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

Class GeoPlatform

  • All Implemented Interfaces:
    Serializable
    public class GeoPlatform
extends GeoData
    Bean describing a microarray platform in GEO
    Author:
    pavlidis
    See Also:
    Serialized Form

    • Constructor Detail

      • GeoPlatform

        public GeoPlatform()

    • Method Detail

      • isAffymetrixExonArray

        public static boolean isAffymetrixExonArray​(String geoPlatformId)
        Parameters:
        geoPlatformId - (GPL)
        Returns:
        true if we know this to be an exon array - so far as we know.

      • alternativeToProperAffyPlatform

        public static String alternativeToProperAffyPlatform​(String geoPlatformId)
        Parameters:
        geoPlatformId - (GPL)
        Returns:
        short name (GPLXXXX) of platform we would actually use, or null if not found

      • isAffyPlatform

        public static boolean isAffyPlatform​(String geoPlatformId)
        Parameters:
        geoPlatformId - (GPL)
        Returns:
        true if we recognize it as an Affymetrix platform. Depends on our mappings, if an error is spotted let us know.

      • isGEOAffyDataUsable

        public static boolean isGEOAffyDataUsable​(String geoPlatformId)
        Refers to a list of platforms for which the data from GEO is usually not usable and/or which we always reanalyze from CEL files - exon arrays. Logic: if this was run on an Affymetrix exon array we won't use the data from GEO, even if it was already using the gene-level version of the platform, because there are several variant versions that just muck up the system with useless probes (we have gone back and forth on this a bit...) Note that we endeavour to reanalyze all Affy data sets at the CEL file level.
        Parameters:
        geoPlatformId - (GPL)
        Returns:
        true if the platform is affymetrix exon array.

      • 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)

      • getWebLink

        public String getWebLink()

      • setWebLink

        public void setWebLink​(String webLink)

      • isUseDataFromGEO

        public boolean isUseDataFromGEO()

      • addToColumnData

        public void addToColumnData​(String columnName,
                            String value)
        Add a value to a column. A special case is when the column is of the probe ids (design element name).
        Parameters:
        columnName - column name
        value - value

      • addToDescription

        public void addToDescription​(String s)
        Parameters:
        s - description

      • addToOrganisms

        public void addToOrganisms​(String org)
        Parameters:
        org - organisation

      • getCatalogNumbers

        public Collection<String> getCatalogNumbers()
        Returns:
        Returns the catalogNumbers.

      • getCoating

        public String getCoating()
        Returns:
        Returns the coating.

      • getColumnData

        public List<List<String>> getColumnData​(Collection<String> columnNames)
        Parameters:
        columnNames - column names
        Returns:
        List of Lists of Strings

      • getContributer

        public Collection<String> getContributer()
        Returns:
        Returns the contributer.

      • getDescription

        public String getDescription()
        Returns:
        Returns the description.

      • getDescriptions

        public String getDescriptions()
        Returns:
        Returns the descriptions.

      • getDistribution

        public String getDistribution()
        Returns:
        Returns the distribution.

      • getIdColumnName

        public String getIdColumnName()
        Returns:
        the name of the column that has the 'ids' for the design elements on this platform. Usually this is "ID".

      • getLastUpdateDate

        public String getLastUpdateDate()
        Returns:
        String

      • getManufactureProtocol

        public String getManufactureProtocol()
        Returns:
        Returns the manufactureProtocol.

      • getManufacturer

        public String getManufacturer()
        Returns:
        Returns the manufacturer.

      • getOrganisms

        public Collection<String> getOrganisms()
        Returns:
        Returns the organisms.

      • getPlatformData

        public List<List<String>> getPlatformData()
        Returns:
        Returns the platformData.

      • getProbeNamesInGemma

        public Map<String,​String> getProbeNamesInGemma()

      • getPubMedIds

        public Collection<Integer> getPubMedIds()
        Returns:
        Returns the pubMedIds.

      • getSample

        public String getSample()
        Returns:
        String

      • getSupplementaryFile

        public String getSupplementaryFile()
        Returns:
        String

      • getSupport

        public String getSupport()
        Returns:
        Returns the support.

      • getWebLinks

        public Collection<String> getWebLinks()
        Returns:
        Returns the webLinks.

      • setCatalogNumbers

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

      • setCoating

        public void setCoating​(String coating)
        Parameters:
        coating - The coating to set.

      • setContributer

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

      • setDescription

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

      • setDistribution

        public void setDistribution​(String distribution)
        Parameters:
        distribution - The distribution to set.

      • setLastUpdateDate

        public void setLastUpdateDate​(String lastUpdateDate)

      • setManufactureProtocol

        public void setManufactureProtocol​(String manufactureProtocol)
        Parameters:
        manufactureProtocol - The manufactureProtocol to set.

      • setManufacturer

        public void setManufacturer​(String manufacturer)
        Parameters:
        manufacturer - The manufacturer to set.

      • setPlatformData

        public void setPlatformData​(List<List<String>> platformData)
        Parameters:
        platformData - The platformData to set.

      • setPubMedIds

        public void setPubMedIds​(Collection<Integer> pubMedIds)
        Parameters:
        pubMedIds - The pubMedIds to set.

      • setSample

        public void setSample​(String sample)

      • setSupplementaryFile

        public void setSupplementaryFile​(String supplementaryFile)

      • setSupport

        public void setSupport​(String support)
        Parameters:
        support - The support to set.

      • setTechnology

        public void setTechnology​(GeoDataset.PlatformType technology)
        Parameters:
        technology - The technology to set.

      • setUseDataFromGEO

        public void setUseDataFromGEO​(boolean b)
        Normally only set this if "false". Default is true, but will be overridden for certain typs of platforms such as MPSS (rna-seq), SAGE or Exon arrays.
        Parameters:
        b - new value

      • setWebLinks

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

      • useDataFromGeo

        public boolean useDataFromGeo()
        Returns:
        true if the data uses a platform that, generally, we can use the data from, if available. Will be false for MPSS, SAGE and transcript- or exon- level exon array data. Note that sometimes this will result in us not using data that was sort of okay - for example, an alternative CDF/MPS version of an Affy Exon array at the gene level. But we'd want to reanalyze it from the official CDF/MPS anyway.