impl/package-tree.html">org.biojavax.ga.impl</a>, </li>
<li><a href="org/biojavax/ga/util/package-tree.html">org.biojavax.ga.util</a>, </li>
<li><a href="org/biojavax/ontology/package-tree.html">org.biojavax.ontology</a>, </li>
<li><a href="org/biojavax/utils/package-tree.html">org.biojavax.utils</a></li>
</ul>
</div>
<div class="contentContainer">
<h2 title="Class Hierarchy">Class Hierarchy</h2>
<ul>
<li type="circle">java.lang.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><span class="typeNameLink">Object</span></a>
<ul>
<li type="circle">org.biojava.bio.proteomics.aaindex.<a href="org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex"><span class="typeNameLink">AAindexStreamReader</span></a> (implements org.biojava.bio.proteomics.aaindex.<a href="org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator.html" title="interface in org.biojava.bio.proteomics.aaindex">SymbolPropertyTableIterator</a>)</li>
<li type="circle">org.biojava.bio.program.abi.<a href="org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi"><span class="typeNameLink">ABIFParser</span></a>
<ul>
<li type="circle">org.biojava.bio.program.abi.<a href="org/biojava/bio/program/abi/ABIFChromatogram.Parser.html" title="class in org.biojava.bio.program.abi"><span class="typeNameLink">ABIFChromatogram.Parser</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.program.abi.<a href="org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi"><span class="typeNameLink">ABIFParser.TaggedDataRecord</span></a></li>
<li type="circle">org.biojava.bio.program.abi.<a href="org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi"><span class="typeNameLink">ABITools</span></a></li>
<li type="circle">org.biojava.bio.program.abi.<a href="org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi"><span class="typeNameLink">ABITrace</span></a></li>
<li type="circle">org.biojava.bio.program.blast2html.<a href="org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html"><span class="typeNameLink">AbstractAlignmentStyler</span></a>
<ul>
<li type="circle">org.biojava.bio.program.blast2html.<a href="org/biojava/bio/program/blast2html/SimpleAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html"><span class="typeNameLink">SimpleAlignmentStyler</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.utils.<a href="org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils"><span class="typeNameLink">AbstractChangeable</span></a> (implements org.biojava.utils.<a href="org/biojava/utils/Changeable.html" title="interface in org.biojava.utils">Changeable</a>)
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">AbiTraceRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>)</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">AbstractAlphabet</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol">FiniteAlphabet</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">IntegerAlphabet.SubIntegerAlphabet</span></a></li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SimpleAlphabet.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">SimpleAlphabet</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SingletonAlphabet.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">SingletonAlphabet</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol">FiniteAlphabet</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio"><span class="typeNameLink">AbstractAnnotation</span></a> (implements org.biojava.bio.<a href="org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio"><span class="typeNameLink">AnnotationChanger</span></a></li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio"><span class="typeNameLink">AnnotationRenamer</span></a></li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/BeanAsAnnotation.html" title="class in org.biojava.bio"><span class="typeNameLink">BeanAsAnnotation</span></a></li>
<li type="circle">org.biojava.bio.seq.io.<a href="org/biojava/bio/seq/io/ReferenceAnnotation.html" title="class in org.biojava.bio.seq.io"><span class="typeNameLink">ReferenceAnnotation</span></a></li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/SimpleAnnotation.html" title="class in org.biojava.bio"><span class="typeNameLink">SimpleAnnotation</span></a></li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/SmallAnnotation.html" title="class in org.biojava.bio"><span class="typeNameLink">SmallAnnotation</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">AbstractBeadRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">BeadFeatureRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">EllipticalBeadRenderer</span></a></li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/RectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">RectangularBeadRenderer</span></a></li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/RoundRectangularBeadRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">RoundRectangularBeadRenderer</span></a></li>
</ul>
</li>
<li type="circle">org.biojavax.bio.db.<a href="org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db"><span class="typeNameLink">AbstractBioEntryDB</span></a> (implements org.biojavax.bio.db.<a href="org/biojavax/bio/db/BioEntryDB.html" title="interface in org.biojavax.bio.db">BioEntryDB</a>)
<ul>
<li type="circle">org.biojavax.bio.db.<a href="org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db"><span class="typeNameLink">AbstractRichSequenceDB</span></a> (implements org.biojavax.bio.db.<a href="org/biojavax/bio/db/RichSequenceDB.html" title="interface in org.biojavax.bio.db">RichSequenceDB</a>)
