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<!DOCTYPE HTML>
<!-- NewPage -->
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<!-- Generated by javadoc (11.0.1) on Thu Jan 03 22:38:55 CET 2019 -->
<title>All Classes (biojava 5.2.0 API)</title>
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<td class="colFirst"><a href="org/biojava/nbio/core/alignment/matrices/AAindexFactory.html" title="class in org.biojava.nbio.core.alignment.matrices">AAindexFactory</a></td>
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<div class="block">Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.</div>
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<td class="colFirst"><a href="org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html" title="class in org.biojava.nbio.core.alignment.matrices">AAIndexFileParser</a></td>
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<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.html" title="class in org.biojava.nbio.structure.align.gui.jmol">AbstractAlignmentJmol</a></td>
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<div class="block">An Abstract Class to generalize the visualization of AFP and
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</tr>
<tr id="i8" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/io/mmcif/model/AbstractBean.html" title="class in org.biojava.nbio.structure.io.mmcif.model">AbstractBean</a></td>
<th class="colLast" scope="row">
<div class="block">a generic class that implements the toString method for a bean</div>
</th>
</tr>
<tr id="i9" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/AbstractCompound.html" title="class in org.biojava.nbio.core.sequence.template">AbstractCompound</a></td>
<th class="colLast" scope="row">
<div class="block">The details of a Compound</div>
</th>
</tr>
<tr id="i10" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html" title="class in org.biojava.nbio.core.sequence.template">AbstractCompoundSet</a><<a href="org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html" title="type parameter in AbstractCompoundSet">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i11" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html" title="class in org.biojava.nbio.core.sequence.template">AbstractCompoundTranslator</a><<a href="org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html" title="type parameter in AbstractCompoundTranslator">F</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>,​<a href="org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html" title="type parameter in AbstractCompoundTranslator">T</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i12" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/features/AbstractFeature.html" title="class in org.biojava.nbio.core.sequence.features">AbstractFeature</a><<a href="org/biojava/nbio/core/sequence/features/AbstractFeature.html" title="type parameter in AbstractFeature">S</a> extends <a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="class in org.biojava.nbio.core.sequence.template">AbstractSequence</a><<a href="org/biojava/nbio/core/sequence/features/AbstractFeature.html" title="type parameter in AbstractFeature">C</a>>,​<a href="org/biojava/nbio/core/sequence/features/AbstractFeature.html" title="type parameter in AbstractFeature">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">A feature is currently any descriptive item that can be associated with a sequence position(s)
A feature has a type and a source which is currently a string to allow flexibility for the user
Ideally well defined features should have a class to describe attributes of that feature</div>
</th>
</tr>
<tr id="i13" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/location/template/AbstractLocation.html" title="class in org.biojava.nbio.core.sequence.location.template">AbstractLocation</a></td>
<th class="colLast" scope="row">
<div class="block">Base abstraction of a location which encodes for the majority of important
features about a location such as the start, end and strand</div>
</th>
</tr>
<tr id="i14" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/template/AbstractMatrixAligner.html" title="class in org.biojava.nbio.alignment.template">AbstractMatrixAligner</a><<a href="org/biojava/nbio/alignment/template/AbstractMatrixAligner.html" title="type parameter in AbstractMatrixAligner">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><<a href="org/biojava/nbio/alignment/template/AbstractMatrixAligner.html" title="type parameter in AbstractMatrixAligner">C</a>>,​<a href="org/biojava/nbio/alignment/template/AbstractMatrixAligner.html" title="type parameter in AbstractMatrixAligner">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Implements common code for an <a href="org/biojava/nbio/alignment/template/Aligner.html" title="interface in org.biojava.nbio.alignment.template"><code>Aligner</code></a> which builds a score matrix during computation.</div>
</th>
</tr>
<tr id="i15" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html" title="class in org.biojava.nbio.core.sequence.template">AbstractNucleotideCompoundSet</a><<a href="org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html" title="type parameter in AbstractNucleotideCompoundSet">C</a> extends <a href="org/biojava/nbio/core/sequence/compound/NucleotideCompound.html" title="class in org.biojava.nbio.core.sequence.compound">NucleotideCompound</a>></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i16" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.template">AbstractPairwiseSequenceAligner</a><<a href="org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html" title="type parameter in AbstractPairwiseSequenceAligner">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><<a href="org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html" title="type parameter in AbstractPairwiseSequenceAligner">C</a>>,​<a href="org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html" title="type parameter in AbstractPairwiseSequenceAligner">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Implements common code for an <a href="org/biojava/nbio/alignment/template/Aligner.html" title="interface in org.biojava.nbio.alignment.template"><code>Aligner</code></a> for a pair of <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template"><code>Sequence</code></a>s.</div>
