gov.nih.nci.caarray.domain.array
Class ArrayDesign

java.lang.Object
  extended by gov.nih.nci.caarray.domain.AbstractCaArrayObject
      extended by gov.nih.nci.caarray.domain.AbstractCaArrayEntity
          extended by gov.nih.nci.caarray.domain.array.ArrayDesign
All Implemented Interfaces:
com.fiveamsolutions.nci.commons.data.persistent.PersistentObject, java.io.Serializable

public class ArrayDesign
extends AbstractCaArrayEntity

The design details for a type of microarray.

See Also:
Serialized Form

Field Summary
 
Fields inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
CAARRAY_LSID_AUTHORITY, CAARRAY_LSID_NAMESPACE
 
Fields inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayObject
DEFAULT_BATCH_SIZE, DEFAULT_STRING_COLUMN_SIZE, LARGE_TEXT_FIELD_LENGTH
 
Constructor Summary
ArrayDesign()
          Default constructor.
ArrayDesign(ArrayDesign arrayDesign)
          Copy constructor.
 
Method Summary
 void addDesignFile(CaArrayFile designFile)
          Add a new design file to this design.
 CaArrayFile getAnnotationFile()
           
 java.util.SortedSet<AssayType> getAssayTypes()
          Gets the assay type for this Experiment.
 java.lang.String getDescription()
           
 ArrayDesignDetails getDesignDetails()
           
 java.util.Set<CaArrayFile> getDesignFiles()
           
 CaArrayFileSet getDesignFileSet()
           
 CaArrayFile getFirstDesignFile()
          Gets the first (or only) design file.
 java.lang.String getGeoAccession()
          GEO accession.
 java.lang.String getName()
          Gets the name.
 java.lang.Integer getNumberOfFeatures()
          Gets the numberOfFeatures.
 Organism getOrganism()
           
 Term getPolymerType()
          Gets the polymerType.
 ProtocolApplication getPrinting()
          Gets the printing.
 Organization getProvider()
          Gets the provider.
 Term getSubstrateType()
          Gets the substrateType.
 Term getSurfaceType()
          Gets the surfaceType.
 Term getTechnologyType()
          Gets the technologyType.
 java.lang.String getVersion()
          Gets the version.
 boolean isImportedAndParsed()
          Check whether this is a array design that has been imported imported but not parsed.
 boolean isUnparsedAndReimportable()
          Check whether this is a array design that was previously imported but not parsed, but now can be imported and parsed (due to a new parsing FileHandler being implemented for it, or because it was previously canceled from the job queue).
 void setAnnotationFile(CaArrayFile annotationFile)
           
 void setAssayTypes(java.util.SortedSet<AssayType> assayTypes)
           
 void setDescription(java.lang.String description)
           
 void setDesignDetails(ArrayDesignDetails designDetails)
           
 void setDesignFileSet(CaArrayFileSet designFileSet)
          Set the design files of this array design to the ones contained in the given set.
 void setGeoAccession(java.lang.String geoAccession)
           
 void setName(java.lang.String nameVal)
          Sets the name.
 void setNumberOfFeatures(java.lang.Integer numberOfFeaturesVal)
          Sets the numberOfFeatures.
 void setOrganism(Organism organism)
           
 void setPolymerType(Term polymerTypeVal)
          Sets the polymerType.
 void setPrinting(ProtocolApplication printingVal)
          Sets the printing.
 void setProvider(Organization providerVal)
          Sets the provider.
 void setSubstrateType(Term substrateTypeVal)
          Sets the substrateType.
 void setSurfaceType(Term surfaceTypeVal)
          Sets the surfaceType.
 void setTechnologyType(Term technologyTypeVal)
          Sets the technologyType.
 void setVersion(java.lang.String versionVal)
          Sets the version.
 java.lang.String toString()
          
 
Methods inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
getLsid, getLsidAuthority, getLsidNamespace, getLsidObjectId, setLsid, setLsid, setLsidForEntity
 
Methods inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayObject
equals, getCaBigId, getId, getPostLoadSecurityPolicies, getRemoteApiSecurityPolicies, hashCode, setCaBigId, setId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ArrayDesign

public ArrayDesign()
Default constructor.


ArrayDesign

public ArrayDesign(ArrayDesign arrayDesign)
Copy constructor. The newly created array design will be a shallow copy of the given design.

Parameters:
arrayDesign - existing array design on which to base the new array design.
Method Detail

getName

@NotNull
@Length(min=1,
        max=254)
public java.lang.String getName()
Gets the name.

Returns:
the name

setName

public void setName(java.lang.String nameVal)
Sets the name.

Parameters:
nameVal - the name

getNumberOfFeatures

public java.lang.Integer getNumberOfFeatures()
Gets the numberOfFeatures.

