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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>demo (biojava 4.2.9 API)</title>

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<li><a href="../overview-summary.html">Overview</a></li>

<li class="navBarCell1Rev">Package</li>

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<h1 title="Package" class="title">Package demo</h1>

</div>

<caption><span>Class Summary</span><span class="tabEnd"> </span></caption>

<tr>

<th class="colFirst" scope="col">Class</th>

<th class="colLast" scope="col">Description</th>

</tr>

<tbody>

<td class="colFirst"><a href="../demo/AFPFromFasta.html" title="class in demo">AFPFromFasta</a></td>

<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>

</td>

</tr>

<td class="colFirst"><a href="../demo/AlignmentGuiDemo.html" title="class in demo">AlignmentGuiDemo</a></td>

<div class="block">Get an instance of the two alignment GUIs.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/BioJavaAADemo.html" title="class in demo">BioJavaAADemo</a></td>

<div class="block">Created by andreas on 8/9/14.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/ChemCompDistribution.html" title="class in demo">ChemCompDistribution</a></td>

</tr>

<td class="colFirst"><a href="../demo/CookBook.html" title="class in demo">CookBook</a></td>

</tr>

<td class="colFirst"><a href="../demo/CookbookMSA.html" title="class in demo">CookbookMSA</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoAlignmentFromFasta.html" title="class in demo">DemoAlignmentFromFasta</a></td>

<div class="block">Demo of how to use the <a href="../org/biojava/nbio/structure/io/FastaStructureParser.html" title="class in org.biojava.nbio.structure.io"><code>FastaStructureParser</code></a> class to read protein

structures from a FASTA file.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoAlignProteins.html" title="class in demo">DemoAlignProteins</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoAsa.html" title="class in demo">DemoAsa</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoAtomCache.html" title="class in demo">DemoAtomCache</a></td>

<div class="block">Example of how to load PDB files using the AtomCache class.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoBerkeleyScop.html" title="class in demo">DemoBerkeleyScop</a></td>

<div class="block">A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoCATH.html" title="class in demo">DemoCATH</a></td>

<div class="block">An example for how to access CATH data.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoCE.html" title="class in demo">DemoCE</a></td>

<div class="block">Example of how to run a structure alignment using the CE algorithm.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoCeSymm.html" title="class in demo">DemoCeSymm</a></td>

<div class="block">Quick demo of how to call CE-Symm programmatically.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoChangeChemCompProvider.html" title="class in demo">DemoChangeChemCompProvider</a></td>

<div class="block">This demo shows how to use an alternative ChemCompProvider.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoCommandLineStartup.html" title="class in demo">DemoCommandLineStartup</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoContacts.html" title="class in demo">DemoContacts</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoCrystalInterfaces.html" title="class in demo">DemoCrystalInterfaces</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoDistanceTree.html" title="class in demo">DemoDistanceTree</a></td>

<div class="block">This demo contains the CookBook example to create a phylogenetic tree from a

multiple sequence alignment (MSA).</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoDomainsplit.html" title="class in demo">DemoDomainsplit</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoFATCAT.html" title="class in demo">DemoFATCAT</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoLoadSecStruc.html" title="class in demo">DemoLoadSecStruc</a></td>

<div class="block">Demonstration of how to load a Structure with the SS information, either from

the PDB file annotation (Author's assignment) or from the DSSP file in the

PDB servers (DSSP assignment).</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoLoadStructure.html" title="class in demo">DemoLoadStructure</a></td>

<div class="block">Example for how to load protein structures (from PDB files).</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoLoadSubstMax.html" title="class in demo">DemoLoadSubstMax</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoMMCIFReader.html" title="class in demo">DemoMMCIFReader</a></td>

<div class="block">An example of how to read MMcif files</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoMultipleMC.html" title="class in demo">DemoMultipleMC</a></td>

<div class="block">Demo for running the MultipleMC Algorithm on a protein family.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoNWALignment.html" title="class in demo">DemoNWALignment</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoOrientBioAssembly.html" title="class in demo">DemoOrientBioAssembly</a></td>

<div class="block">Created by ap3 on 02/04/2015.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoRotationAxis.html" title="class in demo">DemoRotationAxis</a></td>

<div class="block">A demo for how to use <a href="../org/biojava/nbio/structure/align/util/RotationAxis.html" title="class in org.biojava.nbio.structure.align.util"><code>RotationAxis</code></a> to display the rotation for an

alignment.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoSCOP.html" title="class in demo">DemoSCOP</a></td>

<div class="block">A class demonstrating the use of the SCOP parsing tools</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoSecStrucCalc.html" title="class in demo">DemoSecStrucCalc</a></td>

<div class="block">Demonstration on how to use the Secondary Structure Prediction (DSSP)

implementation in BioJava and obtain different SS representations and

outputs.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoShowBiolAssembly.html" title="class in demo">DemoShowBiolAssembly</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoShowCATHDomain.html" title="class in demo">DemoShowCATHDomain</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoShowLargeAssembly.html" title="class in demo">DemoShowLargeAssembly</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoShowValidationResults.html" title="class in demo">DemoShowValidationResults</a></td>

</tr>

<td class="colFirst"><a href="../demo/DemoSixFrameTranslation.html" title="class in demo">DemoSixFrameTranslation</a></td>

<div class="block">Created by andreas on 8/10/15.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoStructureFromFasta.html" title="class in demo">DemoStructureFromFasta</a></td>

structures from a FASTA file.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/DemoSW3DAligner.html" title="class in demo">DemoSW3DAligner</a></td>

</tr>

<td class="colFirst"><a href="../demo/HmmerDemo.html" title="class in demo">HmmerDemo</a></td>

<div class="block">The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/NCBIQBlastServiceDemo.html" title="class in demo">NCBIQBlastServiceDemo</a></td>

<div class="block">A simple demo showing <a href="../org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.html" title="class in org.biojava.nbio.ws.alignment.qblast"><code>NCBIQBlastService</code></a> usage</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/ParseFastaFileDemo.html" title="class in demo">ParseFastaFileDemo</a></td>

<div class="block">Created by andreas on 6/17/15.</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/ParseGO.html" title="class in demo">ParseGO</a></td>

</tr>

<td class="colFirst"><a href="../demo/PredictDisorder.html" title="class in demo">PredictDisorder</a></td>

</tr>

<td class="colFirst"><a href="../demo/ShowStructureInJmol.html" title="class in demo">ShowStructureInJmol</a></td>

<div class="block">Demo how to load and display a structure in Jmol</div>

</td>

</tr>

<td class="colFirst"><a href="../demo/TestDNANeedlemanWunsch.html" title="class in demo">TestDNANeedlemanWunsch</a></td>

</tr>

<td class="colFirst"><a href="../demo/WebStartClientDemo.html" title="class in demo">WebStartClientDemo</a></td>

</tr>

</tbody>

</table>

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