</th>
</tr>
<tr id="i17" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html" title="class in org.biojava.nbio.alignment.template">AbstractProfileProfileAligner</a><<a href="org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html" title="type parameter in AbstractProfileProfileAligner">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><<a href="org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html" title="type parameter in AbstractProfileProfileAligner">C</a>>,​<a href="org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html" title="type parameter in AbstractProfileProfileAligner">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Implements common code for an <a href="org/biojava/nbio/alignment/template/Aligner.html" title="interface in org.biojava.nbio.alignment.template"><code>Aligner</code></a> for a pair of <a href="org/biojava/nbio/core/alignment/template/Profile.html" title="interface in org.biojava.nbio.core.alignment.template"><code>Profile</code></a>s.</div>
</th>
</tr>
<tr id="i18" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/reference/AbstractReference.html" title="class in org.biojava.nbio.core.sequence.reference">AbstractReference</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i19" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/template/AbstractScorer.html" title="class in org.biojava.nbio.alignment.template">AbstractScorer</a></td>
<th class="colLast" scope="row">
<div class="block">Implements common code for algorithms which compute a score.</div>
</th>
</tr>
<tr id="i20" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/multiple/AbstractScoresCache.html" title="class in org.biojava.nbio.structure.align.multiple">AbstractScoresCache</a></td>
<th class="colLast" scope="row">
<div class="block">Abstact implementation of the <a href="org/biojava/nbio/structure/align/multiple/ScoresCache.html" title="interface in org.biojava.nbio.structure.align.multiple"><code>ScoresCache</code></a> with the shared code used
in all objects with a variables cache.</div>
</th>
</tr>
<tr id="i21" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="class in org.biojava.nbio.core.sequence.template">AbstractSequence</a><<a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="type parameter in AbstractSequence">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">The base class for DNA, RNA and Protein sequences.</div>
</th>
</tr>
<tr id="i22" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html" title="enum in org.biojava.nbio.core.sequence.template">AbstractSequence.AnnotationType</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i23" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/AbstractStructureAlignment.html" title="class in org.biojava.nbio.structure.align">AbstractStructureAlignment</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i24" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ontology/AbstractTerm.html" title="class in org.biojava.nbio.ontology">AbstractTerm</a></td>
<th class="colLast" scope="row">
<div class="block">Abstract implementation of term
This provides basic change-forwarding functionality from
the annotation and ontology properties.</div>
</th>
</tr>
<tr id="i25" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce">AbstractUserArgumentProcessor</a></td>
<th class="colLast" scope="row">
<div class="block">Base class for a new structure alignment CLI.</div>
</th>
</tr>
<tr id="i26" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/location/template/AccesionedLocation.html" title="interface in org.biojava.nbio.core.sequence.location.template">AccesionedLocation</a></td>
<th class="colLast" scope="row">
<div class="block">A location which is bound to an AccessionID.</div>
</th>
</tr>
<tr id="i27" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/template/Accessioned.html" title="interface in org.biojava.nbio.core.sequence.template">Accessioned</a></td>
<th class="colLast" scope="row">
<div class="block">Indicates an entity is accessioned</div>
</th>
</tr>
<tr id="i28" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/AccessionID.html" title="class in org.biojava.nbio.core.sequence">AccessionID</a></td>
<th class="colLast" scope="row">
<div class="block">Used in Sequences as the unique indentifier.</div>
</th>
</tr>
<tr id="i29" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/model/AFP.html" title="class in org.biojava.nbio.structure.align.model">AFP</a></td>
<th class="colLast" scope="row">
<div class="block">A class to represent a FATCAT AFP</div>
</th>
</tr>
<tr id="i30" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.html" title="class in org.biojava.nbio.structure.align.util">AFPAlignmentDisplay</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i31" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPCalculator</a></td>
<th class="colLast" scope="row">
<div class="block">a class that performs calculations on AFPCHains</div>
</th>
</tr>
<tr id="i32" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/model/AFPChain.html" title="class in org.biojava.nbio.structure.align.model">AFPChain</a></td>
<th class="colLast" scope="row">
<div class="block">A bean to contain the core of a structure alignment.</div>
</th>
</tr>
