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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioMaterial.BioMaterial
public abstract class BioMaterial
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... Biomaterials can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)).
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasTreatments |
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HasTreatments.Treatments_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCharacteristics |
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HasCharacteristics.Characteristics_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasQualityControlStatistics |
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HasQualityControlStatistics.QualityControlStatistics_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTopBioMaterial |
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HasTopBioMaterial.TopLevelBioMaterials_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 |
characteristics
Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc. |
protected java.lang.Boolean |
copied
caARRAY internal flag to indicate if this BioMaterial is generated by copy of existing biomaterial. |
protected boolean |
imported
caARRAY internal flag to indicate if this BioMaterial is imported. |
protected OntologyEntry |
materialType
The type of material used, i.e. |
protected java.lang.String |
ojbConcreteClass
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protected java.util.List |
qualityControlStatistics
Measures of the quality of the BioMaterial. |
protected java.util.List |
topLevelBioMaterials
This association is one way from BioMaterial to it top most parent biomaterial. |
protected java.util.List |
treatments
This association is one way from BioMaterial to Treatment. |
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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BioMaterial()
Default constructor. |
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BioMaterial(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToCharacteristics(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Characteristics_list |
void |
addToCharacteristics(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Characteristics_list |
void |
addToQualityControlStatistics(int position,
NameValueType nameValueType)
Method to add NameValueType at position to QualityControlStatistics_list |
void |
addToQualityControlStatistics(NameValueType nameValueType)
Method to add NameValueType to QualityControlStatistics_list |
void |
addToTopLevelBioMaterials(BioMaterial bioMaterial)
Method to add Treatment to Treatments_list |
void |
addToTopLevelBioMaterials(int position,
BioMaterial bioMaterial)
Method to add Treatment at position to Treatments_list |
void |
addToTreatments(int position,
Treatment treatment)
Method to add Treatment at position to Treatments_list |
void |
addToTreatments(Treatment treatment)
Method to add Treatment to Treatments_list |
HasCharacteristics.Characteristics_list |
getCharacteristics()
Get method for characteristics |
java.lang.Boolean |
getCopied()
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OntologyEntry |
getFromCharacteristics(int position)
Method to get OntologyEntry from Characteristics_list |
NameValueType |
getFromQualityControlStatistics(int position)
Method to get NameValueType from QualityControlStatistics_list |
BioMaterial |
getFromTopLevelBioMaterials(int position)
Method to get Treatment from Treatments_list |
Treatment |
getFromTreatments(int position)
Method to get Treatment from Treatments_list |
boolean |
getImported()
Method to return if this BioMaterial is imported from MAGEML. |
OntologyEntry |
getMaterialType()
Get method for materialType |
java.lang.String |
getModelClassName()
|
HasQualityControlStatistics.QualityControlStatistics_list |
getQualityControlStatistics()
Get method for qualityControlStatistics |
HasTopBioMaterial.TopLevelBioMaterials_list |
getTopLevelBioMaterials()
Get method for treatments |
HasTreatments.Treatments_list |
getTreatments()
Get method for treatments |
void |
removeElementAtFromCharacteristics(int position)
Method to remove by position from Characteristics_list |
void |
removeElementAtFromQualityControlStatistics(int position)
Method to remove by position from QualityControlStatistics_list |
void |
removeElementAtFromTopLevelBioMaterials(int position)
Method to remove by position from Treatments_list |
void |
removeElementAtFromTreatments(int position)
Method to remove by position from Treatments_list |
void |
removeFromCharacteristics(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Characteristics_list |
void |
removeFromQualityControlStatistics(NameValueType nameValueType)
Method to remove first NameValueType from QualityControlStatistics_list |
void |
removeFromTopLevelBioMaterials(BioMaterial bioMaterial)
Method to remove first Treatment from Treatments_list |
void |
removeFromTreatments(Treatment treatment)
Method to remove first Treatment from Treatments_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setCharacteristics(HasCharacteristics.Characteristics_list characteristics)
Set method for characteristics |
void |
