public void excluir(Oriundo oriundo) throws SQLException {
Connection con =
DriverManager.getConnection(
new conexao().url,
new conexao().config.getString("usuario"),
new conexao().config.getString("senha"));
PreparedStatement ps = null;
String sqlExcluir = "DELETE FROM oriundo WHERE codigo=?";
try {
ps = con.prepareStatement(sqlExcluir);
ps.setInt(1, oriundo.getCodigo());
ps.executeUpdate();
JOptionPane.showMessageDialog(
null, "Ecluido Com Sucesso: ", "Mensagem do Sistema - Excluir", 1);
} catch (NumberFormatException e) {
JOptionPane.showMessageDialog(
null, "NumberFormaterExeption Erro: " + e.getMessage(), "ClasseDAO Func.Excluir", 0);
e.printStackTrace();
} catch (NullPointerException e) {
JOptionPane.showMessageDialog(
null, "NullPointerException Erro: " + e.getMessage(), "ClasseDAO Func. Excluir", 0);
e.printStackTrace();
} catch (SQLException e) {
JOptionPane.showMessageDialog(
null, "SQLException Erro: " + e.getMessage(), "ClasseDAO Func. Excluir", 0);
e.printStackTrace();
} catch (Exception e) {
JOptionPane.showMessageDialog(
null, "Exception Erro: " + e.getMessage(), "ClasseDAO Func. Excluir", 0);
e.printStackTrace();
} finally {
ps.close();
con.close();
}
}
private boolean einlesen() {
int eingabefaktor;
// Faktor
try {
eingabefaktor = Integer.parseInt(feldFaktor.getText());
if (eingabefaktor < 0) {
System.out.println("Faktor < 0");
feldFaktor.selectAll();
return false;
}
} catch (NumberFormatException e) {
System.out.println(e.toString());
feldFaktor.selectAll();
return false;
}
faktor = eingabefaktor;
// Ist die Checkbox angekreuzt?
NUREINSCHRITT = checkbox_nureinSchritt.isSelected();
AUCHSTRAGEGIE2 = checkbox_auchStrategie2.isSelected();
return true;
}
/**
* read the transition matrix from the file
*
* @param fp
* @return
*/
public static Map<Integer, Set<Integer>> readTransitionMatrix(String fp) {
Map<Integer, Set<Integer>> res = new HashMap<Integer, Set<Integer>>();
if (fp == null || fp.length() == 0) return res;
try {
BufferedReader reader =
new BufferedReader(new InputStreamReader(new FileInputStream(new File(fp))));
String line = null;
while ((line = reader.readLine()) != null) {
String[] fields = line.split(" ");
int from = Integer.parseInt(fields[0]);
int to = Integer.parseInt(fields[1]);
if (res.containsKey(from)) {
res.get(from).add(to);
} else {
Set<Integer> cset = new HashSet<Integer>();
cset.add(to);
res.put(from, cset);
}
}
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (NumberFormatException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
return Collections.unmodifiableMap(res);
}
/**
* Analyze the command line options to extract the optional specified strategy and debug level.
*
* @param args options to analyze
*/
private static void analyzeArguments(String args[]) {
int size = args.length;
for (int i = 0; i < size; i++) {
if (args[i].equals("-s")) {
i++;
if (i >= size || args[i].charAt(0) == '-') {
stopError("Missing strategy after '-s'. May be one of:\n" + allStrategies());
} else {
Class strat = allStrategies.get(args[i]);
if (strat == null) {
stopError(
"Unknown strategy '" + args[i] + "'. It should be one of:\n" + allStrategies());
} else {
strategyTag = args[i];
}
}
} else if (args[i].equals("-v")) {
int verb = 1;
i++;
if (i < size && args[i].charAt(0) != '-') {
try {
verb = Integer.decode(args[i]);
} catch (NumberFormatException ex) {
stopError("Non valid verbose level: " + ex.getMessage());
}
}
setVerboseLevel(verb);
} else {
stopError("Unknown argument: " + args[i]);
}
}
}
public static boolean isNumber(String n) {
try {
double d = Double.valueOf(n).doubleValue();
return true;
} catch (NumberFormatException e) {
e.printStackTrace();
return false;
}
}
public static int parseInteger(String s) {
try {
return (Integer.parseInt(s));
} catch (NumberFormatException ex) {
JOptionPane.showMessageDialog(
null, ex.getMessage(), "Invalid number", JOptionPane.ERROR_MESSAGE);
return (-1);
}
}
/**
* Return a integer parsed from the value associated with the given key, or "def" in key wasn't
* found.