<tr id="i33" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">AFPChainCoordManager</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i34" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPChainer</a></td>
<th class="colLast" scope="row">
<div class="block">a class to chain AFPs to an alignment</div>
</th>
</tr>
<tr id="i35" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/xml/AFPChainFlipper.html" title="class in org.biojava.nbio.structure.align.xml">AFPChainFlipper</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i36" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/util/AFPChainScorer.html" title="class in org.biojava.nbio.structure.align.util">AFPChainScorer</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i37" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/model/AfpChainWriter.html" title="class in org.biojava.nbio.structure.align.model">AfpChainWriter</a></td>
<th class="colLast" scope="row">
<div class="block">A class to convert the data in an AfpChain object to various String outputs.</div>
</th>
</tr>
<tr id="i38" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml">AFPChainXMLConverter</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i39" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html" title="class in org.biojava.nbio.structure.align.xml">AFPChainXMLParser</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i40" class="altColor">
<td class="colFirst"><a href="demo/AFPFromFasta.html" title="class in demo">AFPFromFasta</a></td>
<th class="colLast" scope="row">
<div class="block">Demo displaying a structural alignment from a FASTA file using <a href="org/biojava/nbio/structure/io/FastaAFPChainConverter.html" title="class in org.biojava.nbio.structure.io"><code>FastaAFPChainConverter</code></a>.</div>
</th>
</tr>
<tr id="i41" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPOptimizer</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i42" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPPostProcessor</a></td>
<th class="colLast" scope="row">
<div class="block">does post processing after alignment chaingin</div>
</th>
</tr>
<tr id="i43" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/AFPTwister.html" title="class in org.biojava.nbio.structure.align">AFPTwister</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i44" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/survival/cox/stats/AgScore.html" title="class in org.biojava.nbio.survival.cox.stats">AgScore</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i45" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/helper/AligMatEl.html" title="class in org.biojava.nbio.structure.align.helper">AligMatEl</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i46" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.nbio.structure.align.pairwise">Alignable</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i47" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.nbio.structure.gui.util">AlignedPosition</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i48" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/alignment/template/AlignedSequence.html" title="interface in org.biojava.nbio.core.alignment.template">AlignedSequence</a><<a href="org/biojava/nbio/core/alignment/template/AlignedSequence.html" title="type parameter in AlignedSequence">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><<a href="org/biojava/nbio/core/alignment/template/AlignedSequence.html" title="type parameter in AlignedSequence">C</a>>,​<a href="org/biojava/nbio/core/alignment/template/AlignedSequence.html" title="type parameter in AlignedSequence">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Defines a data structure for a <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template"><code>Sequence</code></a> within an alignment.</div>
</th>
</tr>
<tr id="i49" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html" title="enum in org.biojava.nbio.core.alignment.template">AlignedSequence.Step</a></td>
<th class="colLast" scope="row">
<div class="block">Defines an alignment step in order to pass alignment information from an <code>Aligner</code> to a constructor.</div>
</th>
</tr>
<tr id="i50" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/template/Aligner.html" title="interface in org.biojava.nbio.alignment.template">Aligner</a><<a href="org/biojava/nbio/alignment/template/Aligner.html" title="type parameter in Aligner">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><<a href="org/biojava/nbio/alignment/template/Aligner.html" title="type parameter in Aligner">C</a>>,​<a href="org/biojava/nbio/alignment/template/Aligner.html" title="type parameter in Aligner">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Defines an algorithm which computes an alignment <a href="org/biojava/nbio/core/alignment/template/Profile.html" title="interface in org.biojava.nbio.core.alignment.template"><code>Profile</code></a> from a list of <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template"><code>Sequence</code></a>s.</div>
</th>
</tr>
<tr id="i51" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AlignerHelper.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper</a></td>
<th class="colLast" scope="row">
<div class="block">Static utility to construct alignment routines from a common library of methods.</div>
</th>
</tr>
<tr id="i52" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Anchor</a></td>
<th class="colLast" scope="row">
<div class="block">Compounds in query and target sequences that must align</div>
</th>
</tr>
<tr id="i53" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.QueryIndexComparator.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Anchor.QueryIndexComparator</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i54" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Cut.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Cut</a></td>
