List of usage examples for java.awt GridBagConstraints HORIZONTAL
int HORIZONTAL
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From source file:interfaces.InterfazPrincipal.java
private void botonBuscarClienteCrearFacturaActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_botonBuscarClienteCrearFacturaActionPerformed String nombre = nombreClienteCrearFactura.getText(); String identificacion = IdentificacionClienteBuscarFactura.getText(); ControladorCliente controladorCliente = new ControladorCliente(); try {//from ww w . j a v a 2 s. c o m int id = 0; if (!identificacion.equals("")) { id = Integer.parseInt(identificacion); } ArrayList<Cliente> listaClientes = controladorCliente.obtenerClientes(nombre, id); if (listaClientes.isEmpty()) { mensajesBusquedaClientesFactura.setText("La busqueda no arrojo resultados"); return; } final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Buscar clientes"); dialogoEditar.setSize(600, 310); dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel editarTextoPrincipalDialogo = new JLabel("Buscar Cliente"); c.gridx = 0; c.gridy = 0; c.gridwidth = 4; c.insets = new Insets(15, 200, 40, 0); c.ipadx = 100; Font textoGrande = new Font("Arial", 1, 18); editarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(editarTextoPrincipalDialogo, c); /*Vector col = new Vector(); col.add("1"); col.add("2"); col.add("3"); col.add("4"); Vector row = new Vector(); for (int i = 0; i < listaClientes.size(); i++) { Cliente cliente = listaClientes.get(i); Vector temp = new Vector(); temp.add((i + 1) + ""); temp.add(cliente.getNombre()); temp.add(cliente.getCliente_id() + ""); temp.add(cliente.getMonto_prestamo() + ""); System.out.println("info" + cliente.getNombre() + "," + cliente.getMonto_prestamo()); row.add(temp); } final JTable table = new JTable(row, col); */ final JTable table = new JTable(); DefaultTableModel modeloTabla = new DefaultTableModel() { @Override public boolean isCellEditable(int row, int column) { //all cells false return false; } }; ; modeloTabla.addColumn("Numero"); modeloTabla.addColumn("Identificacin"); modeloTabla.addColumn("Nombre"); modeloTabla.addColumn("Monto Prestamo"); //LLenar tabla for (int i = 0; i < listaClientes.size(); i++) { Object[] data = { "1", "2", "3", "4" }; data[0] = (i + 1); data[1] = listaClientes.get(i).getCliente_id(); data[2] = listaClientes.get(i).getNombre(); data[3] = listaClientes.get(i).getMonto_prestamo(); modeloTabla.addRow(data); } table.setModel(modeloTabla); table.getColumn("Numero").setMinWidth(50); table.getColumn("Identificacin").setMinWidth(50); table.getColumn("Nombre").setMinWidth(110); table.getColumn("Monto Prestamo").setMinWidth(110); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); JScrollPane scroll = new JScrollPane(table); scroll.setPreferredSize(new Dimension(320, 150)); table.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent e) { jTextField_Factura_Cliente_Id.setText(table.getValueAt(table.getSelectedRow(), 1).toString()); String identificacion = table.getValueAt(table.getSelectedRow(), 3).toString(); ControladorFlujoFactura controladorFlujoFactura = new ControladorFlujoFactura(); //SELECT * FROM Flujo_Factura where factura_id in (select factura_id from Factura where cliente_id = 1130614506); ArrayList<String[]> flujosCliente = controladorFlujoFactura.getTodosFlujo_Factura( " where factura_id in (select factura_id from Factura where cliente_id = " + String.valueOf(identificacion) + " and estado=\"fiado\") order by factura_id"); double pago = 0.0; for (int i = 0; i < flujosCliente.size(); i++) { String[] datos = flujosCliente.get(i); Object[] rowData = { datos[1], datos[2], datos[3], datos[4] }; if (datos[2].equals("deuda")) { pago += Double.parseDouble(datos[4]); } else { pago -= Double.parseDouble(datos[4]); } } nombreClienteCrearFactura.setText(table.getValueAt(table.getSelectedRow(), 2).toString()); IdentificacionClienteBuscarFactura .setText(table.getValueAt(table.getSelectedRow(), 1).toString()); double montoPrestamo = Double .parseDouble(table.getValueAt(table.getSelectedRow(), 3).toString()); Double totalDisponible = montoPrestamo - pago; valorActualPrestamo.setText(String.valueOf(totalDisponible)); //System.out.println(table.getValueAt(table.getSelectedRow(), 3).toString()); botonAgregarProducto.setEnabled(true); botonGuardarFactura.setEnabled(true); botonEstablecerMontoFactura.setEnabled(true); dialogoEditar.dispose(); } }); c.insets = new Insets(0, 5, 10, 0); c.gridx = 0; c.gridy = 1; c.gridwidth = 1; c.ipadx = 200; //panelDialogo.add(table, c); panelDialogo.add(scroll, c); dialogoEditar.add(panelDialogo); dialogoEditar.setVisible(true); } catch (Exception e) { mensajesBusquedaClientesFactura.setText("La identificacion debe ser un numero"); } }
From source file:interfaces.InterfazPrincipal.java
private void TablaDeFacturaProductoMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_TablaDeFacturaProductoMouseClicked final int fila = TablaDeFacturaProducto.getSelectedRow(); final DefaultTableModel modeloTabla = (DefaultTableModel) TablaDeFacturaProducto.getModel(); //int identificacion = (int) TablaDeFacturaProducto.getValueAt(fila, 0); // TODO add your handling code here: final JDialog dialogoEdicionProducto = new JDialog(this); dialogoEdicionProducto.setTitle("Editar producto"); dialogoEdicionProducto.setSize(250, 150); dialogoEdicionProducto.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel editarTextoPrincipalDialogo = new JLabel("Editar producto"); c.gridx = 0;//from w w w. j a v a 2 s . com c.gridy = 0; c.gridwidth = 3; c.insets = new Insets(15, 40, 10, 0); Font textoGrande = new Font("Arial", 1, 18); editarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(editarTextoPrincipalDialogo, c); c.insets = new Insets(0, 0, 0, 0); c.gridwidth = 0; c.gridy = 1; c.gridx = 0; JLabel textoUnidades = new JLabel("Unidades"); panelDialogo.add(textoUnidades, c); c.gridy = 1; c.gridx = 1; c.gridwidth = 2; final JTextField valorUnidades = new JTextField(); valorUnidades.setText(String.valueOf(modeloTabla.getValueAt(fila, 4))); panelDialogo.add(valorUnidades, c); c.gridwidth = 1; c.gridy = 2; c.gridx = 0; JButton guardarCambios = new JButton("Guardar"); panelDialogo.add(guardarCambios, c); c.gridy = 2; c.gridx = 1; JButton eliminarProducto = new JButton("Eliminar"); panelDialogo.add(eliminarProducto, c); c.gridy = 2; c.gridx = 2; JButton botonCancelar = new JButton("Cerrar"); panelDialogo.add(botonCancelar, c); botonCancelar.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { dialogoEdicionProducto.dispose(); } }); eliminarProducto.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { double precio = (double) modeloTabla.getValueAt(fila, 6); double precioActual = Double.parseDouble(valorActualFactura.getText()); precioActual -= precio; valorActualFactura.setText(String.valueOf(precioActual)); modeloTabla.removeRow(fila); dialogoEdicionProducto.dispose(); } }); guardarCambios.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { try { int numeroUnidades = Integer.parseInt(valorUnidades.getText()); modeloTabla.setValueAt(numeroUnidades, fila, 4); double precioARestar = (double) modeloTabla.getValueAt(fila, 6); double valorUnitario = Double.parseDouble((String) modeloTabla.getValueAt(fila, 5)); double precioNuevo = valorUnitario * numeroUnidades; modeloTabla.setValueAt(precioNuevo, fila, 6); double precioActual = Double.parseDouble(valorActualFactura.getText()); precioActual -= precioARestar; precioActual += precioNuevo; valorActualFactura.setText(String.valueOf(precioActual)); dialogoEdicionProducto.dispose(); } catch (Exception eve) { JOptionPane.showMessageDialog(dialogoEdicionProducto, "Por favor ingrese un valor numrico"); } } }); dialogoEdicionProducto.add(panelDialogo); dialogoEdicionProducto.setVisible(true); }
From source file:interfaces.InterfazPrincipal.java
private void botonAgregarProductoActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_botonAgregarProductoActionPerformed String nombre = jTextField_Factura_Producto_Nombre.getText(); String descripcion = jTextField_Factura_Producto_Descripcion.getText(); ControladorProducto controladorPro = new ControladorProducto(); String restriccion = ""; boolean encounter = true; if (!nombre.equals("")) { if (encounter) { encounter = false;/*from w w w . ja va 2 s. c o m*/ restriccion = " where "; } else { restriccion += " OR "; } restriccion += " nombre like '%" + nombre + "%'"; } if (!descripcion.equals("")) { if (encounter) { encounter = false; restriccion = " where "; } else { restriccion += " OR "; } restriccion += " descripcion like '%" + descripcion + "%'"; } ArrayList<Productos> listaDeProductos = controladorPro.getProducto(restriccion); final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Buscar clientes"); dialogoEditar.setSize(600, 310); dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel editarTextoPrincipalDialogo = new JLabel("Buscar Producto"); c.gridx = 0; c.gridy = 0; c.gridwidth = 6; c.insets = new Insets(15, 200, 40, 0); c.ipadx = 100; Font textoGrande = new Font("Arial", 1, 18); editarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(editarTextoPrincipalDialogo, c); final JTable table = new JTable(); DefaultTableModel modeloTabla = new DefaultTableModel() { @Override public boolean isCellEditable(int row, int column) { //all cells false return false; } }; ; modeloTabla.addColumn("Numero"); modeloTabla.addColumn("Identificacin"); modeloTabla.addColumn("Nombre"); modeloTabla.addColumn("Descripcion"); modeloTabla.addColumn("Unidades Disponibles"); modeloTabla.addColumn("Precio"); //LLenar tabla for (int i = 0; i < listaDeProductos.size(); i++) { Object[] data = { "1", "2", "3", "4", "5", "6" }; data[0] = (i + 1); data[1] = listaDeProductos.get(i).getProductoId(); data[2] = listaDeProductos.get(i).getNombre(); data[3] = listaDeProductos.get(i).getDescripcion(); data[4] = listaDeProductos.get(i).getUnidadesDisponibles(); data[5] = listaDeProductos.get(i).getPrecio(); modeloTabla.addRow(data); } table.setModel(modeloTabla); table.getColumn("Numero").setMinWidth(50); table.getColumn("Identificacin").setMinWidth(50); table.getColumn("Nombre").setMinWidth(110); table.getColumn("Descripcion").setMinWidth(110); table.getColumn("Unidades Disponibles").setMinWidth(40); table.getColumn("Precio").setMinWidth(110); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); JScrollPane scroll = new JScrollPane(table); scroll.setPreferredSize(new Dimension(320, 150)); //final JTable table = new JTable(row, col); table.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent e) { //jTextField_Factura_Cliente_Id.setText(table.getValueAt(table.getSelectedRow(), 1).toString()); //System.out.println(table.getValueAt(table.getSelectedRow(), 3).toString()); DefaultTableModel modelo = (DefaultTableModel) TablaDeFacturaProducto.getModel(); Object[] fila = new Object[7]; fila[0] = table.getValueAt(table.getSelectedRow(), 0).toString(); fila[1] = table.getValueAt(table.getSelectedRow(), 1).toString(); fila[2] = table.getValueAt(table.getSelectedRow(), 2).toString(); fila[3] = table.getValueAt(table.getSelectedRow(), 3).toString(); //fila[4] = table.getValueAt(table.getSelectedRow(), 4).toString(); fila[4] = (String) JOptionPane.showInputDialog("Ingrese el nmero de unidades que va a vender"); fila[5] = table.getValueAt(table.getSelectedRow(), 5).toString(); Double valorProducto = Double.parseDouble((String) fila[5]); String valorActualProducto = String.valueOf(Double.parseDouble(valorActualFactura.getText()) + Double.parseDouble((String) fila[4]) * valorProducto); valorActualFactura.setText(valorActualProducto); fila[6] = Double.parseDouble((String) fila[4]) * valorProducto; modelo.addRow(fila); //modelo.getColumnName(4). /*TablaDeFacturaProducto.setModel(modelo); TablaDeFacturaProducto.getColumnClass(4). ;*/ dialogoEditar.dispose(); } }); c.insets = new Insets(0, 5, 10, 0); c.gridx = 0; c.gridy = 1; c.gridwidth = 1; c.ipadx = 200; panelDialogo.add(scroll, c); //panelDialogo.add(table, c); dialogoEditar.add(panelDialogo); dialogoEditar.setVisible(true); }
From source file:interfaces.InterfazPrincipal.java