*/
public static int parseProperty(Properties preferences, String key, int def) {
String val = preferences.getProperty(key);
if (val == null) return def;
try {
return Integer.parseInt(val);
} catch (NumberFormatException nfe) {
nfe.printStackTrace();
return def;
}
}
public int getInt(String paramName, int defaultInt) {
try {
String temp = getString(paramName);
if (temp == null) return defaultInt;
else return Integer.parseInt(temp);
} catch (NumberFormatException e) {
e.printStackTrace();
}
return 0;
}
public boolean getBoolean(String paramName, boolean defaultBoolean) {
try {
String temp = getString(paramName);
if (temp == null) return defaultBoolean;
else return Boolean.valueOf(temp).booleanValue();
} catch (NumberFormatException e) {
e.printStackTrace();
}
return false;
}
/**
* Returns the editted value.
*
* @return the editted value.
* @throws TagFormatException if the tag value cannot be retrieved with the expected type.
*/
public TagValue getTagValue() throws TagFormatException {
try {
long numer = Long.parseLong(m_numer.getText());
long denom = Long.parseLong(m_denom.getText());
Rational rational = new Rational(numer, denom);
return new TagValue(m_value.getTag(), rational);
} catch (NumberFormatException e) {
e.printStackTrace();
throw new TagFormatException(
m_numer.getText() + "/" + m_denom.getText() + " is not a valid rational");
}
}
@Override
public Optional<Integer> getInt(String elementKey) {
ConfigElement element = elements.get(elementKey);
if (element == null || isNullOrEmpty(element.getValue())) {
return Optional.absent();
}
try {
return Optional.of(Integer.parseInt(element.getValue()));
} catch (NumberFormatException e) {
throw new RuntimeException(
"can't access " + element + " as int" + " (parse exception " + e.getMessage() + ")");
}
}
public static void main(String[] args) {
int myPeerID;
actualPeerProcess pp;
try {
myPeerID = Integer.parseInt(args[0]);
} catch (NumberFormatException exp) {
System.out.println("Exception converting string in main" + exp.getMessage());
return;
}
pp = new actualPeerProcess(myPeerID);
return;
}
private double calcMean(
HashMap<Integer, String> singleGeneCaseValueMap,
String groupType,
String profileStableId) { // group type: altered or unaltered
switch (groupType) {
case "altered":
int _index_altered = 0;
double[] alteredArray = new double[alteredSampleIds.size()];
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
alteredArray[_index_altered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
alteredArray[_index_altered] =
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_altered += 1;
}
}
return StatUtils.mean(alteredArray);
case "unaltered":
int _index_unaltered = 0;
double[] unalteredArray = new double[unalteredSampleIds.size()];
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
unalteredArray[_index_unaltered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
unalteredArray[_index_unaltered] =
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_unaltered += 1;
}
}
return StatUtils.mean(unalteredArray);
default:
return Double.NaN; // error
}
}
public List<Oriundo> listar() throws SQLException {
List<Oriundo> resultado = new ArrayList<Oriundo>();
conexao propCon = new conexao();
Connection con =
DriverManager.getConnection(
new conexao().url,
propCon.config.getString("usuario"),
propCon.config.getString("senha"));