<th class="colLast" scope="row">
<div class="block">Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.</div>
</th>
</tr>
<tr id="i55" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Last.html" title="enum in org.biojava.nbio.alignment.routines">AlignerHelper.Last</a></td>
<th class="colLast" scope="row">
<div class="block">Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound
with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and
insertion (addition of a target compound opening a gap in the query sequence).</div>
</th>
</tr>
<tr id="i56" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Subproblem.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Subproblem</a></td>
<th class="colLast" scope="row">
<div class="block">Alignment subproblem.</div>
</th>
</tr>
<tr id="i57" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/AlignmentCalc.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentCalc</a></td>
<th class="colLast" scope="row">
<div class="block">A class that obtains two structures via DAS and aligns them
This is done in a separate thread.</div>
</th>
</tr>
<tr id="i58" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.nbio.structure.gui.util">AlignmentCalc</a></td>
<th class="colLast" scope="row">
<div class="block">A class that obtains two structures via DAS and aligns them
This is done in a separate thread.</div>
</th>
</tr>
<tr id="i59" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/AlignmentCalcDB.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentCalcDB</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i60" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html" title="interface in org.biojava.nbio.structure.align.gui">AlignmentCalculationRunnable</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i61" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/AlignmentGui.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentGui</a></td>
<th class="colLast" scope="row">
<div class="block">A JFrame that allows to trigger a pairwise structure alignment,
either from files in a directory,
or after manual upload.</div>
</th>
</tr>
<tr id="i62" class="altColor">
<td class="colFirst"><a href="demo/AlignmentGuiDemo.html" title="class in demo">AlignmentGuiDemo</a></td>
<th class="colLast" scope="row">
<div class="block">Get an instance of the two alignment GUIs.</div>
</th>
</tr>
<tr id="i63" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.nbio.structure.gui.events">AlignmentPositionListener</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i64" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/events/AlignmentProgressListener.html" title="interface in org.biojava.nbio.structure.align.events">AlignmentProgressListener</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i65" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/pairwise/AlignmentProgressListener.html" title="class in org.biojava.nbio.structure.align.pairwise">AlignmentProgressListener</a></td>
<th class="colLast" scope="row">
<div class="block">A class to listen to progress of the structure alignment calculations</div>
</th>
</tr>
<tr id="i66" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/pairwise/AlignmentResult.html" title="class in org.biojava.nbio.structure.align.pairwise">AlignmentResult</a></td>
<th class="colLast" scope="row">
<div class="block">A class to track the alignment results in a flat file</div>
</th>
</tr>
<tr id="i67" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/Alignments.html" title="class in org.biojava.nbio.alignment">Alignments</a></td>
<th class="colLast" scope="row">
<div class="block">Static utility to easily run alignment routines.</div>
</th>
</tr>
<tr id="i68" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html" title="enum in org.biojava.nbio.alignment">Alignments.PairInProfileScorerType</a></td>
<th class="colLast" scope="row">
<div class="block">List of implemented sequence pair in a profile scoring routines.</div>
</th>
</tr>
<tr id="i69" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/Alignments.PairwiseSequenceAlignerType.html" title="enum in org.biojava.nbio.alignment">Alignments.PairwiseSequenceAlignerType</a></td>
<th class="colLast" scope="row">
<div class="block">List of implemented pairwise sequence alignment routines.</div>
</th>
</tr>
<tr id="i70" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/Alignments.PairwiseSequenceScorerType.html" title="enum in org.biojava.nbio.alignment">Alignments.PairwiseSequenceScorerType</a></td>
<th class="colLast" scope="row">
<div class="block">List of implemented pairwise sequence scoring routines.</div>
</th>
</tr>
<tr id="i71" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/Alignments.ProfileProfileAlignerType.html" title="enum in org.biojava.nbio.alignment">Alignments.ProfileProfileAlignerType</a></td>
<th class="colLast" scope="row">
<div class="block">List of implemented profile-profile alignment routines.</div>
</th>
</tr>
<tr id="i72" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/Alignments.RefinerType.html" title="enum in org.biojava.nbio.alignment">Alignments.RefinerType</a></td>
<th class="colLast" scope="row">
<div class="block">List of implemented profile refinement routines.</div>
</th>
</tr>
<tr id="i73" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentTextPanel</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i74" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/util/AlignmentTools.html" title="class in org.biojava.nbio.structure.align.util">AlignmentTools</a></td>
<th class="colLast" scope="row">
<div class="block">Methods for analyzing and manipulating AFPChains and for
other pairwise alignment utilities.</div>
</th>
</tr>