private void TablaDeClientesMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_TablaDeClientesMouseClicked // TODO add your handling code here: int fila = TablaDeClientes.getSelectedRow(); int identificacion = (int) TablaDeClientes.getValueAt(fila, 0); final ControladorCliente controladorCliente = new ControladorCliente(); ArrayList<Cliente> listaClientes = controladorCliente.obtenerClientes("", identificacion); final Cliente clienteActual = listaClientes.get(0); final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Editar clientes"); dialogoEditar.setSize(600, 310);//from w ww. java2s . c om dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel editarTextoPrincipalDialogo = new JLabel("Editar clientes"); c.gridx = 0; c.gridy = 0; c.gridwidth = 4; c.insets = new Insets(15, 200, 40, 0); c.ipadx = 100; Font textoGrande = new Font("Arial", 1, 18); editarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(editarTextoPrincipalDialogo, c); c.insets = new Insets(0, 5, 10, 0); c.gridx = 0; c.gridy = 1; c.gridwidth = 1; c.ipadx = 40; JLabel editarNombreClienteDialogo = new JLabel("Nombre:"); panelDialogo.add(editarNombreClienteDialogo, c); c.gridx = 1; c.gridy = 1; c.gridwidth = 1; c.ipadx = 100; c.insets = new Insets(0, 15, 10, 15); final JTextField valorEditarNombreClienteDialogo = new JTextField(); valorEditarNombreClienteDialogo.setText(clienteActual.getNombre()); panelDialogo.add(valorEditarNombreClienteDialogo, c); c.gridx = 0; c.gridy = 2; c.gridwidth = 1; c.ipadx = 40; c.insets = new Insets(0, 5, 10, 0); JLabel editarCelularClienteDialogo = new JLabel("Celular:"); panelDialogo.add(editarCelularClienteDialogo, c); c.gridx = 1; c.gridy = 2; c.gridwidth = 1; c.ipadx = 100; c.insets = new Insets(0, 15, 10, 15); final JTextField valorEditarCelularClienteDialogo = new JTextField(); valorEditarCelularClienteDialogo.setText(clienteActual.getNumero_celular()); panelDialogo.add(valorEditarCelularClienteDialogo, c); c.gridx = 2; c.gridy = 2; c.gridwidth = 1; c.ipadx = 40; c.insets = new Insets(0, 5, 10, 0); JLabel editarMontoClienteDialogo = new JLabel("Monto a prestar:"); panelDialogo.add(editarMontoClienteDialogo, c); c.gridx = 3; c.gridy = 2; c.gridwidth = 1; c.ipadx = 100; c.insets = new Insets(0, 15, 10, 15); final JTextField valorEditarMontoClienteDialogo = new JTextField(); valorEditarMontoClienteDialogo.setText(String.valueOf(clienteActual.getMonto_prestamo())); panelDialogo.add(valorEditarMontoClienteDialogo, c); c.gridx = 2; c.gridy = 1; c.gridwidth = 1; c.ipadx = 40; c.insets = new Insets(0, 15, 10, 0); JLabel editarTelefonoClienteDialogo = new JLabel("Telefono:"); panelDialogo.add(editarTelefonoClienteDialogo, c); c.gridx = 3; c.gridy = 1; c.gridwidth = 1; c.ipadx = 100; c.insets = new Insets(0, 0, 10, 0); final JTextField valorEditarTelefonoClienteDialogo = new JTextField(); valorEditarTelefonoClienteDialogo.setText(clienteActual.getNumero_telefono()); panelDialogo.add(valorEditarTelefonoClienteDialogo, c); c.gridx = 0; c.gridy = 3; c.gridwidth = 1; c.ipadx = 40; c.insets = new Insets(0, 0, 10, 0); JLabel editarAddressClienteDialogo = new JLabel("Direccin:"); panelDialogo.add(editarAddressClienteDialogo, c); c.gridx = 1; c.gridy = 3; c.gridwidth = 3; c.ipadx = 400; c.insets = new Insets(0, 15, 10, 0); final JTextField valorEditarAddressClienteDialogo = new JTextField(); valorEditarAddressClienteDialogo.setText(clienteActual.getDireccion()); panelDialogo.add(valorEditarAddressClienteDialogo, c); c.gridx = 0; c.gridy = 4; c.gridwidth = 2; c.ipadx = 100; c.insets = new Insets(15, 40, 0, 0); JButton botonGuardarClienteDialogo = new JButton("Guardar"); panelDialogo.add(botonGuardarClienteDialogo, c); c.gridx = 2; c.gridy = 4; c.gridwidth = 2; c.insets = new Insets(15, 40, 0, 0); c.ipadx = 100; JButton botonCerrarClienteDialogo = new JButton("Cancelar"); panelDialogo.add(botonCerrarClienteDialogo, c); dialogoEditar.add(panelDialogo); botonCerrarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { dialogoEditar.dispose(); } }); botonGuardarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { try { clienteActual.setDireccion(valorEditarAddressClienteDialogo.getText()); clienteActual.setMonto_prestamo(Double.parseDouble(valorEditarMontoClienteDialogo.getText())); clienteActual.setNombre(valorEditarNombreClienteDialogo.getText()); clienteActual.setNumero_celular(valorEditarCelularClienteDialogo.getText()); clienteActual.setNumero_telefono(valorEditarTelefonoClienteDialogo.getText()); controladorCliente.editarCliente(clienteActual); JOptionPane.showMessageDialog(dialogoEditar, "Se ha editado el cliente xitosamente"); dialogoEditar.dispose(); //Refrescar busqueda actual String nombreCliente = nombreClienteBusqueda.getText(); int identificacionClienteInt = 0; ControladorCliente controladorCliente = new ControladorCliente(); ArrayList<Cliente> listaDeClientes = controladorCliente.obtenerClientes(nombreCliente, identificacionClienteInt); //Agregar filas DefaultTableModel modelo = (DefaultTableModel) TablaDeClientes.getModel(); for (int i = 0; i < modelo.getRowCount(); i++) { modelo.removeRow(i); } modelo.setRowCount(0); for (int i = 0; i < listaDeClientes.size(); i++) { Cliente cliente = listaDeClientes.get(i); Object[] fila = new Object[4]; fila[0] = cliente.getCliente_id(); fila[1] = cliente.getNombre(); fila[2] = cliente.getMonto_prestamo(); //button.setText("<HTML>Click the <FONT color=\"#000099\"><U>link "+i+"</U></FONT>"+ " to go to the Java website.</HTML>"); fila[3] = "Editar"; modelo.addRow(fila); } TablaDeClientes.setModel(modelo); } catch (Exception event) { JOptionPane.showMessageDialog(dialogoEditar, "El valor del monto debe ser numrico"); } } }); dialogoEditar.setVisible(true); /*Action mostrarMensaje; mostrarMensaje = new AbstractAction() { @Override public void actionPerformed(ActionEvent e) { JTable table = (JTable) e.getSource(); int modelRow = Integer.valueOf(e.getActionCommand()); ((DefaultTableModel) table.getModel()).removeRow(modelRow); } }; ButtonColumn buttonColumn = new ButtonColumn(TablaDeClientes, mostrarMensaje, 3); buttonColumn.setMnemonic(KeyEvent.VK_E);*/ }
From source file:MiGA.StatsSelection.java
public StatsSelection(final String[] organisms, final boolean flag) { setTitle("MiGA"); setSize(800, 600);//w w w. j ava 2s . c o m setLocationRelativeTo(null); setResizable(false); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); Image im = Toolkit.getDefaultToolkit().getImage("ssr.png"); this.setIconImage(im); try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { } countmono = new ArrayList<Integer>(); countdi = new ArrayList<Integer>(); counttri = new ArrayList<Integer>(); counttetra = new ArrayList<Integer>(); countpenta = new ArrayList<Integer>(); counthexa = new ArrayList<Integer>(); countmonore = new ArrayList<Integer>(); countdire = new ArrayList<Integer>(); counttrire = new ArrayList<Integer>(); counttetrare = new ArrayList<Integer>(); countpentare = new ArrayList<Integer>(); counthexare = new ArrayList<Integer>(); Amono = new ArrayList<Integer>(); Tmono = new ArrayList<Integer>(); Gmono = new ArrayList<Integer>(); Cmono = new ArrayList<Integer>(); Adi = new ArrayList<Integer>(); Tdi = new ArrayList<Integer>(); Gdi = new ArrayList<Integer>(); Cdi = new ArrayList<Integer>(); Atri = new ArrayList<Integer>(); Ttri = new ArrayList<Integer>(); Gtri = new ArrayList<Integer>(); Ctri = new ArrayList<Integer>(); Atetra = new ArrayList<Integer>(); Ttetra = new ArrayList<Integer>(); Gtetra = new ArrayList<Integer>(); Ctetra = new ArrayList<Integer>(); Apenta = new ArrayList<Integer>(); Tpenta = new ArrayList<Integer>(); Gpenta = new ArrayList<Integer>(); Cpenta = new ArrayList<Integer>(); Ahexa = new ArrayList<Integer>(); Thexa = new ArrayList<Integer>(); Ghexa = new ArrayList<Integer>(); Chexa = new ArrayList<Integer>(); for (int i = 0; i < organisms.length; i++) { countmono.add(0); countdi.add(0); counttri.add(0); counttetra.add(0); countpenta.add(0); counthexa.add(0); countmonore.add(0); countdire.add(0); counttrire.add(0); counttetrare.add(0); countpentare.add(0); counthexare.add(0); Amono.add(0); Tmono.add(0); Gmono.add(0); Cmono.add(0); Adi.add(0); Tdi.add(0); Gdi.add(0); Cdi.add(0); Atri.add(0); Ttri.add(0); Gtri.add(0); Ctri.add(0); Atetra.add(0); Ttetra.add(0); Gtetra.add(0); Ctetra.add(0); Apenta.add(0); Tpenta.add(0); Gpenta.add(0); Cpenta.add(0); Ahexa.add(0); Thexa.add(0); Ghexa.add(0); Chexa.add(0); } lab = new JLabel( "<html><b><p>To retrieve the sequence you want</p><p>simply copy and paste in the fields below</p><p>the data you were given in your result's file</p></b></html>"); startlab = new JLabel("Start:"); endlab = new JLabel("End:"); titlelab = new JLabel("Chromosome or field:"); startnum = new JTextField(); startnum.setColumns(5); endnum = new JTextField(); endnum.setColumns(5); titlef = new JTextField(); titlef.setColumns(30); flankst = new JLabel("Flanking region before: "); flankst.setEnabled(false); flankst.setVisible(false); flankend = new JLabel("Flanking region after: "); flankend.setEnabled(false); flankend.setVisible(false); flankstn = new JTextField(); flankstn.setColumns(5); flankstn.setEnabled(false); flankstn.setVisible(false); flankendn = new JTextField(); flankendn.setColumns(5); flankendn.setEnabled(false); flankendn.setVisible(false); result = new JTextArea("", 6, 90); result.setText(" "); result.setEditable(false); result.setLineWrap(true); result.setAutoscrolls(true); sbrText = new JScrollPane(result); sbrText.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); flk = new JCheckBox("Flanking Regions"); flk.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (flk.isSelected()) { flankst.setEnabled(true); flankst.setVisible(true); flankend.setEnabled(true); flankend.setVisible(true); flankstn.setEnabled(true); flankstn.setVisible(true); flankendn.setEnabled(true); flankendn.setVisible(true); } if (!flk.isSelected()) { flankst.setEnabled(false); flankst.setVisible(false); flankend.setEnabled(false); flankend.setVisible(false); flankstn.setEnabled(false); flankstn.setVisible(false); flankendn.setEnabled(false); flankendn.setVisible(false); } } }); retrieve = new JButton("Retrieve"); retrieve.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { int start = 0; int end = 0; BufferedReader in = null; String location = ""; String newlocation = ""; String bufferpre = ""; String bufferpost = ""; String pre = ""; String post = ""; String mid = ""; try { String[] locationarray = titlef.getText().split("data/"); location = locationarray[0] + locationarray[1]; newlocation = ""; if (location.contains("local")) { in = new BufferedReader(new FileReader(location + ".txt")); } else if (location.contains("organisms")) { String[] loc = location.split("/"); try { if (CheckForKaryotype(loc[1])) { newlocation = loc[0] + "/" + loc[1] + "/chrom-" + loc[2] + "-slices.txt"; } else { newlocation = loc[0] + "/" + loc[1] + "/slice-" + loc[2] + ".txt"; } } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } in = new BufferedReader(new FileReader(newlocation)); } } catch (FileNotFoundException ex) { msg.showMessageDialog(paneldown, "Wrong field", "Error", JOptionPane.ERROR_MESSAGE); } int rest = Integer.parseInt(startnum.getText()) % 20000; int lines = Integer.parseInt(startnum.getText()) / 20000; lines++; String buffer1 = ""; for (int c = 0; c < lines; c++) { try { buffer1 = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } if (flk.isSelected()) { boolean tfs = false, tfe = false; int fs = 0, fe = 0; try { fs = Integer.parseInt(flankstn.getText()); tfs = true; } catch (NumberFormatException ex) { tfs = false; } try { fe = Integer.parseInt(flankendn.getText()); tfe = true; } catch (NumberFormatException ex) { tfe = false; } if (tfs && tfe) { start = rest - Integer.parseInt(flankstn.getText()); end = rest + Integer.parseInt(endnum.getText()) - Integer.parseInt(startnum.getText()) + Integer.parseInt(flankendn.getText()); try { in = new BufferedReader(new FileReader(newlocation)); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } if (start < 0 && lines == 1) { start = 0; } else if (start < 0 && lines > 1) { for (int j = 0; j < lines - 1; j++) { try { bufferpre = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } pre = bufferpre.substring(20000 + start); mid = buffer1.substring(0, end); try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } int cl = 0; try { cl = countlines(newlocation); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } try { in = new BufferedReader(new FileReader(newlocation)); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } if (end > 20000 && lines == cl - 1) { if (end - 20000 >= rest) { end = rest; mid = buffer1.substring(start); post = bufferpost; } else { for (int j = 0; j < lines - 1; j++) { try { bufferpost = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } mid = buffer1.substring(start); post = bufferpre.substring(0, end - 20000); try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } } else if (end > 20000 && lines < cl - 1) { for (int j = 0; j < lines + 1; j++) { try { bufferpost = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } mid = buffer1.substring(start); post = bufferpost.substring(0, end - 20000); try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } if (start >= 0 && (end <= 20000 || end <= rest)) { mid = buffer1.substring(start, end); } } else { if (!tfs) { msg.showMessageDialog(paneldown, "Flanking region start is empty.\nFill in the gap or uncheck the\nflanking regions checkbox", "Error", JOptionPane.ERROR_MESSAGE); } if (!tfe) { msg.showMessageDialog(paneldown, "Flanking region end is empty.