PreparedStatement ps = null;
ResultSet rs = null;
String sqlListar = "SELECT * FROM oriundo Order by codigo DESC";
Oriundo oriundo;
try {
ps = con.prepareStatement(sqlListar);
rs = ps.executeQuery();
// if(rs==null){
// return null;
// }
while (rs.next()) {
oriundo = new Oriundo();
oriundo.setCodigo(rs.getInt("codigo"));
oriundo.setDescricao(rs.getString("descricao"));
oriundo.setData_cadastro(rs.getDate("data_cadastro"));
oriundo.setDia_fechamento(rs.getInt("dia_fechamento"));
oriundo.setDia_pag(rs.getInt("dia_pag"));
resultado.add(oriundo);
}
} catch (NumberFormatException e) {
JOptionPane.showMessageDialog(
null, "NumberFormaterExeption Erro: " + e.getMessage(), "ClasseDAO Func.Localizar", 0);
e.printStackTrace();
} catch (NullPointerException e) {
JOptionPane.showMessageDialog(
null, "NullPointerException Erro: " + e.getMessage(), "ClasseDAO Func. Localizar", 0);
e.printStackTrace();
} catch (SQLException e) {
JOptionPane.showMessageDialog(
null, "SQLException Erro: " + e.getMessage(), "ClasseDAO Func. Localizar", 0);
e.printStackTrace();
} catch (Exception e) {
JOptionPane.showMessageDialog(
null, "Exception Erro: " + e.getMessage(), "ClasseDAO Func. Localizar", 0);
e.printStackTrace();
} finally {
ps.close();
con.close();
}
return resultado;
}
private void feldFaktorActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_feldFaktorActionPerformed
try {
int eingabefaktor = Integer.parseInt(feldFaktor.getText());
if (eingabefaktor < 0) {
System.out.println("Faktor < 0");
feldFaktor.setSelectionStart(0);
feldFaktor.setSelectionEnd(feldFaktor.getText().length());
}
} catch (NumberFormatException e) {
System.out.println(e.toString());
feldFaktor.setSelectionStart(0);
feldFaktor.setSelectionEnd(feldFaktor.getText().length());
}
} // GEN-LAST:event_feldFaktorActionPerformed
/**
* Eclipse compiler hopefully only uses println(String).
*
* <p>{@inheritDoc}
*/
public void println(String x) {
if (x.startsWith("[completed ")) {
int pos = x.lastIndexOf("#");
int endpos = x.lastIndexOf("/");
String fileno_str = x.substring(pos + 1, endpos - pos - 1);
try {
int fileno = Integer.parseInt(fileno_str);
this.listener.progress(fileno, x);
} catch (NumberFormatException _nfe) {
Debug.log("could not parse eclipse compiler output: '" + x + "': " + _nfe.getMessage());
}
}
super.println(x);
}
public void message(String s) {
if (firstLine == null) firstLine = s;
else {
StringTokenizer st = new StringTokenizer(s, " ");
try {
st.nextToken();
st.nextToken();
st.nextToken();
size = (new Integer(st.nextToken().trim())).longValue();
} catch (NoSuchElementException e) {
exception = new RunnerException(e.toString());
} catch (NumberFormatException e) {
exception = new RunnerException(e.toString());
}
}
}
/**
* This method gets called when a property we're interested in is about to change. In case we
* don't like the new value we throw a PropertyVetoException to prevent the actual change from
* happening.
*
* @param evt a <tt>PropertyChangeEvent</tt> object describing the event source and the property
* that will change.
* @exception PropertyVetoException if we don't want the change to happen.
*/
public void vetoableChange(PropertyChangeEvent evt) throws PropertyVetoException {
if (evt.getPropertyName().equals(PROP_STUN_SERVER_ADDRESS)) {
// make sure that we have a valid fqdn or ip address.