<tr id="i75" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html" title="class in org.biojava.nbio.structure.align.util">AlignmentTools.IdentityMap</a><<a href="org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html" title="type parameter in AlignmentTools.IdentityMap">K</a>></td>
<th class="colLast" scope="row">
<div class="block">A Map<K,V> can be viewed as a function from K to V.</div>
</th>
</tr>
<tr id="i76" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/pairwise/AligNPE.html" title="class in org.biojava.nbio.structure.align.pairwise">AligNPE</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i77" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/helper/AlignUtils.html" title="class in org.biojava.nbio.structure.align.helper">AlignUtils</a></td>
<th class="colLast" scope="row">
<div class="block">Low level helper methods for CE and FATCAT algorithms.</div>
</th>
</tr>
<tr id="i78" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">AligPanel</a></td>
<th class="colLast" scope="row">
<div class="block">A JPanel that can display an AFPChain in a nice way and interact with Jmol.</div>
</th>
</tr>
<tr id="i79" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">AligPanelMouseMotionListener</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i80" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/webstart/AligUIManager.html" title="class in org.biojava.nbio.structure.align.webstart">AligUIManager</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i81" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.html" title="class in org.biojava.nbio.structure.io.mmcif">AllChemCompProvider</a></td>
<th class="colLast" scope="row">
<div class="block">A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.</div>
</th>
</tr>
<tr id="i82" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ontology/AlreadyExistsException.html" title="class in org.biojava.nbio.ontology">AlreadyExistsException</a></td>
<th class="colLast" scope="row">
<div class="block">Thrown to indicate that a term or triple can't be added to an ontology
because it is already present.</div>
</th>
</tr>
<tr id="i83" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/pairwise/AltAligComparator.html" title="class in org.biojava.nbio.structure.align.pairwise">AltAligComparator</a></td>
<th class="colLast" scope="row">
<div class="block">a comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.</div>
</th>
</tr>
<tr id="i84" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.nbio.structure.align.pairwise">AlternativeAlignment</a></td>
<th class="colLast" scope="row">
<div class="block">Implements a class which handles one possible (alternative) solution.</div>
</th>
</tr>
<tr id="i85" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.nbio.structure.gui.util">AlternativeAlignmentFrame</a></td>
<th class="colLast" scope="row">
<div class="block">a frame showing the alternative alignments, which are the result of a structure superimposition</div>
</th>
</tr>
<tr id="i86" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AmbiguityDNACompoundSet</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i87" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AmbiguityDNARNAHybridCompoundSet</a></td>
<th class="colLast" scope="row">
<div class="block">Ambiguity set for hybrid DNA/RNA sequences.</div>
</th>
</tr>
<tr id="i88" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AmbiguityRNACompoundSet</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i89" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AminoAcid.html" title="interface in org.biojava.nbio.structure">AminoAcid</a></td>
<th class="colLast" scope="row">
<div class="block">
A <a href="org/biojava/nbio/structure/Group.html" title="interface in org.biojava.nbio.structure"><code>Group</code></a> that represents an AminoAcid.</div>
</th>
</tr>
<tr id="i90" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html" title="class in org.biojava.nbio.aaproperties.xml">AminoAcidComposition</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i91" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html" title="class in org.biojava.nbio.aaproperties.xml">AminoAcidCompositionTable</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i92" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html" title="class in org.biojava.nbio.core.sequence.compound">AminoAcidCompound</a></td>
<th class="colLast" scope="row">
<div class="block">Used to describe an Amino Acid.</div>
</th>
</tr>
<tr id="i93" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AminoAcidCompoundSet</a></td>
<th class="colLast" scope="row">
<div class="block">Set of proteinogenic amino acids.</div>
</th>
</tr>
<tr id="i94" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AminoAcidImpl.html" title="class in org.biojava.nbio.structure">AminoAcidImpl</a></td>
<th class="colLast" scope="row">
<div class="block">AminoAcid inherits most from Hetatom.</div>
</th>
</tr>
<tr id="i95" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/aaproperties/AminoAcidProperties.html" title="class in org.biojava.nbio.aaproperties">AminoAcidProperties</a></td>
<th class="colLast" scope="row">
<div class="block">This class provides the protein properties at the level of individual amino acids.</div>
</th>
</tr>
<tr id="i96" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.routines">AnchoredPairwiseSequenceAligner</a><<a href="org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html" title="type parameter in AnchoredPairwiseSequenceAligner">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><<a href="org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html" title="type parameter in AnchoredPairwiseSequenceAligner">C</a>>,​<a href="org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html" title="type parameter in AnchoredPairwiseSequenceAligner">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the
