Package demo

Class Summary

Class	Description
AFPFromFasta	Demo displaying a structural alignment from a FASTA file using FastaAFPChainConverter.
AlignmentGuiDemo	Get an instance of the two alignment GUIs.
BioJavaAADemo	Created by andreas on 8/9/14.
ChemCompDistribution
CookBook
CookbookMSA
DemoAlignmentFromFasta	Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoAlignProteins
DemoAsa
DemoAtomCache	Example of how to load PDB files using the AtomCache class.
DemoBerkeleyScop	A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
DemoCATH	An example for how to access CATH data.
DemoCE	Example of how to run a structure alignment using the CE algorithm.
DemoCeSymm	Quick demo of how to call CE-Symm programmatically.
DemoChangeChemCompProvider	This demo shows how to use an alternative ChemCompProvider.
DemoCommandLineStartup
DemoContacts
DemoCrystalInterfaces
DemoDistanceTree	This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
DemoDomainsplit
DemoFATCAT
DemoLoadSecStruc	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).
DemoLoadStructure	Example for how to load protein structures (from PDB files).
DemoLoadSubstMax
DemoMMCIFReader	An example of how to read MMcif files
DemoMultipleMC	Demo for running the MultipleMC Algorithm on a protein family.
DemoNWALignment
DemoOrientBioAssembly	Created by ap3 on 02/04/2015.
DemoRotationAxis	A demo for how to use RotationAxis to display the rotation for an alignment.
DemoSCOP	A class demonstrating the use of the SCOP parsing tools
DemoSecStrucCalc	Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.
DemoShowBiolAssembly
DemoShowCATHDomain
DemoShowLargeAssembly
DemoShowValidationResults
DemoSixFrameTranslation	Created by andreas on 8/10/15.
DemoStructureFromFasta	Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoSW3DAligner
HmmerDemo	The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
NCBIQBlastServiceDemo	A simple demo showing NCBIQBlastService usage
ParseFastaFileDemo	Created by andreas on 6/17/15.
ParseGO
PredictDisorder
ShowStructureInJmol	Demo how to load and display a structure in Jmol
TestDNANeedlemanWunsch
WebStartClientDemo