org.biomage.ArrayDesign
Class ZoneGroup

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.ArrayDesign.ZoneGroup

All Implemented Interfaces:

HasDistanceUnit, HasPropertySets, HasZoneLayout, HasZoneLocations, java.io.Serializable

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 inherited from class org.biomage.Interface.HasZoneLocations

HasZoneLocations.ZoneLocations_list

Nested classes inherited from class 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.
protected HasZoneLocations.ZoneLocations_list	zoneLocations Describes the location of different zones within the array design.

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
DistanceUnit	getDistanceUnit() Get method for distanceUnit
Zone	getFromZoneLocations(int position) Method to get Zone from ZoneLocations_list
float	getSpacingsBetweenZonesX() Get method for spacingsBetweenZonesX
float	getSpacingsBetweenZonesY() Get method for spacingsBetweenZonesY
ZoneLayout	getZoneLayout() Get method for zoneLayout
HasZoneLocations.ZoneLocations_list	getZoneLocations() Get method for zoneLocations
int	getZonesPerX() Get method for zonesPerX
int	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	setDistanceUnit(DistanceUnit distanceUnit) Set method for distanceUnit
void	setSpacingsBetweenZonesX(float spacingsBetweenZonesX) Set method for spacingsBetweenZonesX
void	setSpacingsBetweenZonesY(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(int zonesPerX) Set method for zonesPerX
void	setZonesPerY(int 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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

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

zoneLocations

protected HasZoneLocations.ZoneLocations_list zoneLocations

Describes the location of different zones within 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

Method Detail

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

java.io.IOException

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

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

java.io.IOException

setSpacingsBetweenZonesX

public void setSpacingsBetweenZonesX(float spacingsBetweenZonesX)

Set method for spacingsBetweenZonesX

getSpacingsBetweenZonesX

public float getSpacingsBetweenZonesX()

Get method for spacingsBetweenZonesX

Returns:

value of the attribute

setSpacingsBetweenZonesY

public void setSpacingsBetweenZonesY(float spacingsBetweenZonesY)

Set method for spacingsBetweenZonesY

getSpacingsBetweenZonesY

public float getSpacingsBetweenZonesY()

Get method for spacingsBetweenZonesY

Returns:

value of the attribute

setZonesPerX

public void setZonesPerX(int zonesPerX)

Set method for zonesPerX

getZonesPerX

public int getZonesPerX()

Get method for zonesPerX

Returns:

value of the attribute

setZonesPerY

public void setZonesPerY(int zonesPerY)

Set method for zonesPerY

getZonesPerY

public int getZonesPerY()

Get method for zonesPerY

Returns:

value of the attribute

setDistanceUnit

public void setDistanceUnit(DistanceUnit distanceUnit)

Set method for distanceUnit

Specified by:

setDistanceUnit in interface HasDistanceUnit

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

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

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