<ul>
<li type="circle">org.biojavax.bio.db.biosql.<a href="org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql"><span class="typeNameLink">BioSQLRichSequenceDB</span></a></li>
<li type="circle">org.biojavax.bio.db.ncbi.<a href="org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi"><span class="typeNameLink">GenbankRichSequenceDB</span></a> (implements org.biojavax.bio.db.<a href="org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a>)</li>
<li type="circle">org.biojavax.bio.db.ncbi.<a href="org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi"><span class="typeNameLink">GenpeptRichSequenceDB</span></a> (implements org.biojavax.bio.db.<a href="org/biojavax/bio/db/RichSequenceDBLite.html" title="interface in org.biojavax.bio.db">RichSequenceDBLite</a>)</li>
<li type="circle">org.biojavax.bio.db.<a href="org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db"><span class="typeNameLink">HashRichSequenceDB</span></a> (implements org.biojavax.bio.db.<a href="org/biojavax/bio/db/RichSequenceDB.html" title="interface in org.biojavax.bio.db">RichSequenceDB</a>)</li>
</ul>
</li>
<li type="circle">org.biojavax.bio.db.biosql.<a href="org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql"><span class="typeNameLink">BioSQLBioEntryDB</span></a></li>
<li type="circle">org.biojavax.bio.db.<a href="org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db"><span class="typeNameLink">HashBioEntryDB</span></a> (implements org.biojavax.bio.db.<a href="org/biojavax/bio/db/BioEntryDB.html" title="interface in org.biojavax.bio.db">BioEntryDB</a>)</li>
</ul>
</li>
<li type="circle">org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions"><span class="typeNameLink">AbstractCrossOverFunction</span></a> (implements org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions">CrossOverFunction</a>)
<ul>
<li type="circle">org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/OrderCrossover.html" title="class in org.biojavax.ga.functions"><span class="typeNameLink">OrderCrossover</span></a></li>
<li type="circle">org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/SimpleCrossOverFunction.html" title="class in org.biojavax.ga.functions"><span class="typeNameLink">SimpleCrossOverFunction</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">AbstractDistribution</span></a> (implements org.biojava.bio.dist.<a href="org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a>)
<ul>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">AbstractOrderNDistribution</span></a> (implements org.biojava.bio.dist.<a href="org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist">OrderNDistribution</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/SimpleDistribution.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">SimpleDistribution</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/UntrainableDistribution.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">UntrainableDistribution</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/UniformDistribution.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">UniformDistribution</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">AbstractFeatureHolder</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a>)
<ul>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">MergeFeatureHolder</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.projection.<a href="org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection"><span class="typeNameLink">ProjectedFeatureHolder</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/SimpleFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">SimpleFeatureHolder</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
</ul>
</li>
<li type="circle">org.biojavax.ga.impl.<a href="org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl"><span class="typeNameLink">AbstractGeneticAlgorithm</span></a> (implements org.biojavax.ga.<a href="org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga">GeneticAlgorithm</a>)
<ul>
<li type="circle">org.biojavax.ga.impl.<a href="org/biojavax/ga/impl/SimpleGeneticAlgorithm.html" title="class in org.biojavax.ga.impl"><span class="typeNameLink">SimpleGeneticAlgorithm</span></a></li>
</ul>
</li>
<li type="circle">org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions"><span class="typeNameLink">AbstractMutationFunction</span></a> (implements org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions">MutationFunction</a>)
<ul>
<li type="circle">org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/SimpleMutationFunction.html" title="class in org.biojavax.ga.functions"><span class="typeNameLink">SimpleMutationFunction</span></a></li>
<li type="circle">org.biojavax.ga.functions.<a href="org/biojavax/ga/functions/SwapMutationFunction.html" title="class in org.biojavax.ga.functions"><span class="typeNameLink">SwapMutationFunction</span></a></li>
</ul>
</li>
<li type="circle">org.biojavax.ga.impl.<a href="org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl"><span class="typeNameLink">AbstractOrganism</span></a> (implements org.biojavax.ga.<a href="org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga">Organism</a>)
<ul>
