Examples of Taxon

com.psddev.cms.db.Taxon
mesquite.lib.Taxon
org.cipres.treebase.domain.taxon.Taxon
Taxon.java Created on Feb 14, 2006 @author Jin Ruan

Examples of com.psddev.cms.db.Taxon

            Site site = page.getSite();
            Predicate predicate = search.toQuery(page.getSite()).getPredicate();


            if (!ObjectUtils.isBlank(taxonParentUuid)) {


                Taxon parent = Query.findById(Taxon.class, taxonParentUuid);
                taxonResults = (Collection<Taxon>) Taxon.Static.getChildren(parent, predicate);


                if (site != null && !ObjectUtils.isBlank(taxonResults)) {


                    Collection<Taxon> siteTaxons = new ArrayList<Taxon>();

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Examples of mesquite.lib.Taxon

        }


        // FIXME: instead of using a loop, use one query!
        long[] taxaIDs = t.getTaxaIDs();
        for (int j = 0; j < taxaIDs.length; j++) {
          Taxon taxon = t.getTaxon(j);


          String aLabel = taxon.getName();


          TaxonLabel taxonLabel = getTaxonLabelHome().getByDescriptionAndStudy(
            aLabel,
            pStudy);

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Examples of org.cipres.treebase.domain.taxon.Taxon

  
  /**
   * @author mjd 20081204
   */
  public void testFindStudiesByTaxon() {
    Taxon hSap = findHSapTaxon();
    Collection<Study> studies = getFixture().findStudies(hSap);
    logger.info("Query finished; results = " + studies.size() + " studies");
    
    assertTrue(studies.size() > 0);
    for (Study s : studies) {
      boolean thisStudyOK = false;
      for (TaxonLabelSet tls : s.getTaxonLabelSets()) {
        for (TaxonLabel tl : tls.getTaxonLabelsReadOnly()) {
          if (tl.getTaxonVariant() == null || tl.getTaxonVariant().getTaxon() == null) continue;
          if (tl.getTaxonVariant().getTaxon().getId() == hSap.getId()) {
            thisStudyOK = true;
            break;
          }
          if (thisStudyOK) break;
        }

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Examples of org.cipres.treebase.domain.taxon.Taxon

  
  /**
   * @author mjd 20081204
   */
  public void testFindTreesByTaxon() {
    Taxon hSap = findHSapTaxon();
    Collection<PhyloTree> trees = getFixture().findTrees(hSap);
    logger.info("Query finished; results = " + trees.size() + " studies");
    
    assertTrue(trees.size() > 0);
    for (PhyloTree t : trees) {
      boolean thisTreeOK = false;
      for (TaxonLabel tl : t.getAllTaxonLabels()) {
        if (tl.getTaxonVariant() == null || tl.getTaxonVariant().getTaxon() == null) continue;
        if (tl.getTaxonVariant().getTaxon().getId() == hSap.getId()) {
          thisTreeOK = true;
          break;
        }
      }
      assertTrue(thisTreeOK);

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Examples of org.cipres.treebase.domain.taxon.Taxon

  
  /**
   * @author mjd 20081204
   */
  public void testFindMatricesByTaxon() {
    Taxon hSap = findHSapTaxon();
    Collection<Matrix> matrices = getFixture().findMatrices(hSap);
    logger.info("Query finished; results = " + matrices.size() + " studies");
    
    assertTrue(matrices.size() > 0);
    for (Matrix t : matrices) {
      boolean thisMatrixOK = false;
      for (TaxonLabel tl : t.getAllTaxonLabels()) {
        if (tl.getTaxonVariant() == null || tl.getTaxonVariant().getTaxon() == null) continue;
        if (tl.getTaxonVariant().getTaxon().getId() == hSap.getId()) {
          thisMatrixOK = true;
          break;
        }
      }
      assertTrue(thisMatrixOK);

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Examples of org.cipres.treebase.domain.taxon.Taxon

    assertNotNull(expansion);
    assertEquals(14, expansion.size());
  
    // And each one of those TVs should refer to the same taxon
    for (TaxonVariant tv : expansion) {
      Taxon t = tv.getTaxon();
      assertTrue(t == tvEolphus.getTaxon() || t == tvCacatua.getTaxon());
    }  
    
    // And moreover the call should be idempotent
    // That is, the expansion of the expansion should be the same as

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Examples of org.cipres.treebase.domain.taxon.Taxon

    boolean bad = false;
    MergeDuplicateTaxaInterface me = (MergeDuplicateTaxaInterface) ContextManager.getBean("mergeDuplicateTaxa");


    for (String arg : args) {
      Long tId = Long.parseLong(arg);
      Taxon t = getTaxonHome().findPersistedObjectByID(Taxon.class, tId);
      if (t == null) {
        warn("No taxon with id T" + tId);
        bad = true;
      } else 
        taxonClass.add(t);

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Examples of org.cipres.treebase.domain.taxon.Taxon

    Map<String,Set<Taxon>> taxonClasses = new HashMap<String,Set<Taxon>> ();
    
    warn("Scanning database");
    int taxonCount = 0;
    for (TBPersistable obj : getTaxonHome().findAll(Taxon.class)) {
      Taxon t = (Taxon) obj;
      String key = key(t);
      if (! taxonClasses.containsKey(key)) 
        taxonClasses.put(key, new HashSet<Taxon> ());
      taxonClasses.get(key).add(t);
      taxonCount++;

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Examples of org.cipres.treebase.domain.taxon.Taxon

  /* WARNING: This method should modify the TaxonSet and TaxonLink objects too, but doesn't.
   * At the time it was written, there were no such objects.  20090409 MJD 
   */
  public void doMergeTaxonClass(Set<Taxon> taxonClass) {
    Iterator<Taxon> it = taxonClass.iterator();
    Taxon canonicalTaxon = it.next();
        
    // Find the taxon in the set with the lowest ID number
    while (it.hasNext()) {
      Taxon t = it.next();
      if (t.getId() < canonicalTaxon.getId()) canonicalTaxon = t;
    }
    
    {
      StringBuilder s = new StringBuilder ("Merging taxon class : ");
      for (Taxon t : taxonClass) s.append(t.getId()).append(" ");
      s.append("\n");
      warn(s.toString());
    }
    warn("  Canonical taxon for this set is T" + canonicalTaxon.getId());
    
    // Map all the other taxa to the canonical one
    for (Taxon t : taxonClass) {
      if (t.equals(canonicalTaxon)) continue;
      for (TaxonVariant tv : getTaxonHome().findVariantsByTaxon(t)) {
        tv.setTaxon(canonicalTaxon);  
        getTaxonHome().merge(tv);
      }
      getCurrentSession().flush();

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Examples of org.cipres.treebase.domain.taxon.Taxon

  public void createTaxon(String[] args) {
    String name = args[0];
    Long ubio = Long.decode(args[1]);
    Integer ncbi = Integer.decode(args[2]);


    Taxon t = new Taxon(name, ubio, ncbi);
    getTaxonHome().save(t);
  }

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