first until the last <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template"><code>Compound</code></a> of each <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template"><code>Sequence</code></a>) with the restriction that any alignment produced
will connect the query sequence to the target sequence at the <em>anchors</em>.</div>
</th>
</tr>
<tr id="i97" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html" title="class in org.biojava.nbio.structure.symmetry.internal">AngleOrderDetectorPlus</a></td>
<th class="colLast" scope="row">
<div class="block">Guesses an order of rotational symmetry from the angle.</div>
</th>
</tr>
<tr id="i98" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/validation/AngleOutlier.html" title="class in org.biojava.nbio.structure.validation">AngleOutlier</a></td>
<th class="colLast" scope="row">
<div class="block">Java class for anonymous complex type.</div>
</th>
</tr>
<tr id="i99" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/ontology/utils/Annotatable.html" title="interface in org.biojava.nbio.ontology.utils">Annotatable</a></td>
<th class="colLast" scope="row">
<div class="block">Indicates that an object has an associated annotation.</div>
</th>
</tr>
<tr id="i100" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ontology/utils/Annotation.html" title="interface in org.biojava.nbio.ontology.utils">Annotation</a></td>
<th class="colLast" scope="row">
<div class="block">
Arbitrary annotation associated with one or more objects.</div>
</th>
</tr>
<tr id="i101" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/genome/App.html" title="class in org.biojava.nbio.genome">App</a></td>
<th class="colLast" scope="row">
<div class="block">Hello world!</div>
</th>
</tr>
<tr id="i102" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ontology/App.html" title="class in org.biojava.nbio.ontology">App</a></td>
<th class="colLast" scope="row">
<div class="block">Hello world!</div>
</th>
</tr>
<tr id="i103" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader">ArrayListProxySequenceReader</a><<a href="org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html" title="type parameter in ArrayListProxySequenceReader">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i104" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">ArrayListSequenceReader</a><<a href="org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html" title="type parameter in ArrayListSequenceReader">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Stores a Sequence as a collection of compounds in an ArrayList</div>
</th>
</tr>
<tr id="i105" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/asa/AsaCalculator.html" title="class in org.biojava.nbio.structure.asa">AsaCalculator</a></td>
<th class="colLast" scope="row">
<div class="block">Class to calculate Accessible Surface Areas based on
the rolling ball algorithm by Shrake and Rupley.</div>
</th>
</tr>
<tr id="i106" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ontology/utils/AssertionFailure.html" title="class in org.biojava.nbio.ontology.utils">AssertionFailure</a></td>
<th class="colLast" scope="row">
<div class="block">An unchecked exception representing an Assertion failure.</div>
</th>
</tr>
<tr id="i107" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/domain/AssignmentXMLSerializer.html" title="class in org.biojava.nbio.structure.domain">AssignmentXMLSerializer</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i108" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/scop/Astral.html" title="class in org.biojava.nbio.structure.scop">Astral</a></td>
<th class="colLast" scope="row">
<div class="block">Provides programmatic access to ASTRAL representative sets.</div>
</th>
</tr>
<tr id="i109" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/scop/Astral.AstralSet.html" title="enum in org.biojava.nbio.structure.scop">Astral.AstralSet</a></td>
<th class="colLast" scope="row">
<div class="block">An ASTRAL sequence-identity cutoff with an identifier such as:</div>
</th>
</tr>
<tr id="i110" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/Atom.html" title="interface in org.biojava.nbio.structure">Atom</a></td>
<th class="colLast" scope="row">
<div class="block">A simple interface for an Atom.</div>
</th>
</tr>
<tr id="i111" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/util/AtomCache.html" title="class in org.biojava.nbio.structure.align.util">AtomCache</a></td>
<th class="colLast" scope="row">
<div class="block">A utility class that provides easy access to Structure objects.</div>
</th>
</tr>
<tr id="i112" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/contact/AtomContact.html" title="class in org.biojava.nbio.structure.contact">AtomContact</a></td>
<th class="colLast" scope="row">
<div class="block">A pair of atoms that are in contact</div>
</th>
</tr>
<tr id="i113" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/contact/AtomContactSet.html" title="class in org.biojava.nbio.structure.contact">AtomContactSet</a></td>
<th class="colLast" scope="row">
<div class="block">A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations</div>
</th>
</tr>
<tr id="i114" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/contact/AtomIdentifier.html" title="class in org.biojava.nbio.structure.contact">AtomIdentifier</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i115" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AtomImpl.html" title="class in org.biojava.nbio.structure">AtomImpl</a></td>
<th class="colLast" scope="row">
<div class="block">Implementation of an Atom of a PDB file.</div>
</th>
</tr>
<tr id="i116" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/jmol/AtomInfo.html" title="class in org.biojava.nbio.structure.align.gui.jmol">AtomInfo</a></td>
<th class="colLast" scope="row">
<div class="block">This class uniquely describes an atom</div>