// null or empty port is ok since it implies turning STUN off.
if (evt.getNewValue() == null) return;
String host = evt.getNewValue().toString();
if (host.trim().length() == 0) return;
boolean ipv6Expected = false;
if (host.charAt(0) == '[') {
// This is supposed to be an IPv6 litteral
if (host.length() > 2 && host.charAt(host.length() - 1) == ']') {
host = host.substring(1, host.length() - 1);
ipv6Expected = true;
} else {
// This was supposed to be a IPv6 address, but it's not!
throw new PropertyVetoException("Invalid address string" + host, evt);
}
}
for (int i = 0; i < host.length(); i++) {
char c = host.charAt(i);
if (Character.isLetterOrDigit(c)) continue;
if ((c != '.' && c != ':') || (c == '.' && ipv6Expected) || (c == ':' && !ipv6Expected))
throw new PropertyVetoException(host + " is not a valid address nor host name", evt);
}
} // is prop_stun_server_address
else if (evt.getPropertyName().equals(PROP_STUN_SERVER_PORT)) {
// null or empty port is ok since it implies turning STUN off.
if (evt.getNewValue() == null) return;
String port = evt.getNewValue().toString();
if (port.trim().length() == 0) return;
try {
Integer.valueOf(evt.getNewValue().toString());
} catch (NumberFormatException ex) {
throw new PropertyVetoException(port + " is not a valid port! " + ex.getMessage(), evt);
}
}
}
private double runTTest(HashMap<Integer, String> singleGeneCaseValueMap, String profileStableId)
throws IllegalArgumentException {
double[] unalteredArray = new double[unalteredSampleIds.size()];
double[] alteredArray = new double[alteredSampleIds.size()];
int _index_unaltered = 0, _index_altered = 0;
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
alteredArray[_index_altered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
alteredArray[_index_altered] =
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_altered += 1;
}
}
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
unalteredArray[_index_unaltered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
unalteredArray[_index_unaltered] =
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_unaltered += 1;
}
}
if (alteredArray.length < 2 || unalteredArray.length < 2) return Double.NaN;
else {
double pvalue = TestUtils.tTest(alteredArray, unalteredArray);
return pvalue;
}
}
public Oriundo localizar(Integer codigo) throws SQLException {
Connection con =
DriverManager.getConnection(
new conexao().url,
new conexao().config.getString("usuario"),
new conexao().config.getString("senha"));
PreparedStatement ps = null;
ResultSet rs = null;
String sqlLocalizar = "SELECT * FROM oriundo WHERE codigo=?";
Oriundo oriundo = new Oriundo();
try {
ps = con.prepareStatement(sqlLocalizar);
ps.setInt(1, codigo);
rs = ps.executeQuery();
// if(!rs.next()){
// return null;
// }
oriundo.setCodigo(rs.getInt("codigo"));
oriundo.setDescricao(rs.getString("descricao"));
oriundo.setData_cadastro(rs.getDate("data_cadastro"));
oriundo.setDia_fechamento(rs.getInt("dia_fechamento"));
oriundo.setDia_pag(rs.getInt("dia_pag"));
return oriundo;
} catch (NumberFormatException e) {
JOptionPane.showMessageDialog(
null, "NumberFormaterExeption Erro: " + e.getMessage(), "ClasseDAO Func.Localizar", 0);
e.printStackTrace();
} catch (NullPointerException e) {
JOptionPane.showMessageDialog(
null, "NullPointerException Erro: " + e.getMessage(), "ClasseDAO Func. Localizar", 0);
e.printStackTrace();
} catch (SQLException e) {
JOptionPane.showMessageDialog(
null, "SQLException Erro: " + e.getMessage(), "ClasseDAO Func. Localizar", 0);
e.printStackTrace();
} catch (Exception e) {
JOptionPane.showMessageDialog(
null, "Exception Erro: " + e.getMessage(), "ClasseDAO Func. Localizar", 0);
e.printStackTrace();
} finally {
ps.close();
con.close();
}
return oriundo;
}
private double calcSTDev(
