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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.ArrayDesign.ArrayDesign
org.biomage.ArrayDesign.PhysicalArrayDesign
public class PhysicalArrayDesign
A design that is expected to be used to manufacture physical arrays.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasZoneGroups |
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HasZoneGroups.ZoneGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications |
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HasProtocolApplications.ProtocolApplications_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeGroups |
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HasCompositeGroups.CompositeGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDesignProviders |
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HasDesignProviders.DesignProviders_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterGroups |
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HasReporterGroups.ReporterGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureGroups |
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HasFeatureGroups.FeatureGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected OntologyEntry |
surfaceType
The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc. |
protected java.util.List |
zoneGroups
In the case where the array design is specified by one or more zones, allows specifying where those zones are located. |
Fields inherited from class org.biomage.ArrayDesign.ArrayDesign |
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additionalReporterFileLocation, compositeGroups, deleted, designProviderRoles, featureGroups, protocolApplications, reporterFileLocation, reporterFileType, reporterGroups |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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PhysicalArrayDesign()
Default constructor. |
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PhysicalArrayDesign(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToZoneGroups(int position,
ZoneGroup zoneGroup)
Method to add ZoneGroup at position to ZoneGroups_list |
void |
addToZoneGroups(ZoneGroup zoneGroup)
Method to add ZoneGroup to ZoneGroups_list |
boolean |
emptyMAGEobject()
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ZoneGroup |
getFromZoneGroups(int position)
Method to get ZoneGroup from ZoneGroups_list |
java.lang.String |
getModelClassName()
|
OntologyEntry |
getSurfaceType()
Get method for surfaceType |
HasZoneGroups.ZoneGroups_list |
getZoneGroups()
Get method for zoneGroups |
void |
removeElementAtFromZoneGroups(int position)
Method to remove by position from ZoneGroups_list |
void |
removeFromZoneGroups(ZoneGroup zoneGroup)
Method to remove first ZoneGroup from ZoneGroups_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setSurfaceType(OntologyEntry surfaceType)
Set method for surfaceType |
void |
setZoneGroups(HasZoneGroups.ZoneGroups_list zoneGroups)
Set method for zoneGroups |
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.Identifiable |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected OntologyEntry surfaceType
protected java.util.List zoneGroups
Constructor Detail |
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public PhysicalArrayDesign()
public PhysicalArrayDesign(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class ArrayDesign
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class ArrayDesign
java.io.IOException
public boolean emptyMAGEobject()
emptyMAGEobject
in class ArrayDesign
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class ArrayDesign
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class ArrayDesign
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class ArrayDesign
public void setSurfaceType(OntologyEntry surfaceType)
setSurfaceType
in interface HasSurfaceType
value
- to setpublic OntologyEntry getSurfaceType()
getSurfaceType
in interface HasSurfaceType
public void setZoneGroups(HasZoneGroups.ZoneGroups_list zoneGroups)
setZoneGroups
in interface HasZoneGroups
value
- to setpublic HasZoneGroups.ZoneGroups_list getZoneGroups()
getZoneGroups
in interface HasZoneGroups
public void addToZoneGroups(ZoneGroup zoneGroup)
addToZoneGroups
in interface HasZoneGroups
public void addToZoneGroups(int position, ZoneGroup zoneGroup)
addToZoneGroups
in interface HasZoneGroups
public ZoneGroup getFromZoneGroups(int position)
getFromZoneGroups
in interface HasZoneGroups
public void removeElementAtFromZoneGroups(int position)
removeElementAtFromZoneGroups
in interface HasZoneGroups
public void removeFromZoneGroups(ZoneGroup zoneGroup)
removeFromZoneGroups
in interface HasZoneGroups
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