edu.mssm.crover.domain2d.rbdg.xml
Class TmBundle

java.lang.Object
  |
  +--edu.mssm.crover.domain2d.rbdg.xml.TmBundle

All Implemented Interfaces:

java.io.Serializable

public class TmBundle

extends java.lang.Object

implements java.io.Serializable

Use the bundle to layout integral membrane proteins. Specify the number of transmembrane (TM) segment to display, and the bundle will automatically calculate the layout of the diagram. Attributes of the bundle include the direction the N-term will take (up or down). Ids must also be generated for each subunit the tm-bundle contains, so that subunits can be referenced by the secondary -structure section of the diagram. The N and C-term X and Y attributes relate to the spacer values that can be used when drawing the diagram.

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

TmBundle()

Method Summary

void	deleteCTermX()
void	deleteCTermY()
void	deleteNTermX()
void	deleteNTermY()
java.lang.String	getCtermId()
int	getCTermX()
int	getCTermY()
java.lang.String	getDirection()
java.lang.String	getNtermId()
int	getNTermX()
int	getNTermY()
java.lang.String	getTmIdPrefix()
int	getTmNumber()
boolean	hasCTermX()
boolean	hasCTermY()
boolean	hasNTermX()
boolean	hasNTermY()
boolean	hasTmNumber()
boolean	isValid()
void	marshal(org.xml.sax.DocumentHandler handler)
void	marshal(java.io.Writer out)
void	setCtermId(java.lang.String ctermId)
void	setCTermX(int cTermX)
void	setCTermY(int cTermY)
void	setDirection(java.lang.String direction)
void	setNtermId(java.lang.String ntermId)
void	setNTermX(int nTermX)
void	setNTermY(int nTermY)
void	setTmIdPrefix(java.lang.String tmIdPrefix)
void	setTmNumber(int tmNumber)
static TmBundle	unmarshal(java.io.Reader reader)
void	validate()

Methods inherited from class java.lang.Object

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

Constructor Detail

TmBundle

public TmBundle()

Method Detail

deleteCTermX

public void deleteCTermX()

deleteCTermY

public void deleteCTermY()

deleteNTermX

public void deleteNTermX()

deleteNTermY

public void deleteNTermY()

getCTermX

public int getCTermX()

getCTermY

public int getCTermY()

getCtermId

public java.lang.String getCtermId()

getDirection

public java.lang.String getDirection()

getNTermX

public int getNTermX()

getNTermY

public int getNTermY()

getNtermId

public java.lang.String getNtermId()

getTmIdPrefix

public java.lang.String getTmIdPrefix()

getTmNumber

public int getTmNumber()

hasCTermX

public boolean hasCTermX()

hasCTermY

public boolean hasCTermY()

hasNTermX

public boolean hasNTermX()

hasNTermY

public boolean hasNTermY()

hasTmNumber

public boolean hasTmNumber()

isValid

public boolean isValid()

marshal

public void marshal(java.io.Writer out)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException

Parameters:

out -

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

marshal

public void marshal(org.xml.sax.DocumentHandler handler)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException

Parameters:

handler -

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

setCTermX

public void setCTermX(int cTermX)

Parameters:

cTermX -

setCTermY

public void setCTermY(int cTermY)

Parameters:

cTermY -

setCtermId

public void setCtermId(java.lang.String ctermId)

Parameters:

ctermId -

setDirection

public void setDirection(java.lang.String direction)

Parameters:

direction -

setNTermX

public void setNTermX(int nTermX)

Parameters:

nTermX -

setNTermY

public void setNTermY(int nTermY)

Parameters:

nTermY -

setNtermId

public void setNtermId(java.lang.String ntermId)

Parameters:

ntermId -

setTmIdPrefix

public void setTmIdPrefix(java.lang.String tmIdPrefix)

Parameters:

tmIdPrefix -

setTmNumber

public void setTmNumber(int tmNumber)

Parameters:

tmNumber -

unmarshal

public static TmBundle unmarshal(java.io.Reader reader)
                          throws org.exolab.castor.xml.MarshalException,
                                 org.exolab.castor.xml.ValidationException

Parameters:

reader -

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

validate

public void validate()
              throws org.exolab.castor.xml.ValidationException

org.exolab.castor.xml.ValidationException