\nFill in the gap or uncheck the\nflanking regions checkbox", "Error", JOptionPane.ERROR_MESSAGE); } } // } if (!flk.isSelected()) { start = rest; end = rest + Integer.parseInt(endnum.getText()) - Integer.parseInt(startnum.getText()); try { in = new BufferedReader(new FileReader(newlocation)); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } if (start < 0 && lines == 1) { start = 0; } else if (start < 0 && lines > 1) { for (int j = 0; j < lines - 1; j++) { try { bufferpre = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } pre = bufferpre.substring(start); mid = buffer1.substring(0, end); try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } int cl = 0; try { cl = countlines(newlocation); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } try { in = new BufferedReader(new FileReader(newlocation)); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } if (end > 20000 && lines == cl - 1) { if (end - 20000 >= rest) { end = rest; mid = buffer1.substring(start); post = bufferpost; } else { for (int j = 0; j < lines - 1; j++) { try { bufferpost = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } mid = buffer1.substring(start); post = bufferpre.substring(0, end - 20000); try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } } else if (end > 20000 && lines < cl - 1) { for (int j = 0; j < lines + 1; j++) { try { bufferpost = in.readLine(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } mid = buffer1.substring(start); post = bufferpost.substring(0, end - 20000); try { in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } if (start >= 0 && (end <= 20000 || end <= rest)) { mid = buffer1.substring(start, end); } } result.setText(pre + mid + post); } }); mono = new JCheckBox("Mononucleotide"); di = new JCheckBox("Dinucleotide"); tri = new JCheckBox("Trinucleotide"); tetra = new JCheckBox("Tetranucleotide"); penta = new JCheckBox("Pentanucleotide"); hexa = new JCheckBox("Hexanucleotide"); SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); start = new ArrayList<Integer>(); select = new JLabel("Select type: "); minimumssrlen = new JLabel("Minimum SSR length(bp)"); minimumssrlen.setVisible(false); score = new JTextField(); score.setColumns(5); score.setVisible(false); msg = new JOptionPane(); gapmax = new JLabel("Maximum Mismatch length for Imperfect SSRs(bp)"); gapmax.setVisible(false); max = new JTextField(); max.setColumns(5); max.setVisible(false); minlenpregap = new JLabel("Minimum SSR length before given Mismatch length(bp)"); minlenpregap.setVisible(false); minpregap = new JTextField(); minpregap.setColumns(5); minpregap.setVisible(false); gapcomp = new JLabel("Maximum Inter-repeat R for Compound SSRs(bp)"); gapcomp.setVisible(false); maxgapcomp = new JTextField(); maxgapcomp.setColumns(5); maxgapcomp.setVisible(false); box1 = new JCheckBox("Perfect"); box2 = new JCheckBox("Imperfect"); box3 = new JCheckBox("Compound"); com = new JCheckBox("Perfect Compound"); incom = new JCheckBox("Imperfect Compound"); box1.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (box2.isSelected() || box3.isSelected()) { if (box1.isSelected()) { std.setEnabled(true); no_st.setEnabled(true); part_st.setEnabled(true); full_st.setEnabled(true); if (!box3.isSelected()) { minimumssrlen.setVisible(true); score.setVisible(true); } } if (!box1.isSelected()) { std.setEnabled(false); no_st.setEnabled(false); part_st.setEnabled(false); full_st.setEnabled(false); if (!box3.isSelected()) { minimumssrlen.setVisible(false); score.setVisible(false); } } } else { if (box1.isSelected()) { std.setEnabled(true); no_st.setEnabled(true); part_st.setEnabled(true); full_st.setEnabled(true); panel2.setVisible(true); minimumssrlen.setVisible(true); score.setVisible(true); } if (!box1.isSelected()) { std.setEnabled(false); no_st.setEnabled(false); part_st.setEnabled(false); full_st.setEnabled(false); panel2.setVisible(false); minimumssrlen.setVisible(false); score.setVisible(false); } } } }); box2.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (box1.isSelected() || box3.isSelected()) { if (box2.isSelected()) { gapmax.setVisible(true); max.setVisible(true); minlenpregap.setVisible(true); minpregap.setVisible(true); } if (!box2.isSelected()) { gapmax.setVisible(false); max.setVisible(false); minlenpregap.setVisible(false); minpregap.setVisible(false); } } else { if (box2.isSelected()) { panel2.setVisible(true); gapmax.setVisible(true); max.setVisible(true); minlenpregap.setVisible(true); minpregap.setVisible(true); } if (!box2.isSelected()) { panel2.setVisible(false); gapmax.setVisible(false); max.setVisible(false); minlenpregap.setVisible(false); minpregap.setVisible(false); } } } }); box3.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (box1.isSelected() || box2.isSelected()) { if (box3.isSelected()) { paneldownleft.setVisible(true); if (!box1.isSelected()) { minimumssrlen.setVisible(true); score.setVisible(true); } gapcomp.setVisible(true); maxgapcomp.setVisible(true); com.setVisible(true); incom.setVisible(true); } if (!box3.isSelected()) { paneldownleft.setVisible(false); gapcomp.setVisible(false); maxgapcomp.setVisible(false); if (!box1.isSelected()) { minimumssrlen.setVisible(false); score.setVisible(false); com.setVisible(false); incom.setVisible(false); } } } else { if (box3.isSelected()) { paneldownleft.setVisible(true); panel2.setVisible(true); minimumssrlen.setVisible(true); score.setVisible(true); gapcomp.setVisible(true); maxgapcomp.setVisible(true); com.setVisible(true); incom.setVisible(true); } if (!box3.isSelected()) { paneldownleft.setVisible(false); panel2.setVisible(false); minimumssrlen.setVisible(false); score.setVisible(false); gapcomp.setVisible(false); maxgapcomp.setVisible(false); com.setVisible(false); incom.setVisible(false); } } } }); /* incom.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (incom.isSelected()) { if (!box2.isSelected()) { gapmax.setVisible(true); max.setVisible(true); minlenpregap.setVisible(true); minpregap.setVisible(true); } } if (!incom.isSelected()) { if (!box2.isSelected()) { gapmax.setVisible(false); max.setVisible(false); minlenpregap.setVisible(false); minpregap.setVisible(false); } } } });*/ std = new JPanel(); no_st = new JRadioButton("Not Standardized"); part_st = new JRadioButton("Partial Standardized"); full_st = new JRadioButton("Full Standardized"); no_st.setSelected(true); no_st.setEnabled(false); part_st.setEnabled(false); full_st.setEnabled(false); standard = new ButtonGroup(); standard.add(no_st); standard.add(part_st); standard.add(full_st); show = new JButton("Run"); show.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (!box1.isSelected() && !box2.isSelected() && !box3.isSelected()) { msg.showMessageDialog(paneldown, "Please select a type", "Error", JOptionPane.ERROR_MESSAGE); } for (int i = 0; i < organisms.length; i++) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (f.exists()) { f.delete(); } } calendar = Calendar.getInstance(); now = calendar.getTime(); if (box1.isSelected()) { if (!score.getText().isEmpty()) { boolean isnumber = false; int minlen = 0; try { minlen = Integer.parseInt(score.getText()); isnumber = true; } catch (NumberFormatException ex) { isnumber = false; } if (isnumber) { try { getPerfectSSRs(organisms, minlen, flag); for (int i = 0; i < organisms.length; i++) { map = new HashMap<String, motifStats>(); String location = ""; String location2 = ""; PrintWriter out = null; // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here PrintWriter stats = null; PrintWriter html = null; PrintWriter motifstats = null; PrintWriter motifhtml = null; DataOutputStream lt = null; if (filetype.contains("organisms")) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); motifstats = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "motif_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); motifhtml = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "motif_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); html = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); lt = new DataOutputStream(new BufferedOutputStream( new FileOutputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".perf"))); File fi = new File("organisms/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "organisms/" + organisms[i] + "/results/allPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; location = toopen; location2 = "organisms/" + organisms[i] + "/stats/" + "motif_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; out = new PrintWriter(toopen); out.println("Results for organism: " + organisms[i] + "\t Search Parameters --> Minimum SSR Length (bp): " + minlen); out.println( " SSR repeats start-end length Path(../organism/data/chromosome)"); } else if (filetype.contains("local")) { File f = new File("local/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); motifstats = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "motif_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); motifhtml = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "motif_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); lt = new DataOutputStream(new BufferedOutputStream( new FileOutputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".perf"))); html = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("local/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "local/" + organisms[i] + "/results/allPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; location = toopen; location2 = "local/" + organisms[i] + "/stats/" + "motif_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; out = new PrintWriter(toopen); out.println("Results for project: " + organisms[i] + "\t Search Parameters --> Minimum SSR Length (bp): " + minlen); out.println( " SSR repeats start-end length Path(../organism/data/chromosome)"); out.println(); } if (mono.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); //for (int j = 0; j < files.size(); j++) { while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + minlen + "_monoPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int repeats = in.readInt(); int end = in.readInt(); out.println(cell(ssr, 6) + " " + cell(repeats, 11) + " " + cell(Integer .toString(end - repeats * ssr.length() + 1) + "-" + Integer.toString(end + 1), 20) + " " + cell(repeats * ssr.length(), 6) + " " + files.substring(0, files.lastIndexOf('.'))); // map for motifstats if (!map.containsKey(ssr)) { motifStats m = new motifStats(ssr, repeats); map.put(ssr, m); } else { map.get(ssr).update(repeats); } } catch (EOFException exc) { eof = true; } } in.close(); } } if (di.isSelected()) { //for (int j = 0; j < files.size(); j++) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream(new BufferedInputStream( new FileInputStream(files + "_" + minlen + "_diPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int repeats = in.readInt(); int end = in.readInt(); //out.println("SSR: " + ssr + " repeats: " + repeats + " start-end " + (end - repeats * ssr.length()) + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); out.println(cell(ssr, 6) + " " + cell(repeats, 11) + " " + cell(Integer .toString(end - repeats * ssr.length() + 1) + "-" + Integer.toString(end + 1), 20) + " " + cell(repeats * ssr.length(), 6) + " " + files.substring(0, files.lastIndexOf('.'))); if (!map.containsKey(ssr)) { motifStats m = new motifStats(ssr, repeats); map.put(ssr, m); } else { map.get(ssr).update(repeats); } } catch (EOFException exc) { eof = true; } } in.close(); } } if (tri.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //for (int j = 0; j < files.size(); j++) { while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + minlen + "_triPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int repeats = in.readInt(); int end = in.readInt(); //out.println("SSR: " + ssr + " repeats: " + repeats + " start-end " + (end - repeats * ssr.length()) + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); out.println(cell(ssr, 6) + " " + cell(repeats, 11) + " " + cell(Integer .toString(end - repeats * ssr.length() + 1) + "-" + Integer.toString(end + 1), 20) + " " + cell(repeats * ssr.length(), 6) + " " + files.substring(0, files.lastIndexOf('.'))); if (!map.containsKey(ssr)) { motifStats m = new motifStats(ssr, repeats); map.put(ssr, m); } else { map.get(ssr).update(repeats); } } catch (EOFException exc) { eof = true; } } in.close(); } } if (tetra.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + minlen + "_tetraPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int repeats = in.readInt(); int end = in.readInt(); // out.println("SSR: " + ssr + " repeats: " + repeats + " start-end " + (end - repeats * ssr.length()) + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); out.println(cell(ssr, 6) + " " + cell(repeats, 11) + " " + cell(Integer .toString(end - repeats * ssr.length() + 1) + "-" + Integer.toString(end + 1), 20) + " " + cell(repeats * ssr.length(), 6) + " " + files.substring(0, files.lastIndexOf('.'))); if (!map.containsKey(ssr)) { motifStats m = new motifStats(ssr, repeats); map.put(ssr, m); } else { map.get(ssr).update(repeats); } } catch (EOFException exc) { eof = true; } } in.close(); } } if (penta.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + minlen + "_pentaPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int repeats = in.readInt(); int end = in.readInt(); // out.println("SSR: " + ssr + " repeats: " + repeats + " start-end " + (end - repeats * ssr.length()) + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); out.println(cell(ssr, 6) + " " + cell(repeats, 11) + " " + cell(Integer .toString(end - repeats * ssr.length() + 1) + "-" + Integer.toString(end + 1), 20) + " " + cell(repeats * ssr.length(), 6) + " " + files.substring(0, files.lastIndexOf('.'))); if (!map.containsKey(ssr)) { motifStats m = new motifStats(ssr, repeats); map.put(ssr, m); } else { map.get(ssr).update(repeats); } } catch (EOFException exc) { eof = true; } } in.close(); } } if (hexa.