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:

Serialized Form

Constructor Summary

Constructors
Constructor Description

GeoPlatform()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addToColumnData(String columnName, String value)`	Add a value to a column.
`void`	`addToDescription(String s)`
`void`	`addToOrganisms(String org)`
`static String`	`alternativeToProperAffyPlatform(String geoPlatformId)`
`Collection<String>`	`getCatalogNumbers()`
`String`	`getCoating()`
`List<String>`	`getColumnData(String columnName)`
`List<List<String>>`	`getColumnData(Collection<String> columnNames)`
`Collection<String>`	`getContributer()`
`String`	`getDescription()`
`String`	`getDescriptions()`
`Collection<String>`	`getDesignElements()`
`String`	`getDistribution()`
`String`	`getId()`
`String`	`getIdColumnName()`
`String`	`getLastUpdateDate()`
`String`	`getManufactureProtocol()`
`String`	`getManufacturer()`
`Collection<String>`	`getOrganisms()`
`List<List<String>>`	`getPlatformData()`
`Map<String,List<String>>`	`getPlatformInformation()`
`Map<String,String>`	`getProbeNamesInGemma()`
`Collection<Integer>`	`getPubMedIds()`
`String`	`getSample()`
`String`	`getStatus()`
`String`	`getSubmissionDate()`
`String`	`getSupplementaryFile()`
`String`	`getSupport()`
`GeoDataset.PlatformType`	`getTechnology()`
`String`	`getWebLink()`
`Collection<String>`	`getWebLinks()`
`static boolean`	`isAffymetrixExonArray(String geoPlatformId)`
`static boolean`	`isAffyPlatform(String geoPlatformId)`
`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.
`boolean`	`isUseDataFromGEO()`
`void`	`setCatalogNumbers(Collection<String> catalogNumbers)`
`void`	`setCoating(String coating)`
`void`	`setContributer(Collection<String> contributer)`
`void`	`setDescription(String description)`
`void`	`setDistribution(String distribution)`
`void`	`setId(String id)`
`void`	`setLastUpdateDate(String lastUpdateDate)`
`void`	`setManufactureProtocol(String manufactureProtocol)`
`void`	`setManufacturer(String manufacturer)`
`void`	`setOrganisms(Collection<String> organism)`
`void`	`setPlatformData(List<List<String>> platformData)`
`void`	`setPubMedIds(Collection<Integer> pubMedIds)`
`void`	`setSample(String sample)`
`void`	`setStatus(String status)`
`void`	`setSubmissionDate(String submissionDate)`
`void`	`setSupplementaryFile(String supplementaryFile)`
`void`	`setSupport(String support)`
`void`	`setTechnology(GeoDataset.PlatformType technology)`
`void`	`setUseDataFromGEO(boolean b)`	Normally only set this if "false".
`void`	`setWebLink(String webLink)`
`void`	`setWebLinks(Collection<String> webLinks)`
`boolean`	`useDataFromGeo()`

Methods inherited from class ubic.gemma.core.loader.expression.geo.model.GeoData
addColumnName, equals, getColumnDescriptions, getColumnNames, getContact, getGeoAccession, getTitle, hashCode, setGeoAccession, setTitle, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- 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)
```
  - 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.

Class GeoPlatform

Constructor Summary

Method Summary

Methods inherited from class ubic.gemma.core.loader.expression.geo.model.GeoData

Methods inherited from class java.lang.Object

Constructor Detail

GeoPlatform

Method Detail

isAffymetrixExonArray

alternativeToProperAffyPlatform

isAffyPlatform

isGEOAffyDataUsable

getId

setId

getStatus

setStatus

getSubmissionDate

setSubmissionDate

getWebLink

setWebLink

getPlatformInformation

isUseDataFromGEO

addToColumnData

addToDescription

addToOrganisms

getCatalogNumbers

getCoating

getColumnData

getColumnData

getContributer

getDescription

getDescriptions

getDesignElements

getDistribution

getIdColumnName

getLastUpdateDate

getManufactureProtocol

getManufacturer

getOrganisms

getPlatformData

getProbeNamesInGemma

getPubMedIds

getSample

getSupplementaryFile

getSupport

getTechnology

getWebLinks

setCatalogNumbers

setCoating

setContributer

setDescription

setDistribution

setLastUpdateDate

setManufactureProtocol

setManufacturer

setOrganisms

setPlatformData

setPubMedIds

setSample

setSupplementaryFile

setSupport

setTechnology

setUseDataFromGEO

setWebLinks

useDataFromGeo