/**
* 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();
}
/**
* 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();
}
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");
}
}
}