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + minlen + "_hexaPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int repeats = in.readInt(); int end = in.readInt(); // out.println("SSR: " + ssr + " repeats: " + repeats + " start-end " + (end - repeats * ssr.length()) + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); out.println(cell(ssr, 6) + " " + cell(repeats, 11) + " " + cell(Integer .toString(end - repeats * ssr.length() + 1) + "-" + Integer.toString(end + 1), 20) + " " + cell(repeats * ssr.length(), 6) + " " + files.substring(0, files.lastIndexOf('.'))); if (!map.containsKey(ssr)) { motifStats m = new motifStats(ssr, repeats); map.put(ssr, m); } else { map.get(ssr).update(repeats); } } catch (EOFException exc) { eof = true; } } in.close(); } } out.close(); Runtime.getRuntime().exec("notepad " + location); DecimalFormat round = new DecimalFormat("#.###"); html.println("<html><h1>******* Perfect SSRs *******</h1>"); html.println("<h4>Results for project: " + organisms[i] + "</h4><h4>Search Parameters --> Minimum SSR Length (bp): " + minlen + "</h4>"); html.println( "<table border=\"1\"><tr><td><b>motif</b></td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); stats.println("******* Perfect SSRs *******"); stats.println("Results for project: " + organisms[i] + "\n Search Parameters --> Minimum SSR Length (bp): " + minlen); stats.println( " ____________________________________________________________________________________________________________ "); stats.println( "| | | | | | | | Relative | | Relative |"); stats.println( "| motif | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); stats.println( "|=======|=======|============|=======|=======|=======|=======|===============|===============|===============|"); int totalcount = 0; long bpcount = 0; int Aperc = 0; int Tperc = 0; int Gperc = 0; int Cperc = 0; float relfreq = 0; float abfreq = 0; long seqcount = 0; if (mono.isSelected()) { totalcount += countmono.get(i); bpcount += countmonore.get(i); } if (di.isSelected()) { totalcount += countdi.get(i); bpcount += countdire.get(i) * 2; } if (tri.isSelected()) { totalcount += counttri.get(i); bpcount += counttrire.get(i) * 3; } if (tetra.isSelected()) { totalcount += counttetra.get(i); bpcount += counttetrare.get(i) * 4; } if (penta.isSelected()) { totalcount += countpenta.get(i); bpcount += countpentare.get(i) * 5; } if (hexa.isSelected()) { totalcount += counthexa.get(i); bpcount += counthexare.get(i) * 6; } try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Connection con = null; try { con = DriverManager.getConnection("jdbc:mysql://localhost:3306", "biouser", "thesis2012"); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Statement st = null; try { st = con.createStatement(); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } st.executeUpdate("use lobid"); seqcount = 0; if (filetype.contains("organisms")) { ResultSet rs = st.executeQuery( "SELECT end FROM slices INNER JOIN organism WHERE slices.org_id=organism.org_id AND organism.name='" + organisms[i] + "'"); while (rs.next()) { seqcount += Long.parseLong(rs.getString(1)); } } else if (filetype.contains("local")) { BufferedReader in = new BufferedReader( new FileReader("local/" + organisms[i] + "/index.txt")); int count = countlines("local/" + organisms[i] + "/index.txt"); for (int c = 0; c < count; c++) { String temp = in.readLine(); BufferedReader tmp = new BufferedReader( new FileReader("local/" + organisms[i] + "/" + temp + ".txt")); boolean eof = false; while (!eof) { String s = tmp.readLine(); if (s != null) { seqcount += s.length(); } else { eof = true; } } tmp.close(); } } if (mono.isSelected()) { Aperc += Amono.get(i); Tperc += Tmono.get(i); Gperc += Gmono.get(i); Cperc += Cmono.get(i); //lt.writeInt(countmono);lt.writeInt(countmonore);lt.writeFloat((float)Amono*100/countmonore);lt.writeFloat((float)Tmono*100/countmonore);lt.writeFloat((float)Gmono*100/countmonore);lt.writeFloat((float)Cmono*100/countmonore);lt.writeFloat((float) countmono / totalcount);lt.writeFloat((float) countmonore / seqcount);lt.writeFloat((float) countmonore / bpcount); stats.printf("|mono |" + cell(Integer.toString(countmono.get(i)), 7) + "|" + cell(Integer.toString(1 * countmonore.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) countmono.get(i) / totalcount, 15) + "|" + cell((float) countmonore.get(i) / seqcount, 15) + "|" + cell((float) countmonore.get(i) / bpcount, 15) + "|\n", cell((float) (Amono.get(i) * 100) / (countmonore.get(i)), 7), cell((float) (Tmono.get(i) * 100) / (countmonore.get(i)), 7), cell((float) (Cmono.get(i) * 100) / (countmonore.get(i)), 7), cell((float) (Gmono.get(i) * 100) / (countmonore.get(i)), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>mono</b></td><td>" + countmono.get(i) + "</td><td>" + (1 * countmonore.get(i)) + "</td><td>" + round.format((float) (Amono.get(i) * 100) / (countmonore.get(i))) + "</td><td>" + round.format((float) (Tmono.get(i) * 100) / (countmonore.get(i))) + "</td><td>" + round.format((float) (Cmono.get(i) * 100) / (countmonore.get(i))) + "</td><td>" + round.format((float) (Gmono.get(i) * 100) / (countmonore.get(i))) + "</td><td>" + round.format((float) countmono.get(i) / totalcount) + "</td><td>" + round.format((float) countmonore.get(i) / seqcount) + "</td><td>" + round.format((float) countmonore.get(i) / bpcount) + "</td></tr>"); } if (di.isSelected()) { Aperc += Adi.get(i); Tperc += Tdi.get(i); Gperc += Gdi.get(i); Cperc += Cdi.get(i); //lt.writeInt(countdi);lt.writeInt(countdire*2);lt.writeFloat((float)Adi*100/countdire*2);lt.writeFloat((float)Tdi*100/countdire*2);lt.writeFloat((float)Gdi*100/countdire*2);lt.writeFloat((float)Cdi*100/countdire*2);lt.writeFloat((float) countdi / totalcount);lt.writeFloat((float) countdire*2 / seqcount);lt.writeFloat((float) countdire*2 / bpcount); stats.printf("|di |" + cell(Integer.toString(countdi.get(i)), 7) + "|" + cell(Integer.toString(countdire.get(i) * 2), 12) + "|%s|%s|%s|%s|" + cell((float) countdi.get(i) / totalcount, 15) + "|" + cell((float) countdire.get(i) * 2 / seqcount, 15) + "|" + cell((float) countdire.get(i) * 2 / bpcount, 15) + "|\n", cell((float) (Adi.get(i) * 100) / (countdire.get(i) * 2), 7), cell((float) (Tdi.get(i) * 100) / (countdire.get(i) * 2), 7), cell((float) (Cdi.get(i) * 100) / (countdire.get(i) * 2), 7), cell((float) (Gdi.get(i) * 100) / (countdire.get(i) * 2), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>di</b></td><td>" + countdi.get(i) + "</td><td>" + (2 * countdire.get(i)) + "</td><td>" + round.format((float) (Adi.get(i) * 100) / (2 * countdire.get(i))) + "</td><td>" + round.format((float) (Tdi.get(i) * 100) / (2 * countdire.get(i))) + "</td><td>" + round.format((float) (Cdi.get(i) * 100) / (2 * countdire.get(i))) + "</td><td>" + round.format((float) (Gdi.get(i) * 100) / (2 * countdire.get(i))) + "</td><td>" + round.format((float) countdi.get(i) / totalcount) + "</td><td>" + round.format((float) 2 * countdire.get(i) / seqcount) + "</td><td>" + round.format((float) 2 * countdire.get(i) / bpcount) + "</td></tr>"); } if (tri.isSelected()) { Aperc += Atri.get(i); Tperc += Ttri.get(i); Gperc += Gtri.get(i); Cperc += Ctri.get(i); //lt.writeInt(counttri);lt.writeInt(counttrire*3);lt.writeFloat((float)Atri*100/counttrire*3);lt.writeFloat((float)Ttri*100/counttrire*3);lt.writeFloat((float)Gtri*100/counttrire*3);lt.writeFloat((float)Ctri*100/counttrire*3);lt.writeFloat((float) counttri / totalcount);lt.writeFloat((float) counttrire*3 / seqcount);lt.writeFloat((float) counttrire*3 / bpcount); stats.printf("|tri |" + cell(Integer.toString(counttri.get(i)), 7) + "|" + cell(Integer.toString(counttrire.get(i) * 3), 12) + "|%s|%s|%s|%s|" + cell((float) counttri.get(i) / totalcount, 15) + "|" + cell((float) counttrire.get(i) * 3 / seqcount, 15) + "|" + cell((float) counttrire.get(i) * 3 / bpcount, 15) + "|\n", cell((float) (Atri.get(i) * 100) / (counttrire.get(i) * 3), 7), cell((float) (Ttri.get(i) * 100) / (counttrire.get(i) * 3), 7), cell((float) (Ctri.get(i) * 100) / (counttrire.get(i) * 3), 7), cell((float) (Gtri.get(i) * 100) / (counttrire.get(i) * 3), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>tri</b></td><td>" + counttri.get(i) + "</td><td>" + (3 * counttrire.get(i)) + "</td><td>" + round.format( (float) (Atri.get(i) * 100) / (3 * counttrire.get(i))) + "</td><td>" + round.format( (float) (Ttri.get(i) * 100) / (3 * counttrire.get(i))) + "</td><td>" + round.format( (float) (Ctri.get(i) * 100) / (3 * counttrire.get(i))) + "</td><td>" + round.format( (float) (Gtri.get(i) * 100) / (3 * counttrire.get(i))) + "</td><td>" + round.format((float) counttri.get(i) / totalcount) + "</td><td>" + round.format((float) 3 * counttrire.get(i) / seqcount) + "</td><td>" + round.format((float) 3 * counttrire.get(i) / bpcount) + "</td></tr>"); } if (tetra.isSelected()) { Aperc += Atetra.get(i); Tperc += Ttetra.get(i); Gperc += Gtetra.get(i); Cperc += Ctetra.get(i); //lt.writeInt(counttetra);lt.writeInt(counttetrare*4);lt.writeFloat((float)Atetra*100/counttetrare*4);lt.writeFloat((float)Ttetra*100/counttetrare*4);lt.writeFloat((float)Gtetra*100/counttetrare*4);lt.writeFloat((float)Ctetra*100/counttetrare*4);lt.writeFloat((float) counttetra / totalcount);lt.writeFloat((float) counttetrare*4 / seqcount);lt.writeFloat((float) counttetrare*4 / bpcount); stats.printf("|tetra |" + cell(Integer.toString(counttetra.get(i)), 7) + "|" + cell(Integer.toString(counttetrare.get(i) * 4), 12) + "|%s|%s|%s|%s|" + cell((float) counttetra.get(i) / totalcount, 15) + "|" + cell((float) counttetrare.get(i) * 4 / seqcount, 15) + "|" + cell((float) counttetrare.get(i) * 4 / bpcount, 15) + "|\n", cell((float) (Atetra.get(i) * 100) / (counttetrare.get(i) * 4), 7), cell((float) (Ttetra.get(i) * 100) / (counttetrare.get(i) * 4), 7), cell((float) (Ctetra.get(i) * 100) / (counttetrare.get(i) * 4), 7), cell((float) (Gtetra.get(i) * 100) / (counttetrare.get(i) * 4), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>tetra</b></td><td>" + counttetra.get(i) + "</td><td>" + (4 * counttetrare.get(i)) + "</td><td>" + round.format( (float) (Atetra.get(i) * 100) / (4 * counttetrare.get(i))) + "</td><td>" + round.format( (float) (Ttetra.get(i) * 100) / (4 * counttetrare.get(i))) + "</td><td>" + round.format( (float) (Ctetra.get(i) * 100) / (4 * counttetrare.get(i))) + "</td><td>" + round.format( (float) (Gtetra.get(i) * 100) / (4 * counttetrare.get(i))) + "</td><td>" + round.format((float) counttetra.get(i) / totalcount) + "</td><td>" + round.format((float) 4 * counttetrare.get(i) / seqcount) + "</td><td>" + round.format((float) 4 * counttetrare.get(i) / bpcount) + "</td></tr>"); } if (penta.isSelected()) { Aperc += Apenta.get(i); Tperc += Tpenta.get(i); Gperc += Gpenta.get(i); Cperc += Cpenta.get(i); //lt.writeInt(countpenta);lt.writeInt(countpentare*5);lt.writeFloat((float)Apenta*100/countpentare*5);lt.writeFloat((float)Tpenta*100/countpentare*5);lt.writeFloat((float)Gpenta*100/countpentare*5);lt.writeFloat((float)Cpenta*100/countpentare*5);lt.writeFloat((float) countpenta / totalcount);lt.writeFloat((float) countpentare*5 / seqcount);lt.writeFloat((float) countpentare*5 / bpcount); stats.printf("|penta |" + cell(Integer.toString(countpenta.get(i)), 7) + "|" + cell(Integer.toString(countpentare.get(i) * 5), 12) + "|%s|%s|%s|%s|" + cell((float) countpenta.get(i) / totalcount, 15) + "|" + cell((float) countpentare.get(i) * 5 / seqcount, 15) + "|" + cell((float) countpentare.get(i) * 5 / bpcount, 15) + "|\n", cell((float) (Apenta.get(i) * 100) / (countpentare.get(i) * 5), 7), cell((float) (Tpenta.get(i) * 100) / (countpentare.get(i) * 5), 7), cell((float) (Cpenta.get(i) * 100) / (countpentare.get(i) * 5), 7), cell((float) (Gpenta.get(i) * 100) / (countpentare.get(i) * 5), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>penta</b></td><td>" + countpenta.get(i) + "</td><td>" + (5 * countpentare.get(i)) + "</td><td>" + round.format( (float) (Apenta.get(i) * 100) / (5 * countpentare.get(i))) + "</td><td>" + round.format( (float) (Tpenta.get(i) * 100) / (5 * countpentare.get(i))) + "</td><td>" + round.format( (float) (Cpenta.get(i) * 100) / (5 * countpentare.get(i))) + "</td><td>" + round.format( (float) (Gpenta.get(i) * 100) / (5 * countpentare.get(i))) + "</td><td>" + round.format((float) countpenta.get(i) / totalcount) + "</td><td>" + round.format((float) 5 * countpentare.get(i) / seqcount) + "</td><td>" + round.format((float) 5 * countpentare.get(i) / bpcount) + "</td></tr>"); } if (hexa.isSelected()) { Aperc += Ahexa.get(i); Tperc += Thexa.get(i); Gperc += Ghexa.get(i); Cperc += Chexa.get(i); //lt.writeInt(counthexa);lt.writeInt(counthexare*6);lt.writeFloat((float)Ahexa*100/counthexare*6);lt.writeFloat((float)Thexa*100/counthexare*6);lt.writeFloat((float)Ghexa*100/counthexare*6);lt.writeFloat((float)Chexa*100/counthexare*6);lt.writeFloat((float) counthexa / totalcount);lt.writeFloat((float) counthexare*6 / seqcount);lt.writeFloat((float) counthexare*6 / bpcount); stats.printf("|hexa |" + cell(Integer.toString(counthexa.get(i)), 7) + "|" + cell(Integer.toString(counthexare.get(i) * 6), 12) + "|%s|%s|%s|%s|" + cell((float) counthexa.get(i) / totalcount, 15) + "|" + cell((float) counthexare.get(i) * 6 / seqcount, 15) + "|" + cell((float) counthexare.get(i) * 6 / bpcount, 15) + "|\n", cell((float) (Ahexa.get(i) * 100) / (counthexare.get(i) * 6), 7), cell((float) (Thexa.get(i) * 100) / (counthexare.get(i) * 6), 7), cell((float) (Chexa.get(i) * 100) / (counthexare.get(i) * 6), 7), cell((float) (Ghexa.get(i) * 100) / (counthexare.get(i) * 6), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>hexa</b></td><td>" + counthexa.get(i) + "</td><td>" + (6 * counthexare.get(i)) + "</td><td>" + round.format( (float) (Ahexa.get(i) * 100) / (6 * counthexare.get(i))) + "</td><td>" + round.format( (float) (Thexa.get(i) * 100) / (6 * counthexare.get(i))) + "</td><td>" + round.format( (float) (Chexa.get(i) * 100) / (6 * counthexare.get(i))) + "</td><td>" + round.format( (float) (Ghexa.get(i) * 100) / (6 * counthexare.get(i))) + "</td><td>" + round.format((float) counthexa.get(i) / totalcount) + "</td><td>" + round.format((float) 6 * counthexare.get(i) / seqcount) + "</td><td>" + round.format((float) 6 * counthexare.get(i) / bpcount) + "</td></tr>"); } if (mono.isSelected()) { relfreq += (float) countmono.get(i) / totalcount; abfreq += (float) countmonore.get(i) / bpcount; } if (di.isSelected()) { relfreq += (float) countdi.get(i) / totalcount; abfreq += (float) countdire.get(i) * 2 / bpcount; } if (tri.isSelected()) { relfreq += (float) counttri.get(i) / totalcount; abfreq += (float) counttrire.get(i) * 3 / bpcount; } if (tetra.isSelected()) { relfreq += (float) counttetra.get(i) / totalcount; abfreq += (float) counttetrare.get(i) * 4 / bpcount; } if (penta.isSelected()) { relfreq += (float) countpenta.get(i) / totalcount; abfreq += (float) countpentare.get(i) * 5 / bpcount; } if (hexa.isSelected()) { relfreq += (float) counthexa.get(i) / totalcount; abfreq += (float) counthexare.get(i) * 6 / bpcount; } Globals.A = Aperc; Globals.T = Tperc; Globals.G = Gperc; Globals.C = Cperc; lt.writeLong(seqcount); lt.writeInt(totalcount); lt.writeLong(bpcount); lt.writeInt(Aperc); lt.writeInt(Tperc); lt.writeInt(Gperc); lt.writeInt(Cperc); stats.println("|TOTAL |" + cell(Integer.toString(totalcount), 7) + "|" + cell(Long.toString(bpcount), 12) + "|" + cell((float) Aperc * 100 / bpcount, 7) + "|" + cell((float) Tperc * 100 / bpcount, 7) + "|" + cell((float) Cperc * 100 / bpcount, 7) + "|" + cell((float) Gperc * 100 / bpcount, 7) + "|" + cell(relfreq, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) abfreq, 15) + "|"); stats.println( "|_______|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); stats.println("Genome length (bp): " + seqcount); stats.println("Relative Frequency: Count of each motif type / total SSR count"); stats.println("Abundance: bp of each motif type / total sequence bp"); stats.println( "Relative Abundance: bp of each motif type / total microsatellites bp"); stats.println(); stats.println(); stats.close(); lt.close(); html.println("<tr><td><b>TOTAL</b></td><td>" + totalcount + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) relfreq) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) abfreq) + "</td></tr></table></html>"); html.close(); // it = map.keySet().iterator(); for (String key : map.keySet()) { map.get(key).refresh(); } List<String> n1 = new ArrayList<String>(); List<String> n2 = new ArrayList<String>(); List<String> n3 = new ArrayList<String>(); List<String> n4 = new ArrayList<String>(); List<String> n5 = new ArrayList<String>(); List<String> n6 = new ArrayList<String>(); Iterator<String> it = map.keySet().iterator(); while (it.hasNext()) { String next = it.next(); int len = next.length(); if (len == 1) n1.add(next); else if (len == 2) n2.add(next); else if (len == 3) n3.add(next); else if (len == 4) n4.add(next); else if (len == 5) n5.add(next); else if (len == 6) n6.add(next); } Collections.sort(n1); Collections.sort(n2); Collections.sort(n3); Collections.sort(n4); Collections.sort(n5); Collections.sort(n6); boolean[] id1 = new boolean[n1.size()]; boolean[] id2 = new boolean[n2.size()]; boolean[] id3 = new boolean[n3.size()]; boolean[] id4 = new boolean[n4.size()]; boolean[] id5 = new boolean[n5.size()]; boolean[] id6 = new boolean[n6.size()]; motifhtml.println("<html><head><title>Motif Statistics</title></head><body>"); int stand = checkStandardize(); // stand=2; debug if (stand == 0) { motifstats.println("**** Not Standardized ****"); motifhtml.println("<h1>**** Not Standardized ****</h1>"); Arrays.fill(id1, true); Arrays.fill(id2, true); Arrays.fill(id3, true); Arrays.fill(id4, true); Arrays.fill(id5, true); Arrays.fill(id6, true); } else { if (stand == 1) { motifstats.println("**** Partially Standardized ****"); motifhtml.println("<h1>**** Partially Standardized ****</h1>"); matrix = new parser(1); } if (stand == 2) { motifstats.println("**** Fully Standardized ****"); motifhtml.println("<h1>**** Fully Standardized ****</h1>"); matrix = new parser(2); } Arrays.fill(id1, true); Arrays.fill(id2, true); Arrays.fill(id3, true); Arrays.fill(id4, true); Arrays.fill(id5, true); Arrays.fill(id6, true); for (int n = 0; n < n1.size(); n++) { int id = -2; id = matrix.SearchMap(1, n1.get(n)); if (id >= 0) { int found = matrix.checkFound(1, id); if (found >= 0) { map.get(n1.get(found)).merge(map.get(n1.get(n))); id1[n] = false; // gia clean twn listwn apo merged TODO * } if (found == -4) { matrix.makeFound(1, id, n); } } } for (int n = 0; n < n2.size(); n++) { int id = -2; id = matrix.SearchMap(2, n2.get(n)); if (id >= 0) { int found = matrix.checkFound(2, id); if (found >= 0) { map.get(n2.get(found)).merge(map.get(n2.get(n))); id2[n] = false; // gia clean twn listwn apo merged TODO * } else { matrix.makeFound(2, id, n); id2[n] = true; } } } for (int n = 0; n < n3.size(); n++) { int id = -2; id = matrix.SearchMap(3, n3.get(n)); if (id >= 0) { int found = matrix.checkFound(3, id); if (found >= 0) { map.get(n3.get(found)).merge(map.get(n3.get(n))); id3[n] = false; // gia clean twn listwn apo merged TODO * } else { matrix.makeFound(3, id, n); id3[n] = true; } } } for (int n = 0; n < n4.size(); n++) { int id = -2; id = matrix.SearchMap(4, n4.get(n)); if (id >= 0) { int found = matrix.checkFound(4, id); if (found >= 0) { map.get(n4.get(found)).merge(map.get(n4.get(n))); id4[n] = false; // gia clean twn listwn apo merged TODO * } else { matrix.makeFound(4, id, n); id4[n] = true; } } } for (int n = 0; n < n5.size(); n++) { int id = -2; id = matrix.SearchMap(5, n5.get(n)); if (id >= 0) { int found = matrix.checkFound(5, id); if (found >= 0) { map.get(n5.get(found)).merge(map.get(n5.get(n))); id5[n] = false; // gia clean twn listwn apo merged TODO * } else { matrix.makeFound(5, id, n); id5[n] = true; } } } for (int n = 0; n < n6.size(); n++) { int id = -2; id = matrix.SearchMap(6, n6.get(n)); if (id >= 0) { int found = matrix.checkFound(6, id); if (found >= 0) { map.get(n6.get(found)).merge(map.get(n6.get(n))); id6[n] = false; // gia clean twn listwn apo merged TODO * } else { matrix.makeFound(6, id, n); id6[n] = true; } } } } for (String key : map.keySet()) { map.get(key).refresh(); } motifstats.println( " Motif Count Repeats bp Avg_Length SD_Length Max_Length Avg_Repeats A% T% C% G% "); motifhtml.println( "<table border=\"1\"><tr><td><b>Motif</b></td><td><b>Count</b></td><td><b>Repeats</b></td><td><b>bp</b></td><td><b>Avg_Length</b></td><td><b>SD_Length</b></td><td><b>Max_Length</b></td><td><b>Avg_Repeats</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td></tr>"); if (mono.isSelected()) { for (int z = 0; z < n1.size(); z++) { if (id1[z] && !map.get(n1.get(z)).getMotif().contains("N")) { motifstats.println(map.get(n1.get(z)).toString()); motifhtml.println(map.get(n1.get(z)).toHTML()); } } } if (di.isSelected()) { for (int z = 0; z < n2.size(); z++) { if (id2[z] && !map.get(n2.get(z)).getMotif().contains("N")) { motifstats.println(map.get(n2.get(z)).toString()); motifhtml.println(map.get(n2.get(z)).toHTML()); } } } if (tri.isSelected()) { for (int z = 0; z < n3.size(); z++) { if (id3[z] && !map.get(n3.get(z)).getMotif().contains("N")) { motifstats.println(map.get(n3.get(z)).toString()); motifhtml.println(map.get(n3.get(z)).toHTML()); } } } if (tetra.isSelected()) { for (int z = 0; z < n4.size(); z++) { if (id4[z] && !map.get(n4.get(z)).getMotif().contains("N")) { motifstats.println(map.get(n4.get(z)).toString()); motifhtml.println(map.get(n4.get(z)).toHTML()); } } } if (penta.isSelected()) { for (int z = 0; z < n5.size(); z++) { if (id5[z] && !map.get(n5.get(z)).getMotif().contains("N")) { motifstats.println(map.get(n5.get(z)).toString()); motifhtml.println(map.get(n5.get(z)).toHTML()); } } } if (hexa.isSelected()) { for (int z = 0; z < n6.size(); z++) { if (id6[z] && !map.get(n6.get(z)).getMotif().contains("N")) { motifstats.println(map.get(n6.get(z)).toString()); motifhtml.println(map.get(n6.get(z)).toHTML()); } } } motifstats.close(); motifhtml.println("</table></body></html>"); motifhtml.close(); Runtime.getRuntime().exec("notepad " + location2); } } catch (FileNotFoundException ex) { //msg.showMessageDialog(paneldown, "Update your selected species", "Error", JOptionPane.ERROR_MESSAGE); Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } else { msg.showMessageDialog(paneldown, "Minimum length requires an Integer", "Error", JOptionPane.ERROR_MESSAGE); } } else { msg.showMessageDialog(paneldown, "Please fill in the minimum length (Integers only)", "Error", JOptionPane.ERROR_MESSAGE); } } if (box2.isSelected()) { boolean gapisnumber = false; boolean minisnumber = false; int gap = 0; int min = 0; try { gap = Integer.parseInt(max.getText()); gapisnumber = true; } catch (NumberFormatException ex) { gapisnumber = false; } try { min = Integer.parseInt(minpregap.getText()); minisnumber = true; } catch (NumberFormatException ex) { minisnumber = false; } if (gapisnumber && minisnumber) { try { getImPerfectSSRs(organisms, min, flag, gap); for (int i = 0; i < organisms.length; i++) { PrintWriter stats = null; PrintWriter html = null; String location = ""; // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here PrintWriter out = null; DataOutputStream lt = null; if (filetype.contains("organisms")) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter( "organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream( new FileOutputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".imperf"))); html = new PrintWriter(new FileWriter( "organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("organisms/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "organisms/" + organisms[i] + "/results/allImPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; location = toopen; out = new PrintWriter(toopen); out.println("Results for organism: " + organisms[i] + "\t Search Parameters --> Maximum Mismatch length for ImPerfect SSRs : " + gap + " minimum SSR length before given gap: " + min); } else if (filetype.contains("local")) { File f = new File("local/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter( "local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".imperf"))); html = new PrintWriter(new FileWriter( "local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("local/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "local/" + organisms[i] + "/results/allImPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; location = toopen; out = new PrintWriter(toopen); out.println("Results for project: " + organisms[i] + "\t Search Parameters --> Maximum Mismatch length for ImPerfect SSRs : " + gap + " minimum SSR length before given gap: " + min); } if (mono.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + min + "_" + gap + "_monoImPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int start = in.readInt(); int end = in.readInt(); if (!ssr.contains("N")) out.println("SSR: " + ssr + " start-end " + start + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } catch (EOFException exc) { eof = true; } } in.close(); } } if (di.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + min + "_" + gap + "_diImPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int start = in.readInt(); int end = in.readInt(); if (!ssr.contains("N")) out.println("SSR: " + ssr + " start-end " + start + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } catch (EOFException exc) { eof = true; } } in.close(); } } if (tri.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + min + "_" + gap + "_triImPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int start = in.readInt(); int end = in.readInt(); if (!ssr.contains("N")) out.println("SSR: " + ssr + " start-end " + start + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } catch (EOFException exc) { eof = true; } } in.close(); } } if (tetra.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + min + "_" + gap + "_tetraImPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int start = in.readInt(); int end = in.readInt(); if (!ssr.contains("N")) out.println("SSR: " + ssr + " start-end " + start + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } catch (EOFException exc) { eof = true; } } in.close(); } } if (penta.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + min + "_" + gap + "_pentaImPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int start = in.readInt(); int end = in.readInt(); if (!ssr.contains("N")) out.println("SSR: " + ssr + " start-end " + start + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } catch (EOFException exc) { eof = true; } } in.close(); } } if (hexa.isSelected()) { // 18/11/2013 added starting here if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream( new BufferedInputStream(new FileInputStream( files + "_" + min + "_" + gap + "_hexaImPerfect.temp"))); boolean eof = false; while (!eof) { try { String ssr = in.readUTF(); int start = in.readInt(); int end = in.readInt(); if (!ssr.contains("N")) out.println("SSR: " + ssr + " start-end " + start + "-" + end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } catch (EOFException exc) { eof = true; } } in.close(); } } out.close(); Runtime.getRuntime().exec("notepad " + location); DecimalFormat round = new DecimalFormat("#.