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

Class GeoPlatform

java.lang.Object
ubic.gemma.core.loader.expression.geo.model.GeoData
ubic.gemma.core.loader.expression.geo.model.GeoPlatform
All Implemented Interfaces:
Serializable
public class GeoPlatform extends GeoData
Bean describing a microarray platform in GEO
Author:
pavlidis
See Also:

  • Constructor Details

    • GeoPlatform

      public GeoPlatform()

  • Method Details

    • 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)

    • getPlatformInformation

      public Map<String,List<String>> getPlatformInformation()

    • 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

    • getColumnData

      public List<String> getColumnData(String columnName)

    • 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.

    • getDesignElements

      public Collection<String> getDesignElements()

    • 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.

    • getTechnology

      public GeoDataset.PlatformType getTechnology()
      Returns:
      Returns the technology.

    • 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.

    • setOrganisms

      public void setOrganisms(Collection<String> organism)

    • 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.