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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.CompositeCompositeMap
public class CompositeCompositeMap
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositePositionSources |
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HasCompositePositionSources.CompositePositionSources_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 java.util.List |
compositePositionSources
Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur. |
protected CompositeSequence |
compositeSequence
A map to the compositeSequences 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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CompositeCompositeMap()
Default constructor. |
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CompositeCompositeMap(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToCompositePositionSources(CompositePosition compositePosition)
Method to add CompositePosition to CompositePositionSources_list |
void |
addToCompositePositionSources(int position,
CompositePosition compositePosition)
Method to add CompositePosition at position to CompositePositionSources_list |
boolean |
emptyMAGEobject()
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HasCompositePositionSources.CompositePositionSources_list |
getCompositePositionSources()
Get method for compositePositionSources |
CompositeSequence |
getCompositeSequence()
Get method for compositeSequence |
CompositePosition |
getFromCompositePositionSources(int position)
Method to get CompositePosition from CompositePositionSources_list |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromCompositePositionSources(int position)
Method to remove by position from CompositePositionSources_list |
void |
removeFromCompositePositionSources(CompositePosition compositePosition)
Method to remove first CompositePosition from CompositePositionSources_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list compositePositionSources)
Set method for compositePositionSources |
void |
setCompositeSequence(CompositeSequence compositeSequence)
Set method for compositeSequence |
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
protected java.util.List compositePositionSources
Constructor Detail |
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public CompositeCompositeMap()
public CompositeCompositeMap(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 setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list compositePositionSources)
setCompositePositionSources
in interface HasCompositePositionSources
value
- to setpublic HasCompositePositionSources.CompositePositionSources_list getCompositePositionSources()
getCompositePositionSources
in interface HasCompositePositionSources
public void addToCompositePositionSources(CompositePosition compositePosition)
addToCompositePositionSources
in interface HasCompositePositionSources
public void addToCompositePositionSources(int position, CompositePosition compositePosition)
addToCompositePositionSources
in interface HasCompositePositionSources
public CompositePosition getFromCompositePositionSources(int position)
getFromCompositePositionSources
in interface HasCompositePositionSources
public void removeElementAtFromCompositePositionSources(int position)
removeElementAtFromCompositePositionSources
in interface HasCompositePositionSources
public void removeFromCompositePositionSources(CompositePosition compositePosition)
removeFromCompositePositionSources
in interface HasCompositePositionSources
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