setCopied(java.lang.Boolean copied)
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void |
setImported(boolean imported)
Flags this BioMaterial if it is imported from MAGEML. |
void |
setMaterialType(OntologyEntry materialType)
Set method for materialType |
void |
setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
Set method for qualityControlStatistics |
void |
setTopLevelBioMaterials(HasTopBioMaterial.TopLevelBioMaterials_list biomaterials)
Set method for treatments |
void |
setTreatments(HasTreatments.Treatments_list treatments)
Set method for treatments |
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.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.lang.String ojbConcreteClass
protected boolean imported
protected java.lang.Boolean copied
protected java.util.List qualityControlStatistics
protected java.util.List characteristics
protected OntologyEntry materialType
protected java.util.List treatments
protected java.util.List topLevelBioMaterials
Constructor Detail |
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public BioMaterial()
public BioMaterial(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 Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
setQualityControlStatistics
in interface HasQualityControlStatistics
value
- to setpublic HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()
getQualityControlStatistics
in interface HasQualityControlStatistics
public void addToQualityControlStatistics(NameValueType nameValueType)
addToQualityControlStatistics
in interface HasQualityControlStatistics
public void addToQualityControlStatistics(int position, NameValueType nameValueType)
addToQualityControlStatistics
in interface HasQualityControlStatistics
public NameValueType getFromQualityControlStatistics(int position)
getFromQualityControlStatistics
in interface HasQualityControlStatistics
public void removeElementAtFromQualityControlStatistics(int position)
removeElementAtFromQualityControlStatistics
in interface HasQualityControlStatistics
public void removeFromQualityControlStatistics(NameValueType nameValueType)
removeFromQualityControlStatistics
in interface HasQualityControlStatistics
public void setCharacteristics(HasCharacteristics.Characteristics_list characteristics)
setCharacteristics
in interface HasCharacteristics
value
- to setpublic HasCharacteristics.Characteristics_list getCharacteristics()
getCharacteristics
in interface HasCharacteristics
public void addToCharacteristics(OntologyEntry ontologyEntry)
addToCharacteristics
in interface HasCharacteristics
public void addToCharacteristics(int position, OntologyEntry ontologyEntry)
addToCharacteristics
in interface HasCharacteristics
public OntologyEntry getFromCharacteristics(int position)
getFromCharacteristics
in interface HasCharacteristics
public void removeElementAtFromCharacteristics(int position)
removeElementAtFromCharacteristics
in interface HasCharacteristics
public void removeFromCharacteristics(OntologyEntry ontologyEntry)
removeFromCharacteristics
in interface HasCharacteristics
public void setMaterialType(OntologyEntry materialType)
setMaterialType
in interface HasMaterialType
value
- to setpublic OntologyEntry getMaterialType()
getMaterialType
in interface HasMaterialType
public void setTopLevelBioMaterials(HasTopBioMaterial.TopLevelBioMaterials_list biomaterials)
setTopLevelBioMaterials
in interface HasTopBioMaterial
value
- to setpublic HasTopBioMaterial.TopLevelBioMaterials_list getTopLevelBioMaterials()
getTopLevelBioMaterials
in interface HasTopBioMaterial
public void addToTopLevelBioMaterials(BioMaterial bioMaterial)
addToTopLevelBioMaterials
in interface HasTopBioMaterial
public void addToTopLevelBioMaterials(int position, BioMaterial bioMaterial)
addToTopLevelBioMaterials
in interface HasTopBioMaterial
public BioMaterial getFromTopLevelBioMaterials(int position)
getFromTopLevelBioMaterials
in interface HasTopBioMaterial
public void removeElementAtFromTopLevelBioMaterials(int position)
removeElementAtFromTopLevelBioMaterials
in interface HasTopBioMaterial
public void removeFromTopLevelBioMaterials(BioMaterial bioMaterial)
removeFromTopLevelBioMaterials
in interface HasTopBioMaterial
public boolean getImported()
public void setImported(boolean imported)
imported
- - True to indicate this BioMaterial is imported from MAGEML.public java.lang.Boolean getCopied()
public void setCopied(java.lang.Boolean copied)
copied
- The copied to set.public void setTreatments(HasTreatments.Treatments_list treatments)
setTreatments
in interface HasTreatments
value
- to setpublic HasTreatments.Treatments_list getTreatments()
getTreatments
in interface HasTreatments
public void addToTreatments(Treatment treatment)
addToTreatments
in interface HasTreatments
public void addToTreatments(int position, Treatment treatment)
addToTreatments
in interface HasTreatments
public Treatment getFromTreatments(int position)
getFromTreatments
in interface HasTreatments
public void removeElementAtFromTreatments(int position)
removeElementAtFromTreatments
in interface HasTreatments
public void removeFromTreatments(Treatment treatment)
removeFromTreatments
in interface HasTreatments
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