Returns:
the numberOfFeatures

setNumberOfFeatures

public void setNumberOfFeatures(java.lang.Integer numberOfFeaturesVal)
Sets the numberOfFeatures.

Parameters:
numberOfFeaturesVal - the numberOfFeatures

getPolymerType

public Term getPolymerType()
Gets the polymerType.

Returns:
the polymerType

setPolymerType

public void setPolymerType(Term polymerTypeVal)
Sets the polymerType.

Parameters:
polymerTypeVal - the polymerType

getSubstrateType

public Term getSubstrateType()
Gets the substrateType.

Returns:
the substrateType

setSubstrateType

public void setSubstrateType(Term substrateTypeVal)
Sets the substrateType.

Parameters:
substrateTypeVal - the substrateType

getSurfaceType

public Term getSurfaceType()
Gets the surfaceType.

Returns:
the surfaceType

setSurfaceType

public void setSurfaceType(Term surfaceTypeVal)
Sets the surfaceType.

Parameters:
surfaceTypeVal - the surfaceType

getTechnologyType

@NotNull
public Term getTechnologyType()
Gets the technologyType.

Returns:
the technologyType

setTechnologyType

public void setTechnologyType(Term technologyTypeVal)
Sets the technologyType.

Parameters:
technologyTypeVal - the technologyType

getVersion

@NotNull
public java.lang.String getVersion()
Gets the version.

Returns:
the version

setVersion

public void setVersion(java.lang.String versionVal)
Sets the version.

Parameters:
versionVal - the version

getProvider

@NotNull
public Organization getProvider()
Gets the provider.

Returns:
the provider

setProvider

public void setProvider(Organization providerVal)
Sets the provider.

Parameters:
providerVal - the provider

getPrinting

public ProtocolApplication getPrinting()
Gets the printing.

Returns:
the printing

setPrinting

public void setPrinting(ProtocolApplication printingVal)
Sets the printing.

Parameters:
printingVal - the printing

getDesignFiles

@NotNull
@Size(min=1)
public java.util.Set<CaArrayFile> getDesignFiles()
Returns:
the designFiles

getDesignFileSet

public CaArrayFileSet getDesignFileSet()
Returns:
the design files as a set.

setDesignFileSet

public void setDesignFileSet(CaArrayFileSet designFileSet)
Set the design files of this array design to the ones contained in the given set.

Parameters:
designFileSet - files to set

addDesignFile

public void addDesignFile(CaArrayFile designFile)
Add a new design file to this design.

Parameters:
designFile - design file to add

getFirstDesignFile

public CaArrayFile getFirstDesignFile()
Gets the first (or only) design file.

Returns:
the design file

setAnnotationFile

public void setAnnotationFile(CaArrayFile annotationFile)
Parameters:
annotationFile - the annotationFile to set

getAnnotationFile

public CaArrayFile getAnnotationFile()
Returns:
the annotationFile

toString

public java.lang.String toString()

Overrides:
toString in class AbstractCaArrayObject

getAssayTypes

@AttributePolicy(allow="Browse")
@NotNull
@Size(min=1)
public java.util.SortedSet<AssayType> getAssayTypes()
Gets the assay type for this Experiment.

Returns:
the assay type

setAssayTypes

public void setAssayTypes(java.util.SortedSet<AssayType> assayTypes)
Parameters:
assayTypes - the assayTypes to set

getOrganism

@NotNull
public Organism getOrganism()
Returns:
the organism

setOrganism

public void setOrganism(Organism organism)
Parameters:
organism - the organism to set

getDesignDetails

public ArrayDesignDetails getDesignDetails()
Returns:
the designDetails

setDesignDetails

public void setDesignDetails(ArrayDesignDetails designDetails)
Parameters:
designDetails - the designDetails to set

getDescription

@Length(max=2000)
public java.lang.String getDescription()
Returns:
the description

setDescription

public void setDescription(java.lang.String description)
Parameters:
description - the description to set

getGeoAccession

@Length(max=254)
public java.lang.String getGeoAccession()
GEO accession.

Returns:
the GEO accession.

setGeoAccession

public void setGeoAccession(java.lang.String geoAccession)
Parameters:
geoAccession - GEO accession.

isUnparsedAndReimportable

public boolean isUnparsedAndReimportable()
Check whether this is a array design that was previously imported but not parsed, but now can be imported and parsed (due to a new parsing FileHandler being implemented for it, or because it was previously canceled from the job queue). This will be the case if any of the design files associated with the array design meet this condition.

Returns:
true if the design can be re-imported and parsed, false otherwise.

isImportedAndParsed

public boolean isImportedAndParsed()
Check whether this is a array design that has been imported imported but not parsed. implemented for it). This will be the case if any of the design files associated with the array design meet this condition.

Returns:
true if the design has been imported and parsed, false otherwise.