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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.DesignElement.DesignElement
org.biomage.DesignElement.CompositeSequence
public class CompositeSequence
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasBiologicalCharacteristics |
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HasBiologicalCharacteristics.BiologicalCharacteristics_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterCompositeMaps |
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HasReporterCompositeMaps.ReporterCompositeMaps_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeCompositeMaps |
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HasCompositeCompositeMaps.CompositeCompositeMaps_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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Fields inherited from class org.biomage.DesignElement.DesignElement |
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controlType |
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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CompositeSequence()
Default constructor. |
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CompositeSequence(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBiologicalCharacteristics(BioSequence bioSequence)
Method to add BioSequence to BiologicalCharacteristics_list |
void |
addToBiologicalCharacteristics(int position,
BioSequence bioSequence)
Method to add BioSequence at position to BiologicalCharacteristics_list |
void |
addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap to CompositeCompositeMaps_list |
void |
addToCompositeCompositeMaps(int position,
CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list |
void |
addToReporterCompositeMaps(int position,
ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list |
void |
addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap to ReporterCompositeMaps_list |
boolean |
emptyMAGEobject()
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HasBiologicalCharacteristics.BiologicalCharacteristics_list |
getBiologicalCharacteristics()
Get method for biologicalCharacteristics |
HasCompositeCompositeMaps.CompositeCompositeMaps_list |
getCompositeCompositeMaps()
Get method for compositeCompositeMaps |
BioSequence |
getFromBiologicalCharacteristics(int position)
Method to get BioSequence from BiologicalCharacteristics_list |
CompositeCompositeMap |
getFromCompositeCompositeMaps(int position)
Method to get CompositeCompositeMap from CompositeCompositeMaps_list |
ReporterCompositeMap |
getFromReporterCompositeMaps(int position)
Method to get ReporterCompositeMap from ReporterCompositeMaps_list |
java.lang.String |
getModelClassName()
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HasReporterCompositeMaps.ReporterCompositeMaps_list |
getReporterCompositeMaps()
Get method for reporterCompositeMaps |
void |
removeElementAtFromBiologicalCharacteristics(int position)
Method to remove by position from BiologicalCharacteristics_list |
void |
removeElementAtFromCompositeCompositeMaps(int position)
Method to remove by position from CompositeCompositeMaps_list |
void |
removeElementAtFromReporterCompositeMaps(int position)
Method to remove by position from ReporterCompositeMaps_list |
void |
removeFromBiologicalCharacteristics(BioSequence bioSequence)
Method to remove first BioSequence from BiologicalCharacteristics_list |
void |
removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list |
void |
removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)
Set method for biologicalCharacteristics |
void |
setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)
Set method for compositeCompositeMaps |
void |
setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)
Set method for reporterCompositeMaps |
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.DesignElement.DesignElement |
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getControlType, setControlType |
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 |
Constructor Detail |
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public CompositeSequence()
public CompositeSequence(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 DesignElement
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class DesignElement
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class DesignElement
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class DesignElement
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class DesignElement
public void setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)
setBiologicalCharacteristics
in interface HasBiologicalCharacteristics
value
- to setpublic HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()
getBiologicalCharacteristics
in interface HasBiologicalCharacteristics
public void addToBiologicalCharacteristics(BioSequence bioSequence)
addToBiologicalCharacteristics
in interface HasBiologicalCharacteristics
public void addToBiologicalCharacteristics(int position, BioSequence bioSequence)
addToBiologicalCharacteristics
in interface HasBiologicalCharacteristics
public BioSequence getFromBiologicalCharacteristics(int position)
getFromBiologicalCharacteristics
in interface HasBiologicalCharacteristics
public void removeElementAtFromBiologicalCharacteristics(int position)
removeElementAtFromBiologicalCharacteristics
in interface HasBiologicalCharacteristics
public void removeFromBiologicalCharacteristics(BioSequence bioSequence)
removeFromBiologicalCharacteristics
in interface HasBiologicalCharacteristics
public void setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)
setReporterCompositeMaps
in interface HasReporterCompositeMaps
value
- to setpublic HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()
getReporterCompositeMaps
in interface HasReporterCompositeMaps
public void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
addToReporterCompositeMaps
in interface HasReporterCompositeMaps
public void addToReporterCompositeMaps(int position, ReporterCompositeMap reporterCompositeMap)
addToReporterCompositeMaps
in interface HasReporterCompositeMaps
public ReporterCompositeMap getFromReporterCompositeMaps(int position)
getFromReporterCompositeMaps
in interface HasReporterCompositeMaps
public void removeElementAtFromReporterCompositeMaps(int position)
removeElementAtFromReporterCompositeMaps
in interface HasReporterCompositeMaps
public void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
removeFromReporterCompositeMaps
in interface HasReporterCompositeMaps
public void setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)
setCompositeCompositeMaps
in interface HasCompositeCompositeMaps
value
- to setpublic HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()
getCompositeCompositeMaps
in interface HasCompositeCompositeMaps
public void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
addToCompositeCompositeMaps
in interface HasCompositeCompositeMaps
public void addToCompositeCompositeMaps(int position, CompositeCompositeMap compositeCompositeMap)
addToCompositeCompositeMaps
in interface HasCompositeCompositeMaps
public CompositeCompositeMap getFromCompositeCompositeMaps(int position)
getFromCompositeCompositeMaps
in interface HasCompositeCompositeMaps
public void removeElementAtFromCompositeCompositeMaps(int position)
removeElementAtFromCompositeCompositeMaps
in interface HasCompositeCompositeMaps
public void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
removeFromCompositeCompositeMaps
in interface HasCompositeCompositeMaps
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