Examples of TBPersistable

org.cipres.treebase.domain.TBPersistable
A tagging interface for all persisted treebase objects. Created on Sep 27, 2005 @author Jin Ruan

Examples of org.cipres.treebase.domain.TBPersistable

            request.setAttribute("hasNeXML", true);
            request.setAttribute("hasRdf", true);
          }
          phyloWSPath = new PhyloWSPath(theClass.getPackage(),namespacedGUID);
          
          TBPersistable theObject = getStudyService().findByID(theClass, treebaseIDString.getId());
          if ( null != theObject ) {
            Study theContainingStudy = theObject.getStudy();
            if (null != theContainingStudy && ! theContainingStudy.isPublished()) {
                  response.setContentType("text/plain");
                  response.setStatus(HttpServletResponse.SC_SEE_OTHER);        
                  response.setHeader("Location", "/treebase-web/accessviolation.html");
                  return null;

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Examples of org.cipres.treebase.domain.TBPersistable

   * @param pID
   * @return
   */
  public TBPersistable loadObject(Class pClass, Long pID) {


    TBPersistable obj = null;
    try {
      obj = (TBPersistable) hibernateTemplate.load(pClass, pID);
    } catch (DataAccessException ex) {
      obj = null;
    }

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Examples of org.cipres.treebase.domain.TBPersistable

   * @param prefix - a prefix as defined by TreebaseIDString 
   * @param objects - a set of TBPersistable objects, one of which has a matching id
   * @return the TBPersistable object whose prefix + primary key == id
   */
  private TBPersistable findEquivalentObject(String id,String prefix,Set<?> objects) {
    TBPersistable result = null;
    for ( Object oObject : objects ) {
      TBPersistable object = (TBPersistable)oObject; 
      if ( id.equals(prefix + object.getId()) ) {
        result = object;
        break;
      }
    }
    Assert.assertNotNull("Found object with id "+id, result);

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Examples of org.cipres.treebase.domain.TBPersistable

      sr = initialSearchResults();
    } 
    else if (sr.hasResultsList()) {
      Object[] resultsArray = ((Set<TBPersistable>)((SearchResults)sr).getResults()).toArray();
      REFINE: for ( int i = 0; i < resultsArray.length; i++ ) {
        TBPersistable refineCandidate = (TBPersistable)resultsArray[i];  
        if ( selectedItems != null ) {
          for ( int j = 0; j < selectedItems.length; j++ ) {
            Long id = Long.parseLong(selectedItems[j]);
            if ( id.compareTo(refineCandidate.getId()) == 0 ) {
              LOGGER.debug("Keeping result "+refineCandidate.getId());
              continue REFINE;
            }
          }
        }
        LOGGER.debug("Removing result "+refineCandidate.getId());
        sr.getResults().remove(refineCandidate);
      }
      sr.announceSize(LOGGER);
      AbstractService service = getSearchService().getAppropriateService(sr);
      service.resurrectAll(sr.getResults());

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Examples of org.cipres.treebase.domain.TBPersistable

  }
  
  public Collection<? extends TBPersistable> doSearchByIDString(HttpServletRequest req, 
      AbstractService service, Class expectedClass, String idString) {
    Collection<TBPersistable> matches = new ArrayList<TBPersistable> ();
    TBPersistable t;
    try {
      TreebaseIDString ids = new TreebaseIDString(idString, expectedClass);
      if (ids.getTBClass() != expectedClass) {
        String expectedPrefix = TreebaseIDString.getPrefixForClass(expectedClass);
        addMessage(req, "ID number '" + idString + "' is not valid; try " + expectedPrefix + "#### or just ####");

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