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
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

  • 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.

    • getMergedInto

      @Nullable public ArrayDesignReferenceValueObject getMergedInto()
      The platform this one was merged into, or null when it was not merged.

      The companion to isMergee, which says only THAT a merge happened. Batch-hydrated in ArrayDesignDaoImpl.populateMergeRelations; the association is LAZY on the entity, so reading shortName off the proxy inside the constructor would fire one extra query per row of a listing.

    • getMergees

      @Nullable public List<ArrayDesignReferenceValueObject> getMergees()
      The platforms merged INTO this one — the inverse of mergedInto, empty when there are none. Companion to isMerged.

    • 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.

      Report-era field: a String, written by ArrayDesignReportService into a disk-serialized report and never populated on the REST path. Left as-is because those report files are Java-serialized on production and retyping the field would break reading them. The live, typed counterpart on the wire is numberOfGenes.

    • getNumberOfGenes

      @Nullable public Long getNumberOfGenes()
      Distinct genes the platform's elements map to, or null when the caller did not ask.

      Opt-in via ?withGeneCounts=true; see ArrayDesignDao.getGeneCounts(Collection) for why it is not computed by default.

    • getNumberOfMappedElements

      @Nullable public Long getNumberOfMappedElements()
      Elements on the platform that map to at least one gene, or null when the caller did not ask. Pairs with numberOfGenes and comes from the same query — the difference between the two is what tells a reader whether a platform is densely or sparsely annotated.

    • getGeneCountsLastUpdated

      @Nullable public String getGeneCountsLastUpdated()
      When the report backing numberOfGenes / numberOfMappedElements was written, as yyyy.MM.dd HH:mm.

      Null when the counts were derived live rather than read from a report (gene-list platforms, where the element count answers both), or when no counts were populated at all. Exposed because a count read from a monthly report is not the same claim as a fresh one, and a client showing the number should be able to say how old it is.

    • 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.

    • setMergedInto

      public void setMergedInto(@Nullable ArrayDesignReferenceValueObject mergedInto)
      The platform this one was merged into, or null when it was not merged.

      The companion to isMergee, which says only THAT a merge happened. Batch-hydrated in ArrayDesignDaoImpl.populateMergeRelations; the association is LAZY on the entity, so reading shortName off the proxy inside the constructor would fire one extra query per row of a listing.

    • setMergees

      public void setMergees(@Nullable List<ArrayDesignReferenceValueObject> mergees)
      The platforms merged INTO this one — the inverse of mergedInto, empty when there are none. Companion to isMerged.

    • 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.

      Report-era field: a String, written by ArrayDesignReportService into a disk-serialized report and never populated on the REST path. Left as-is because those report files are Java-serialized on production and retyping the field would break reading them. The live, typed counterpart on the wire is numberOfGenes.

    • setNumberOfGenes

      public void setNumberOfGenes(@Nullable Long numberOfGenes)
      Distinct genes the platform's elements map to, or null when the caller did not ask.

      Opt-in via ?withGeneCounts=true; see ArrayDesignDao.getGeneCounts(Collection) for why it is not computed by default.

    • setNumberOfMappedElements

      public void setNumberOfMappedElements(@Nullable Long numberOfMappedElements)
      Elements on the platform that map to at least one gene, or null when the caller did not ask. Pairs with numberOfGenes and comes from the same query — the difference between the two is what tells a reader whether a platform is densely or sparsely annotated.

    • setGeneCountsLastUpdated

      public void setGeneCountsLastUpdated(@Nullable String geneCountsLastUpdated)
      When the report backing numberOfGenes / numberOfMappedElements was written, as yyyy.MM.dd HH:mm.

      Null when the counts were derived live rather than read from a report (gene-list platforms, where the element count answers both), or when no counts were populated at all. Exposed because a count read from a monthly report is not the same claim as a fresh one, and a client showing the number should be able to say how old it is.

    • 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>