<li type="circle">org.biojavax.ga.impl.<a href="org/biojavax/ga/impl/SimpleOrganism.html" title="class in org.biojavax.ga.impl"><span class="typeNameLink">SimpleOrganism</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.program.homologene.<a href="org/biojava/bio/program/homologene/AbstractOrthologueSet.html" title="class in org.biojava.bio.program.homologene"><span class="typeNameLink">AbstractOrthologueSet</span></a> (implements org.biojava.bio.program.homologene.<a href="org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene">OrthologueSet</a>)
<ul>
<li type="circle">org.biojava.bio.program.homologene.<a href="org/biojava/bio/program/homologene/SimpleOrthologueSet.html" title="class in org.biojava.bio.program.homologene"><span class="typeNameLink">SimpleOrthologueSet</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.program.homologene.<a href="org/biojava/bio/program/homologene/AbstractOrthoPairSet.html" title="class in org.biojava.bio.program.homologene"><span class="typeNameLink">AbstractOrthoPairSet</span></a> (implements org.biojava.bio.program.homologene.<a href="org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene">OrthoPairSet</a>)
<ul>
<li type="circle">org.biojava.bio.program.homologene.<a href="org/biojava/bio/program/homologene/SimpleOrthoPairSet.html" title="class in org.biojava.bio.program.homologene"><span class="typeNameLink">SimpleOrthoPairSet</span></a></li>
</ul>
</li>
<li type="circle">org.biojavax.ga.impl.<a href="org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl"><span class="typeNameLink">AbstractPopulation</span></a> (implements org.biojavax.ga.<a href="org/biojavax/ga/Population.html" title="interface in org.biojavax.ga">Population</a>)
<ul>
<li type="circle">org.biojavax.ga.impl.<a href="org/biojavax/ga/impl/SimplePopulation.html" title="class in org.biojavax.ga.impl"><span class="typeNameLink">SimplePopulation</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">AbstractSequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>)
<ul>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">AnnotatedSequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.distributed.<a href="org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed"><span class="typeNameLink">DistributedSequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>)</li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">DummySequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>)</li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">HashSequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">IndexedSequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDBWrapper.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">SequenceDBWrapper</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">CachingSequenceDB</span></a></li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SubSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">SubSequenceDB</span></a></li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/ViewingSequenceDB.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">ViewingSequenceDB</span></a></li>
</ul>
</li>
</ul>
</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">AbstractSymbol</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/Symbol.html" title="interface in org.biojava.bio.symbol">Symbol</a>)
<ul>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">FundamentalAtomicSymbol</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/AtomicSymbol.html" title="interface in org.biojava.bio.symbol">AtomicSymbol</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.dp.<a href="org/biojava/bio/dp/SimpleDotState.html" title="class in org.biojava.bio.dp"><span class="typeNameLink">SimpleDotState</span></a> (implements org.biojava.bio.dp.<a href="org/biojava/bio/dp/DotState.html" title="interface in org.biojava.bio.dp">DotState</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.dp.<a href="org/biojava/bio/dp/SimpleModelInState.html" title="class in org.biojava.bio.dp"><span class="typeNameLink">SimpleModelInState</span></a> (implements org.biojava.bio.dp.<a href="org/biojava/bio/dp/ModelInState.html" title="interface in org.biojava.bio.dp">ModelInState</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SimpleAtomicSymbol.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">SimpleAtomicSymbol</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/AtomicSymbol.html" title="interface in org.biojava.bio.symbol">AtomicSymbol</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">AbstractSymbolList</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>)
<ul>
<li type="circle">org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment"><span class="typeNameLink">AbstractULAlignment</span></a> (implements org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/UnequalLengthAlignment.html" title="interface in org.biojava.bio.alignment">UnequalLengthAlignment</a>)
<ul>
