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

Class GeoSample

  • All Implemented Interfaces:
    Serializable, Comparable<GeoData>
    public class GeoSample
extends GeoData
implements Comparable<GeoData>
    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:
    Serialized Form

    • Constructor Detail

      • GeoSample

        public GeoSample()

    • Method Detail

      • 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.

      • getId

        public String getId()

      • setId

        public void setId​(String id)

      • getStatus

        public String getStatus()

      • setStatus

        public void setStatus​(String status)

      • getSubmissionDate

        public String getSubmissionDate()

      • setSubmissionDate

        public void setSubmissionDate​(String submissionDate)

      • setChannelCount

        public void setChannelCount​(int channelCount)

      • setGenePix

        public void setGenePix​(boolean genePix)

      • isWarnedAboutGenePix

        public boolean isWarnedAboutGenePix()

      • setWarnedAboutGenePix

        public void setWarnedAboutGenePix​(boolean warnedAboutGenePix)

      • getAnchor

        public String getAnchor()
        Returns:
        Returns the anchor. (SAGE)

      • getChannel

        public GeoChannel getChannel​(int i)

      • getChannelCount

        public int getChannelCount()
        Returns:
        Returns the channelCount.

      • getChannels

        public List<GeoChannel> getChannels()
        Returns:
        Returns the channels.

      • getDataProcessing

        public String getDataProcessing()
        Returns:
        Returns the dataProcessing.

      • getDescription

        public String getDescription()
        Returns:
        Returns the description.

      • getHybProtocol

        public String getHybProtocol()
        Returns:
        Returns the hybProtocol.

      • getLastUpdateDate

        public String getLastUpdateDate()
        Returns:
        String

      • 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.

      • getScanProtocol

        public String getScanProtocol()
        Returns:
        Returns the scanProtocol.

      • getSupplementaryFile

        public String getSupplementaryFile()
        Returns:
        String

      • getTagCount

        public int getTagCount()
        Returns:
        Returns the tagCount. (SAGE)

      • getTagLength

        public int getTagLength()
        Returns:
        Returns the tagLength. (SAGE)

      • getTitleInDataset

        public String getTitleInDataset()

      • getType

        public String getType()
        Returns the sample type (ie. DNA, RNA, etc.)
        Returns:
        String

      • 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.

      • isGenePix

        public boolean isGenePix()

      • isMightNotHaveDataInFile

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

      • setAnchor

        public void setAnchor​(String anchor)
        Parameters:
        anchor - The anchor to set. (SAGE)

      • setChannels

        public void setChannels​(List<GeoChannel> channelData)

      • setDataProcessing

        public void setDataProcessing​(String dataProcessing)
        Parameters:
        dataProcessing - The dataProcessing to set.

      • setDescription

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

      • setHybProtocol

        public void setHybProtocol​(String hybProtocol)
        Parameters:
        hybProtocol - The hybProtocol to set.

      • setLastUpdateDate

        public void setLastUpdateDate​(String lastUpdateDate)

      • setLibStrategy

        public void setLibStrategy​(@Nullable
                           String libStrategy)

      • setMightNotHaveDataInFile

        public void setMightNotHaveDataInFile​(boolean mightNotHaveDataInFile)

      • setScanProtocol

        public void setScanProtocol​(String scanProtocol)
        Parameters:
        scanProtocol - The scanProtocol to set.

      • setSeriesAppearsIn

        public void setSeriesAppearsIn​(Collection<String> otherSeriesAppearsIn)

      • setSupplementaryFile

        public void setSupplementaryFile​(String supplementaryFile)

      • setTagCount

        public void setTagCount​(int tagCount)
        Parameters:
        tagCount - The tagCount to set. (SAGE)

      • setTagLength

        public void setTagLength​(int tagLength)
        Parameters:
        tagLength - The tagLength to set. (SAGE)

      • setTitleInDataset

        public void setTitleInDataset​(String titleInDataset)

      • setType

        public void setType​(String type)
        Sets the sample type (ie. DNA, RNA, etc.)
        Parameters:
        type - new type