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java.lang.Objectgov.nih.nci.caarray.domain.AbstractCaArrayObject
gov.nih.nci.caarray.domain.AbstractCaArrayEntity
gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
@UniqueConstraint(fields={@UniqueConstraintField(name="externalId"),@UniqueConstraintField(name="experiment",nullsEqual=false)}, generateDDLConstraint=false, message="{biomaterial.externalId.uniqueConstraint}") public abstract class AbstractBioMaterial
AbstractBiomaterial represents a biomaterial at some stage prior to being hybridized to an array.
Field Summary |
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Fields inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayEntity |
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CAARRAY_LSID_AUTHORITY, CAARRAY_LSID_NAMESPACE |
Fields inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayObject |
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DEFAULT_BATCH_SIZE, DEFAULT_STRING_COLUMN_SIZE, LARGE_TEXT_FIELD_LENGTH |
Constructor Summary | |
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AbstractBioMaterial()
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Method Summary | |
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void |
addProtocolApplication(ProtocolApplication protocolApplication)
Add the given protocol application to the protocol applications of this. |
void |
clearProtocolApplications()
Remove all protocol applications of this. |
java.util.Set<CaArrayFile> |
getAllDataFiles()
The data files related to this biomaterial is the set of files that is related to at least one hybridization that is related to this biomaterial (@see getRelatedHybs()). |
Term |
getCellType()
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AbstractCharacteristic |
getCharacteristic(java.lang.String categoryName)
Return the characteristic with given category name in this biomaterial. |
java.util.Set<AbstractCharacteristic> |
getCharacteristics()
Gets the characteristics. |
java.util.Set<AbstractCharacteristic> |
getCharacteristics(Category category)
Return the characteristics with given category in this biomaterial. |
java.lang.String |
getDescription()
Gets the description. |
Term |
getDiseaseState()
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Experiment |
getExperiment()
Get the experiment to which this node belongs. |
java.lang.String |
getExternalId()
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java.util.Date |
getLastModifiedDataTime()
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Term |
getMaterialType()
Gets the materialType. |
java.lang.String |
getName()
Gets the name. |
Organism |
getOrganism()
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java.util.List<ProtocolApplication> |
getProtocolApplications()
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java.util.Set<Hybridization> |
getRelatedHybridizations()
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protected java.util.Map<ExperimentOntologyCategory,Term> |
getSpecialCharacteristics()
Returns the characteristics that are handled specially and have their own fields in AbstractBioMaterial or one of its subclasses, rather than being placed in the general characteristics collection. |
Term |
getTissueSite()
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void |
merge(AbstractExperimentDesignNode node)
Merges another AbstractExperimentDesignNode into this one. |
void |
propagateLastModifiedDataTime(java.util.Date lastModifiedDate)
Propagates the last modified data time up the chain. |
void |
setCellType(Term cellType)
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void |
setDescription(java.lang.String descriptionVal)
Sets the description. |
void |
setDiseaseState(Term diseaseState)
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void |
setExperiment(Experiment experiment)
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void |
setExternalId(java.lang.String externalId)
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void |
setLastModifiedDataTime(java.util.Date lastModifiedDataTime)
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void |
setMaterialType(Term materialTypeVal)
Sets the materialType. |
void |
setName(java.lang.String nameVal)
Sets the name. |
void |
setOrganism(Organism organism)
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void |
setTissueSite(Term tissueSite)
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java.lang.String |
toString()
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Methods inherited from class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode |
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addDirectPredecessor, addDirectSuccessor, doAddDirectPredecessor, doAddDirectSuccessor, getCharacteristicsRecursively, getDirectPredecessors, getDirectSuccessors, getNodeType, getPredecessorsOfType, getSuccessorsOfType |
Methods inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayEntity |
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getLsid, getLsidAuthority, getLsidNamespace, getLsidObjectId, setLsid, setLsid, setLsidForEntity |
Methods inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayObject |
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equals, getCaBigId, getId, getPostLoadSecurityPolicies, getRemoteApiSecurityPolicies, hashCode, setCaBigId, setId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public AbstractBioMaterial()
Method Detail |
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public Experiment getExperiment()
getExperiment
in class AbstractExperimentDesignNode
public void setExperiment(Experiment experiment)
experiment
- the experiment to setpublic Term getTissueSite()
public void setTissueSite(Term tissueSite)
tissueSite
- the tissueSite to setpublic Term getMaterialType()
public void setMaterialType(Term materialTypeVal)
materialTypeVal
- the materialTypepublic Term getCellType()
public void setCellType(Term cellType)
cellType
- the cellType to setpublic Term getDiseaseState()
public void setDiseaseState(Term diseaseState)
diseaseState
- the diseaseState to set@NotNull @Length(min=1, max=254) public java.lang.String getName()
getName
in class AbstractExperimentDesignNode
public void setName(java.lang.String nameVal)
nameVal
- the name@Length(max=2000) public java.lang.String getDescription()
public void setDescription(java.lang.String descriptionVal)
descriptionVal
- the description@Length(max=254) public java.lang.String getExternalId()
public void setExternalId(java.lang.String externalId)
externalId
- the externalId to setpublic java.util.Set<AbstractCharacteristic> getCharacteristics()
public java.util.Date getLastModifiedDataTime()
public void setLastModifiedDataTime(java.util.Date lastModifiedDataTime)
lastModifiedDataTime
- the lastDataModificationDate to set.public void propagateLastModifiedDataTime(java.util.Date lastModifiedDate)
propagateLastModifiedDataTime
in class AbstractExperimentDesignNode
lastModifiedDate
- the lastDataModificationDate to set.public AbstractCharacteristic getCharacteristic(java.lang.String categoryName)
categoryName
- name of category for which to find a characteristic.
public java.util.Set<AbstractCharacteristic> getCharacteristics(Category category)
getCharacteristics
in class AbstractExperimentDesignNode
category
- category
protected java.util.Map<ExperimentOntologyCategory,Term> getSpecialCharacteristics()
public java.util.List<ProtocolApplication> getProtocolApplications()
public void addProtocolApplication(ProtocolApplication protocolApplication)
protocolApplication
- the protocol application to addpublic void clearProtocolApplications()
public Organism getOrganism()
public void setOrganism(Organism organism)
organism
- the organism to setpublic java.util.Set<Hybridization> getRelatedHybridizations()
public java.util.Set<CaArrayFile> getAllDataFiles()
getAllDataFiles
in class AbstractExperimentDesignNode
public void merge(AbstractExperimentDesignNode node)
Most of the information will actually be moved from node
to this in preparation
for deleting node
.
merge
in class AbstractExperimentDesignNode
node
- node to merge into thispublic java.lang.String toString()
toString
in class AbstractCaArrayObject
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