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 OrthologyPair(ResultSet rs, OrthologyLoader loader) throws NotFoundException {
try {
dbid = rs.getInt(1);
int mappingID = rs.getInt(2);
mapping = loader.loadMapping(mappingID);
name1 = rs.getString(3);
int gid1 = rs.getInt(4);
name2 = rs.getString(5);
int gid2 = rs.getInt(6);
genome1 = Organism.findGenome(gid1);
genome2 = Organism.findGenome(gid2);
} catch (SQLException se) {
throw new DatabaseException("Error: " + se.getMessage(), se);
}
}