<li type="circle">org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment"><span class="typeNameLink">FlexibleAlignment</span></a> (implements org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment">ARAlignment</a>, org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment">EditableAlignment</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/AbstractULAlignment.SubULAlignment.html" title="class in org.biojava.bio.alignment"><span class="typeNameLink">AbstractULAlignment.SubULAlignment</span></a> (implements org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/UnequalLengthAlignment.html" title="interface in org.biojava.bio.alignment">UnequalLengthAlignment</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">AssembledSymbolList</span></a></li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">ChunkedSymbolList</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">DummySymbolList</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">NewAssembledSymbolList</span></a></li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">PackedSymbolList</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/SimpleAlignment.html" title="class in org.biojava.bio.alignment"><span class="typeNameLink">SimpleAlignment</span></a> (implements org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/Alignment.html" title="interface in org.biojava.bio.alignment">Alignment</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.alignment.<a href="org/biojava/bio/alignment/AlignmentPair.html" title="class in org.biojava.bio.alignment"><span class="typeNameLink">AlignmentPair</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SimpleGappedSymbolList.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">SimpleGappedSymbolList</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol">GappedSymbolList</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleGappedSequence.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleGappedSequence</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/GappedSequence.html" title="interface in org.biojava.bio.seq">GappedSequence</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SimpleSymbolList.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">SimpleSymbolList</span></a> (implements org.biojava.utils.<a href="org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils">ChangeListener</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
</ul>
</li>
<li type="circle">org.biojava.bio.taxa.<a href="org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa"><span class="typeNameLink">AbstractTaxon</span></a> (implements org.biojava.bio.taxa.<a href="org/biojava/bio/taxa/Taxon.html" title="interface in org.biojava.bio.taxa">Taxon</a>)
<ul>
<li type="circle">org.biojava.bio.taxa.<a href="org/biojava/bio/taxa/SimpleTaxon.html" title="class in org.biojava.bio.taxa"><span class="typeNameLink">SimpleTaxon</span></a></li>
<li type="circle">org.biojava.bio.taxa.<a href="org/biojava/bio/taxa/WeakTaxon.html" title="class in org.biojava.bio.taxa"><span class="typeNameLink">WeakTaxon</span></a></li>
</ul>
</li>
<li type="circle">org.biojava.ontology.<a href="org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology"><span class="typeNameLink">AbstractTerm</span></a> (implements org.biojava.ontology.<a href="org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a>)
<ul>
<li type="circle">org.biojava.ontology.<a href="org/biojava/ontology/RemoteTerm.Impl.html" title="class in org.biojava.ontology"><span class="typeNameLink">RemoteTerm.Impl</span></a> (implements org.biojava.ontology.<a href="org/biojava/ontology/RemoteTerm.html" title="interface in org.biojava.ontology">RemoteTerm</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.ontology.<a href="org/biojava/ontology/Term.Impl.html" title="class in org.biojava.ontology"><span class="typeNameLink">Term.Impl</span></a> (implements java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>, org.biojava.ontology.<a href="org/biojava/ontology/Term.html" title="interface in org.biojava.ontology">Term</a>)
<ul>
<li type="circle">org.biojava.ontology.<a href="org/biojava/ontology/Variable.Impl.html" title="class in org.biojava.ontology"><span class="typeNameLink">Variable.Impl</span></a> (implements org.biojava.ontology.<a href="org/biojava/ontology/Variable.html" title="interface in org.biojava.ontology">Variable</a>)</li>
</ul>
</li>
</ul>
</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">BasicFeatureRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a>)</li>
<li type="circle">org.biojava.bio.seq.db.biosql.<a href="org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql"><span class="typeNameLink">BioSQLSequenceDB</span></a> (implements org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/SequenceDB.html" title="interface in org.biojava.bio.seq.db">SequenceDB</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">CrosshairRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">DummySequence</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq">Sequence</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">FeatureBlockSequenceRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">FeatureLabelRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureTypes.RepositoryImpl</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureTypes.Repository.html" title="interface in org.biojava.bio.seq">FeatureTypes.Repository</a>)</li>
<li type="circle">org.biojava.bio.program.gff3.<a href="org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3"><span class="typeNameLink">GFF3Record.Impl</span></a> (implements org.biojava.bio.program.gff3.<a href="org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3">GFF3Record</a>)</li>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">IndexedCount</span></a> (implements org.biojava.bio.dist.<a href="org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist">Count</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">LabelledSequenceRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">LazyFeatureHolder</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq">FeatureHolder</a>)</li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio"><span class="typeNameLink">MergeAnnotation</span></a> (implements org.biojava.bio.<a href="org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">MultiLineRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">AbstractPeptideDigestRenderer</span></a>