###"); html.println("<html><h1>******* ImPerfect SSRs *******</h1>"); html.println("<h4>Results for project: " + organisms[i] + "</h4><h4>Search Parameters --> Maximum Mismatch length for ImPerfect SSRs (bp): " + gap + "</h4><h4>minimum SSR length before given Mismatch length (bp): " + min + "</h4>"); html.println( "<table border=\"1\"><tr><td><b>motif</b></td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); stats.println("******* ImPerfect SSRs *******"); stats.println("Results for project: " + organisms[i] + "\n Search Parameters --> Maximum Mismatch length for ImPerfect SSRs (bp): " + gap + " \nminimum SSR length before given Mismatch length (bp): " + min); stats.println( " ____________________________________________________________________________________________________________ "); stats.println( "| | | | | | | | Relative | | Relative |"); stats.println( "| motif | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); stats.println( "|=======|=======|============|=======|=======|=======|=======|===============|===============|===============|"); int totalcount = 0; long bpcount = 0; int Aperc = 0; int Tperc = 0; int Gperc = 0; int Cperc = 0; float relfreq = 0; float abfreq = 0; long seqcount = 0; if (mono.isSelected()) { totalcount += countmono.get(i); bpcount += countmonore.get(i); } if (di.isSelected()) { totalcount += countdi.get(i); bpcount += countdire.get(i); } if (tri.isSelected()) { totalcount += counttri.get(i); bpcount += counttrire.get(i); } if (tetra.isSelected()) { totalcount += counttetra.get(i); bpcount += counttetrare.get(i); } if (penta.isSelected()) { totalcount += countpenta.get(i); bpcount += countpentare.get(i); } if (hexa.isSelected()) { totalcount += counthexa.get(i); bpcount += counthexare.get(i); } try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Connection con = null; try { con = DriverManager.getConnection("jdbc:mysql://localhost:3306", "biouser", "thesis2012"); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Statement st = null; try { st = con.createStatement(); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } st.executeUpdate("use lobid"); seqcount = 0; if (filetype.contains("organisms")) { ResultSet rs = st.executeQuery( "SELECT end FROM slices INNER JOIN organism WHERE slices.org_id=organism.org_id AND organism.name='" + organisms[i] + "'"); while (rs.next()) { seqcount += Long.parseLong(rs.getString(1)); } } else if (filetype.contains("local")) { BufferedReader in = new BufferedReader( new FileReader("local/" + organisms[i] + "/index.txt")); int count = countlines("local/" + organisms[i] + "/index.txt"); for (int c = 0; c < count; c++) { String temp = in.readLine(); BufferedReader tmp = new BufferedReader( new FileReader("local/" + organisms[i] + "/" + temp + ".txt")); boolean eof = false; while (!eof) { String s = tmp.readLine(); if (s != null) { seqcount += s.length(); } else { eof = true; } } tmp.close(); } } int tempmono = countmonore.get(i); int tempdi = countdire.get(i); int temptri = counttrire.get(i); int temptetra = counttetrare.get(i); int temppenta = countpentare.get(i); int temphexa = counthexare.get(i); if (tempmono == 0) tempmono = 1; if (tempdi == 0) tempdi = 1; if (temptri == 0) temptri = 1; if (temptetra == 0) temptetra = 1; if (temppenta == 0) temppenta = 1; if (temphexa == 0) temphexa = 1; if (mono.isSelected()) { Aperc += Amono.get(i); Tperc += Tmono.get(i); Gperc += Gmono.get(i); Cperc += Cmono.get(i); //lt.writeInt(countmono.get(i));lt.writeInt(countmonore.get(i));lt.writeFloat((float)Amono.get(i)*100/tempmono);lt.writeFloat((float)Tmono.get(i)*100/tempmono);lt.writeFloat((float)Gmono.get(i)*100/tempmono);lt.writeFloat((float)Cmono.get(i)*100/tempmono);lt.writeFloat((float) countmono.get(i) / totalcount);lt.writeFloat((float) countmonore.get(i) / seqcount);lt.writeFloat((float) countmonore.get(i) / bpcount); stats.printf("|mono |" + cell(Integer.toString(countmono.get(i)), 7) + "|" + cell(Integer.toString(countmonore.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) countmono.get(i) / totalcount, 15) + "|" + cell((float) countmonore.get(i) / seqcount, 15) + "|" + cell((float) countmonore.get(i) / bpcount, 15) + "|\n", cell((float) (Amono.get(i) * 100) / (tempmono), 7), cell((float) (Tmono.get(i) * 100) / (tempmono), 7), cell((float) (Cmono.get(i) * 100) / (tempmono), 7), cell((float) (Gmono.get(i) * 100) / (tempmono), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>mono</b></td><td>" + countmono.get(i) + "</td><td>" + (countmonore.get(i)) + "</td><td>" + round.format((float) (Amono.get(i) * 100) / (tempmono)) + "</td><td>" + round.format((float) (Tmono.get(i) * 100) / (tempmono)) + "</td><td>" + round.format((float) (Cmono.get(i) * 100) / (tempmono)) + "</td><td>" + round.format((float) (Gmono.get(i) * 100) / (tempmono)) + "</td><td>" + round.format((float) countmono.get(i) / totalcount) + "</td><td>" + round.format((float) countmonore.get(i) / seqcount) + "</td><td>" + round.format((float) countmonore.get(i) / bpcount) + "</td></tr>"); } if (di.isSelected()) { Aperc += Adi.get(i); Tperc += Tdi.get(i); Gperc += Gdi.get(i); Cperc += Cdi.get(i); //lt.writeInt(countdi.get(i));lt.writeInt(countdi.get(i)re.get(i));lt.writeFloat((float)Adi.get(i)*100/tempdi);lt.writeFloat((float)Tdi.get(i)*100/tempdi);lt.writeFloat((float)Gdi.get(i)*100/tempdi);lt.writeFloat((float)Cdi.get(i)*100/tempdi);lt.writeFloat((float) countdi.get(i) / totalcount);lt.writeFloat((float) countdi.get(i)re.get(i) / seqcount);lt.writeFloat((float) countdi.get(i)re.get(i) / bpcount); stats.printf( "|di |" + cell(Integer.toString(countdi.get(i)), 7) + "|" + cell(Integer.toString(countdire.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) countdi.get(i) / totalcount, 15) + "|" + cell((float) countdi.get(i) / seqcount, 15) + "|" + cell((float) countdi.get(i) / bpcount, 15) + "|\n", cell((float) (Adi.get(i) * 100) / (tempdi), 7), cell((float) (Tdi.get(i) * 100) / (tempdi), 7), cell((float) (Cdi.get(i) * 100) / (tempdi), 7), cell((float) (Gdi.get(i) * 100) / (tempdi), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>di</b></td><td>" + countdi.get(i) + "</td><td>" + (countdire.get(i)) + "</td><td>" + round.format((float) (Adi.get(i) * 100) / (tempdi)) + "</td><td>" + round.format((float) (Tdi.get(i) * 100) / (tempdi)) + "</td><td>" + round.format((float) (Cdi.get(i) * 100) / (tempdi)) + "</td><td>" + round.format((float) (Gdi.get(i) * 100) / (tempdi)) + "</td><td>" + round.format((float) countdi.get(i) / totalcount) + "</td><td>" + round.format((float) countdire.get(i) / seqcount) + "</td><td>" + round.format((float) countdire.get(i) / bpcount) + "</td></tr>"); } if (tri.isSelected()) { Aperc += Atri.get(i); Tperc += Ttri.get(i); Gperc += Gtri.get(i); Cperc += Ctri.get(i); //lt.writeInt(counttri.get(i));lt.writeInt(counttrire.get(i).get(i));lt.writeFloat((float)Atri.get(i)*100/temptri);lt.writeFloat((float)Ttri.get(i)*100/temptri);lt.writeFloat((float)Gtri.get(i)*100/temptri);lt.writeFloat((float)Ctri.get(i)*100/temptri);lt.writeFloat((float) counttri.get(i) / totalcount);lt.writeFloat((float) counttrire.get(i).get(i) / seqcount);lt.writeFloat((float) counttrire.get(i).get(i) / bpcount); stats.printf("|tri |" + cell(Integer.toString(counttri.get(i)), 7) + "|" + cell(Integer.toString(counttrire.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) counttri.get(i) / totalcount, 15) + "|" + cell((float) counttrire.get(i) / seqcount, 15) + "|" + cell((float) counttrire.get(i) / bpcount, 15) + "|\n", cell((float) (Atri.get(i) * 100) / (temptri), 7), cell((float) (Ttri.get(i) * 100) / (temptri), 7), cell((float) (Ctri.get(i) * 100) / (temptri), 7), cell((float) (Gtri.get(i) * 100) / (temptri), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>tri</b></td><td>" + counttri.get(i) + "</td><td>" + (counttrire.get(i)) + "</td><td>" + round.format((float) (Atri.get(i) * 100) / (temptri)) + "</td><td>" + round.format((float) (Ttri.get(i) * 100) / (temptri)) + "</td><td>" + round.format((float) (Ctri.get(i) * 100) / (temptri)) + "</td><td>" + round.format((float) (Gtri.get(i) * 100) / (temptri)) + "</td><td>" + round.format((float) counttri.get(i) / totalcount) + "</td><td>" + round.format((float) counttrire.get(i) / seqcount) + "</td><td>" + round.format((float) counttrire.get(i) / bpcount) + "</td></tr>"); } if (tetra.isSelected()) { Aperc += Atetra.get(i); Tperc += Ttetra.get(i); Gperc += Gtetra.get(i); Cperc += Ctetra.get(i); //lt.writeInt(counttetra.get(i));lt.writeInt(counttetrare.get(i));lt.writeFloat((float)Atetra.get(i)*100/temptetra);lt.writeFloat((float)Ttetra.get(i)*100/temptetra);lt.writeFloat((float)Gtetra.get(i)*100/temptetra);lt.writeFloat((float)Ctetra.get(i)*100/temptetra);lt.writeFloat((float) counttetra.get(i) / totalcount);lt.writeFloat((float) counttetrare.get(i) / seqcount);lt.writeFloat((float) counttetrare.get(i) / bpcount); stats.printf("|tetra |" + cell(Integer.toString(counttetra.get(i)), 7) + "|" + cell(Integer.toString(counttetrare.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) counttetra.get(i) / totalcount, 15) + "|" + cell((float) counttetrare.get(i) / seqcount, 15) + "|" + cell((float) counttetrare.get(i) / bpcount, 15) + "|\n", cell((float) (Atetra.get(i) * 100) / (temptetra), 7), cell((float) (Ttetra.get(i) * 100) / (temptetra), 7), cell((float) (Ctetra.get(i) * 100) / (temptetra), 7), cell((float) (Gtetra.get(i) * 100) / (temptetra), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>tetra</b></td><td>" + counttetra.get(i) + "</td><td>" + (counttetrare.get(i)) + "</td><td>" + round.format((float) (Atetra.get(i) * 100) / (temptetra)) + "</td><td>" + round.format((float) (Ttetra.get(i) * 100) / (temptetra)) + "</td><td>" + round.format((float) (Ctetra.get(i) * 100) / (temptetra)) + "</td><td>" + round.format((float) (Gtetra.get(i) * 100) / (temptetra)) + "</td><td>" + round.format((float) counttetra.get(i) / totalcount) + "</td><td>" + round.format((float) counttetrare.get(i) / seqcount) + "</td><td>" + round.format((float) counttetrare.get(i) / bpcount) + "</td></tr>"); } if (penta.isSelected()) { Aperc += Apenta.get(i); Tperc += Tpenta.get(i); Gperc += Gpenta.get(i); Cperc += Cpenta.get(i); //lt.writeInt(countpenta.get(i));lt.writeInt(countpentare.get(i));lt.writeFloat((float)Apenta.get(i)*100/temppenta);lt.writeFloat((float)Tpenta.get(i)*100/temppenta);lt.writeFloat((float)Gpenta.get(i)*100/temppenta);lt.writeFloat((float)Cpenta.get(i)*100/temppenta);lt.writeFloat((float) countpenta.get(i) / totalcount);lt.writeFloat((float) countpentare.get(i) / seqcount);lt.writeFloat((float) countpentare.get(i) / bpcount); stats.printf("|penta |" + cell(Integer.toString(countpenta.get(i)), 7) + "|" + cell(Integer.toString(countpentare.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) countpenta.get(i) / totalcount, 15) + "|" + cell((float) countpentare.get(i) / seqcount, 15) + "|" + cell((float) countpentare.get(i) / bpcount, 15) + "|\n", cell((float) (Apenta.get(i) * 100) / (temppenta), 7), cell((float) (Tpenta.get(i) * 100) / (temppenta), 7), cell((float) (Cpenta.get(i) * 100) / (temppenta), 7), cell((float) (Gpenta.get(i) * 100) / (temppenta), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>penta</b></td><td>" + countpenta.get(i) + "</td><td>" + (countpentare.get(i)) + "</td><td>" + round.format((float) (Apenta.get(i) * 100) / (temppenta)) + "</td><td>" + round.format((float) (Tpenta.get(i) * 100) / (temppenta)) + "</td><td>" + round.format((float) (Cpenta.get(i) * 100) / (temppenta)) + "</td><td>" + round.format((float) (Gpenta.get(i) * 100) / (temppenta)) + "</td><td>" + round.format((float) countpenta.get(i) / totalcount) + "</td><td>" + round.format((float) countpentare.get(i) / seqcount) + "</td><td>" + round.format((float) countpentare.get(i) / bpcount) + "</td></tr>"); } if (hexa.isSelected()) { Aperc += Ahexa.get(i); Tperc += Thexa.get(i); Gperc += Ghexa.get(i); Cperc += Chexa.get(i); //lt.writeInt(counthexa.get(i));lt.writeInt(counthexare.get(i));lt.writeFloat((float)Ahexa.get(i)*100/temphexa);lt.writeFloat((float)Thexa.get(i)*100/temphexa);lt.writeFloat((float)Ghexa.get(i)*100/temphexa);lt.writeFloat((float)Chexa.get(i)*100/temphexa);lt.writeFloat((float) counthexa.get(i) / totalcount);lt.writeFloat((float) counthexare.get(i) / seqcount);lt.writeFloat((float) counthexare.get(i) / bpcount); stats.printf("|hexa |" + cell(Integer.toString(counthexa.get(i)), 7) + "|" + cell(Integer.toString(counthexare.get(i)), 12) + "|%s|%s|%s|%s|" + cell((float) counthexa.get(i) / totalcount, 15) + "|" + cell((float) counthexare.get(i) / seqcount, 15) + "|" + cell((float) counthexare.get(i) / bpcount, 15) + "|\n", cell((float) (Ahexa.get(i) * 100) / (temphexa), 7), cell((float) (Thexa.get(i) * 100) / (temphexa), 7), cell((float) (Chexa.get(i) * 100) / (temphexa), 7), cell((float) (Ghexa.get(i) * 100) / (temphexa), 7)); stats.println( "|-------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>hexa</b></td><td>" + counthexa.get(i) + "</td><td>" + (counthexare.get(i)) + "</td><td>" + round.format((float) (Ahexa.get(i) * 100) / (temphexa)) + "</td><td>" + round.format((float) (Thexa.get(i) * 100) / (temphexa)) + "</td><td>" + round.format((float) (Chexa.get(i) * 