Package ubic.gemma.model.expression.arrayDesign

Class ArrayDesignValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<ArrayDesign>
ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<ArrayDesign>
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject
All Implemented Interfaces:
Serializable, Versioned, Identifiable
Direct Known Subclasses:
ArrayDesignValueObjectExt, DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
public class ArrayDesignValueObject extends AbstractCuratableValueObject<ArrayDesign> implements Versioned
Value object for quickly displaying varied information about Array Designs.
Author:
paul et al
See Also:

  • Constructor Details

    • ArrayDesignValueObject

      public ArrayDesignValueObject()

    • ArrayDesignValueObject

      public ArrayDesignValueObject(Long id)

    • ArrayDesignValueObject

      public ArrayDesignValueObject(ArrayDesign ad)
      This will only work if the object is thawed (lightly). Not everything will be filled in -- test before using!
      Parameters:
      ad - ad

    • ArrayDesignValueObject

      protected ArrayDesignValueObject(ArrayDesignValueObject arrayDesignValueObject)
      Copies constructor from other ArrayDesignValueObject

  • Method Details

    • create

      public static Collection<ArrayDesignValueObject> create(Collection<ArrayDesign> subsumees)

    • getExpressionExperimentCount

      @Deprecated public Long getExpressionExperimentCount()
      Deprecated.
      use getNumberOfExpressionExperiments() instead.

    • getNumberOfExpressionExperiments

      public Long getNumberOfExpressionExperiments()

    • getTaxon

      public String getTaxon()

    • getTaxonID

      @Deprecated public Long getTaxonID()
      Deprecated.
      use getTaxonObject() instead

    • toString

      public String toString()
      Overrides:
      toString in class IdentifiableValueObject<ArrayDesign>

    • getBlackListed

      public Boolean getBlackListed()

    • getColor

      @Deprecated public String getColor()
      Deprecated.

    • getDateCached

      public String getDateCached()

    • getDescription

      public String getDescription()

    • getDesignElementCount

      public Integer getDesignElementCount()

    • getHasBlatAssociations

      public Boolean getHasBlatAssociations()

    • getHasGeneAssociations

      public Boolean getHasGeneAssociations()

    • getHasSequenceAssociations

      public Boolean getHasSequenceAssociations()

    • getIsAffymetrixAltCdf

      public Boolean getIsAffymetrixAltCdf()

    • getIsMerged

      public Boolean getIsMerged()
      Indicates this array design is the merger of other array designs.

    • getIsMergee

      public Boolean getIsMergee()
      Indicates that this array design has been merged into another.

    • getIsSubsumed

      public Boolean getIsSubsumed()
      Indicate if this array design is subsumed by some other array design.

    • getIsSubsumer

      public Boolean getIsSubsumer()
      Indicates if this array design subsumes some other array design(s)

    • getLastGeneMapping

      public Date getLastGeneMapping()

    • getLastRepeatMask

      public Date getLastRepeatMask()

    • getLastSequenceAnalysis

      public Date getLastSequenceAnalysis()

    • getLastSequenceUpdate

      public Date getLastSequenceUpdate()

    • getName

      public String getName()

    • getCreateDate

      public Date getCreateDate()

    • getNumGenes

      public String getNumGenes()
      The number of unique genes that this array design maps to.

    • getNumProbeAlignments

      public String getNumProbeAlignments()
      The number of probes that have BLAT alignments.

    • getNumProbeSequences

      public String getNumProbeSequences()
      The number of probes that map to bioSequences.

    • getNumProbesToGenes

      public String getNumProbesToGenes()
      The number of probes that map to genes. This count includes probe-aligned regions, predicted genes, and known genes.

