/* Need to special-case some URLs. It's yucky to do this,
* but that's the only way this will work for some of the Drosophila
* result types. The assumption in the code is that there is one URL
* per type, but for us it depends on which database the hit is on. */
protected String getURLPrefix(FeatureProperty prop, SeqFeatureI f, String id) {
String defaultURL = prop.getURLString();
if (!(f instanceof FeaturePair)) return (defaultURL);
FeaturePair fp = (FeaturePair) f;
SeqFeatureI fs = (SeqFeatureI) fp.getRefFeature();
String database = fs.getDatabase();
String url = defaultURL;
/* Here we go--a bunch of special cases.
* It sucks that these are in the code--
* these should be in the style file or something! */
String nucleotide = "nucleotide";
String protein = "protein";
String ENTREZ_N =
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db="
+ nucleotide
+ "&doptcmdl=GenBank&term=";
String ENTREZ_P =
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db="
+ protein
+ "&doptcmdl=GenBank&term=";
// In most cases, the IDs for BLASTX Similarity to Fly seem to work better
// with the default SWALL URL; however, the AA ones seem not to be in SWALL
// and we have to look in Entrez. Yuck.
// if (prop.typeEquals("BLASTX Similarity to Fly") && id.startsWith("AA")) {
if (prop.getDisplayType().startsWith("BLASTX") && id.startsWith("AA")) {
url = ENTREZ_P;
} else if (prop.typeEquals("Rodent") && (database.indexOf("unigene") >= 0)) {
url = ENTREZ_N;
} else if (prop.typeEquals("Insect") && (database.indexOf("dbEST") >= 0)) {
url = ENTREZ_N;
}
// This isn't working right yet. The tRNA ids look like:
// gb|AE002593|AE002593.trna5-ArgTCG
// and we want just the part between the first two ||s.
else {
String acc;
if (prop.typeEquals("tRNA-result") && (database.indexOf("na_tRNA.dros") >= 0)) {
acc = id.substring(id.indexOf("|") + 1);
acc = acc.substring(0, acc.indexOf("|"));
} else if (prop.typeEquals("New Fly Sequence")) {
// These accs look like gi||gb|AY135216|AY135216
acc = id;
if (acc.indexOf("|") >= 0) acc = acc.substring(acc.lastIndexOf("|") + 1);
/* We've already appended the correct acc,
* but the URL constructor will automatically
* slap the uncorrected one at the end.
* The last # is so that when the whole ID is appended at the end, it
* won't have any effect. */
url = ENTREZ_N + acc + "#";
}
}
return url;
}
/** 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;
}