HashMap<Integer, String> singleGeneCaseValueMap, String groupType, String profileStableId) {
switch (groupType) {
case "altered":
DescriptiveStatistics stats_altered = new DescriptiveStatistics();
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_altered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_altered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_altered.getStandardDeviation();
case "unaltered":
DescriptiveStatistics stats_unaltered = new DescriptiveStatistics();
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_unaltered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_unaltered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_unaltered.getStandardDeviation();
default:
return Double.NaN; // error
}
}
public List<Object> readExcel(Workbook wb, Class clz, int readLine, int tailLine) {
Sheet sheet = wb.getSheetAt(0); // 取第一张表
List<Object> objs = null;
try {
Row row = sheet.getRow(readLine); // 开始行，主题栏
objs = new ArrayList<Object>();
Map<Integer, String> maps = getHeaderMap(row, clz); // 设定对应的字段顺序与方法名
if (maps == null || maps.size() <= 0)
throw new RuntimeException("要读取的Excel的格式不正确，检查是否设定了合适的行"); // 与order顺序不符
for (int i = readLine + 1; i <= sheet.getLastRowNum() - tailLine; i++) { // 取数据
row = sheet.getRow(i);
Object obj = clz.newInstance(); // 调用无参结构
for (Cell c : row) {
int ci = c.getColumnIndex();
String mn = maps.get(ci).substring(3); // 消除get
mn = mn.substring(0, 1).toLowerCase() + mn.substring(1);
Map<String, Object> params = new HashMap<String, Object>();
if (!"enterDate".equals(mn)) c.setCellType(Cell.CELL_TYPE_STRING); // 设置单元格格式
else c.setCellType(Cell.CELL_TYPE_NUMERIC);
if (this.getCellValue(c).trim().equals("是")) {
BeanUtils.copyProperty(obj, mn, 1);
} else if (this.getCellValue(c).trim().equals("否")) {
BeanUtils.copyProperty(obj, mn, 0);
} else BeanUtils.copyProperty(obj, mn, this.getCellValue(c));
}
objs.add(obj);
}
} catch (InstantiationException e) {
e.printStackTrace();
logger.error(e);
} catch (IllegalAccessException e) {
e.printStackTrace();
logger.error(e);
} catch (InvocationTargetException e) {
e.printStackTrace();
logger.error(e);
} catch (NumberFormatException e) {
e.printStackTrace();
logger.error(e);
}
return objs;
}
private void processFrames(Element element) {
NodeList elements = element.getChildNodes();
if (elements.getLength() > 0) {
Map<String, ReferenceFrame> frames = new HashMap();
for (ReferenceFrame f : FrameManager.getFrames()) {
frames.put(f.getName(), f);
}
List<ReferenceFrame> reorderedFrames = new ArrayList();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equalsIgnoreCase(SessionElement.FRAME.getText())) {
String frameName = getAttribute((Element) childNode, SessionAttribute.NAME.getText());
ReferenceFrame f = frames.get(frameName);
if (f != null) {
reorderedFrames.add(f);
try {
String chr = getAttribute((Element) childNode, SessionAttribute.CHR.getText());
final String startString =
getAttribute((Element) childNode, SessionAttribute.START.getText())
.replace(",", "");
final String endString =
getAttribute((Element) childNode, SessionAttribute.END.getText())
.replace(",", "");
int start = ParsingUtils.parseInt(startString);
int end = ParsingUtils.parseInt(endString);
org.broad.igv.feature.Locus locus = new Locus(chr, start, end);
f.jumpTo(locus);
} catch (NumberFormatException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings |
// File Templates.
}
}
}
}
if (reorderedFrames.size() > 0) {
FrameManager.setFrames(reorderedFrames);
}
}
IGV.getInstance().resetFrames();
}
/**
* @return a double parsed from the value associated with the given key in the given Properties.
* returns "def" in key wasn't found, or if a parsing error occured. If "value" contains a "%"
* sign, we use a <code>NumberFormat.getPercentInstance</code> to convert it to a double.
