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();
}
}
private void execute() {
gResult.clear();
String sCmd = null;
if (4096 <= ifHuge.length()) {
sCmd = ifHuge;
} else {
sCmd = txtCommand.getText();
}
if (sCmd.startsWith("-->>>TEST<<<--")) {
testPerformance();
return;
}
String g[] = new String[1];
try {
lTime = System.currentTimeMillis();
sStatement.execute(sCmd);
int r = sStatement.getUpdateCount();
if (r == -1) {
formatResultSet(sStatement.getResultSet());
} else {
g[0] = "update count";
gResult.setHead(g);
g[0] = "" + r;
gResult.addRow(g);
}
lTime = System.currentTimeMillis() - lTime;
addToRecent(txtCommand.getText());
gResult.fireTableChanged(null);
} catch (SQLException e) {
lTime = System.currentTimeMillis() - lTime;
g[0] = "SQL Error";
gResult.setHead(g);
String s = e.getMessage();
s += " / Error Code: " + e.getErrorCode();
s += " / State: " + e.getSQLState();
g[0] = s;
gResult.addRow(g);
gResult.fireTableChanged(null);
}
updateResult();
System.gc();
}
public void actionPerformed(ActionEvent ev) {
String s = ev.getActionCommand();
if (s == null) {
if (ev.getSource() instanceof JMenuItem) {
JMenuItem i;
s = ((JMenuItem) ev.getSource()).getText();
}
}
/*
// button replace by toolbar
if (s.equals("Execute")) {
execute();
} else
*/
if (s.equals("Exit")) {
windowClosing(null);
} else if (s.equals("Transfer")) {
Transfer.work(null);
} else if (s.equals("Dump")) {
Transfer.work(new String[] {"-d"});
} else if (s.equals("Restore")) {
Transfer.work(new String[] {"-r"});
} else if (s.equals("Logging on")) {
javaSystem.setLogToSystem(true);
} else if (s.equals("Logging off")) {
javaSystem.setLogToSystem(false);
} else if (s.equals("Refresh Tree")) {
refreshTree();
} else if (s.startsWith("#")) {
int i = Integer.parseInt(s.substring(1));
txtCommand.setText(sRecent[i]);
} else if (s.equals("Connect...")) {
connect(ConnectionDialogSwing.createConnection(fMain, "Connect"));
refreshTree();
} else if (s.equals("Results in Grid")) {
iResult = 0;
pResult.removeAll();
pResult.add(gScrollPane, BorderLayout.CENTER);
pResult.doLayout();
gResult.fireTableChanged(null);
pResult.repaint();
} else if (s.equals("Open Script...")) {
JFileChooser f = new JFileChooser(".");
f.setDialogTitle("Open Script...");
// (ulrivo): set default directory if set from command line
if (defDirectory != null) {
f.setCurrentDirectory(new File(defDirectory));
}
int option = f.showOpenDialog(fMain);
if (option == JFileChooser.APPROVE_OPTION) {
File file = f.getSelectedFile();
if (file != null) {
StringBuffer buf = new StringBuffer();
ifHuge = DatabaseManagerCommon.readFile(file.getAbsolutePath());
if (4096 <= ifHuge.length()) {
buf.append("This huge file cannot be edited. Please execute\n");
txtCommand.setText(buf.toString());
} else {
txtCommand.setText(ifHuge);
}
}
}
} else if (s.equals("Save Script...")) {
JFileChooser f = new JFileChooser(".");
f.setDialogTitle("Save Script");
// (ulrivo): set default directory if set from command line
if (defDirectory != null) {
f.setCurrentDirectory(new File(defDirectory));
}
int option = f.showSaveDialog(fMain);
if (option == JFileChooser.APPROVE_OPTION) {
File file = f.getSelectedFile();
if (file != null) {
DatabaseManagerCommon.writeFile(file.getAbsolutePath(), txtCommand.getText());
}
}
} else if (s.equals("Save Result...")) {
JFileChooser f = new JFileChooser(".");
f.setDialogTitle("Save Result...");
// (ulrivo): set default directory if set from command line
if (defDirectory != null) {
f.setCurrentDirectory(new File(defDirectory));
}
int option = f.showSaveDialog(fMain);
if (option == JFileChooser.APPROVE_OPTION) {
File file = f.getSelectedFile();
if (file != null) {
showResultInText();
DatabaseManagerCommon.writeFile(file.getAbsolutePath(), txtResult.getText());
}
}
} else if (s.equals("Results in Text")) {
iResult = 1;
pResult.removeAll();
pResult.add(txtResultScroll, BorderLayout.CENTER);
pResult.doLayout();
showResultInText();
pResult.repaint();
} else if (s.equals("AutoCommit on")) {
try {
cConn.setAutoCommit(true);
} catch (SQLException e) {
}
} else if (s.equals("AutoCommit off")) {
try {
cConn.setAutoCommit(false);
} catch (SQLException e) {
}
} else if (s.equals("Commit")) {
try {
cConn.commit();
} catch (SQLException e) {
}
} else if (s.equals("Insert test data")) {
insertTestData();
} else if (s.equals("Rollback")) {
try {
cConn.rollback();
} catch (SQLException e) {
}
} else if (s.equals("Disable MaxRows")) {
try {
sStatement.setMaxRows(0);
} catch (SQLException e) {
}
} else if (s.equals("Set MaxRows to 100")) {
try {
sStatement.setMaxRows(100);
} catch (SQLException e) {
}
} else if (s.equals("SELECT")) {
showHelp(DatabaseManagerCommon.selectHelp);
} else if (s.equals("INSERT")) {
showHelp(DatabaseManagerCommon.insertHelp);
} else if (s.equals("UPDATE")) {
showHelp(DatabaseManagerCommon.updateHelp);
} else if (s.equals("DELETE")) {
showHelp(DatabaseManagerCommon.deleteHelp);
} else if (s.equals("CREATE TABLE")) {
showHelp(DatabaseManagerCommon.createTableHelp);
} else if (s.equals("DROP TABLE")) {
showHelp(DatabaseManagerCommon.dropTableHelp);
} else if (s.equals("CREATE INDEX")) {
showHelp(DatabaseManagerCommon.createIndexHelp);
} else if (s.equals("DROP INDEX")) {
showHelp(DatabaseManagerCommon.dropIndexHelp);
} else if (s.equals("CHECKPOINT")) {
showHelp(DatabaseManagerCommon.checkpointHelp);
} else if (s.equals("SCRIPT")) {
showHelp(DatabaseManagerCommon.scriptHelp);
} else if (s.equals("SHUTDOWN")) {
showHelp(DatabaseManagerCommon.shutdownHelp);
} else if (s.equals("SET")) {
showHelp(DatabaseManagerCommon.setHelp);
} else if (s.equals("Test Script")) {
showHelp(DatabaseManagerCommon.testHelp);
}
}