List of addAnalysis() Examples

Examples of addAnalysis()

org.cipres.treebase.domain.study.Study.addAnalysis()
Append a new analysis to the end of the list. Manage bi-directional relationship. Creation date: Feb 22, 2006 12:06:25 PM @param pAnalysis Analysis
ptolemy.actor.Manager.addAnalysis()
Add a static analysis to this manager. A static analysis is simply an object that is recorded in a hash table and cleared at the end of preinitialize(), with no semantics associated with that object. The intent is for that object to serve as a repository for static analysis results, but clearing it and the end of preinitialize isn't quite right. The idea is that it is cleared at a point when the analysis has to be redone after that point. But doing this at the end of preinitialize means this won't work with models that mutate either during preinitialize() (as in higher- order actors) or during execution. @param name The name of the analysis. @param analysis The analysis to record. @see #getAnalysis(String)

Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

    Study s = new Study();
    s.setName(newName);
    s.setStudyStatus(inprogress);
    s.setCitation(c);
    c.setStudy(s);
    s.addAnalysis(a1);
    s.addAnalysis(a2);


    TaxonLabel label = new TaxonLabel();
    label.setTaxonLabel(newName);
    label.setStudy(s);

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

    s.setName(newName);
    s.setStudyStatus(inprogress);
    s.setCitation(c);
    c.setStudy(s);
    s.addAnalysis(a1);
    s.addAnalysis(a2);


    TaxonLabel label = new TaxonLabel();
    label.setTaxonLabel(newName);
    label.setStudy(s);

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

    // s.addAnalysis(a2);


    Analysis updatedA1 = getFixture().update(a1);
    Analysis updatedA2 = getFixture().update(a2);


    s.addAnalysis(updatedA1);
    s.addAnalysis(updatedA2);
    Study updatedS = getFixture().update(s);


    // Note: a1.getID() and a2.getID() will return false.
    logger.info("analysis created: " + a1.getName() + "id = " + updatedA1.getId());

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()


    Analysis updatedA1 = getFixture().update(a1);
    Analysis updatedA2 = getFixture().update(a2);


    s.addAnalysis(updatedA1);
    s.addAnalysis(updatedA2);
    Study updatedS = getFixture().update(s);


    // Note: a1.getID() and a2.getID() will return false.
    logger.info("analysis created: " + a1.getName() + "id = " + updatedA1.getId());
    logger.info("analysis created: " + a2.getName() + "id = " + updatedA2.getId());

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()


    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);
    s.addAnalysis(a1);
    s.addAnalysis(a2);


    getStudyHome().store(s);


    // force commit immeidately, important:

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);
    s.addAnalysis(a1);
    s.addAnalysis(a2);


    getStudyHome().store(s);


    // force commit immeidately, important:
    setComplete();

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

      theAnalysisStep.setSoftwareInfo(theSoftware);
          
      theAnalysisStep.setNotes("Imported from TB1");
      ContextManager.getAnalysisStepService().save(theAnalysisStep);
      
      theStudy.addAnalysis(theAnalysis);
      ContextManager.getStudyService().save(theStudy);
    }


    warn("  Commiting the study (" + theStudy.getId() + ") to the database");
//    t.commit();

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()


    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);
    s.addAnalysis(a1);
    s.addAnalysis(a2);


    getStudyHome().store(s);


    // force commit immediately, important:

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    Analysis a2 = new Analysis();
    a2.setName("2 " + newName);
    s.addAnalysis(a1);
    s.addAnalysis(a2);


    getStudyHome().store(s);


    // force commit immediately, important:
    setComplete();

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Examples of org.cipres.treebase.domain.study.Study.addAnalysis()

    Study s = getTestStudy();
    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);
    AnalysisStep step1 = new AnalysisStep();
    step1.setName("step1 " + newName);
    s.addAnalysis(a1);
    a1.addAnalysisStep(step1);


    AnalyzedTree treeData = new AnalyzedTree();
    treeData.setTree(tree);
    treeData.setInput(Boolean.FALSE);

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