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">PeptideDigestRenderer</span></a></li>
</ul>
</li>
</ul>
</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">NewSimpleAssembly</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/RealizingFeatureHolder.html" title="interface in org.biojava.bio.seq">RealizingFeatureHolder</a>, org.biojava.bio.seq.<a href="org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq">Sequence</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">OffsetRulerRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>)</li>
<li type="circle">org.biojava.ontology.<a href="org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology"><span class="typeNameLink">Ontology.Impl</span></a> (implements org.biojava.ontology.<a href="org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology">Ontology</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.ontology.<a href="org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology"><span class="typeNameLink">OntologyTerm.Impl</span></a> (implements org.biojava.ontology.<a href="org/biojava/ontology/OntologyTerm.html" title="interface in org.biojava.ontology">OntologyTerm</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.<a href="org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio"><span class="typeNameLink">OverlayAnnotation</span></a> (implements org.biojava.bio.<a href="org/biojava/bio/Annotation.html" title="interface in org.biojava.bio">Annotation</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">OverlayRendererWrapper</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/OverlayMarker.html" title="interface in org.biojava.bio.gui.sequence">OverlayMarker</a>, org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.dist.<a href="org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist"><span class="typeNameLink">PairDistribution</span></a> (implements org.biojava.bio.dist.<a href="org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist">Distribution</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">PairwiseDiagonalRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">PairwiseFilteringRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">PairwiseOverlayRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/SequenceDBSearchHit.html" title="class in org.biojava.bio.search"><span class="typeNameLink">SequenceDBSearchHit</span></a> (implements org.biojava.bio.<a href="org/biojava/bio/Annotatable.html" title="interface in org.biojava.bio">Annotatable</a>, org.biojava.bio.search.<a href="org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a>)</li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/SequenceDBSearchResult.html" title="class in org.biojava.bio.search"><span class="typeNameLink">SequenceDBSearchResult</span></a> (implements org.biojava.bio.<a href="org/biojava/bio/Annotatable.html" title="interface in org.biojava.bio">Annotatable</a>, org.biojava.bio.search.<a href="org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchResult</a>)</li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/SequenceDBSearchSubHit.html" title="class in org.biojava.bio.search"><span class="typeNameLink">SequenceDBSearchSubHit</span></a> (implements org.biojava.bio.search.<a href="org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRendererWrapper.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">SequenceRendererWrapper</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence">SequenceRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">AlignmentRenderer</span></a></li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">BumpedRenderer</span></a></li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">FilteringRenderer</span></a>
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">GlyphFeatureRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a>)
<ul>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SecondaryStructureFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">SecondaryStructureFeatureRenderer</span></a></li>
</ul>
</li>
</ul>
</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">GappedRenderer</span></a></li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">PaddingRenderer</span></a></li>
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<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/SimpleAssembly.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">SimpleAssembly</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/RealizingFeatureHolder.html" title="interface in org.biojava.bio.seq">RealizingFeatureHolder</a>, org.biojava.bio.seq.<a href="org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq">Sequence</a>)</li>
<li type="circle">org.biojavax.bio.<a href="org/biojavax/bio/SimpleBioEntry.html" title="class in org.biojavax.bio"><span class="typeNameLink">SimpleBioEntry</span></a> (implements org.biojavax.bio.<a href="org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio">BioEntry</a>)
