public ExptLocatorTree(Genome g) {
super();
try {
java.sql.Connection c = DatabaseFactory.getConnection(ExptLocator.dbRole);
int species = g.getSpeciesDBID();
int genome = g.getDBID();
Statement s = c.createStatement();
ResultSet rs = null;
rs =
s.executeQuery(
"select e.name, e.version from experiment e, exptToGenome eg where e.active=1 and "
+ "e.id=eg.experiment and eg.genome="
+ genome);
while (rs.next()) {
String name = rs.getString(1);
String version = rs.getString(2);
ChipChipLocator loc = new ChipChipLocator(g, name, version);
this.addElement(loc.getTreeAddr(), loc);
}
rs.close();
rs =
s.executeQuery(
"select ra.name, ra.version from rosettaanalysis ra, rosettaToGenome rg where "
+ "ra.id = rg.analysis and ra.active=1 and rg.genome="
+ genome);
while (rs.next()) {
String name = rs.getString(1);
String version = rs.getString(2);
MSPLocator msp = new MSPLocator(g, name, version);
this.addElement(msp.getTreeAddr(), msp);
}
rs.close();
rs =
s.executeQuery(
"select ra.name, ra.version from bayesanalysis ra, bayesToGenome rg where "
+ "ra.id = rg.analysis and ra.active=1 and rg.genome="
+ genome);
while (rs.next()) {
String name2 = rs.getString(1);
String version2 = rs.getString(2);
ExptLocator loc2 = new BayesLocator(g, name2, version2);
addElement(loc2.getTreeAddr(), loc2);
}
rs.close();
s.close();
DatabaseFactory.freeConnection(c);
} catch (SQLException se) {
se.printStackTrace(System.err);
throw new RuntimeException(se);
} catch (UnknownRoleException e) {
e.printStackTrace();
}
}
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);
}