</th>
</tr>
<tr id="i117" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.html" title="class in org.biojava.nbio.structure.align.gui.jmol">AtomInfoParser</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i118" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AtomIterator.html" title="class in org.biojava.nbio.structure">AtomIterator</a></td>
<th class="colLast" scope="row">
<div class="block">an iterator over all atoms of a structure / group.</div>
</th>
</tr>
<tr id="i119" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AtomPositionMap.html" title="class in org.biojava.nbio.structure">AtomPositionMap</a></td>
<th class="colLast" scope="row">
<div class="block">A map from <a href="org/biojava/nbio/structure/ResidueNumber.html" title="class in org.biojava.nbio.structure"><code>ResidueNumbers</code></a> to ATOM record positions in a PDB file.</div>
</th>
</tr>
<tr id="i120" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AtomPositionMap.GroupMatcher.html" title="interface in org.biojava.nbio.structure">AtomPositionMap.GroupMatcher</a></td>
<th class="colLast" scope="row">
<div class="block">Used as a Predicate to indicate whether a particular Atom should be mapped</div>
</th>
</tr>
<tr id="i121" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.nbio.structure.io.mmcif.model">AtomSite</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i122" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/io/mmcif/model/AtomSites.html" title="class in org.biojava.nbio.structure.io.mmcif.model">AtomSites</a></td>
<th class="colLast" scope="row">
<div class="block">A class containing the _atom_sites data.</div>
</th>
</tr>
<tr id="i123" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/io/mmcif/model/AuditAuthor.html" title="class in org.biojava.nbio.structure.io.mmcif.model">AuditAuthor</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i124" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/AugmentedResidueRange.html" title="class in org.biojava.nbio.structure">AugmentedResidueRange</a></td>
<th class="colLast" scope="row">
<div class="block">Created by douglas on 1/23/15.</div>
</th>
</tr>
<tr id="i125" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/Author.html" title="class in org.biojava.nbio.structure">Author</a></td>
<th class="colLast" scope="row">
<div class="block">Describes author attributes for author information in a PDB file.</div>
</th>
</tr>
<tr id="i126" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.html" title="interface in org.biojava.nbio.structure.align.gui.autosuggest">AutoSuggestProvider</a></td>
<th class="colLast" scope="row">
<div class="block">A class that provides auto-completion suggestions for JAutoSuggest</div>
</th>
</tr>
<tr id="i127" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/symmetry/axis/AxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.axis">AxisAligner</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i128" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/basepairs/BasePairParameters.html" title="class in org.biojava.nbio.structure.basepairs">BasePairParameters</a></td>
<th class="colLast" scope="row">
<div class="block">This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic
acid containing structure that has the information about the core base-pair rings.</div>
</th>
</tr>
<tr id="i129" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/BasicSequence.html" title="class in org.biojava.nbio.core.sequence">BasicSequence</a><<a href="org/biojava/nbio/core/sequence/BasicSequence.html" title="type parameter in BasicSequence">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">Bare bones version of the Sequence object to be used sparingly.</div>
</th>
</tr>
<tr id="i130" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/scop/BerkeleyScopInstallation.html" title="class in org.biojava.nbio.structure.scop">BerkeleyScopInstallation</a></td>
<th class="colLast" scope="row">
<div class="block">SCOPe:
The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley
(<a href="http://scop.berkeley.edu/">http://scop.berkeley.edu/</a>).</div>
</th>
</tr>
<tr id="i131" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/secstruc/BetaBridge.html" title="class in org.biojava.nbio.structure.secstruc">BetaBridge</a></td>
<th class="colLast" scope="row">
<div class="block">Container that represents a beta Bridge between two residues.</div>
</th>
</tr>
<tr id="i132" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/BioAssemblyIdentifier.html" title="class in org.biojava.nbio.structure">BioAssemblyIdentifier</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i133" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/quaternary/BioAssemblyInfo.html" title="class in org.biojava.nbio.structure.quaternary">BioAssemblyInfo</a></td>
<th class="colLast" scope="row">
<div class="block">Representation of a Biological Assembly annotation as provided by the PDB.</div>
</th>
</tr>
<tr id="i134" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/quaternary/BioAssemblyTools.html" title="class in org.biojava.nbio.structure.quaternary">BioAssemblyTools</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i135" class="rowColor">
<td class="colFirst"><a href="demo/BioJavaAADemo.html" title="class in demo">BioJavaAADemo</a></td>
<th class="colLast" scope="row">
<div class="block">Created by andreas on 8/9/14.</div>
</th>
</tr>
<tr id="i136" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/gui/BiojavaJmol.html" title="class in org.biojava.nbio.structure.gui">BiojavaJmol</a></td>
<th class="colLast" scope="row">
<div class="block">A class that provides a simple GUI for Jmol</div>
</th>
</tr>
<tr id="i137" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/align/BioJavaStructureAlignment.html" title="class in org.biojava.nbio.structure.align">BioJavaStructureAlignment</a></td>
