membranModel
Class MembranModel

java.lang.Object
  membranModel.MembranModel

Direct Known Subclasses:

MembranModelSingleton

public class MembranModel
extends java.lang.Object

This class implements a membrane model

Constructor Summary

MembranModel()

Method Summary

void	addComponent(java.lang.String PDBCode, java.lang.String sub_componente) This function adds a protein to a subcomponent of the mebrane model
void	addComponents(java.util.Vector PDBCodes) This function adds proteins to the membrane model
void	addProtein(Protein protein) This function adds one protein to the membrane model
void	complete_scaling_proteins() Does the completeScaling() function for any Protein the membrane consists of
int	countProteins()
java.util.Vector	getAllProteins()
java.awt.Color	getBackground_color()
double	getBiLayerSpace()
Protein	getBiLayerType()
java.lang.String	getCelltype()
java.awt.Color	getColor(int i)
java.awt.Color[]	getColors()
java.lang.String	getDate()
java.lang.String	getDescription()
java.util.Hashtable	getHash()
java.lang.String	getMembraneTitle()
java.lang.String	getName()
int	getPercent()
Protein	getProtein(java.lang.String PDBCode)
java.util.Set	getProteinNames()
java.awt.Color	getSelection_color()
java.lang.String[]	getSpecies()
java.lang.String	getVRMLFile()
double	getXz_area()
void	removeAllComponents() this function removes all proteins that are in the membrane model
void	removeComponent(java.lang.String PDBCode) This function removes a given protein
void	removeComponents(java.util.Set PDBCodes) this function removes all proteins with given PDBcode
void	setBackground_color(java.awt.Color background_color)
void	setBiLayerSpace(double biLayerSpace)
void	setBiLayerType(java.lang.String name)
void	setCelltype(java.lang.String celltype)
void	setDate(java.lang.String date)
void	setDescription(java.lang.String Description) sets the dirscription of the membrane model
void	setHash(java.util.Hashtable hash)
void	setMembraneTitle(java.lang.String title) sets the membrane title
void	setName(java.lang.String name)
void	setPercent(int percent)
void	setSelection_color(java.awt.Color selection_color)
void	setSpecies(java.lang.String[] species)
void	setVRMLFile(java.lang.String vrml)
void	setxz_area() Computes the value of the xz_area of the membrane, the area of the membrane in x- and z-dimension in angstrom^2.
void	setxz_area(double xz_area)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MembranModel

public MembranModel()

Method Detail

getProtein

public Protein getProtein(java.lang.String PDBCode)

Parameters:

PDBCode -

Returns:

Protein

addComponent

public void addComponent(java.lang.String PDBCode,
                         java.lang.String sub_componente)
                  throws java.io.IOException

This function adds a protein to a subcomponent of the mebrane model

Parameters:

PDBCode -

sub_componente -

Throws:

java.io.IOException

addProtein

public void addProtein(Protein protein)

This function adds one protein to the membrane model

Parameters:

protein -

addComponents

public void addComponents(java.util.Vector PDBCodes)

This function adds proteins to the membrane model

Parameters:

PDBCodes -

removeComponent

public void removeComponent(java.lang.String PDBCode)

This function removes a given protein

Parameters:

PDBCode -

removeComponents

public void removeComponents(java.util.Set PDBCodes)

this function removes all proteins with given PDBcode

Parameters:

PDBCodes -

removeAllComponents

public void removeAllComponents()

this function removes all proteins that are in the membrane model

setDescription

public void setDescription(java.lang.String Description)

sets the dirscription of the membrane model

Parameters:

Description -

getDescription

public java.lang.String getDescription()

Returns:

description of the membrane model

setBiLayerType

public void setBiLayerType(java.lang.String name)
                    throws java.io.IOException

Parameters:

name - The name of the new BilayerType Sets a new lipid a BiLayerType

Throws:

java.io.IOException

getAllProteins

public java.util.Vector getAllProteins()

Returns:

all proteins in the membrane model

getProteinNames

public java.util.Set getProteinNames()

Returns:

the names of the proteins in the membrane model

getCelltype

public java.lang.String getCelltype()

Returns:

Returns the celltype.

setCelltype

public void setCelltype(java.lang.String celltype)

Parameters:

celltype - The celltype to set.

getMembraneTitle

public java.lang.String getMembraneTitle()

Returns:

the membrane title

setMembraneTitle

public void setMembraneTitle(java.lang.String title)

sets the membrane title

Parameters:

title -

setDate

public void setDate(java.lang.String date)

Parameters:

date - The date to set.

getName

public java.lang.String getName()

Returns:

Returns the name.

setName

public void setName(java.lang.String name)

Parameters:

name - The name to set.

getSpecies

public java.lang.String[] getSpecies()

Returns:

Returns the species.

setSpecies

public void setSpecies(java.lang.String[] species)

Parameters:

species - The species to set.

getDate

public java.lang.String getDate()

Returns:

Returns the date.

countProteins

public int countProteins()

Returns:

the amount of the proteins in the membrane model

getPercent

public int getPercent()

Returns:

Returns the percent.

setPercent

public void setPercent(int percent)

Parameters:

percent - The percent to set.

getBiLayerType

public Protein getBiLayerType()

Returns:

Returns the biLayerType.

getColors

public java.awt.Color[] getColors()

Returns:

Returns the colors.

getColor

public java.awt.Color getColor(int i)

Parameters:

i -

Returns:

the color

getHash

public java.util.Hashtable getHash()

Returns:

Returns the hash.

setHash

public void setHash(java.util.Hashtable hash)

Parameters:

hash - The hash to set.

complete_scaling_proteins

public void complete_scaling_proteins()

Does the completeScaling() function for any Protein the membrane consists of

See Also:

in ProteinClass

getBackground_color

public java.awt.Color getBackground_color()

Returns:

Returns the background_color.

setBackground_color

public void setBackground_color(java.awt.Color background_color)

Parameters:

background_color - The background_color to set.

getSelection_color

public java.awt.Color getSelection_color()

Returns:

Returns the selection_color.

setSelection_color

public void setSelection_color(java.awt.Color selection_color)

Parameters:

selection_color - The selection_color to set.

getBiLayerSpace

public double getBiLayerSpace()

Returns:

Returns the biLayerSpace.

setBiLayerSpace

public void setBiLayerSpace(double biLayerSpace)

Parameters:

biLayerSpace - The biLayerSpace to set.

getXz_area

public double getXz_area()

Returns:

Returns the value of the xz_area, the space of the membrane in x- and z-dimension in angstrom^2.

setxz_area

public void setxz_area(double xz_area)

Parameters:

xz_area - The xz_area to set.

setxz_area

public void setxz_area()

Computes the value of the xz_area of the membrane, the area of the membrane in x- and z-dimension in angstrom^2.

getVRMLFile

public java.lang.String getVRMLFile()

Returns:

Returns the vrml.

setVRMLFile

public void setVRMLFile(java.lang.String vrml)

Parameters:

vrml - The vrml to set.