    • getShortName

      public String getShortName()

    • getSwitchedExpressionExperimentCount

      public Long getSwitchedExpressionExperimentCount()

    • getTaxonObject

      @Nullable public TaxonValueObject getTaxonObject()

    • getTechnologyType

      public String getTechnologyType()

    • getReleaseVersion

      public String getReleaseVersion()
      Description copied from interface: Versioned
      The version of the release, if applicable.
      Specified by:
      getReleaseVersion in interface Versioned

    • getReleaseUrl

      public URL getReleaseUrl()
      Description copied from interface: Versioned
      External URL to the release, if applicable.
      Specified by:
      getReleaseUrl in interface Versioned

    • getExternalReferences

      @Nullable public Set<DatabaseEntryValueObject> getExternalReferences()
      Main external reference.

    • setBlackListed

      public void setBlackListed(Boolean blackListed)

    • setColor

      @Deprecated public void setColor(String color)
      Deprecated.

    • setDateCached

      public void setDateCached(String dateCached)

    • setDescription

      public void setDescription(String description)

    • setDesignElementCount

      public void setDesignElementCount(Integer designElementCount)

    • setExpressionExperimentCount

      public void setExpressionExperimentCount(Long expressionExperimentCount)

    • setHasBlatAssociations

      public void setHasBlatAssociations(Boolean hasBlatAssociations)

    • setHasGeneAssociations

      public void setHasGeneAssociations(Boolean hasGeneAssociations)

    • setHasSequenceAssociations

      public void setHasSequenceAssociations(Boolean hasSequenceAssociations)

    • setIsAffymetrixAltCdf

      public void setIsAffymetrixAltCdf(Boolean isAffymetrixAltCdf)

    • setIsMerged

      public void setIsMerged(Boolean isMerged)
      Indicates this array design is the merger of other array designs.

    • setIsMergee

      public void setIsMergee(Boolean isMergee)
      Indicates that this array design has been merged into another.

    • setIsSubsumed

      public void setIsSubsumed(Boolean isSubsumed)
      Indicate if this array design is subsumed by some other array design.

    • setIsSubsumer

      public void setIsSubsumer(Boolean isSubsumer)
      Indicates if this array design subsumes some other array design(s)

    • setLastGeneMapping

      public void setLastGeneMapping(Date lastGeneMapping)

    • setLastRepeatMask

      public void setLastRepeatMask(Date lastRepeatMask)

    • setLastSequenceAnalysis

      public void setLastSequenceAnalysis(Date lastSequenceAnalysis)

    • setLastSequenceUpdate

      public void setLastSequenceUpdate(Date lastSequenceUpdate)

    • setName

      public void setName(String name)

    • setCreateDate

      public void setCreateDate(Date createDate)

    • setNumGenes

      public void setNumGenes(String numGenes)
      The number of unique genes that this array design maps to.

    • setNumProbeAlignments

      public void setNumProbeAlignments(String numProbeAlignments)
      The number of probes that have BLAT alignments.

    • setNumProbeSequences

      public void setNumProbeSequences(String numProbeSequences)
      The number of probes that map to bioSequences.

    • setNumProbesToGenes

      public void setNumProbesToGenes(String numProbesToGenes)
      The number of probes that map to genes. This count includes probe-aligned regions, predicted genes, and known genes.

    • setShortName

      public void setShortName(String shortName)

    • setSwitchedExpressionExperimentCount

      public void setSwitchedExpressionExperimentCount(Long switchedExpressionExperimentCount)

    • setTaxonObject

      public void setTaxonObject(@Nullable TaxonValueObject taxonObject)

    • setTechnologyType

      public void setTechnologyType(String technologyType)

    • setReleaseVersion

      public void setReleaseVersion(String releaseVersion)

    • setReleaseUrl

      public void setReleaseUrl(URL releaseUrl)

    • setExternalReferences

      public void setExternalReferences(@Nullable Set<DatabaseEntryValueObject> externalReferences)
      Main external reference.

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class IdentifiableValueObject<ArrayDesign>

    • canEqual

      protected boolean canEqual(Object other)
      Overrides:
      canEqual in class IdentifiableValueObject<ArrayDesign>

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class IdentifiableValueObject<ArrayDesign>