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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.BioAssayMap
public class BioAssayMap
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourceBioAssays |
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HasSourceBioAssays.SourceBioAssays_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 DerivedBioAssay |
bioAssayMapTarget
The DerivedBioAssay that is produced by the sources of the BioAssayMap. |
protected java.util.List |
sourceBioAssays
The sources of the BioAssayMap that are used to produce a target DerivedBioAssay. |
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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BioAssayMap()
Default constructor. |
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BioAssayMap(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToSourceBioAssays(BioAssay bioAssay)
Method to add BioAssay to SourceBioAssays_list |
void |
addToSourceBioAssays(int position,
BioAssay bioAssay)
Method to add BioAssay at position to SourceBioAssays_list |
boolean |
emptyMAGEobject()
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DerivedBioAssay |
getBioAssayMapTarget()
Get method for bioAssayMapTarget |
BioAssay |
getFromSourceBioAssays(int position)
Method to get BioAssay from SourceBioAssays_list |
java.lang.String |
getModelClassName()
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HasSourceBioAssays.SourceBioAssays_list |
getSourceBioAssays()
Get method for sourceBioAssays |
void |
removeElementAtFromSourceBioAssays(int position)
Method to remove by position from SourceBioAssays_list |
void |
removeFromSourceBioAssays(BioAssay bioAssay)
Method to remove first BioAssay from SourceBioAssays_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setBioAssayMapTarget(DerivedBioAssay bioAssayMapTarget)
Set method for bioAssayMapTarget |
void |
setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)
Set method for sourceBioAssays |
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 DerivedBioAssay bioAssayMapTarget
protected java.util.List sourceBioAssays
Constructor Detail |
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public BioAssayMap()
public BioAssayMap(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 Map
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Map
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Map
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Map
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Map
public void setBioAssayMapTarget(DerivedBioAssay bioAssayMapTarget)
setBioAssayMapTarget
in interface HasBioAssayMapTarget
value
- to setpublic DerivedBioAssay getBioAssayMapTarget()
getBioAssayMapTarget
in interface HasBioAssayMapTarget
public void setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)
setSourceBioAssays
in interface HasSourceBioAssays
value
- to setpublic HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()
getSourceBioAssays
in interface HasSourceBioAssays
public void addToSourceBioAssays(BioAssay bioAssay)
addToSourceBioAssays
in interface HasSourceBioAssays
public void addToSourceBioAssays(int position, BioAssay bioAssay)
addToSourceBioAssays
in interface HasSourceBioAssays
public BioAssay getFromSourceBioAssays(int position)
getFromSourceBioAssays
in interface HasSourceBioAssays
public void removeElementAtFromSourceBioAssays(int position)
removeElementAtFromSourceBioAssays
in interface HasSourceBioAssays
public void removeFromSourceBioAssays(BioAssay bioAssay)
removeFromSourceBioAssays
in interface HasSourceBioAssays
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