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<li type="circle">org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/SimpleRichSequence.html" title="class in org.biojavax.bio.seq"><span class="typeNameLink">SimpleRichSequence</span></a></li>
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<li type="circle">org.biojavax.bio.<a href="org/biojavax/bio/SimpleBioEntryRelationship.html" title="class in org.biojavax.bio"><span class="typeNameLink">SimpleBioEntryRelationship</span></a> (implements org.biojavax.bio.<a href="org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio">BioEntryRelationship</a>)</li>
<li type="circle">org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/SimpleCodonPref.html" title="class in org.biojava.bio.symbol"><span class="typeNameLink">SimpleCodonPref</span></a> (implements org.biojava.bio.symbol.<a href="org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol">CodonPref</a>)</li>
<li type="circle">org.biojavax.<a href="org/biojavax/SimpleComment.html" title="class in org.biojavax"><span class="typeNameLink">SimpleComment</span></a> (implements org.biojavax.<a href="org/biojavax/Comment.html" title="interface in org.biojavax">Comment</a>)</li>
<li type="circle">org.biojavax.ontology.<a href="org/biojavax/ontology/SimpleComparableOntology.html" title="class in org.biojavax.ontology"><span class="typeNameLink">SimpleComparableOntology</span></a> (implements org.biojavax.ontology.<a href="org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology">ComparableOntology</a>)</li>
<li type="circle">org.biojavax.ontology.<a href="org/biojavax/ontology/SimpleComparableTerm.html" title="class in org.biojavax.ontology"><span class="typeNameLink">SimpleComparableTerm</span></a> (implements org.biojavax.ontology.<a href="org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology">ComparableTerm</a>)</li>
<li type="circle">org.biojavax.ontology.<a href="org/biojavax/ontology/SimpleComparableTriple.html" title="class in org.biojavax.ontology"><span class="typeNameLink">SimpleComparableTriple</span></a> (implements org.biojavax.ontology.<a href="org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology">ComparableTriple</a>)</li>
<li type="circle">org.biojavax.<a href="org/biojavax/SimpleDocRef.html" title="class in org.biojavax"><span class="typeNameLink">SimpleDocRef</span></a> (implements org.biojavax.<a href="org/biojavax/DocRef.html" title="interface in org.biojavax">DocRef</a>)</li>
<li type="circle">org.biojava.bio.dp.<a href="org/biojava/bio/dp/SimpleEmissionState.html" title="class in org.biojava.bio.dp"><span class="typeNameLink">SimpleEmissionState</span></a> (implements org.biojava.bio.dp.<a href="org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp">EmissionState</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
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<li type="circle">org.biojava.bio.dp.<a href="org/biojava/bio/dp/MagicalState.html" title="class in org.biojava.bio.dp"><span class="typeNameLink">MagicalState</span></a></li>
<li type="circle">org.biojava.bio.program.hmmer.<a href="org/biojava/bio/program/hmmer/ProfileEmissionState.html" title="class in org.biojava.bio.program.hmmer"><span class="typeNameLink">ProfileEmissionState</span></a></li>
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<ul>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleStrandedFeature.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleStrandedFeature</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/StrandedFeature.html" title="interface in org.biojava.bio.seq">StrandedFeature</a>)
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<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleHomologyFeature.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleHomologyFeature</span></a> (implements org.biojava.bio.seq.homol.<a href="org/biojava/bio/seq/homol/HomologyFeature.html" title="interface in org.biojava.bio.seq.homol">HomologyFeature</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleRemoteFeature.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleRemoteFeature</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/RemoteFeature.html" title="interface in org.biojava.bio.seq">RemoteFeature</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleRestrictionSite.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleRestrictionSite</span></a> (implements org.biojava.bio.molbio.<a href="org/biojava/bio/molbio/RestrictionSite.html" title="interface in org.biojava.bio.molbio">RestrictionSite</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleSimilarityPairFeature.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleSimilarityPairFeature</span></a> (implements org.biojava.bio.seq.homol.<a href="org/biojava/bio/seq/homol/SimilarityPairFeature.html" title="interface in org.biojava.bio.seq.homol">SimilarityPairFeature</a>)</li>
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<li type="circle">org.biojava.bio.seq.homol.<a href="org/biojava/bio/seq/homol/SimpleHomology.html" title="class in org.biojava.bio.seq.homol"><span class="typeNameLink">SimpleHomology</span></a> (implements org.biojava.bio.seq.homol.<a href="org/biojava/bio/seq/homol/Homology.html" title="interface in org.biojava.bio.seq.homol">Homology</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SimpleLabelRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">SimpleLabelRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/LabelRenderer.html" title="interface in org.biojava.bio.gui.sequence">LabelRenderer</a>)</li>
