DatabaseDocument.java

    {
      GmodDAO dao;
      DatabaseEntrySource src = new DatabaseEntrySource();
      src.setLocation(true);
      
      if(System.getProperty("ibatis") == null)
        dao = new JdbcDAO(src.getLocation(), src.getPfield()); 
      else
        dao = new IBatisDAO(src.getPfield());
      
      Feature feature = new Feature();
      feature.setUniqueName(args[0]);
      List schemas = new Vector();
      schemas.add(args[1]);
      List featureList = new Vector();
      featureList.add(dao.getFeatureByUniqueName(args[0], "polypeptide")); 
      System.out.println("FINISHED getFeature()");
      for(int i = 0; i < featureList.size(); i++)
      {
        feature = (Feature)featureList.get(i);
        
        String abb  = feature.getOrganism().getAbbreviation();
        String type = feature.getCvTerm().getName();
        int fmin    = feature.getFeatureLoc().getFmin().intValue() + 1;
        int fmax    = feature.getFeatureLoc().getFmax().intValue();
        String featprop = 
          ((FeatureProp)(new Vector(feature.getFeatureProps()).get(0))).getCvTerm().getName();
        
        System.out.print(fmin+".."+fmax);
        System.out.print(" "+type);
        System.out.print(" "+featprop);
        System.out.print(" "+feature.getFeatureLoc().getStrand());
        System.out.print(" "+feature.getUniqueName());
        System.out.print(" "+abb);
        System.out.println(" "+Integer.toString(feature.getFeatureId()));
        
/*      Hashtable synonyms = getAllFeatureSynonyms(dao, null);
        Vector syns = (Vector)synonyms.get(new Integer(feature.getId()));
        for(int j=0; j<syns.size(); j++)
        {
          FeatureSynonym alias = (FeatureSynonym)syns.get(j);
          System.out.print(" "+alias.getSynonym().getCvterm().getName()+
                           "="+alias.getSynonym().getName());
        }*/
        
        System.out.println(" "); 
      }
    }
    catch(SQLException sqle)
    {
      sqle.printStackTrace();
    }
    catch(RuntimeException re)
    {
      re.printStackTrace();
    }
    catch(ConnectException e)
    {
      e.printStackTrace();
    }
  }

  public Document getParent()
  {
    return null;
  }
  
  /**
   * Find from a list the FeatureLoc with a given srcFeature
   * @param locs
   * @param srcfeature_id
   * @return
   */
  public static FeatureLoc getFeatureLoc(List locs, int srcfeature_id)
  {
    for(int i=0; i<locs.size(); i++)
    {
      FeatureLoc loc = (FeatureLoc)locs.get(i);
      if(loc.getFeatureBySrcFeatureId().getFeatureId() == srcfeature_id)
        return loc;
    }
    return null;
  }


  public String getSrcFeatureId()
  {
    return srcFeatureId;
  }


  private JPasswordField getPfield()
  {
    return pfield;
  }


  /**
   * Return true if this looks like a single schema postgres
   * database
   * @return
   */
  public boolean isSingleSchema()
  {
    return singleSchema;
  }
  
  /**
   * Ensure exon featurelocs are in the correct order
   */
  class LocationComarator implements Comparator
  {

    public int compare(Object o1, Object o2)
    {
      int loc1 = ((FeatureLoc)o1).getFmin().intValue();
      int loc2 = ((FeatureLoc)o2).getFmin().intValue();
      
      if(loc2 == loc1)
        return 0;
      int strand = ((FeatureLoc)o1).getStrand().intValue();
      
      if(strand < 0)
      {
        if(loc2 > loc1)
          return 1;
        else
          return -1;
      }
      else
      {
        if(loc2 > loc1)
          return -1;
        else
          return 1;
      }
    } 
  }
  
  class CvTermThread extends Thread 
  {
    private GmodDAO dao;
    CvTermThread(final GmodDAO dao) 
    {
      this.dao = dao;
    }

    public void run() 
    {
      getCvterms(dao);
    }
  }

  public void setRange(Range range)
  {
    this.range = range;
  }


  public Hashtable getIdFeatureStore()
  {
    return idFeatureStore;
  }


  public boolean isLazyFeatureLoad()
  {
    return lazyFeatureLoad;
  }


  public void setLazyFeatureLoad(boolean lazyFeatureLoad)
  {
    this.lazyFeatureLoad = lazyFeatureLoad;
  }
}