Package ubic.gemma.model.genome.gene

Class GeneValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<Gene>
ubic.gemma.model.genome.gene.GeneValueObject
All Implemented Interfaces:
Serializable, Identifiable
public class GeneValueObject extends IdentifiableValueObject<Gene> implements Serializable
Author:
kelsey
See Also:

  • Constructor Details

    • GeneValueObject

      public GeneValueObject()
      Required when using the class as a spring bean.

    • GeneValueObject

      public GeneValueObject(Long id)

    • GeneValueObject

      public GeneValueObject(Gene gene)
      Parameters:
      gene - gene

    • GeneValueObject

      public GeneValueObject(Gene gene, boolean includeTaxon)
      Parameters:
      includeTaxon - include full taxon details in getTaxonForGemmaRest(), otherwise only getTaxonIdForGemmaRest() is filled

    • GeneValueObject

      public GeneValueObject(GeneValueObject otherBean)
      Copies constructor from other GeneValueObject
      Parameters:
      otherBean - , cannot be null
      Throws:
      NullPointerException - if the argument is null

    • GeneValueObject

      public GeneValueObject(Long geneId, String geneSymbol, String geneOfficialName, Taxon taxon)

  • Method Details

    • convert2ValueObject

      public static GeneValueObject convert2ValueObject(Gene gene)
      Converts a Gene to a GeneValueObject
      Parameters:
      gene - a gene to be converted to a value object
      Returns:
      value object with the same basic characteristics as the given gene, including aliases.

    • convertMembers2GeneValueObjects

      public static Collection<GeneValueObject> convertMembers2GeneValueObjects(Collection<GeneSetMember> setMembers)
      A static method for easily converting GeneSetMembers into GeneValueObjects
      Parameters:
      setMembers - gene set members
      Returns:
      gene VOs

    • getTaxonId

      public Long getTaxonId()

    • getTaxonForGemmaRest

      public TaxonValueObject getTaxonForGemmaRest()

    • getTaxonIdForGemmaRest

      public Long getTaxonIdForGemmaRest()

    • getTaxonCommonName

      public String getTaxonCommonName()

    • getTaxonScientificName

      public String getTaxonScientificName()

    • toString

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

    • getAliases

      @Nullable public SortedSet<String> getAliases()
      Gene aliases, sorted alphabetically.

    • getAssociatedExperimentCount

      public Integer getAssociatedExperimentCount()
      How many experiments "involve" (manipulate, etc.) this gene

    • getCompositeSequenceCount

      public Integer getCompositeSequenceCount()

    • getDescription

      public String getDescription()

    • getGeneSets

      public Collection<GeneSetValueObject> getGeneSets()

    • getHomologues

      public Collection<GeneValueObject> getHomologues()

    • getIsQuery

      public Boolean getIsQuery()
      Was this gene directly used in a query? Or is it inferred somehow. The default is true, use this when you need to differentiate

    • getMultifunctionalityRank

      @Nullable public Double getMultifunctionalityRank()

    • getName

      public String getName()

    • getNcbiId

      public Integer getNcbiId()

    • getEnsemblId

      public String getEnsemblId()

    • getAccessions

      @Nullable public Set<DatabaseEntryValueObject> getAccessions()

    • getNodeDegreeNegRanks

      public double[] getNodeDegreeNegRanks()

    • getNodeDegreePosRanks

      public double[] getNodeDegreePosRanks()

    • getNodeDegreesNeg

      public int[] getNodeDegreesNeg()
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for negative correlation coexpression

    • getNodeDegreesPos

      public int[] getNodeDegreesPos()
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for positive coexpression

    • getNumGoTerms

      public Integer getNumGoTerms()

    • getOfficialName

      public String getOfficialName()

    • getOfficialSymbol

      public String getOfficialSymbol()

    • getPlatformCount

      public Integer getPlatformCount()

    • getScore

      public Double getScore()

    • getTaxon

      @Nullable public TaxonValueObject getTaxon()

    • isIncludeTaxon

      public boolean isIncludeTaxon()

    • setAliases

      public void setAliases(@Nullable SortedSet<String> aliases)
      Gene aliases, sorted alphabetically.

    • setAssociatedExperimentCount

      public void setAssociatedExperimentCount(Integer associatedExperimentCount)
      How many experiments "involve" (manipulate, etc.) this gene

    • setCompositeSequenceCount

      public void setCompositeSequenceCount(Integer compositeSequenceCount)

    • setDescription

      public void setDescription(String description)

    • setGeneSets

      public void setGeneSets(Collection<GeneSetValueObject> geneSets)

    • setHomologues

      public void setHomologues(Collection<GeneValueObject> homologues)

    • setIsQuery

      public void setIsQuery(Boolean isQuery)
      Was this gene directly used in a query? Or is it inferred somehow. The default is true, use this when you need to differentiate

    • setMultifunctionalityRank

      public void setMultifunctionalityRank(@Nullable Double multifunctionalityRank)

    • setName

      public void setName(String name)

    • setNcbiId

      public void setNcbiId(Integer ncbiId)

    • setEnsemblId

      public void setEnsemblId(String ensemblId)

    • setAccessions

      public void setAccessions(@Nullable Set<DatabaseEntryValueObject> accessions)

    • setNodeDegreeNegRanks

      public void setNodeDegreeNegRanks(double[] nodeDegreeNegRanks)

    • setNodeDegreePosRanks

      public void setNodeDegreePosRanks(double[] nodeDegreePosRanks)

    • setNodeDegreesNeg

      public void setNodeDegreesNeg(int[] nodeDegreesNeg)
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for negative correlation coexpression

    • setNodeDegreesPos

      public void setNodeDegreesPos(int[] nodeDegreesPos)
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for positive coexpression

    • setNumGoTerms

      public void setNumGoTerms(Integer numGoTerms)

    • setOfficialName

      public void setOfficialName(String officialName)

    • setOfficialSymbol

      public void setOfficialSymbol(String officialSymbol)

    • setPlatformCount

      public void setPlatformCount(Integer platformCount)

    • setScore

      public void setScore(Double score)

    • setTaxon

      public void setTaxon(@Nullable TaxonValueObject taxon)

    • setIncludeTaxon

      public void setIncludeTaxon(boolean includeTaxon)

    • equals

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

    • canEqual

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

    • hashCode

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