Package ubic.gemma.model.expression.bioAssay

Class BioAssay

  • All Implemented Interfaces:
    gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Serializable, Describable, Identifiable
    @Indexed
public class BioAssay
extends AbstractDescribable
implements gemma.gsec.model.SecuredChild, Serializable
    Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay). We don't distinguish between "physical" and "computational" BioAssays, so this is a concrete class. This has several slots that are used specifically to support sequence-based data, but is intended to be generic.
    See Also:
    Serialized Form

    • Constructor Detail

      • BioAssay

        public BioAssay()

    • 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

      • getAccession

        @IndexedEmbedded
public DatabaseEntry getAccession()

      • setAccession

        public void setAccession​(DatabaseEntry accession)

      • getArrayDesignUsed

        public ArrayDesign getArrayDesignUsed()

      • setArrayDesignUsed

        public void setArrayDesignUsed​(ArrayDesign arrayDesignUsed)

      • getIsOutlier

        public Boolean getIsOutlier()
        Returns:
        Used to indicate if the sample should be considered an outlier based on QC. The audit trail for the entity tracks when this was done.

      • setIsOutlier

        public void setIsOutlier​(Boolean isOutlier)

      • getProcessingDate

        public Date getProcessingDate()
        Returns:
        Indicates the date that the assay was processed in the original study. This would correspond to "batch" information and will often be a "scan date" or similar information extracted from the raw data files.

      • setProcessingDate

        public void setProcessingDate​(Date processingDate)

      • getSampleUsed

        @IndexedEmbedded
public BioMaterial getSampleUsed()

      • setSampleUsed

        public void setSampleUsed​(BioMaterial sampleUsed)

      • getSecurityOwner

        public gemma.gsec.model.Securable getSecurityOwner()
        Specified by:
        getSecurityOwner in interface gemma.gsec.model.SecuredChild

      • getSequencePairedReads

        @Nullable
public Boolean getSequencePairedReads()
        Returns:
        For sequence-based data, this should be set to true if the sequencing was paired-end reads and false otherwise. It should be left as null if it isn't known.

      • setSequencePairedReads

        public void setSequencePairedReads​(@Nullable
                                   Boolean sequencePairedReads)

      • getSequenceReadCount

        @Nullable
public Long getSequenceReadCount()
        Returns:
        For sequence-read based data, the total number of reads in the sample, computed from the data as the total of the values for the elements assayed.

      • setSequenceReadCount

        public void setSequenceReadCount​(@Nullable
                                 Long sequenceReadCount)

      • getSequenceReadLength

        @Nullable
public Integer getSequenceReadLength()
        Returns:
        For sequencing-based data, the length of the reads. If it was paired reads, this is understood to be the length for each "end". If the read length was variable (due to quality trimming, etc.) this will be treated as representing the mean read length.

      • setSequenceReadLength

        public void setSequenceReadLength​(@Nullable
                                  Integer sequenceReadLength)

      • getMetadata

        public String getMetadata()

      • setMetadata

        public void setMetadata​(String metadata)

      • getOriginalPlatform

        public ArrayDesign getOriginalPlatform()

      • setOriginalPlatform

        public void setOriginalPlatform​(ArrayDesign originalPlatform)

      • getFastqHeaders

        public String getFastqHeaders()

      • setFastqHeaders

        public void setFastqHeaders​(String fastqHeaders)