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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.ArrayDesign.DesignElementGroup
public abstract class DesignElementGroup
The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
Nested Class Summary |
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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 java.lang.String |
ojbConcreteClass
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protected OntologyEntry |
species
The organism from which the biosequences of this group are from. |
protected java.util.List |
types
The specific type of a feature, reporter, or composite. |
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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DesignElementGroup()
Default constructor. |
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DesignElementGroup(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list |
void |
addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list |
OntologyEntry |
getFromTypes(int position)
Method to get OntologyEntry from Types_list |
java.lang.String |
getModelClassName()
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OntologyEntry |
getSpecies()
Get method for species |
HasTypes.Types_list |
getTypes()
Get method for types |
void |
removeElementAtFromTypes(int position)
Method to remove by position from Types_list |
void |
removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setSpecies(OntologyEntry species)
Set method for species |
void |
setTypes(HasTypes.Types_list types)
Set method for types |
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 java.lang.String ojbConcreteClass
protected java.util.List types
protected OntologyEntry species
Constructor Detail |
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public DesignElementGroup()
public DesignElementGroup(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 Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setTypes(HasTypes.Types_list types)
setTypes
in interface HasTypes
value
- to setpublic HasTypes.Types_list getTypes()
getTypes
in interface HasTypes
public void addToTypes(OntologyEntry ontologyEntry)
addToTypes
in interface HasTypes
public void addToTypes(int position, OntologyEntry ontologyEntry)
addToTypes
in interface HasTypes
public OntologyEntry getFromTypes(int position)
getFromTypes
in interface HasTypes
public void removeElementAtFromTypes(int position)
removeElementAtFromTypes
in interface HasTypes
public void removeFromTypes(OntologyEntry ontologyEntry)
removeFromTypes
in interface HasTypes
public void setSpecies(OntologyEntry species)
setSpecies
in interface HasSpecies
value
- to setpublic OntologyEntry getSpecies()
getSpecies
in interface HasSpecies
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