*/
public static double parseProperty(Properties preferences, String key, double def) {
NumberFormat formatPercent = NumberFormat.getPercentInstance(Locale.US); // for zoom factor
String val = preferences.getProperty(key);
if (val == null) return def;
if (val.indexOf("%") == -1) { // not in percent format !
try {
return Double.parseDouble(val);
} catch (NumberFormatException nfe) {
nfe.printStackTrace();
return def;
}
}
// else it's a percent format -> parse it
try {
Number n = formatPercent.parse(val);
return n.doubleValue();
} catch (ParseException ex) {
ex.printStackTrace();
return def;
}
}
public void atualizar(Oriundo oriundo) throws SQLException {
Connection con =
DriverManager.getConnection(
new conexao().url,
new conexao().config.getString("usuario"),
new conexao().config.getString("senha"));
PreparedStatement ps = null;
String sqlAtualizar =
"UPDATE oriundo SET descricao=?, data_cadastro=?, dia_fechamento=?, dia_pag=? WHERE codigo=?";
try {
ps = con.prepareStatement(sqlAtualizar);
ps.setString(1, oriundo.getDescricao());
ps.setDate(2, oriundo.getData_cadastro());
ps.setInt(3, oriundo.getDia_fechamento());
ps.setInt(4, oriundo.getDia_pag());
ps.setInt(5, oriundo.getCodigo());
ps.executeUpdate();
JOptionPane.showMessageDialog(
null, "Atualizado Com Sucesso: ", "Mensagem do Sistema - Atualizar", 1);
} catch (NumberFormatException e) {
JOptionPane.showMessageDialog(
null, "NumberFormaterExeption Erro: " + e.getMessage(), "ClasseDAO Func.Atualizar", 0);
e.printStackTrace();
} catch (NullPointerException e) {
JOptionPane.showMessageDialog(
null, "NullPointerException Erro: " + e.getMessage(), "ClasseDAO Func. Atualizar", 0);
e.printStackTrace();
} catch (SQLException e) {
JOptionPane.showMessageDialog(
null, "SQLException Erro: " + e.getMessage(), "ClasseDAO Func. Atualizar", 0);
e.printStackTrace();
} catch (Exception e) {
JOptionPane.showMessageDialog(
null, "Exception Erro: " + e.getMessage(), "ClasseDAO Func. Atualizar", 0);
e.printStackTrace();
} finally {
ps.close();
con.close();
}
}
public void salvar(Oriundo oriundo) throws SQLException {
Connection con =
DriverManager.getConnection(
new conexao().url,
new conexao().config.getString("usuario"),
new conexao().config.getString("senha"));
PreparedStatement ps = null;
String sqlSalvar =
"INSERT INTO oriundo (descricao, data_cadastro, dia_fechamento, dia_pag ) VALUES (?, ?, ?, ?)";
try {
ps = con.prepareStatement(sqlSalvar);
ps.setString(1, oriundo.getDescricao());
ps.setDate(2, oriundo.getData_cadastro());
ps.setInt(3, oriundo.getDia_fechamento());
ps.setInt(4, oriundo.getDia_pag());
ps.executeUpdate();
// JOptionPane.showMessageDialog(null, "Inserido Com Sucesso: ", "Mensagem do Sistema -
// Salvar", 1);
} catch (NumberFormatException e) {
JOptionPane.showMessageDialog(
null, "NumberFormaterExeption Erro: " + e.getMessage(), "ClasseDAO Func.Salvar", 0);
e.printStackTrace();
} catch (NullPointerException e) {
JOptionPane.showMessageDialog(
null, "NullPointerException Erro: " + e.getMessage(), "ClasseDAO Func. Salvar", 0);
e.printStackTrace();
} catch (SQLException e) {
JOptionPane.showMessageDialog(
null, "SQLException Erro: " + e.getMessage(), "ClasseDAO Func. Salvar", 0);
e.printStackTrace();
} catch (Exception e) {
JOptionPane.showMessageDialog(
null, "Exception Erro: " + e.getMessage(), "ClasseDAO Func. Salvar", 0);
e.printStackTrace();
} finally {
ps.close();
con.close();
}
}
protected void getDimensionsFromLogFile(BufferedReader reader, PicText text) {
if (reader == null) {
return;
}
String line = ""; // il rale si j'initialise pas ...
