public IdTouple getIdTouple(String symbol) {
BiologicalEntity entity = guessEntity(symbol);
IdTouple touple = new IdTouple();
if (entity != null) {
touple.gid = entity.getId();
touple.pname = entity.getName();
}
// if (entity != null) {
// touple.pname = guessProtein(entity.getName());
// } else {
// touple.pname = guessProtein(symbol);
// }
return touple;
}
private BiologicalEntity guessEntity(String key) {
String sql;
if (key.endsWith("_HUMAN")) {
sql = "SELECT * FROM proteinGene WHERE pname='" + key + "'";
HashMap<String, String> line = DBUtil.fillFirstRow(sql);
if (line != null) {
BiologicalEntity be = new BiologicalEntity();
be.setId(line.get("geneid"));
be.setId_src(BiologicalEntity.ENTREZ);
be.setType(BiologicalEntity.GENE);
be.setName(key); // line.get("pname"));
return be;
}
}
sql = "SELECT geneid FROM gene WHERE symbol='" + key + "' AND taxid=9606";
String s = DBUtil.querySingle(sql);
if (s != null) {
BiologicalEntity be = new BiologicalEntity();
be.setId(s);
be.setName(key);
be.setId_src(BiologicalEntity.ENTREZ);
be.setType(BiologicalEntity.GENE);
return be;
}
sql =
"SELECT geneid FROM geneAlias, gene WHERE gene.taxid=9606 AND geneAlias.alias='"
+ key
+ "' AND geneAlias.id_list=geneid";
s = DBUtil.querySingle(sql);
if (s != null) {
BiologicalEntity be = new BiologicalEntity();
be.setId(s);
be.setName(key);
be.setId_src(BiologicalEntity.ENTREZ);
be.setType(BiologicalEntity.GENE);
return be;
}
System.err.println("Cannot find an entry for " + key);
return null;
}
