org.biomage.ArrayDesign
Class ZoneGroup

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.ArrayDesign.ZoneGroup
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasDistanceUnit, HasPropertySets, HasZoneLayout, HasZoneLocations

public class ZoneGroup
extends Extendable
implements java.io.Serializable, HasZoneLayout, HasZoneLocations, HasDistanceUnit

Specifies a repeating area on an array. This is useful for printing when the same pattern is repeated in a regular fashion.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasZoneLocations
HasZoneLocations.ZoneLocations_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  DistanceUnit distanceUnit
          Unit for the ZoneGroup attributes.
protected  ZoneLayout zoneLayout
          Describes the rectangular layout of features in the array design.
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ZoneGroup()
          Default constructor.
ZoneGroup(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToZoneLocations(int position, Zone zone)
          Method to add Zone at position to ZoneLocations_list
 void addToZoneLocations(Zone zone)
          Method to add Zone to ZoneLocations_list
 boolean emptyMAGEobject()
           
 DistanceUnit getDistanceUnit()
          Get method for distanceUnit
 Zone getFromZoneLocations(int position)
          Method to get Zone from ZoneLocations_list
 java.lang.String getModelClassName()
           
 java.lang.Float getSpacingsBetweenZonesX()
          Get method for spacingsBetweenZonesX
 java.lang.Float getSpacingsBetweenZonesY()
          Get method for spacingsBetweenZonesY
 ZoneLayout getZoneLayout()
          Get method for zoneLayout
 HasZoneLocations.ZoneLocations_list getZoneLocations()
          Get method for zoneLocations
 java.lang.Integer getZonesPerX()
          Get method for zonesPerX
 java.lang.Integer getZonesPerY()
          Get method for zonesPerY
 void removeElementAtFromZoneLocations(int position)
          Method to remove by position from ZoneLocations_list
 void removeFromZoneLocations(Zone zone)
          Method to remove first Zone from ZoneLocations_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setDistanceUnit(DistanceUnit distanceUnit)
          Set method for distanceUnit
 void setSpacingsBetweenZonesX(java.lang.Float spacingsBetweenZonesX)
          Set method for spacingsBetweenZonesX
 void setSpacingsBetweenZonesY(java.lang.Float spacingsBetweenZonesY)
          Set method for spacingsBetweenZonesY
 void setZoneLayout(ZoneLayout zoneLayout)
          Set method for zoneLayout
 void setZoneLocations(HasZoneLocations.ZoneLocations_list zoneLocations)
          Set method for zoneLocations
 void setZonesPerX(java.lang.Integer zonesPerX)
          Set method for zonesPerX
 void setZonesPerY(java.lang.Integer zonesPerY)
          Set method for zonesPerY
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

distanceUnit

protected DistanceUnit distanceUnit
Unit for the ZoneGroup attributes.


zoneLayout

protected ZoneLayout zoneLayout
Describes the rectangular layout of features in the array design.

Constructor Detail

ZoneGroup

public ZoneGroup()
Default constructor.


ZoneGroup

public ZoneGroup(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Extendable

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:
writeMAGEML in class Extendable
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:
writeAttributes in class Extendable
Throws:
java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:
writeAssociations in class Extendable
Throws:
java.io.IOException

setSpacingsBetweenZonesX

public void setSpacingsBetweenZonesX(java.lang.Float spacingsBetweenZonesX)
Set method for spacingsBetweenZonesX

Parameters:
value - to set

getSpacingsBetweenZonesX

public java.lang.Float getSpacingsBetweenZonesX()
Get method for spacingsBetweenZonesX

Returns:
value of the attribute

setSpacingsBetweenZonesY

public void setSpacingsBetweenZonesY(java.lang.Float spacingsBetweenZonesY)
Set method for spacingsBetweenZonesY

Parameters:
value - to set

getSpacingsBetweenZonesY

public java.lang.Float getSpacingsBetweenZonesY()
Get method for spacingsBetweenZonesY

Returns:
value of the attribute

setZonesPerX

public void setZonesPerX(java.lang.Integer zonesPerX)
Set method for zonesPerX

Parameters:
value - to set

getZonesPerX

public java.lang.Integer getZonesPerX()
Get method for zonesPerX

Returns:
value of the attribute

setZonesPerY

public void setZonesPerY(java.lang.Integer zonesPerY)
Set method for zonesPerY

Parameters:
value - to set

getZonesPerY

public java.lang.Integer getZonesPerY()
Get method for zonesPerY

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Extendable

setDistanceUnit

public void setDistanceUnit(DistanceUnit distanceUnit)
Set method for distanceUnit

Specified by:
setDistanceUnit in interface HasDistanceUnit
Parameters:
value - to set

getDistanceUnit

public DistanceUnit getDistanceUnit()
Get method for distanceUnit

Specified by:
getDistanceUnit in interface HasDistanceUnit
Returns:
value of the attribute

setZoneLayout

public void setZoneLayout(ZoneLayout zoneLayout)
Set method for zoneLayout

Specified by:
setZoneLayout in interface HasZoneLayout
Parameters:
value - to set

getZoneLayout

public ZoneLayout getZoneLayout()
Get method for zoneLayout

Specified by:
getZoneLayout in interface HasZoneLayout
Returns:
value of the attribute

setZoneLocations

public void setZoneLocations(HasZoneLocations.ZoneLocations_list zoneLocations)
Set method for zoneLocations

Specified by:
setZoneLocations in interface HasZoneLocations
Parameters:
value - to set

getZoneLocations

public HasZoneLocations.ZoneLocations_list getZoneLocations()
Get method for zoneLocations

Specified by:
getZoneLocations in interface HasZoneLocations
Returns:
value of the attribute

addToZoneLocations

public void addToZoneLocations(Zone zone)
Method to add Zone to ZoneLocations_list

Specified by:
addToZoneLocations in interface HasZoneLocations

addToZoneLocations

public void addToZoneLocations(int position,
                               Zone zone)
Method to add Zone at position to ZoneLocations_list

Specified by:
addToZoneLocations in interface HasZoneLocations

getFromZoneLocations

public Zone getFromZoneLocations(int position)
Method to get Zone from ZoneLocations_list

Specified by:
getFromZoneLocations in interface HasZoneLocations

removeElementAtFromZoneLocations

public void removeElementAtFromZoneLocations(int position)
Method to remove by position from ZoneLocations_list

Specified by:
removeElementAtFromZoneLocations in interface HasZoneLocations

removeFromZoneLocations

public void removeFromZoneLocations(Zone zone)
Method to remove first Zone from ZoneLocations_list

Specified by:
removeFromZoneLocations in interface HasZoneLocations