Package ubic.gemma.core.loader.expression.geo.model

Class GeoChannel

  • public class GeoChannel
extends Object
    Represents data for one channel on a microarray in GEO. Corresponds (roughly) to a BioMaterial in Gemma.
    Author:
    pavlidis

    • Constructor Detail

      • GeoChannel

        public GeoChannel()

    • Method Detail

      • addToExtractProtocol

        public void addToExtractProtocol​(String s)

      • addToGrowthProtocol

        public void addToGrowthProtocol​(String s)

      • addCharacteristic

        public void addCharacteristic​(String characteristic)

      • addToTreatmentProtocol

        public void addToTreatmentProtocol​(String s)

      • getBioMaterialProvider

        public String getBioMaterialProvider()
        Returns:
        Returns the bioMaterialProvider.

      • setBioMaterialProvider

        public void setBioMaterialProvider​(String bioMaterialProvider)
        Parameters:
        bioMaterialProvider - The bioMaterialProvider to set.

      • getCharacteristic

        public Collection<String> getCharacteristic()
        Returns:
        Returns the characteristic.

      • setCharacteristic

        public void setCharacteristic​(Collection<String> characteristics)
        Parameters:
        characteristics - The characteristics to set.

      • getExtractProtocol

        public String getExtractProtocol()
        Returns:
        Returns the extractProtocol.

      • setExtractProtocol

        public void setExtractProtocol​(String extractProtocol)
        Parameters:
        extractProtocol - The extractProtocol to set.

      • getLabel

        public String getLabel()
        Returns:
        Returns the label.

      • setLabel

        public void setLabel​(String label)
        Parameters:
        label - The label to set.

      • getLabelProtocol

        public String getLabelProtocol()
        Returns:
        Returns the labelProtocol.

      • setLabelProtocol

        public void setLabelProtocol​(String labelProtocol)
        Parameters:
        labelProtocol - The labelProtocol to set.

      • getMoleculeAsCharacteristic

        public Characteristic getMoleculeAsCharacteristic()
        Convert the molecule into a MGED Ontology-based MaterialType Characteristic. If "other" we just return a plain text value. URIs checked 8/2024
        Returns:
        characteristic

      • getOrganism

        public String getOrganism()
        Returns:
        Returns the organism.

      • setOrganism

        public void setOrganism​(String organism)
        Parameters:
        organism - The organism to set.

      • getSourceName

        public String getSourceName()
        Returns:
        Returns the sourceName.

      • setSourceName

        public void setSourceName​(String sourceName)
        Parameters:
        sourceName - The sourceName to set.

      • getTreatmentProtocol

        public String getTreatmentProtocol()
        Returns:
        Returns the treatmentProtocol.

      • setTreatmentProtocol

        public void setTreatmentProtocol​(String treatmentProtocol)
        Parameters:
        treatmentProtocol - The treatmentProtocol to set.

      • getChannelNumber

        public int getChannelNumber()
        Returns:
        Returns the channelNumber.

      • setChannelNumber

        public void setChannelNumber​(int channelNumber)
        Parameters:
        channelNumber - The channelNumber to set.

      • getCharacteristics

        public Collection<String> getCharacteristics()
        Returns:
        Returns the characteristics.

      • setCharacteristics

        public void setCharacteristics​(Collection<String> characteristics)
        Parameters:
        characteristics - The characteristics to set.

      • getGrowthProtocol

        public String getGrowthProtocol()

      • setGrowthProtocol

        public void setGrowthProtocol​(String growthProtocol)