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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.ArrayDesign.DesignElementGroup
org.biomage.ArrayDesign.FeatureGroup
public class FeatureGroup
A collection of like features.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatures |
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HasFeatures.Features_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTypes |
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HasTypes.Types_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 DistanceUnit |
distanceUnit
The unit for the feature measures. |
protected java.util.List |
features
The features that belong to this group. |
protected OntologyEntry |
featureShape
The expected shape of the feature on the array: circular, oval, square, etc. |
protected OntologyEntry |
technologyType
The technology type of this design. |
Fields inherited from class org.biomage.ArrayDesign.DesignElementGroup |
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ojbConcreteClass, species, types |
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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FeatureGroup()
Default constructor. |
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FeatureGroup(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToFeatures(Feature feature)
Method to add Feature to Features_list |
void |
addToFeatures(int position,
Feature feature)
Method to add Feature at position to Features_list |
boolean |
emptyMAGEobject()
|
DistanceUnit |
getDistanceUnit()
Get method for distanceUnit |
java.lang.Float |
getFeatureHeight()
Get method for featureHeight |
java.lang.Float |
getFeatureLength()
Get method for featureLength |
HasFeatures.Features_list |
getFeatures()
Get method for features |
OntologyEntry |
getFeatureShape()
Get method for featureShape |
java.lang.Float |
getFeatureWidth()
Get method for featureWidth |
Feature |
getFromFeatures(int position)
Method to get Feature from Features_list |
java.lang.String |
getModelClassName()
|
OntologyEntry |
getTechnologyType()
Get method for technologyType |
void |
removeElementAtFromFeatures(int position)
Method to remove by position from Features_list |
void |
removeFromFeatures(Feature feature)
Method to remove first Feature from Features_list |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setDistanceUnit(DistanceUnit distanceUnit)
Set method for distanceUnit |
void |
setFeatureHeight(java.lang.Float featureHeight)
Set method for featureHeight |
void |
setFeatureLength(java.lang.Float featureLength)
Set method for featureLength |
void |
setFeatures(HasFeatures.Features_list features)
Set method for features |
void |
setFeatureShape(OntologyEntry featureShape)
Set method for featureShape |
void |
setFeatureWidth(java.lang.Float featureWidth)
Set method for featureWidth |
void |
setTechnologyType(OntologyEntry technologyType)
Set method for technologyType |
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.ArrayDesign.DesignElementGroup |
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addToTypes, addToTypes, getFromTypes, getSpecies, getTypes, removeElementAtFromTypes, removeFromTypes, setSpecies, setTypes |
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 technologyType
protected OntologyEntry featureShape
protected DistanceUnit distanceUnit
protected java.util.List features
Constructor Detail |
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public FeatureGroup()
public FeatureGroup(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 DesignElementGroup
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class DesignElementGroup
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class DesignElementGroup
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class DesignElementGroup
java.io.IOException
public void setFeatureWidth(java.lang.Float featureWidth)
value
- to setpublic java.lang.Float getFeatureWidth()
public void setFeatureLength(java.lang.Float featureLength)
value
- to setpublic java.lang.Float getFeatureLength()
public void setFeatureHeight(java.lang.Float featureHeight)
value
- to setpublic java.lang.Float getFeatureHeight()
public java.lang.String getModelClassName()
getModelClassName
in class DesignElementGroup
public void setTechnologyType(OntologyEntry technologyType)
setTechnologyType
in interface HasTechnologyType
value
- to setpublic OntologyEntry getTechnologyType()
getTechnologyType
in interface HasTechnologyType
public void setFeatureShape(OntologyEntry featureShape)
setFeatureShape
in interface HasFeatureShape
value
- to setpublic OntologyEntry getFeatureShape()
getFeatureShape
in interface HasFeatureShape
public void setDistanceUnit(DistanceUnit distanceUnit)
setDistanceUnit
in interface HasDistanceUnit
value
- to setpublic DistanceUnit getDistanceUnit()
getDistanceUnit
in interface HasDistanceUnit
public void setFeatures(HasFeatures.Features_list features)
setFeatures
in interface HasFeatures
value
- to setpublic HasFeatures.Features_list getFeatures()
getFeatures
in interface HasFeatures
public void addToFeatures(Feature feature)
addToFeatures
in interface HasFeatures
public void addToFeatures(int position, Feature feature)
addToFeatures
in interface HasFeatures
public Feature getFromFeatures(int position)
getFromFeatures
in interface HasFeatures
public void removeElementAtFromFeatures(int position)
removeElementAtFromFeatures
in interface HasFeatures
public void removeFromFeatures(Feature feature)
removeFromFeatures
in interface HasFeatures
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