Interface GeoConverter

All Superinterfaces:
Converter<GeoData, Identifiable>
All Known Implementing Classes:
GeoConverterImpl
public interface GeoConverter extends Converter<GeoData, Identifiable>
Author:
paul

  • Method Details

    • clear

      void clear()
      Clear the state of the converter.

      Call this prior to starting conversion of a full dataset.

    • convert

      Collection<Identifiable> convert(Collection<? extends GeoData> geoObjects)
      Specified by:
      convert in interface Converter<GeoData, Identifiable>

    • convert

      <T extends Identifiable> Collection<T> convert(Collection<? extends GeoData> geoObjects, Class<T> dataType)
      Convert a collection of GeoData objects, retaining only elements of the specified data type.

    • convert

      Identifiable convert(GeoData geoObject)
      Specified by:
      convert in interface Converter<GeoData, Identifiable>

    • convert

      ArrayDesign convert(GeoPlatform geoPlatform)

    • convert

      Collection<ExpressionExperiment> convert(GeoSeries geoSeries)

    • convert

      Collection<ExpressionExperiment> convert(GeoSeries geoSeries, boolean skipDataVectors)

    • convert

      ExpressionExperiment convert(GeoDataset geoDataset, boolean skipDataVectors)

    • convertSubsetToExperimentalFactor

      void convertSubsetToExperimentalFactor(ExpressionExperiment expExp, GeoSubset geoSubSet)
      Converts Geo subsets to experimental factors. This adds a new factor value to the experimental factor of an experimental design, and adds the factor value to each BioMaterial of a specific BioAssay.
      Parameters:
      expExp - experiment
      geoSubSet - geo subset

    • getPrimaryArrayTaxon

      @Nullable Taxon getPrimaryArrayTaxon(Collection<Taxon> platformTaxa, Collection<String> probeTaxa) throws IllegalArgumentException
      Throws:
      IllegalArgumentException

    • setSplitByPlatform

      void setSplitByPlatform(boolean splitByPlatform)
      Parameters:
      splitByPlatform - If true, and the series uses more than one platform, split it up. This often isn't necessary/desirable. This is overridden if the series uses more than one species, in which case it is always split up.

    • setForceConvertElements

      void setForceConvertElements(boolean forceConvertElements)
      Parameters:
      forceConvertElements - Set the behaviour when a platform that normally would not be loaded in detail is encountered, such as an Exon array.

    • setElementLimitForStrictness

      void setElementLimitForStrictness(int i)
      Parameters:
      i - this is here for tests only. The default value should be okay otherwise.