public static String buildQuery(SequenceI seq)
{
- String query = seq.getName();
- StringBuilder queryBuilder = new StringBuilder();
- int count = 0;
+ HashSet<String> seqRefs = new LinkedHashSet<String>();
+ String seqName = seq.getName();
+ String[] names = seqName.toLowerCase().split("\\|");
+ for (String name : names)
+ {
+ System.out.println("Found name : " + name);
+ name.trim();
+ if (isValidSeqName(name))
+ {
+ seqRefs.add(name);
+ }
+ }
if (seq.getPDBId() != null)
{
for (PDBEntry entry : seq.getPDBId())
{
- queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+ seqRefs.add(entry.getId());
}
}
if (seq.getDBRef() != null && seq.getDBRef().length != 0)
{
+ int count = 0;
for (DBRefEntry dbRef : seq.getDBRef())
{
- queryBuilder.append("text:")
- .append(dbRef.getAccessionId().replaceAll("GO:", ""))
- .append(" OR ");
+ seqRefs.add(getDBRefId(dbRef));
++count;
if (count > 10)
{
break;
}
}
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- query = queryBuilder.toString().substring(5, endIndex);
}
+
+ StringBuilder queryBuilder = new StringBuilder();
+ for (String seqRef : seqRefs)
+ {
+ queryBuilder.append("text:").append(seqRef).append(" OR ");
+ }
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ String query = queryBuilder.toString().substring(5, endIndex);
return query;
}
/**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ public static boolean isValidSeqName(String seqName)
+ {
+ String ignoreList = "pdb,uniprot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.equalsIgnoreCase(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ /**
* Filters a given list of discovered structures based on supplied argument
*
* @param fieldToFilterBy