uk.ac.ed.simulator_pdb.model
Class PDBFile

java.lang.Object
  uk.ac.ed.simulator_pdb.model.PDBFile

public class PDBFile

extends java.lang.Object

User: nix Date: 17-Aug-2004 Time: 13:30:58 To change this template_file_object use Options | File TemplateBuilderModel.

Nested Class Summary

class	PDBFile.AminoAcid
class	PDBFile.Atom
class	PDBFile.Cluster
static interface	PDBFile.DataPoint
static class	PDBFile.PDBAdapter
static class	PDBFile.PDBEvent
static interface	PDBFile.PDBListener

Field Summary

protected java.util.HashMap	amino_acids
static int	AMINO_ACIDS
protected java.util.ArrayList	atoms
static int	ATOMS
protected java.util.ArrayList	clusters
protected java.util.ArrayList	data_points
static javax.vecmath.Color3f	DEFAULT_AMINO_ACID_COLOUR
static float	DEFAULT_CLUSTER_ALPHA
static javax.vecmath.Color3f	DEFAULT_CLUSTER_COLOUR
static boolean	DEFAULT_CLUSTERED
static int	DEFAULT_NUMBER_OF_CLUSTERS
static double	DEFAULT_SCALE
static int	DEFAULT_TYPE
protected java.io.File	file
protected SimLandscapeTemplate	landscape
protected int	number_of_clusters
protected java.util.ArrayList	pdb_listeners
protected java.util.ArrayList	sub_particles
protected java.util.HashMap	template_hashmap
protected int	type

Constructor Summary

PDBFile(java.io.File file)

Method Summary

void	addAtom(SimParticleTemplate particle_template, javax.vecmath.Vector3d position, int amino_acid_id)
void	addPDBFileListener(PDBFile.PDBListener listener)
void	addTemplate(TemplateFileObject template_object_file_object)
void	addTo(TemplateFile templateFile)
double	getHalfScale()
SimLandscapeTemplate	getLandscape()
java.lang.String	getName()
int	getNumberOfClusters()
double	getScale()
java.lang.String	getShortName()
SimSubParticle[]	getSubParticles()
int	getType()
boolean	isClustered()
void	removePDBFileListener(PDBFile.PDBListener listener)
void	removeTemplate(TemplateFileObject template_object_file_object)
void	revalidate()
void	setClustered(boolean clustered)
void	setLandscape(SimLandscapeTemplate landscape)
void	setNumberOfClusters(int number_of_clusters)
void	setScale(double scale)
void	setType(int type)
java.lang.String	toString()
void	validate()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ATOMS

public static final int ATOMS

See Also:

Constant Field Values

AMINO_ACIDS

public static final int AMINO_ACIDS

See Also:

Constant Field Values

DEFAULT_SCALE

public static final double DEFAULT_SCALE

DEFAULT_TYPE

public static final int DEFAULT_TYPE

See Also:

Constant Field Values

DEFAULT_CLUSTERED

public static final boolean DEFAULT_CLUSTERED

See Also:

Constant Field Values

DEFAULT_NUMBER_OF_CLUSTERS

public static final int DEFAULT_NUMBER_OF_CLUSTERS

See Also:

Constant Field Values

DEFAULT_CLUSTER_COLOUR

public static final javax.vecmath.Color3f DEFAULT_CLUSTER_COLOUR

DEFAULT_CLUSTER_ALPHA

public static final float DEFAULT_CLUSTER_ALPHA

See Also:

Constant Field Values

DEFAULT_AMINO_ACID_COLOUR

public static final javax.vecmath.Color3f DEFAULT_AMINO_ACID_COLOUR

landscape

protected SimLandscapeTemplate landscape

type

protected int type

number_of_clusters

protected int number_of_clusters

file

protected java.io.File file

atoms

protected java.util.ArrayList atoms

amino_acids

protected java.util.HashMap amino_acids

clusters

protected java.util.ArrayList clusters

data_points

protected java.util.ArrayList data_points

template_hashmap

protected java.util.HashMap template_hashmap

sub_particles

protected java.util.ArrayList sub_particles

pdb_listeners

protected java.util.ArrayList pdb_listeners

Constructor Detail

PDBFile

public PDBFile(java.io.File file)

Method Detail

toString

public java.lang.String toString()

getName

public java.lang.String getName()

getShortName

public java.lang.String getShortName()

setScale

public void setScale(double scale)

getScale

public double getScale()

getHalfScale

public double getHalfScale()

addTemplate

public void addTemplate(TemplateFileObject template_object_file_object)

removeTemplate

public void removeTemplate(TemplateFileObject template_object_file_object)

addAtom

public void addAtom(SimParticleTemplate particle_template,
                    javax.vecmath.Vector3d position,
                    int amino_acid_id)

setLandscape

public void setLandscape(SimLandscapeTemplate landscape)

getLandscape

public SimLandscapeTemplate getLandscape()

getType

public int getType()

setType

public void setType(int type)

isClustered

public boolean isClustered()

setClustered

public void setClustered(boolean clustered)

getNumberOfClusters

public int getNumberOfClusters()

setNumberOfClusters

public void setNumberOfClusters(int number_of_clusters)

getSubParticles

public SimSubParticle[] getSubParticles()

addTo

public void addTo(TemplateFile templateFile)

validate

public void validate()

revalidate

public void revalidate()

addPDBFileListener

public void addPDBFileListener(PDBFile.PDBListener listener)

removePDBFileListener

public void removePDBFileListener(PDBFile.PDBListener listener)