<li type="circle">org.biojava.bio.dp.<a href="org/biojava/bio/dp/SimpleMarkovModel.html" title="class in org.biojava.bio.dp"><span class="typeNameLink">SimpleMarkovModel</span></a> (implements org.biojava.bio.dp.<a href="org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
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<li type="circle">org.biojava.bio.program.hmmer.<a href="org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer"><span class="typeNameLink">FullHmmerProfileHMM</span></a></li>
<li type="circle">org.biojava.bio.dp.<a href="org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp"><span class="typeNameLink">ProfileHMM</span></a>
<ul>
<li type="circle">org.biojava.bio.program.hmmer.<a href="org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer"><span class="typeNameLink">HmmerProfileHMM</span></a></li>
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<li type="circle">org.biojavax.bio.taxa.<a href="org/biojavax/bio/taxa/SimpleNCBITaxon.html" title="class in org.biojavax.bio.taxa"><span class="typeNameLink">SimpleNCBITaxon</span></a> (implements org.biojavax.bio.taxa.<a href="org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa">NCBITaxon</a>)</li>
<li type="circle">org.biojavax.<a href="org/biojavax/SimpleNote.html" title="class in org.biojavax"><span class="typeNameLink">SimpleNote</span></a> (implements org.biojavax.<a href="org/biojavax/Note.html" title="interface in org.biojavax">Note</a>)</li>
<li type="circle">org.biojavax.<a href="org/biojavax/SimpleRankedCrossRef.html" title="class in org.biojavax"><span class="typeNameLink">SimpleRankedCrossRef</span></a> (implements org.biojavax.<a href="org/biojavax/RankedCrossRef.html" title="interface in org.biojavax">RankedCrossRef</a>)</li>
<li type="circle">org.biojavax.<a href="org/biojavax/SimpleRankedDocRef.html" title="class in org.biojavax"><span class="typeNameLink">SimpleRankedDocRef</span></a> (implements org.biojavax.<a href="org/biojavax/RankedDocRef.html" title="interface in org.biojavax">RankedDocRef</a>)</li>
<li type="circle">org.biojavax.<a href="org/biojavax/SimpleRichAnnotation.html" title="class in org.biojavax"><span class="typeNameLink">SimpleRichAnnotation</span></a> (implements org.biojavax.<a href="org/biojavax/RichAnnotation.html" title="interface in org.biojavax">RichAnnotation</a>)</li>
<li type="circle">org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/SimpleRichFeature.html" title="class in org.biojavax.bio.seq"><span class="typeNameLink">SimpleRichFeature</span></a> (implements org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/RichFeature.html" title="interface in org.biojavax.bio.seq">RichFeature</a>)</li>
<li type="circle">org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/SimpleRichFeatureRelationship.html" title="class in org.biojavax.bio.seq"><span class="typeNameLink">SimpleRichFeatureRelationship</span></a> (implements org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/RichFeatureRelationship.html" title="interface in org.biojavax.bio.seq">RichFeatureRelationship</a>)</li>
<li type="circle">org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/SimpleRichLocation.html" title="class in org.biojavax.bio.seq"><span class="typeNameLink">SimpleRichLocation</span></a> (implements org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a>)
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<li type="circle">org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq"><span class="typeNameLink">CompoundRichLocation</span></a> (implements org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a>)
<ul>
<li type="circle">org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq"><span class="typeNameLink">MultiSourceCompoundRichLocation</span></a> (implements org.biojavax.bio.seq.<a href="org/biojavax/bio/seq/RichLocation.html" title="interface in org.biojavax.bio.seq">RichLocation</a>)</li>
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<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/SimpleSeqSimilaritySearchHit.html" title="class in org.biojava.bio.search"><span class="typeNameLink">SimpleSeqSimilaritySearchHit</span></a> (implements org.biojava.bio.search.<a href="org/biojava/bio/search/SeqSimilaritySearchHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchHit</a>)</li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/SimpleSeqSimilaritySearchResult.html" title="class in org.biojava.bio.search"><span class="typeNameLink">SimpleSeqSimilaritySearchResult</span></a> (implements org.biojava.bio.search.<a href="org/biojava/bio/search/SeqSimilaritySearchResult.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchResult</a>)</li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit.html" title="class in org.biojava.bio.search"><span class="typeNameLink">SimpleSeqSimilaritySearchSubHit</span></a> (implements org.biojava.bio.search.<a href="org/biojava/bio/search/SeqSimilaritySearchSubHit.html" title="interface in org.biojava.bio.search">SeqSimilaritySearchSubHit</a>)</li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/SimpleSequence.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">SimpleSequence</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/RealizingFeatureHolder.html" title="interface in org.biojava.bio.seq">RealizingFeatureHolder</a>, org.biojava.bio.seq.<a href="org/biojava/bio/seq/Sequence.html" title="interface in org.biojava.bio.seq">Sequence</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)
