Class ArrayDesign

    • Constructor Detail

      • ArrayDesign

        public ArrayDesign()
        No-arg constructor added to satisfy javabean contract
    • Method Detail

      • equals

        public boolean equals​(Object object)
        Description copied from class: AbstractDescribable
        Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.
        Overrides:
        equals in class AbstractDescribable
      • getName

        @Field
        public String getName()
        Description copied from interface: Describable
        Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
        Specified by:
        getName in interface Describable
        Overrides:
        getName in class AbstractDescribable
      • getAdvertisedNumberOfDesignElements

        public Integer getAdvertisedNumberOfDesignElements()
        Returns:
        The number of design elements, according to the manufactuerer or determined at the time the array design was entered into the system. The actual number of design elements can only be determined by looking at the associated Set of DesignElements.
      • getAlternateNames

        @IndexedEmbedded
        public Set<AlternateName> getAlternateNames()
      • getAlternativeTo

        public ArrayDesign getAlternativeTo()
        Returns:
        true if this is an Affymetrix platform that has a related "canonical" platform we use instead.
      • getDesignProvider

        public Contact getDesignProvider()
      • getExternalReferences

        @IndexedEmbedded
        public Set<DatabaseEntry> getExternalReferences()
        Returns:
        Accessions for this array design in other databases, e.g., GEO, ArrayExpression.
      • getPrimaryTaxon

        public Taxon getPrimaryTaxon()
        Returns:
        The taxon the array design is for. This could be a non-specific taxon ("salmonid"). It may not match the sequences on the array exactly. For example, a mouse array might have some non-mouse sequences as controls, but the primary taxon is still mouse.
      • getShortName

        @Field(analyze=NO)
        public String getShortName()
        Returns:
        A brief unique (but optional) human-readable name for the expression experiment. For example in the past we often used names like "HG-U95A".
      • getSubsumedArrayDesigns

        public Set<ArrayDesign> getSubsumedArrayDesigns()
        Returns:
        Array designs that this array design "covers". For example, the HG-U133_Plus_2 array includes all the elements that are on the HG-U133A and HG-U133B, so they are subsumed by the HG-U133_Plus_2.
      • getSubsumingArrayDesign

        public ArrayDesign getSubsumingArrayDesign()
        Returns:
        An array design that subsumes this one (contains DesignElements that are equivalent to the ones on this arraydesign).
      • setAdvertisedNumberOfDesignElements

        public void setAdvertisedNumberOfDesignElements​(Integer advertisedNumberOfDesignElements)
      • setAlternateNames

        public void setAlternateNames​(Set<AlternateName> alternateNames)
      • setAlternativeTo

        public void setAlternativeTo​(ArrayDesign alternativeTo)
      • setCompositeSequences

        public void setCompositeSequences​(Set<CompositeSequence> compositeSequences)
      • setDesignProvider

        public void setDesignProvider​(Contact designProvider)
      • setExternalReferences

        public void setExternalReferences​(Set<DatabaseEntry> externalReferences)
      • setMergedInto

        public void setMergedInto​(ArrayDesign mergedInto)
      • setPrimaryTaxon

        public void setPrimaryTaxon​(Taxon primaryTaxon)
      • setShortName

        public void setShortName​(String shortName)
      • setSubsumedArrayDesigns

        public void setSubsumedArrayDesigns​(Set<ArrayDesign> subsumedArrayDesigns)
      • setSubsumingArrayDesign

        public void setSubsumingArrayDesign​(ArrayDesign subsumingArrayDesign)
      • setTechnologyType

        public void setTechnologyType​(TechnologyType technologyType)