boolean finished = false;
while (!finished) {
try {
line = reader.readLine();
} catch (IOException ioex) {
ioex.printStackTrace();
return;
}
if (line == null) {
System.out.println("Size of text not found in log file...");
return;
}
System.out.println(line);
Matcher matcher = LogFilePattern.matcher(line);
if (line != null && matcher.find()) {
System.out.println("FOUND :" + line);
finished = true;
try {
text.setDimensions(
0.3515 * Double.parseDouble(matcher.group(1)), // height, pt->mm (1pt=0.3515 mm)
0.3515 * Double.parseDouble(matcher.group(2)), // width
0.3515 * Double.parseDouble(matcher.group(3))); // depth
areDimensionsComputed = true;
} catch (NumberFormatException e) {
System.out.println("Logfile number format problem: $line" + e.getMessage());
} catch (IndexOutOfBoundsException e) {
System.out.println("Logfile regexp problem: $line" + e.getMessage());
}
}
}
return;
}
public static Dice parse(String dt) {
Dice ret = null;
try {
dt = dt.toUpperCase();
String[] diceparts = dt.split(DICE_TOKEN_S);
if (diceparts.length == 2) {
int nThrows = Integer.valueOf(diceparts[0]), nFaces = 0, modifier = 0;
String nFacesBld = "";
OperatorType opType = null;
char[] faceParts = diceparts[1].toCharArray();
for (char c : faceParts) {
String current = String.valueOf(c);
if (Utils.isInteger(current)) {
nFacesBld = nFacesBld.concat(current);
} else if ((opType = OperatorType.parseOperator(c)) != null) {
break;
} else {
break;
}
}
nFaces = Integer.valueOf(nFacesBld);
if (opType != null) {
String[] bonusParts = diceparts[1].split(opType.toEscapedString());
if ((bonusParts.length == 2) && Utils.isInteger(bonusParts[1])) {
modifier = Integer.valueOf(bonusParts[1]);
}
ret = new Dice(nThrows, nFaces, opType, modifier);
} else {
ret = new Dice(nThrows, nFaces);
}
}
} catch (NumberFormatException e) {
e.printStackTrace();
ret = null;
}
return ret;
}
public static double TCSValue(
int[][] alignmentInstance, AlignmentMaker am, Configuration config) {
String filename =
config.temporaryFileDirectory
+ "tmp"
+ alignmentInstance.hashCode()
+ "_"
+ am.hashCode()
+ "_"
+ config.hashCode()
+ "_"
+ am.in.hashCode();
int oldVerbosity = am.in.verbosity;
am.in.verbosity = -1;
am.printOutput(alignmentInstance, filename);
am.in.verbosity = oldVerbosity;
String command =
config.tcoffeeDirectory
+ "t_coffee -infile "
+ filename
+ " -evaluate -method proba_pair -output score_ascii -outfile=stdout";
String result = "-1";
try {
result = execCmd(command);
execCmd("rm " + filename);
} catch (NumberFormatException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// System.err.println("Command: \""+command+"\"\nPre Parse Line: \""+result+"\"");
return Double.parseDouble(result) / 100.0;
}
public VirtualMachine attach(Map arguments)
throws IOException, IllegalConnectorArgumentsException {
int pid = 0;
try {
pid = Integer.parseInt(argument(ARG_PID, arguments).value());
} catch (NumberFormatException nfe) {
throw (IllegalConnectorArgumentsException)
new IllegalConnectorArgumentsException(nfe.getMessage(), ARG_PID).initCause(nfe);
}
checkProcessAttach(pid);
VirtualMachine myVM = null;
try {
try {
Class vmImplClass = loadVirtualMachineImplClass();
myVM = createVirtualMachine(vmImplClass, pid);
} catch (InvocationTargetException ite) {
Class vmImplClass = handleVMVersionMismatch(ite);
if (vmImplClass != null) {
return createVirtualMachine(vmImplClass, pid);
} else {
throw ite;
}
}
} catch (Exception ee) {
if (DEBUG) {
System.out.println("VirtualMachineImpl() got an exception:");
ee.printStackTrace();
System.out.println("pid = " + pid);
}
throw (IOException) new IOException().initCause(ee);
}
setVMDisposeObserver(myVM);
return myVM;
}