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<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/RevCompSequence.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">RevCompSequence</span></a></li>
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<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/SixFrameZiggyRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">SixFrameZiggyRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a>, java.io.<a href="https://docs.oracle.com/javase/1.5.0/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/StackedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">StackedFeatureRenderer</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence">FeatureRenderer</a>)</li>
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<li type="circle">org.biojava.bio.chromatogram.<a href="org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram"><span class="typeNameLink">AbstractChromatogram</span></a> (implements org.biojava.bio.chromatogram.<a href="org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram">Chromatogram</a>)
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<ul>
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<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByAnnotation.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByAnnotation</span></a></li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.HasAnnotation.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.HasAnnotation</span></a></li>
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<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByChild</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByClass</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByComponentName</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByDescendant</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByFeature</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByPairwiseScore</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByParent</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.BySequenceName</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.BySource</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ByType</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
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<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.OnlyChildren</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.OnlyDescendants</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.Or</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq">FeatureFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.OverlapsLocation</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ShadowContainedByLocation</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.ShadowOverlapsLocation</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureFilter.StrandFilter</span></a> (implements org.biojava.bio.seq.<a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq">OptimizableFilter</a>)</li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureHolderUtils</span></a></li>
<li type="circle">org.biojava.bio.seq.impl.<a href="org/biojava/bio/seq/impl/FeatureImpl.html" title="class in org.biojava.bio.seq.impl"><span class="typeNameLink">FeatureImpl</span></a></li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">FeatureLabelRenderer.AnnotationLabelMaker</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html" title="interface in org.biojava.bio.gui.sequence">FeatureLabelRenderer.LabelMaker</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">FeatureLabelRenderer.SourceLabelMaker</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html" title="interface in org.biojava.bio.gui.sequence">FeatureLabelRenderer.LabelMaker</a>)</li>
<li type="circle">org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html" title="class in org.biojava.bio.gui.sequence"><span class="typeNameLink">FeatureLabelRenderer.TypeLabelMaker</span></a> (implements org.biojava.bio.gui.sequence.<a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html" title="interface in org.biojava.bio.gui.sequence">FeatureLabelRenderer.LabelMaker</a>)</li>
<li type="circle">org.biojava.bio.seq.io.<a href="org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io"><span class="typeNameLink">FeatureTableParser</span></a></li>
<li type="circle">org.biojava.bio.seq.<a href="org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq"><span class="typeNameLink">FeatureTypes</span></a></li>
<li type="circle">org.biojava.bio.seq.db.<a href="org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db"><span class="typeNameLink">FetchURL</span></a></li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/FilteringContentHandler.FilterVisitor.html" title="class in org.biojava.bio.search"><span class="typeNameLink">FilteringContentHandler.FilterVisitor</span></a> (implements org.biojava.utils.walker.<a href="org/biojava/utils/walker/Visitor.html" title="interface in org.biojava.utils.walker">Visitor</a>)</li>
<li type="circle">org.biojava.bio.search.<a href="org/biojava/bio/search/FilterTest.Equals.html" title="class in org.biojava.bio.search"><span class="typeNameLink">FilterTest.Equals</span></a> (implements org.biojava.bio.search.<a href="org/biojava/bio/search/FilterTest.html" title="interface in org.biojava.bio.search">FilterTest</a>)</li>