<th class="colLast" scope="row">
<div class="block">Wrapper for the BioJava Structure Alignment Implementation</div>
</th>
</tr>
<tr id="i138" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.html" title="class in org.biojava.nbio.structure.quaternary">BiologicalAssemblyBuilder</a></td>
<th class="colLast" scope="row">
<div class="block">Reconstructs the quaternary structure of a protein from an asymmetric unit</div>
</th>
</tr>
<tr id="i139" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.html" title="class in org.biojava.nbio.structure.quaternary">BiologicalAssemblyTransformation</a></td>
<th class="colLast" scope="row">
<div class="block">The transformation needed for generation of biological assemblies
from the contents of a PDB/mmCIF file.</div>
</th>
</tr>
<tr id="i140" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">BitSequenceReader</a><<a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.html" title="type parameter in BitSequenceReader">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">An implementation of the popular bit encodings.</div>
</th>
</tr>
<tr id="i141" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html" title="class in org.biojava.nbio.core.sequence.storage">BitSequenceReader.BitArrayWorker</a><<a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html" title="type parameter in BitSequenceReader.BitArrayWorker">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></td>
<th class="colLast" scope="row">
<div class="block">The logic of working with a bit has been separated out into this class
to help developers create the bit data structures without having to
put the code into an intermediate format and to also use the format
without the need to copy this code.</div>
</th>
</tr>
<tr id="i142" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastAlignmentParameterEnum</a></td>
<th class="colLast" scope="row">
<div class="block">Alignment request parameters accepted by QBlast service.<br/>
Not all are mandatory.</div>
</th>
</tr>
<tr id="i143" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/structure/symmetry/utils/BlastClustReader.html" title="class in org.biojava.nbio.structure.symmetry.utils">BlastClustReader</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i144" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/search/io/blast/BlastHitBuilder.html" title="class in org.biojava.nbio.core.search.io.blast">BlastHitBuilder</a></td>
<th class="colLast" scope="row">
<div class="block">Designed by Paolo Pavan.</div>
</th>
</tr>
<tr id="i145" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/genome/homology/BlastHomologyHits.html" title="class in org.biojava.nbio.genome.homology">BlastHomologyHits</a></td>
<th class="colLast" scope="row"> </th>
</tr>
<tr id="i146" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/search/io/blast/BlastHspBuilder.html" title="class in org.biojava.nbio.core.search.io.blast">BlastHspBuilder</a></td>
<th class="colLast" scope="row">
<div class="block">Designed by Paolo Pavan.</div>
</th>
</tr>
<tr id="i147" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastJob.html" title="class in org.biojava.nbio.ws.alignment.qblast">BlastJob</a></td>
<th class="colLast" scope="row">
<div class="block">Information about QBlast search job</div>
</th>
</tr>
<tr id="i148" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastMatrixEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastMatrixEnum</a></td>
<th class="colLast" scope="row">
<div class="block">Enum representing matrices supported by QBlast</div>
</th>
</tr>
<tr id="i149" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastOutputAlignmentFormatEnum</a></td>
<th class="colLast" scope="row">
<div class="block">Enum representing available output alignment types.</div>
</th>
</tr>
<tr id="i150" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastOutputFormatEnum</a></td>
<th class="colLast" scope="row">
<div class="block">Enum representing available output formats.</div>
</th>
</tr>
<tr id="i151" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastOutputParameterEnum</a></td>
<th class="colLast" scope="row">
<div class="block">Output parameters accepted by QBlast service.</div>
</th>
</tr>
<tr id="i152" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastProgramEnum</a></td>
<th class="colLast" scope="row">
<div class="block">Enum representing available blast programs.</div>
</th>
</tr>
<tr id="i153" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/search/io/blast/BlastResult.html" title="class in org.biojava.nbio.core.search.io.blast">BlastResult</a></td>
<th class="colLast" scope="row">
<div class="block">This class models a Blast/Blast plus result.</div>
</th>
</tr>
<tr id="i154" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/search/io/blast/BlastResultBuilder.html" title="class in org.biojava.nbio.core.search.io.blast">BlastResultBuilder</a></td>
<th class="colLast" scope="row">
<div class="block">Designed by Paolo Pavan.</div>
</th>
</tr>
<tr id="i155" class="rowColor">
<td class="colFirst"><a href="org/biojava/nbio/core/search/io/blast/BlastTabularParser.html" title="class in org.biojava.nbio.core.search.io.blast">BlastTabularParser</a></td>
<th class="colLast" scope="row">
<div class="block">Designed by Paolo Pavan.</div>
</th>
</tr>
<tr id="i156" class="altColor">
<td class="colFirst"><a href="org/biojava/nbio/core/search/io/blast/BlastXMLParser.html" title="class in org.biojava.nbio.core.search.io.blast">BlastXMLParser</a></td>
<th class="colLast" scope="row">
<div class="block">Re-designed by Paolo Pavan on the footprint of:
org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis <willishf at gmail dot com>
You may want to find my contacts on Github and LinkedIn for code info
or discuss major changes.</div>
</th>
</tr>