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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.hybridization.Hybridization
public class Hybridization
The act of hybridizing extracted genetic material to the probes on a microarray.
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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Hybridization()
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Method Summary | |
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void |
addArrayData(AbstractArrayData arrayData)
Add a new array data to this hybridization. |
void |
addProtocolApplication(ProtocolApplication pa)
Add the given protocol application to the protocol applications of this. |
void |
clearProtocolApplications()
Remove all protocol applications of this. |
protected void |
doAddDirectPredecessor(AbstractExperimentDesignNode predecessor)
Actually add the new node as a direct predecessor of this node. |
protected void |
doAddDirectSuccessor(AbstractExperimentDesignNode successor)
Actually add the new node as a direct successor of this node. |
java.util.Set<CaArrayFile> |
getAllDataFiles()
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float |
getAmountOfMaterial()
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Term |
getAmountOfMaterialUnit()
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Array |
getArray()
Gets the array. |
java.util.Set<DerivedArrayData> |
getDerivedDataCollection()
Gets the derivedDatas. |
java.lang.String |
getDescription()
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java.util.Set<? extends AbstractExperimentDesignNode> |
getDirectPredecessors()
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java.util.Set<? extends AbstractExperimentDesignNode> |
getDirectSuccessors()
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Experiment |
getExperiment()
Get the experiment to which this node belongs. |
AbstractFactorValue |
getFactorValue(java.lang.String factorName)
Return the factor value for the factor with given name in this hybridization. |
java.util.Set<AbstractFactorValue> |
getFactorValues()
Gets the factorValues. |
java.util.Set<HybridizationData> |
getHybridizationData()
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java.util.Set<Image> |
getImages()
Gets the images. |
java.util.Set<LabeledExtract> |
getLabeledExtracts()
Gets the labeledExtract. |
java.lang.String |
getName()
Gets the name. |
ExperimentDesignNodeType |
getNodeType()
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java.util.List<ProtocolApplication> |
getProtocolApplications()
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java.util.Set<RawArrayData> |
getRawDataCollection()
Gets the rawArrayDatas. |
int |
getUncompressedSizeOfDataFiles()
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void |
merge(AbstractExperimentDesignNode node)
Merges another AbstractExperimentDesignNode into this one. |
java.util.Collection<? extends gov.nih.nci.caarray.security.Protectable> |
relatedProtectables()
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void |
removeArrayData(AbstractArrayData arrayData)
Remove an array data from this hybridization. |
void |
setAmountOfMaterial(float amountOfMaterial)
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void |
setAmountOfMaterialUnit(Term amountOfMaterialUnit)
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void |
setArray(Array arrayVal)
Sets the array. |
void |
setDescription(java.lang.String description)
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void |
setExperiment(Experiment experiment)
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void |
setHybridizationData(java.util.Set<HybridizationData> hybridizationData)
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void |
setName(java.lang.String nameVal)
Sets the name. |
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, getCharacteristics, getCharacteristicsRecursively, getPredecessorsOfType, getSuccessorsOfType, propagateLastModifiedDataTime |
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 |
Methods inherited from interface com.fiveamsolutions.nci.commons.data.persistent.PersistentObject |
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getId |
Constructor Detail |
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public Hybridization()
Method Detail |
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@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=254) public java.lang.String getDescription()
public void setDescription(java.lang.String description)
description
- the description to setpublic java.util.Set<Image> getImages()
public java.util.Set<DerivedArrayData> getDerivedDataCollection()
public Array getArray()
public void setArray(Array arrayVal)
arrayVal
- the arraypublic java.util.Set<RawArrayData> getRawDataCollection()
public void addArrayData(AbstractArrayData arrayData)
arrayData
- the array data to addpublic void removeArrayData(AbstractArrayData arrayData)
arrayData
- the array data to removepublic java.util.Set<AbstractFactorValue> getFactorValues()
public AbstractFactorValue getFactorValue(java.lang.String factorName)
factorName
- name of factor for which to find a value.
public java.util.List<ProtocolApplication> getProtocolApplications()
getProtocolApplications
in interface ProtocolApplicable
public void addProtocolApplication(ProtocolApplication pa)
addProtocolApplication
in interface ProtocolApplicable
pa
- the protocol application to addpublic void clearProtocolApplications()
clearProtocolApplications
in interface ProtocolApplicable
public java.util.Set<LabeledExtract> getLabeledExtracts()
public Experiment getExperiment()
getExperiment
in class AbstractExperimentDesignNode
public void setExperiment(Experiment experiment)
experiment
- the experiment to setpublic java.lang.String toString()
toString
in class AbstractCaArrayObject
public float getAmountOfMaterial()
public void setAmountOfMaterial(float amountOfMaterial)
amountOfMaterial
- the amountOfMaterial to setpublic Term getAmountOfMaterialUnit()
public void setAmountOfMaterialUnit(Term amountOfMaterialUnit)
amountOfMaterialUnit
- the amountOfMaterialUnit to setpublic java.util.Set<HybridizationData> getHybridizationData()
public void setHybridizationData(java.util.Set<HybridizationData> hybridizationData)
hybridizationData
- the hybridizationData to setpublic java.util.Set<CaArrayFile> getAllDataFiles()
getAllDataFiles
in class AbstractExperimentDesignNode
public java.util.Collection<? extends gov.nih.nci.caarray.security.Protectable> relatedProtectables()
relatedProtectables
in interface gov.nih.nci.caarray.security.ProtectableDescendent
public int getUncompressedSizeOfDataFiles()
public ExperimentDesignNodeType getNodeType()
getNodeType
in class AbstractExperimentDesignNode
public java.util.Set<? extends AbstractExperimentDesignNode> getDirectPredecessors()
getDirectPredecessors
in class AbstractExperimentDesignNode
public java.util.Set<? extends AbstractExperimentDesignNode> getDirectSuccessors()
getDirectSuccessors
in class AbstractExperimentDesignNode
protected void doAddDirectPredecessor(AbstractExperimentDesignNode predecessor)
doAddDirectPredecessor
in class AbstractExperimentDesignNode
predecessor
- the new node. it is assumed this node is of the correct typeprotected void doAddDirectSuccessor(AbstractExperimentDesignNode successor)
doAddDirectSuccessor
in class AbstractExperimentDesignNode
successor
- the new node. it is assumed this node is of the correct typepublic 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 this
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