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

Class GeoSample

java.lang.Object
ubic.gemma.core.loader.expression.geo.model.GeoData
ubic.gemma.core.loader.expression.geo.model.GeoSample
All Implemented Interfaces:
Serializable, Comparable<GeoSample>
public class GeoSample extends GeoData implements Comparable<GeoSample>
Represents a sample (GSM) in GEO. The channels correspond to BioMaterials; the sample itself corresponds to a BioAssay in Gemma. Some fields are only relevant for SAGE.
Author:
pavlidis
See Also:

  • Constructor Details

    • GeoSample

      public GeoSample()

  • Method Details

    • addChannel

      public void addChannel()

    • addPlatform

      public void addPlatform(GeoPlatform platform)

    • addReplication

      public void addReplication(GeoReplication replication)

    • addSeriesAppearsIn

      public void addSeriesAppearsIn(String value)

    • addToDataProcessing

      public void addToDataProcessing(String s)

    • addToDescription

      public void addToDescription(String s)

    • addToHybProtocol

      public void addToHybProtocol(String s)

    • addToScanProtocol

      public void addToScanProtocol(String s)

    • addVariable

      public void addVariable(GeoVariable variable)

    • appearsInMultipleSeries

      public boolean appearsInMultipleSeries()
      Returns:
      true if this sample appears in more than one GEO Series.

    • getChannel

      public GeoChannel getChannel(int i)

    • getNthQuantitationType

      public String getNthQuantitationType(int n)
      Given a column number (count starts from zero) get the name of the corresponding quantitation type for this sample.
      Parameters:
      n - column number
      Returns:
      column name.

    • getOrganism

      public String getOrganism()
      Returns:
      organism name. This is obtained from the 'channels'.
      Throws:
      IllegalArgumentException - if there are two different organisms. This is kind of temporary, it's not nice.

    • hasUsableData

      public boolean hasUsableData()
      Returns:
      true if the data uses a platform that, generally, we can use the data from. Will be false for MPSS, SAGE and Exon array data.

    • setDescription

      public void setDescription(String description)
      Parameters:
      description - The description to set.

    • addToSupplementaryFiles

      public void addToSupplementaryFiles(String s)

    • compareTo

      public int compareTo(GeoSample o)
      Specified by:
      compareTo in interface Comparable<GeoSample>

    • toString

      public String toString()
      Overrides:
      toString in class GeoData

    • getStatus

      public String getStatus()

    • getSubmissionDate

      public String getSubmissionDate()

    • getId

      public String getId()

    • getChannels

      public List<GeoChannel> getChannels()

    • getDataProcessing

      public String getDataProcessing()

    • getDescription

      public String getDescription()

    • getHybProtocol

      public String getHybProtocol()

    • isGenePix

      public boolean isGenePix()

    • getLastUpdateDate

      public String getLastUpdateDate()

    • getLibSource

      @Nullable public GeoLibrarySource getLibSource()

    • getLibStrategy

      @Nullable public GeoLibraryStrategy getLibStrategy()

    • isMightNotHaveDataInFile

      public boolean isMightNotHaveDataInFile()
      Indicate if the data might be separate, as for some RNA-seq studies.

    • getPlatforms

      public Collection<GeoPlatform> getPlatforms()

    • getReplicates

      public Collection<GeoReplication> getReplicates()

    • getScanProtocol

      public String getScanProtocol()

    • getSeriesAppearsIn

      public Collection<String> getSeriesAppearsIn()

    • getSupplementaryFiles

      public Collection<String> getSupplementaryFiles()

    • getAnchor

      public String getAnchor()

    • getTagCount

      public int getTagCount()

    • getTagLength

      public int getTagLength()

    • getTitleInDataset

      @Nullable public String getTitleInDataset()
      This is used to store the title for the sample as found in the GDS file, if it differs from the one in the GSE file

    • getType

      public GeoSampleType getType()
      The sample type (ie. DNA, RNA, etc.)

    • getVariables

      public Collection<GeoVariable> getVariables()

    • isWarnedAboutGenePix

      public boolean isWarnedAboutGenePix()

    • setStatus

      public void setStatus(String status)

    • setSubmissionDate

      public void setSubmissionDate(String submissionDate)

    • setId

      public void setId(String id)

    • setDataProcessing

      public void setDataProcessing(String dataProcessing)

    • setHybProtocol

      public void setHybProtocol(String hybProtocol)

    • setGenePix

      public void setGenePix(boolean isGenePix)

    • setLastUpdateDate

      public void setLastUpdateDate(String lastUpdateDate)

    • setLibSource

      public void setLibSource(@Nullable GeoLibrarySource libSource)

    • setLibStrategy

      public void setLibStrategy(@Nullable GeoLibraryStrategy libStrategy)

    • setMightNotHaveDataInFile

      public void setMightNotHaveDataInFile(boolean mightNotHaveDataInFile)
      Indicate if the data might be separate, as for some RNA-seq studies.

    • setPlatforms

      public void setPlatforms(Collection<GeoPlatform> platforms)

    • setScanProtocol

      public void setScanProtocol(String scanProtocol)

    • setAnchor

      public void setAnchor(String anchor)

    • setTagCount

      public void setTagCount(int tagCount)

    • setTagLength

      public void setTagLength(int tagLength)

    • setTitleInDataset

      public void setTitleInDataset(@Nullable String titleInDataset)
      This is used to store the title for the sample as found in the GDS file, if it differs from the one in the GSE file

    • setType

      public void setType(GeoSampleType type)
      The sample type (ie. DNA, RNA, etc.)

    • setWarnedAboutGenePix

      public void setWarnedAboutGenePix(boolean warnedAboutGenePix)