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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.CompositeGroup
public class CompositeGroup
Allows specification of the type of Composite Design Element.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeSequences |
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HasCompositeSequences.CompositeSequences_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 java.util.List |
compositeSequences
The compositeSequences that belong to this group. |
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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CompositeGroup()
Default constructor. |
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CompositeGroup(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToCompositeSequences(CompositeSequence compositeSequence)
Method to add CompositeSequence to CompositeSequences_list |
void |
addToCompositeSequences(int position,
CompositeSequence compositeSequence)
Method to add CompositeSequence at position to CompositeSequences_list |
boolean |
emptyMAGEobject()
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HasCompositeSequences.CompositeSequences_list |
getCompositeSequences()
Get method for compositeSequences |
CompositeSequence |
getFromCompositeSequences(int position)
Method to get CompositeSequence from CompositeSequences_list |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromCompositeSequences(int position)
Method to remove by position from CompositeSequences_list |
void |
removeFromCompositeSequences(CompositeSequence compositeSequence)
Method to remove first CompositeSequence from CompositeSequences_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setCompositeSequences(HasCompositeSequences.CompositeSequences_list compositeSequences)
Set method for compositeSequences |
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 java.util.List compositeSequences
Constructor Detail |
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public CompositeGroup()
public CompositeGroup(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 java.lang.String getModelClassName()
getModelClassName
in class DesignElementGroup
public void setCompositeSequences(HasCompositeSequences.CompositeSequences_list compositeSequences)
setCompositeSequences
in interface HasCompositeSequences
value
- to setpublic HasCompositeSequences.CompositeSequences_list getCompositeSequences()
getCompositeSequences
in interface HasCompositeSequences
public void addToCompositeSequences(CompositeSequence compositeSequence)
addToCompositeSequences
in interface HasCompositeSequences
public void addToCompositeSequences(int position, CompositeSequence compositeSequence)
addToCompositeSequences
in interface HasCompositeSequences
public CompositeSequence getFromCompositeSequences(int position)
getFromCompositeSequences
in interface HasCompositeSequences
public void removeElementAtFromCompositeSequences(int position)
removeElementAtFromCompositeSequences
in interface HasCompositeSequences
public void removeFromCompositeSequences(CompositeSequence compositeSequence)
removeFromCompositeSequences
in interface HasCompositeSequences
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