100) / (temphexa)) + "</td><td>" + round.format((float) (Ghexa.get(i) * 100) / (temphexa)) + "</td><td>" + round.format((float) counthexa.get(i) / totalcount) + "</td><td>" + round.format((float) counthexare.get(i) / seqcount) + "</td><td>" + round.format((float) counthexare.get(i) / bpcount) + "</td></tr>"); } if (mono.isSelected()) { relfreq += (float) countmono.get(i) / totalcount; abfreq += (float) countmonore.get(i) / bpcount; } if (di.isSelected()) { relfreq += (float) countdi.get(i) / totalcount; abfreq += (float) countdire.get(i) / bpcount; } if (tri.isSelected()) { relfreq += (float) counttri.get(i) / totalcount; abfreq += (float) counttrire.get(i) / bpcount; } if (tetra.isSelected()) { relfreq += (float) counttetra.get(i) / totalcount; abfreq += (float) counttetrare.get(i) / bpcount; } if (penta.isSelected()) { relfreq += (float) countpenta.get(i) / totalcount; abfreq += (float) countpentare.get(i) / bpcount; } if (hexa.isSelected()) { relfreq += (float) counthexa.get(i) / totalcount; abfreq += (float) counthexare.get(i) / bpcount; } lt.writeLong(seqcount); lt.writeInt(totalcount); lt.writeLong(bpcount); lt.writeInt(Aperc); lt.writeInt(Tperc); lt.writeInt(Gperc); lt.writeInt(Cperc); stats.println("|TOTAL |" + cell(Integer.toString(totalcount), 7) + "|" + cell(Long.toString(bpcount), 12) + "|" + cell((float) Aperc * 100 / bpcount, 7) + "|" + cell((float) Tperc * 100 / bpcount, 7) + "|" + cell((float) Cperc * 100 / bpcount, 7) + "|" + cell((float) Gperc * 100 / bpcount, 7) + "|" + cell(relfreq, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) abfreq, 15) + "|"); stats.println( "|_______|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); stats.println("Genome length (bp): " + seqcount); stats.println("Relative Frequency: Count of each motif type / total SSR count"); stats.println("Abundance: bp of each motif type / total sequence bp"); stats.println( "Relative Abundance: bp of each motif type / total microsatellites bp"); stats.println(); stats.println(); stats.close(); lt.close(); html.println("<tr><td><b>TOTAL</b></td><td>" + totalcount + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) relfreq) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) abfreq) + "</td></tr></table></html>"); html.close(); } } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); //msg.showMessageDialog(paneldown, "Update your selected species", "Error", JOptionPane.ERROR_MESSAGE); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } else { if (!gapisnumber && !minisnumber) { msg.showMessageDialog(paneldown, "Fill in Mismatch length for Imperfect SSRs \n and the minimum sequence length before the Mismatch length\n (Integers only)", "Error", JOptionPane.ERROR_MESSAGE); } else { if (!gapisnumber) { msg.showMessageDialog(paneldown, "Fill in Mismatch length for Imperfect SSRs (Integer only)", "Error", JOptionPane.ERROR_MESSAGE); } if (!minisnumber) { msg.showMessageDialog(paneldown, "Fill in the minimum sequence length before the Mismatch length (Integer only)", "Error", JOptionPane.ERROR_MESSAGE); } } } } if (box3.isSelected()) { boolean lenisnumber; boolean gapisnumber; int minlen = 0; int gap = 0; if (!com.isSelected() && !incom.isSelected()) { msg.showMessageDialog(paneldown, "Select a Compound SSR Option", "Error", JOptionPane.ERROR_MESSAGE); } else { try { minlen = Integer.parseInt(score.getText()); lenisnumber = true; } catch (NumberFormatException ex) { lenisnumber = false; } try { gap = Integer.parseInt(maxgapcomp.getText()); gapisnumber = true; } catch (NumberFormatException ex) { gapisnumber = false; } if (lenisnumber && gapisnumber) { if (com.isSelected()) { try { getCompoundPerfectSSRs(organisms, minlen, flag, gap); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); //msg.showMessageDialog(paneldown, "Update your selected species", "Error", JOptionPane.ERROR_MESSAGE); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } if (incom.isSelected()) { try { getImPerfectCompoundSSRs(organisms, minlen, flag, gap); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); //msg.showMessageDialog(paneldown, "Update your selected species", "Error", JOptionPane.ERROR_MESSAGE); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } } else { if (!lenisnumber) { msg.showMessageDialog(paneldown, "Minimum length requires an Integer", "Error", JOptionPane.ERROR_MESSAGE); } if (!gapisnumber) { msg.showMessageDialog(paneldown, "Inter-repeat Region between compound SSRs requires an Integer", "Error", JOptionPane.ERROR_MESSAGE); } } } } if (box1.isSelected() || box2.isSelected() || box3.isSelected() || com.isSelected() || incom.isSelected()) { PrintWriter out = null; PrintWriter html = null; boolean orgs = true; DecimalFormat round = new DecimalFormat("#.###"); //String file=""; for (int i = 0; i < organisms.length; i++) { String file = "organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; File stats = new File(file); if (!stats.exists()) { orgs = false; file = "local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; } try { html = new PrintWriter( new FileWriter(file.substring(0, file.indexOf(".")) + ".html", true)); html.println("<html><h1>******* SUMMARY TABLE *******</h1>"); html.println( "<table border=\"1\"><tr><td>type</td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); out = new PrintWriter(new FileWriter(file, true)); out.println("******* SUMMARY TABLE *******"); out.println( " _________________________________________________________________________________________________________________ "); out.println( "| | | | | | | | Relative | | Relative |"); out.println( "| type | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); out.println( "|============|=======|============|=======|=======|=======|=======|===============|===============|===============|"); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } //TOTAL long seqcount = 0; int SSRcount = 0; int SSRbpcount = 0; int A = 0, T = 0, G = 0, C = 0; float relfreq = 0; float abfreq = 0; //perfect int pcount = 0; long pbpcount = 0; int Ap = 0, Tp = 0, Gp = 0, Cp = 0; //imperfect int imcount = 0; long imbpcount = 0; int Aim = 0, Tim = 0, Gim = 0, Cim = 0; //compound perfect int ccount = 0; long cbpcount = 0; int Ac = 0, Tc = 0, Gc = 0, Cc = 0; //compound imperfect int cicount = 0; long cibpcount = 0; int Aci = 0, Tci = 0, Gci = 0, Cci = 0; if (box1.isSelected()) { DataInputStream in = null; if (orgs) { try { in = new DataInputStream( new BufferedInputStream(new FileInputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".perf"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } else { try { in = new DataInputStream(new BufferedInputStream(new FileInputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".perf"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } try { seqcount = in.readLong(); pcount = in.readInt(); pbpcount = in.readLong(); Ap = in.readInt(); Tp = in.readInt(); Gp = in.readInt(); Cp = in.readInt(); A += Ap; T += Tp; G += Gp; C += Cp; SSRcount += pcount; SSRbpcount += pbpcount; in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } if (box2.isSelected()) { DataInputStream in = null; if (orgs) { try { in = new DataInputStream( new BufferedInputStream(new FileInputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".imperf"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } else { try { in = new DataInputStream(new BufferedInputStream(new FileInputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".imperf"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } try { seqcount = in.readLong(); imcount = in.readInt(); imbpcount = in.readLong(); Aim = in.readInt(); Tim = in.readInt(); Gim = in.readInt(); Cim = in.readInt(); A += Aim; T += Tim; G += Gim; C += Cim; SSRcount += imcount; SSRbpcount += imbpcount; in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } if (box3.isSelected()) { if (com.isSelected()) { DataInputStream in = null; if (orgs) { try { in = new DataInputStream(new BufferedInputStream( new FileInputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compp"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } else { try { in = new DataInputStream(new BufferedInputStream( new FileInputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compp"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } try { seqcount = in.readLong(); ccount = in.readInt(); cbpcount = in.readInt(); Ac = in.readInt(); Tc = in.readInt(); Gc = in.readInt(); Cc = in.readInt(); A += Ac; T += Tc; G += Gc; C += Cc; SSRcount += ccount; SSRbpcount += cbpcount; in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } if (incom.isSelected()) { DataInputStream in = null; if (orgs) { try { in = new DataInputStream(new BufferedInputStream( new FileInputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compim"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } else { try { in = new DataInputStream(new BufferedInputStream( new FileInputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compim"))); } catch (FileNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } try { seqcount = in.readLong(); cicount = in.readInt(); cibpcount = in.readInt(); Aci = in.readInt(); Tci = in.readInt(); Gci = in.readInt(); Cci = in.readInt(); A += Aci; T += Tci; G += Gci; C += Cci; SSRcount += cicount; SSRbpcount += cibpcount; in.close(); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } } if (box1.isSelected()) { relfreq += (float) pcount / SSRcount; abfreq += (float) pbpcount / SSRbpcount; out.printf( "|Perfect |" + cell(Integer.toString(pcount), 7) + "|" + cell(Long.toString(pbpcount), 12) + "|%s|%s|%s|%s|" + cell((float) pcount / SSRcount, 15) + "|" + cell((float) pbpcount / seqcount, 15) + "|" + cell((float) pbpcount / SSRbpcount, 15) + "|\n", cell((float) (Ap * 100) / (SSRbpcount), 7), cell((float) (Tp * 100) / (SSRbpcount), 7), cell((float) (Cp * 100) / (SSRbpcount), 7), cell((float) (Gp * 100) / (SSRbpcount), 7)); out.println( "|------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>Perfect</b></td><td>" + pcount + "</td><td>" + pbpcount + "</td><td>" + round.format((float) Ap * 100 / SSRbpcount) + "</td><td>" + round.format((float) Tp * 100 / SSRbpcount) + "</td><td>" + round.format((float) Cp * 100 / SSRbpcount) + "</td><td>" + round.format((float) Gp * 100 / SSRbpcount) + "</td><td>" + round.format((float) pcount / SSRcount) + "</td><td>" + round.format((float) pbpcount / seqcount) + "</td><td>" + round.format((float) pbpcount / SSRbpcount) + "</td></tr>"); } if (box2.isSelected()) { relfreq += (float) imcount / SSRcount; abfreq += (float) imbpcount / SSRbpcount; out.printf( "|Imperfect |" + cell(Integer.toString(imcount), 7) + "|" + cell(Long.toString(imbpcount), 12) + "|%s|%s|%s|%s|" + cell((float) imcount / SSRcount, 15) + "|" + cell((float) imbpcount / seqcount, 15) + "|" + cell((float) imbpcount / SSRbpcount, 15) + "|\n", cell((float) (Aim * 100) / (SSRbpcount), 7), cell((float) (Tim * 100) / (SSRbpcount), 7), cell((float) (Cim * 100) / (SSRbpcount), 7), cell((float) (Gim * 100) / (SSRbpcount), 7)); out.println( "|------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>Imperfect</b></td><td>" + imcount + "</td><td>" + imbpcount + "</td><td>" + round.format((float) Aim * 100 / SSRbpcount) + "</td><td>" + round.format((float) Tim * 100 / SSRbpcount) + "</td><td>" + round.format((float) Cim * 100 / SSRbpcount) + "</td><td>" + round.format((float) Gim * 100 / SSRbpcount) + "</td><td>" + round.format((float) imcount / SSRcount) + "</td><td>" + round.format((float) imbpcount / seqcount) + "</td><td>" + round.format((float) imbpcount / SSRbpcount) + "</td></tr>"); } if (box3.isSelected()) { if (com.isSelected()) { abfreq += (float) cbpcount / SSRbpcount; relfreq += (float) ccount / SSRcount; out.printf( "|Compound Per|" + cell(Integer.toString(ccount), 7) + "|" + cell(Long.toString(cbpcount), 12) + "|%s|%s|%s|%s|" + cell((float) ccount / SSRcount, 15) + "|" + cell((float) cbpcount / seqcount, 15) + "|" + cell((float) cbpcount / SSRbpcount, 15) + "|\n", cell((float) (Ac * 100) / (SSRbpcount), 7), cell((float) (Tc * 100) / (SSRbpcount), 7), cell((float) (Cc * 100) / (SSRbpcount), 7), cell((float) (Gc * 100) / (SSRbpcount), 7)); out.println( "|------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>Compound Perf.</b></td><td>" + ccount + "</td><td>" + cbpcount + "</td><td>" + round.format((float) Ac * 100 / SSRbpcount) + "</td><td>" + round.format((float) Tc * 100 / SSRbpcount) + "</td><td>" + round.format((float) Cc * 100 / SSRbpcount) + "</td><td>" + round.format((float) Gc * 100 / SSRbpcount) + "</td><td>" + round.format((float) ccount / SSRcount) + "</td><td>" + round.format((float) cbpcount / seqcount) + "</td><td>" + round.format((float) cbpcount / SSRbpcount) + "</td></tr>"); } if (incom.isSelected()) { abfreq += (float) cibpcount / SSRbpcount; relfreq += (float) cicount / SSRcount; out.printf( "|Compound Imp|" + cell(Integer.toString(cicount), 7) + "|" + cell(Long.toString(cibpcount), 12) + "|%s|%s|%s|%s|" + cell((float) cicount / SSRcount, 15) + "|" + cell((float) cibpcount / seqcount, 15) + "|" + cell((float) cibpcount / SSRbpcount, 15) + "|\n", cell((float) (Aci * 100) / (SSRbpcount), 7), cell((float) (Tci * 100) / (SSRbpcount), 7), cell((float) (Cci * 100) / (SSRbpcount), 7), cell((float) (Gci * 100) / (SSRbpcount), 7)); out.println( "|------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); html.println("<tr><td><b>Compound Imperf.