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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioEvent.BioEvent
org.biomage.BioEvent.Map
org.biomage.BioAssayData.DesignElementMap
org.biomage.DesignElement.ReporterCompositeMap
public class ReporterCompositeMap
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterPositionSources |
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HasReporterPositionSources.ReporterPositionSources_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.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 CompositeSequence |
compositeSequence
A map to the reporters that compose this CompositeSequence. |
Fields inherited from class org.biomage.BioAssayData.DesignElementMap |
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ojbConcreteClass |
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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ReporterCompositeMap()
Default constructor. |
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ReporterCompositeMap(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToReporterPositionSources(int position,
ReporterPosition reporterPosition)
Method to add ReporterPosition at position to ReporterPositionSources_list |
void |
addToReporterPositionSources(ReporterPosition reporterPosition)
Method to add ReporterPosition to ReporterPositionSources_list |
boolean |
emptyMAGEobject()
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CompositeSequence |
getCompositeSequence()
Get method for compositeSequence |
ReporterPosition |
getFromReporterPositionSources(int position)
Method to get ReporterPosition from ReporterPositionSources_list |
java.lang.String |
getModelClassName()
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HasReporterPositionSources.ReporterPositionSources_list |
getReporterPositionSources()
Get method for reporterPositionSources |
void |
removeElementAtFromReporterPositionSources(int position)
Method to remove by position from ReporterPositionSources_list |
void |
removeFromReporterPositionSources(ReporterPosition reporterPosition)
Method to remove first ReporterPosition from ReporterPositionSources_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setCompositeSequence(CompositeSequence compositeSequence)
Set method for compositeSequence |
void |
setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)
Set method for reporterPositionSources |
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.BioEvent.BioEvent |
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addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications |
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 CompositeSequence compositeSequence
Constructor Detail |
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public ReporterCompositeMap()
public ReporterCompositeMap(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 DesignElementMap
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class DesignElementMap
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class DesignElementMap
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class DesignElementMap
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class DesignElementMap
public void setCompositeSequence(CompositeSequence compositeSequence)
setCompositeSequence
in interface HasCompositeSequence
value
- to setpublic CompositeSequence getCompositeSequence()
getCompositeSequence
in interface HasCompositeSequence
public void setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)
setReporterPositionSources
in interface HasReporterPositionSources
value
- to setpublic HasReporterPositionSources.ReporterPositionSources_list getReporterPositionSources()
getReporterPositionSources
in interface HasReporterPositionSources
public void addToReporterPositionSources(ReporterPosition reporterPosition)
addToReporterPositionSources
in interface HasReporterPositionSources
public void addToReporterPositionSources(int position, ReporterPosition reporterPosition)
addToReporterPositionSources
in interface HasReporterPositionSources
public ReporterPosition getFromReporterPositionSources(int position)
getFromReporterPositionSources
in interface HasReporterPositionSources
public void removeElementAtFromReporterPositionSources(int position)
removeElementAtFromReporterPositionSources
in interface HasReporterPositionSources
public void removeFromReporterPositionSources(ReporterPosition reporterPosition)
removeFromReporterPositionSources
in interface HasReporterPositionSources
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