public void run(String[] args) {
DatabaseFactory factory = new DatabaseFactory();
if (System.getProperty("user.dir").isEmpty()) {
System.out.println("user.dir is incorrect");
}
if (System.getProperty("fizteh.db.dir").isEmpty()) {
System.out.println("fizteh.db.dir is incorrect");
}
Path pathDirection =
Paths.get(System.getProperty("user.dir")).resolve(System.getProperty("fizteh.db.dir"));
String dir = pathDirection.toString();
DatabaseProvider dProvider = factory.create(dir);
if (args.length == 0) {
interactiveMode(dProvider);
} else {
pocketMode(args, dProvider);
}
}
/* takes the two experiment ids for which to retrieve data.
*/
public PairedSQLData(int one, int two) throws SQLException {
exptone = one;
expttwo = two;
try {
corecxn = DatabaseFactory.getConnection("core");
} catch (UnknownRoleException ex) {
throw new DatabaseException("Couldn't connect with role core", ex);
} catch (SQLException ex) {
throw new DatabaseException("Couldn't connect to database for role core", ex);
}
try {
chipcxn = DatabaseFactory.getConnection("chipchip");
basicstmt =
chipcxn.prepareStatement(
"select a.channelone, a.channeltwo, a.ratio, b.channelone, b.channeltwo, b.ratio "
+ " from data a, data b where a.probe = b.probe and a.experiment = ? and "
+ " b.experiment = ?");
samplestmt =
chipcxn.prepareStatement(
"select * from (select a.channelone, a.channeltwo, a.ratio, b.channelone, b.channeltwo, b.ratio, dbms_random.value as randval "
+ " from data a, data b where a.probe = b.probe and a.experiment = ? and "
+ " b.experiment = ? order by dbms_random.value) where randval < ?");
limitstmt =
chipcxn.prepareStatement(
"select aone, atwo, arat, bone, btwo, brat from (select a.channelone aone, a.channeltwo atwo, a.ratio arat, b.channelone bone, b.channeltwo btwo, b.ratio brat "
+ " from data a, data b where a.probe = b.probe and a.experiment = ? and "
+ " b.experiment = ? order by dbms_random.value) where rownum < ?");
} catch (UnknownRoleException ex) {
throw new DatabaseException("Couldn't connect with role chipchip", ex);
} catch (SQLException ex) {
throw new DatabaseException("Couldn't connect to database for role chipchip", ex);
}
}
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 void close() {
try {
basicstmt.close();
DatabaseFactory.freeConnection(corecxn);
DatabaseFactory.freeConnection(chipcxn);
corecxn = null;
chipcxn = null;
basicstmt = null;
} catch (SQLException e) {
throw new DatabaseException(e.toString(), e);
}
}
