Examples with Protocol ubic.gemma.model.common.protocol.Protocol used on opensource projects

Example 1 with Protocol

use of ubic.gemma.model.common.protocol.Protocol in project Gemma by PavlidisLab.

the class ProtocolDaoImpl method find.

@Override
public Protocol find(Protocol protocol) {
    Criteria queryObject = this.getSessionFactory().getCurrentSession().createCriteria(Protocol.class);
    queryObject.add(Restrictions.eq("name", protocol.getName()));
    if (protocol.getDescription() != null)
        queryObject.add(Restrictions.eq("description", protocol.getDescription()));
    return (Protocol) queryObject.uniqueResult();
}

Example 2 with Protocol

use of ubic.gemma.model.common.protocol.Protocol in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalysisConfig method toAnalysis.

/**
 * @return representation of this analysis with populated protocol holding information from this.
 */
public DifferentialExpressionAnalysis toAnalysis() {
    DifferentialExpressionAnalysis analysis = DifferentialExpressionAnalysis.Factory.newInstance();
    Protocol protocol = Protocol.Factory.newInstance();
    protocol.setName("Differential expression analysis settings");
    protocol.setDescription(this.toString());
    analysis.setProtocol(protocol);
    return analysis;
}

Example 3 with Protocol

use of ubic.gemma.model.common.protocol.Protocol in project Gemma by PavlidisLab.

the class LinkAnalysisConfig method toAnalysis.

/**
 * @return representation of this analysis (not completely filled in - only the basic parameters)
 */
public CoexpressionAnalysis toAnalysis() {
    CoexpressionAnalysis analysis = CoexpressionAnalysis.Factory.newInstance();
    Protocol protocol = Protocol.Factory.newInstance();
    protocol.setName("Link analysis settings");
    protocol.setDescription(this.toString());
    analysis.setProtocol(protocol);
    return analysis;
}

Example 4 with Protocol

use of ubic.gemma.model.common.protocol.Protocol in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method addTestAnalyses.

public void addTestAnalyses(ExpressionExperiment ee) {
    /*
         * Add analyses
         */
    CoexpressionAnalysis pca = CoexpressionAnalysis.Factory.newInstance();
    pca.setName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    pca.setExperimentAnalyzed(ee);
    persisterHelper.persist(pca);
    /*
         * Diff
         */
    DifferentialExpressionAnalysis expressionAnalysis = DifferentialExpressionAnalysis.Factory.newInstance();
    Protocol protocol = Protocol.Factory.newInstance();
    protocol.setName("Differential expression analysis settings");
    protocol.setDescription("qvalue: " + true);
    expressionAnalysis.setProtocol(protocol);
    expressionAnalysis.setExperimentAnalyzed(ee);
    persisterHelper.persist(expressionAnalysis);
}