public Collection<Experiment> findExpts(CellLine cells, ExptCondition cond) throws SQLException {
LinkedList<Integer> dbids = new LinkedList<Integer>();
String tables = "experiment e";
if (genome != null) {
tables += ", probe_platform_to_genome p2g";
}
String query = "select e.id from " + tables;
Vector<String> conds = new Vector<String>();
if (genome != null) {
int gid = genome.getDBID();
conds.add("e.platform=p2g.platform and p2g.genome=" + gid);
}
if (cells != null) {
conds.add("e.cells=" + cells.getDBID());
}
if (cond != null) {
conds.add("e.condition=" + cond.getDBID());
}
for (int i = 0; i < conds.size(); i++) {
if (i == 0) {
query += " where ";
} else {
query += " and ";
}
query += conds.get(i);
}
System.out.println("Final Query: \"" + query + "\"");
java.sql.Connection cxn = loader.getConnection();
Statement s = cxn.createStatement();
ResultSet rs = s.executeQuery(query);
while (rs.next()) {
int dbid = rs.getInt(1);
dbids.addLast(dbid);
}
rs.close();
s.close();
Collection<Experiment> expts = loader.loadExperiments(dbids);
return expts;
}
public CellLine getCells(Experiment expt) throws SQLException, UnknownRoleException {
java.sql.Connection cxn = loader.getConnection();
PreparedStatement ps = cxn.prepareStatement("select cells from experiment" + " where id=?");
ps.setInt(1, expt.getDBID());
ResultSet rs = ps.executeQuery();
int cellsID = -1;
if (rs.next()) {
cellsID = rs.getInt(1);
}
rs.close();
ps.close();
return chipLoader.loadCellLine(cellsID);
}