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


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.