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

Class GeoChannel

java.lang.Object
ubic.gemma.core.loader.expression.geo.model.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 Details

    • GeoChannel

      public GeoChannel()

  • Method Details

    • convertStringToMolecule

      public static GeoChannel.ChannelMolecule convertStringToMolecule(String string)

    • 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.

    • 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.

    • getMolecule

      public GeoChannel.ChannelMolecule getMolecule()
      Returns:
      Returns the molecule.

    • setMolecule

      public void setMolecule(GeoChannel.ChannelMolecule molecule)
      Parameters:
      molecule - The molecule 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.

    • getGrowthProtocol

      public String getGrowthProtocol()

    • setGrowthProtocol

      public void setGrowthProtocol(String growthProtocol)