Examples with PlatformType ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType used on opensource projects

Example 1 with PlatformType

use of ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType in project Gemma by PavlidisLab.

the class GeoConverterImpl method createMinimalArrayDesign.

private ArrayDesign createMinimalArrayDesign(GeoPlatform platform) {
    ArrayDesign arrayDesign = ArrayDesign.Factory.newInstance();
    arrayDesign.setName(platform.getTitle());
    arrayDesign.setShortName(platform.getGeoAccession());
    arrayDesign.setDescription(platform.getDescriptions());
    PlatformType technology = platform.getTechnology();
    if (technology == PlatformType.dualChannel || technology == PlatformType.dualChannelGenomic || technology == PlatformType.spottedOligonucleotide || technology == PlatformType.spottedDNAOrcDNA) {
        arrayDesign.setTechnologyType(TechnologyType.TWOCOLOR);
    } else if (technology == PlatformType.singleChannel || technology == PlatformType.oligonucleotideBeads || technology == PlatformType.inSituOligonucleotide) {
        arrayDesign.setTechnologyType(TechnologyType.ONECOLOR);
    } else if (technology == null) {
        GeoConverterImpl.log.warn("No technology type available for " + platform + ", provisionally setting to 'dual mode'");
        arrayDesign.setTechnologyType(TechnologyType.DUALMODE);
    } else if (technology.equals(PlatformType.MPSS)) {
        // we don't support this directly
        arrayDesign.setTechnologyType(TechnologyType.NONE);
    } else if (technology.equals(PlatformType.SAGE) || technology.equals(PlatformType.SAGENlaIII) || technology.equals(PlatformType.SAGERsaI) || technology.equals(PlatformType.SAGESau3A) || technology.equals(PlatformType.other)) {
        // we don't support this directly
        arrayDesign.setTechnologyType(TechnologyType.NONE);
    } else {
        throw new IllegalArgumentException("Don't know how to interpret technology type " + technology);
    }
    return arrayDesign;
}