/**
* Fills the copyObj with the contents of this object. If deepcopy is true, The associated objects
* are also copied and treated as new objects.
*
* @param copyObj the object to fill.
* @param deepcopy whether the associated objects should be copied.
*/
protected Synonym copyInto(Synonym copyObj, boolean deepcopy) throws TorqueException {
copyObj.setId(id);
copyObj.setKeywords(keywords);
copyObj.setState(state);
copyObj.setId(0);
if (deepcopy) {}
return copyObj;
}
/** For annotations, try to find the appropriate identifier to add to the base URL. */
protected String generateAnnotURL(AnnotatedFeatureI g, String baseAnnotURL) {
if (baseAnnotURL == null || baseAnnotURL.equals("")) return null;
Hashtable id_hash = new Hashtable();
String id;
for (int i = 0; i < g.getDbXrefs().size(); i++) {
DbXref ref = (DbXref) g.getDbXrefs().elementAt(i);
id = ref.getIdValue();
// Apparently, if the id starts with FBan we want to replace "FBan" with "CG".
if (id.startsWith("FBan")) {
id = id.substring("FBan".length());
try {
int cg_num = Integer.parseInt(id);
id = "CG" + cg_num;
id_hash.put(id, id);
} catch (Exception e) {
}
} else if (id.startsWith("FB")) { // FBgn, FBab, etc.
id_hash.put(id, id);
} else if (id.startsWith("TE")) { // FBgn, FBab, etc.
id_hash.put(id, id);
}
}
id = getCG(g.getId(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "CR");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "FB");
if (id != null) id_hash.put(id, id);
}
}
id = getCG(g.getName(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getName(), "CR");
if (id != null) id_hash.put(id, id);
}
for (int i = 0; i < g.getSynonyms().size(); i++) {
Synonym syn = (Synonym) (g.getSynonyms().elementAt(i));
id = getCG(syn.getName(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(syn.getName(), "CR");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "FB");
if (id != null) id_hash.put(id, id);
}
}
}
// The code here was glomming together all the elements into one
// big |ed string, but that's not what the FlyBase annotation report CGI wants.
// An FB or CG or CR identifier should be sufficient.
StringBuffer query_str = new StringBuffer();
for (Enumeration e = id_hash.elements(); e.hasMoreElements(); ) {
String namepart = (String) e.nextElement();
// System.out.println("Considering namepart " + namepart); // DEL
if (namepart.indexOf("FB") == 0
|| namepart.indexOf("CG") == 0
|| namepart.indexOf("CR") == 0) {
if (query_str.length() > 0) query_str.replace(0, query_str.length(), namepart);
else query_str.append(namepart);
break;
}
if (query_str.length() > 0) query_str.append('|');
query_str.append(namepart);
}
// if not FlyBase ID, use the annotation's regular ID
if (query_str.length() == 0) {
query_str.append(g.getId());
}
String url = null;
// System.out.println("generateAnnotUrl: query = " + query_str); // DEL
if (query_str.length() > 0) {
// if a custom URL is setup for this type in the tiers file, use that - otherwise use the
// global
// one setup in the style file
FeatureProperty fp = Config.getPropertyScheme().getFeatureProperty(g.getTopLevelType());
if (fp.getURLString() != null && fp.getURLString().length() > 0) {
url = fp.getURLString() + g.getId();
} else {
url = baseAnnotURL + query_str.toString();
}
}
return url;
}
