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org.biomage.ArrayDesign
Class ZoneGroup  view ZoneGroup download ZoneGroup.java

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

public class ZoneGroup
extends org.biomage.Common.Extendable
implements java.io.Serializable, org.biomage.Interface.HasZoneLayout, org.biomage.Interface.HasZoneLocations, org.biomage.Interface.HasDistanceUnit

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasZoneLocations
org.biomage.Interface.HasZoneLocations.ZoneLocations_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Measurement.DistanceUnit distanceUnit
          Unit for the ZoneGroup attributes.
(package private)  float spacingsBetweenZonesX
          Spacing between zones, if applicable.
(package private)  float spacingsBetweenZonesY
          Spacing between zones, if applicable.
private  ZoneLayout zoneLayout
          Describes the rectangular layout of features in the array design.
private  org.biomage.Interface.HasZoneLocations.ZoneLocations_list zoneLocations
          Describes the location of different zones within the array design.
(package private)  int zonesPerX
          The number of zones on the x-axis.
(package private)  int zonesPerY
          The number of zones on the y-axis.
 
Fields inherited from class org.biomage.Common.Extendable
 
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
 org.biomage.Measurement.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
 org.biomage.Interface.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(org.biomage.Measurement.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(org.biomage.Interface.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
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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

spacingsBetweenZonesX

float spacingsBetweenZonesX
Spacing between zones, if applicable.


spacingsBetweenZonesY

float spacingsBetweenZonesY
Spacing between zones, if applicable.


zonesPerX

int zonesPerX
The number of zones on the x-axis.


zonesPerY

int zonesPerY
The number of zones on the y-axis.


zoneLayout

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


zoneLocations

private org.biomage.Interface.HasZoneLocations.ZoneLocations_list zoneLocations
Describes the location of different zones within the array design.


distanceUnit

private org.biomage.Measurement.DistanceUnit distanceUnit
Unit for the ZoneGroup attributes.

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.


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.


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.


setSpacingsBetweenZonesX

public void setSpacingsBetweenZonesX(float spacingsBetweenZonesX)
Set method for spacingsBetweenZonesX


getSpacingsBetweenZonesX

public float getSpacingsBetweenZonesX()
Get method for spacingsBetweenZonesX


setSpacingsBetweenZonesY

public void setSpacingsBetweenZonesY(float spacingsBetweenZonesY)
Set method for spacingsBetweenZonesY


getSpacingsBetweenZonesY

public float getSpacingsBetweenZonesY()
Get method for spacingsBetweenZonesY


setZonesPerX

public void setZonesPerX(int zonesPerX)
Set method for zonesPerX


getZonesPerX

public int getZonesPerX()
Get method for zonesPerX


setZonesPerY

public void setZonesPerY(int zonesPerY)
Set method for zonesPerY


getZonesPerY

public int getZonesPerY()
Get method for zonesPerY


setZoneLayout

public void setZoneLayout(ZoneLayout zoneLayout)
Set method for zoneLayout

Specified by:
setZoneLayout in interface org.biomage.Interface.HasZoneLayout

getZoneLayout

public ZoneLayout getZoneLayout()
Get method for zoneLayout

Specified by:
getZoneLayout in interface org.biomage.Interface.HasZoneLayout

setZoneLocations

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

Specified by:
setZoneLocations in interface org.biomage.Interface.HasZoneLocations

getZoneLocations

public org.biomage.Interface.HasZoneLocations.ZoneLocations_list getZoneLocations()
Get method for zoneLocations

Specified by:
getZoneLocations in interface org.biomage.Interface.HasZoneLocations

addToZoneLocations

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

Specified by:
addToZoneLocations in interface org.biomage.Interface.HasZoneLocations

addToZoneLocations

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

Specified by:
addToZoneLocations in interface org.biomage.Interface.HasZoneLocations

getFromZoneLocations

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

Specified by:
getFromZoneLocations in interface org.biomage.Interface.HasZoneLocations

removeElementAtFromZoneLocations

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

Specified by:
removeElementAtFromZoneLocations in interface org.biomage.Interface.HasZoneLocations

removeFromZoneLocations

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

Specified by:
removeFromZoneLocations in interface org.biomage.Interface.HasZoneLocations

setDistanceUnit

public void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)
Set method for distanceUnit

Specified by:
setDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

getDistanceUnit

public org.biomage.Measurement.DistanceUnit getDistanceUnit()
Get method for distanceUnit

Specified by:
getDistanceUnit in interface org.biomage.Interface.HasDistanceUnit