Esempio n. 1
0
  /**
   * For a collection of items return the count of given class name.
   *
   * @param items the Item collection to count
   * @return the count for a given classname in the collection
   */
  public static int countItemByClass(Collection<Item> items, String className) {
    Map<String, List> counts = new TreeMap<String, List>();
    for (Item item : items) {
      List<String> clsItems = counts.get(item.getClassName());
      if (clsItems == null) {
        clsItems = new ArrayList<String>();
        counts.put(item.getClassName(), clsItems);
      }
      clsItems.add(item.getIdentifier());
    }

    return counts.get(className).size();
  }
Esempio n. 2
0
  /**
   * For a collection of items return a string containing counts of each item classname - useful for
   * degugging tests.
   *
   * @param items the Item collection to count
   * @return a formatted string with counts for each classname in the collection
   */
  public static String countItemClasses(Collection<Item> items) {
    Map<String, List> counts = new TreeMap<String, List>();
    for (Item item : items) {
      List<String> clsItems = counts.get(item.getClassName());
      if (clsItems == null) {
        clsItems = new ArrayList<String>();
        counts.put(item.getClassName(), clsItems);
      }
      clsItems.add(item.getIdentifier());
    }

    StringBuffer sb = new StringBuffer();
    for (Map.Entry<String, List> entry : counts.entrySet()) {
      sb.append(entry.getKey() + " - " + entry.getValue().size() + " " + entry.getValue() + ENDL);
    }
    return sb.toString();
  }
Esempio n. 3
0
 private void setRefsAndCollections(List<String> parents, Item feature) {
   String clsName = feature.getClassName();
   Map<String, String> refsAndCollections = handler.getRefsAndCollections();
   if (refsAndCollections != null
       && refsAndCollections.containsKey(clsName)
       && parents != null
       && !parents.isEmpty()) {
     ClassDescriptor cld =
         tgtModel.getClassDescriptorByName(tgtModel.getPackageName() + "." + clsName);
     String refName = refsAndCollections.get(clsName);
     Iterator<String> parentIter = parents.iterator();
     if (cld.getReferenceDescriptorByName(refName, true) != null) {
       String parent = parentIter.next();
       feature.setReference(refName, getRefId(parent));
       if (parentIter.hasNext()) {
         String primaryIdent = feature.getAttribute("primaryIdentifier").getValue();
         throw new RuntimeException(
             "Feature has multiple relations for reference: "
                 + refName
                 + " for feature: "
                 + feature.getClassName()
                 + ", "
                 + feature.getIdentifier()
                 + ", "
                 + primaryIdent);
       }
     } else if (cld.getCollectionDescriptorByName(refName, true) != null) {
       List<String> refIds = new ArrayList<String>();
       while (parentIter.hasNext()) {
         refIds.add(getRefId(parentIter.next()));
       }
       feature.setCollection(refName, refIds);
     } else if (parentIter.hasNext()) {
       throw new RuntimeException(
           "No '"
               + refName
               + "' reference/collection found in "
               + "class: "
               + clsName
               + " - is map configured correctly?");
     }
   }
 }
    /*    @Override necessary */
    public void process(GFF3Record record) {
        Item feature = getFeature();
	
        String clsName = feature.getClassName();
	
        if ("Gene".equals(clsName)) {
            // move Gene.primaryIdentifier to Gene.secondaryIdentifier
            // move Gene.symbol to Gene.primaryIdentifier
	    
            if (feature.getAttribute("primaryIdentifier") != null) {
                String secondary = feature.getAttribute("primaryIdentifier").getValue();
                feature.setAttribute("secondaryIdentifier", secondary);
            }
            if (feature.getAttribute("symbol") != null) {
                String primary = feature.getAttribute("symbol").getValue();
                feature.setAttribute("primaryIdentifier", primary);
                feature.removeAttribute("symbol");
            }
        }
    }