</b></td><td>" + cicount + "</td><td>" + cibpcount + "</td><td>" + round.format((float) Aci * 100 / SSRbpcount) + "</td><td>" + round.format((float) Tci * 100 / SSRbpcount) + "</td><td>" + round.format((float) Cci * 100 / SSRbpcount) + "</td><td>" + round.format((float) Gci * 100 / SSRbpcount) + "</td><td>" + round.format((float) cicount / SSRcount) + "</td><td>" + round.format((float) cibpcount / seqcount) + "</td><td>" + round.format((float) cibpcount / SSRbpcount) + "</td></tr>"); } } out.println("|TOTAL |" + cell(Integer.toString(SSRcount), 7) + "|" + cell(Long.toString(SSRbpcount), 12) + "|" + cell((float) A * 100 / SSRbpcount, 7) + "|" + cell((float) T * 100 / SSRbpcount, 7) + "|" + cell((float) C * 100 / SSRbpcount, 7) + "|" + cell((float) G * 100 / SSRbpcount, 7) + "|" + cell(relfreq, 15) + "|" + cell((float) SSRbpcount / seqcount, 15) + "|" + cell((float) abfreq, 15) + "|"); out.println( "|____________|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); out.println("Genome length (bp): " + seqcount); out.println("Relative Frequency: Count of each motif type / total SSR count"); out.println("Abundance: bp of each motif type / total sequence bp"); out.println("Relative Abundance: bp of each motif type / total microsatellites bp"); out.println(); out.println(); out.close(); html.println("<tr><td><b>TOTAL</b></td><td>" + SSRcount + "</td><td>" + SSRbpcount + "</td><td>" + round.format((float) A * 100 / SSRbpcount) + "</td><td>" + round.format((float) T * 100 / SSRbpcount) + "</td><td>" + round.format((float) C * 100 / SSRbpcount) + "</td><td>" + round.format((float) G * 100 / SSRbpcount) + "</td><td>" + round.format((float) relfreq) + "</td><td>" + round.format((float) SSRbpcount / seqcount) + "</td><td>" + round.format((float) abfreq) + "</td></tr></table></html>"); html.close(); try { Runtime.getRuntime().exec("notepad " + file); } catch (IOException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } } } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }); selectsp = new JButton("Select new Species"); selectsp.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { try { input_frame frame = new input_frame(); } catch (ClassNotFoundException ex) { Logger.getLogger(updateframe.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(updateframe.class.getName()).log(Level.SEVERE, null, ex); } dispose(); } }); quit = new JButton("Quit"); quit.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { System.exit(0); } }); tab = new JTabbedPane(); tab.setSize(790, 590); // about us panel ImageIcon image = new ImageIcon("miga.png"); JLabel label = new JLabel("", image, JLabel.CENTER); contact = new JLabel( "<html><b><p>Machine Learning and Knowledge Discovery Group</p><p>Computer Science Department</p><p>Aristotle University of Thessaloniki</p><p> </p><p>In collaboration with the laboratory of</p><p> </p><p>Population Genetics of Animal Organisms</p><p>Department of Genetics, Development and Molecular Biology</p><p>School of Biology</p><p>Aristotle University of Thessaloniki</p><p> </p><p> </p><p>For any comments or information please contact with:</p><p><a href=\"mailto:ikavak@csd.auth.gr\">ikavak@csd.auth.gr</a></p></b></html>"); about = new JPanel(); about.setLayout(new GridBagLayout()); GridBagConstraints ab = new GridBagConstraints(); ab.fill = GridBagConstraints.WEST; ab.weightx = 0.5; ab.weighty = 0.5; ab.gridx = 0; ab.gridy = 0; about.add(label, ab); ab.fill = GridBagConstraints.WEST; ab.weightx = 0.5; ab.weighty = 0.5; ab.gridx = 0; ab.gridy = 1; about.add(contact, ab); //end of about us //below are the rest of th panels paneltop = new JPanel(); TitledBorder t = BorderFactory.createTitledBorder("Select Period"); paneltop.setBorder(t); paneltop.setLayout(new GridBagLayout()); GridBagConstraints pt = new GridBagConstraints(); pt.fill = GridBagConstraints.HORIZONTAL; pt.weightx = 0.5; pt.weighty = 0.5; pt.gridx = 0; pt.gridy = 0; paneltop.add(mono, pt); pt.fill = GridBagConstraints.HORIZONTAL; pt.weightx = 0.5; pt.weighty = 0.5; pt.gridx = 0; pt.gridy = -1; paneltop.add(di, pt); pt.fill = GridBagConstraints.HORIZONTAL; pt.weightx = 0.5; pt.weighty = 0.5; pt.gridx = 0; pt.gridy = -2; paneltop.add(tri, pt); pt.fill = GridBagConstraints.HORIZONTAL; pt.weightx = 0.5; pt.weighty = 0.5; pt.gridx = 0; pt.gridy = -3; paneltop.add(tetra, pt); pt.fill = GridBagConstraints.HORIZONTAL; pt.weightx = 0.5; pt.weighty = 0.5; pt.gridx = 0; pt.gridy = -4; paneltop.add(penta, pt); pt.fill = GridBagConstraints.HORIZONTAL; pt.weightx = 0.5; pt.weighty = 0.5; pt.gridx = 0; pt.gridy = -5; paneltop.add(hexa, pt); panel1 = new JPanel(); TitledBorder title = BorderFactory.createTitledBorder("Type"); panel1.setBorder(title); panel1.setLayout(new GridBagLayout()); GridBagConstraints a = new GridBagConstraints(); a.fill = GridBagConstraints.HORIZONTAL; a.weightx = 0.5; a.weighty = 0.5; a.gridx = 0; a.gridy = 0; panel1.add(select, a); a.fill = GridBagConstraints.HORIZONTAL; a.weightx = 0.5; a.weighty = 0.5; a.gridx = 0; a.gridy = -1; panel1.add(box1, a); a.fill = GridBagConstraints.HORIZONTAL; a.weightx = 0.5; a.weighty = 0.5; a.gridx = 0; a.gridy = -2; panel1.add(box2, a); a.fill = GridBagConstraints.HORIZONTAL; a.weightx = 0.5; a.weighty = 0.5; a.gridx = 0; a.gridy = -3; panel1.add(box3, a); panel2 = new JPanel(); panel2.setVisible(false); TitledBorder title2 = BorderFactory.createTitledBorder("More Options"); panel2.setBorder(title2); panel2.setLayout(new GridBagLayout()); GridBagConstraints b = new GridBagConstraints(); b.fill = GridBagConstraints.HORIZONTAL; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 0; b.gridy = 0; panel2.add(minimumssrlen, b); b.fill = GridBagConstraints.CENTER; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 1; b.gridy = 0; panel2.add(score, b); b.fill = GridBagConstraints.HORIZONTAL; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 0; b.gridy = -1; panel2.add(gapmax, b); b.fill = GridBagConstraints.CENTER; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 1; b.gridy = -1; panel2.add(max, b); b.fill = GridBagConstraints.HORIZONTAL; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 0; b.gridy = -2; panel2.add(minlenpregap, b); b.fill = GridBagConstraints.CENTER; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 1; b.gridy = -2; panel2.add(minpregap, b); b.fill = GridBagConstraints.HORIZONTAL; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 0; b.gridy = -3; panel2.add(gapcomp, b); b.fill = GridBagConstraints.CENTER; b.weightx = 0.5; b.weighty = 0.5; b.gridx = 1; b.gridy = -3; panel2.add(maxgapcomp, b); paneldownleft = new JPanel(); paneldownleft.setVisible(false); TitledBorder titledl = BorderFactory.createTitledBorder("Compound SSR options"); paneldownleft.setBorder(titledl); paneldownleft.setLayout(new GridBagLayout()); GridBagConstraints dl = new GridBagConstraints(); dl.fill = GridBagConstraints.CENTER; dl.weightx = 0.5; dl.weighty = 0.5; dl.gridx = 0; dl.gridy = 0; paneldownleft.add(com, dl); dl.fill = GridBagConstraints.CENTER; dl.weightx = 0.5; dl.weighty = 0.5; dl.gridx = 0; dl.gridy = -1; paneldownleft.add(incom, dl); paneldownright = new JPanel(); paneldownright.setLayout(new GridBagLayout()); GridBagConstraints dr = new GridBagConstraints(); dr.fill = GridBagConstraints.CENTER; dr.weightx = 0.5; dr.weighty = 0.5; dr.gridx = 0; dr.gridy = 0; paneldownright.add(show, dr); dr.fill = GridBagConstraints.CENTER; dr.weightx = 0.5; dr.weighty = 0.5; dr.gridx = 0; dr.gridy = -1; paneldownright.add(selectsp, dr); dr.fill = GridBagConstraints.CENTER; dr.weightx = 0.5; dr.weighty = 0.5; dr.gridx = 0; dr.gridy = -2; paneldownright.add(quit, dr); panelup = new JPanel(); TitledBorder titleup = BorderFactory.createTitledBorder("Statistics"); panelup.setBorder(titleup); panelup.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; c.weightx = 0.5; c.weighty = 0.5; c.gridx = 0; c.gridy = 0; panelup.add(paneltop, c); c.fill = GridBagConstraints.HORIZONTAL; c.weightx = 0.5; c.weighty = 0.5; c.gridx = 1; c.gridy = 0; panelup.add(panel1, c); c.fill = GridBagConstraints.HORIZONTAL; c.weightx = 0.5; c.weighty = 0.5; c.gridx = 0; c.gridy = -1; panelup.add(paneldownleft, c); c.fill = GridBagConstraints.HORIZONTAL; c.weightx = 0.5; c.weighty = 0.5; c.gridx = 1; c.gridy = -1; panelup.add(panel2, c); c.fill = GridBagConstraints.HORIZONTAL; c.weightx = 0.5; c.weighty = 0.5; c.gridx = 0; c.gridy = -2; panelup.add(paneldownright, c); TitledBorder s = BorderFactory.createTitledBorder("Standardization"); std.setBorder(s); std.add(no_st); std.add(part_st); std.add(full_st); std.setEnabled(false); c.fill = GridBagConstraints.HORIZONTAL; c.weightx = 0.5; c.weighty = 0.5; c.gridx = 0; c.gridy = -3; panelup.add(std, c); tab.add(panelup, "Statistics"); panelshow = new JPanel(); TitledBorder ps = BorderFactory.createTitledBorder("Sequence Retrieval"); panelshow.setBorder(ps); panelshow.setLayout(new GridBagLayout()); GridBagConstraints psg = new GridBagConstraints(); panelshowup = new JPanel(); panelshowup.setLayout(new GridBagLayout()); GridBagConstraints p = new GridBagConstraints(); p.fill = GridBagConstraints.WEST; p.weightx = 0.5; p.weighty = 0.5; p.gridx = 0; p.gridy = 0; panelshowup.add(lab, p); panelshowd = new JPanel(); panelshowd.setLayout(new GridBagLayout()); GridBagConstraints pd = new GridBagConstraints(); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 0; pd.gridy = -1; panelshowd.add(startlab, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -1; panelshowd.add(startnum, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 0; pd.gridy = -2; panelshowd.add(endlab, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -2; panelshowd.add(endnum, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 0; pd.gridy = -3; panelshowd.add(titlelab, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -3; panelshowd.add(titlef, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 0; pd.gridy = -4; panelshowd.add(flk, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -4; panelshowd.add(new JLabel(" "), pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 0; pd.gridy = -5; panelshowd.add(flankst, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -5; panelshowd.add(flankstn, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 0; pd.gridy = -6; panelshowd.add(flankend, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -6; panelshowd.add(flankendn, pd); pd.fill = GridBagConstraints.CENTER; pd.weightx = 0.5; pd.weighty = 0.5; pd.gridx = 1; pd.gridy = -7; panelshowd.add(retrieve, pd); psg.fill = GridBagConstraints.CENTER; psg.weightx = 0.5; psg.weighty = 0.5; psg.gridx = 0; psg.gridy = 0; panelshow.add(panelshowup, psg); psg.fill = GridBagConstraints.CENTER; psg.weightx = 0.5; psg.weighty = 0.5; psg.gridx = 0; psg.gridy = -1; panelshow.add(panelshowd, psg); psg.fill = GridBagConstraints.CENTER; psg.weightx = 0.5; psg.weighty = 0.5; psg.gridx = 0; psg.gridy = -2; panelshow.add(sbrText, psg); tab.add(panelshow, "Sequence Retrieval"); tab.add(about, "About us"); add(tab); setVisible(true); }
From source file:interfaces.InterfazPrincipal.java
private void BotonBuscarClienteSaldoActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_BotonBuscarClienteSaldoActionPerformed String nombreCliente = nombreClienteBusquedaSaldo.getText(); //08-11-2014 listar clientes por nombre ControladorCliente controladorCliente = new ControladorCliente(); ArrayList<Cliente> listaClientes = new ArrayList<>(); if (nombreCliente.equals("")) { listaClientes = controladorCliente.obtenerClientes(); } else {// w ww. j a v a 2 s . c o m listaClientes = controladorCliente.obtenerClientes(nombreCliente, 0); } //08-11-2014 Crear dialogo de bsqueda final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Buscar clientes"); dialogoEditar.setSize(300, 300); dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel ediitarTextoPrincipalDialogo = new JLabel("Buscar cliente"); c.gridx = 0; c.gridy = 0; c.gridwidth = 2; c.insets = new Insets(10, 60, 10, 10); Font textoGrande = new Font("Arial", 1, 16); ediitarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(ediitarTextoPrincipalDialogo, c); c.gridx = 0; c.gridy = 1; c.gridwidth = 2; c.insets = new Insets(10, 10, 10, 10); final JTable tablaDialogo = new JTable(); DefaultTableModel modeloTabla = new DefaultTableModel() { @Override public boolean isCellEditable(int row, int column) { //all cells false return false; } }; ; modeloTabla.addColumn("Identificacin"); modeloTabla.addColumn("Nombre"); //LLenar tabla for (int i = 0; i < listaClientes.size(); i++) { Object[] data = { "1", "2" }; data[0] = listaClientes.get(i).getCliente_id(); data[1] = listaClientes.get(i).getNombre(); modeloTabla.addRow(data); } tablaDialogo.setModel(modeloTabla); tablaDialogo.getColumn("Identificacin").setMinWidth(110); tablaDialogo.getColumn("Nombre").setMinWidth(110); tablaDialogo.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); JScrollPane scroll = new JScrollPane(tablaDialogo); scroll.setPreferredSize(new Dimension(220, 150)); panelDialogo.add(scroll, c); c.insets = new Insets(0, 0, 0, 10); c.gridx = 0; c.gridy = 2; c.gridwidth = 1; JButton botonGuardarClienteDialogo = new JButton("Elegir"); panelDialogo.add(botonGuardarClienteDialogo, c); c.gridx = 1; c.gridy = 2; c.gridwidth = 1; JButton botonCerrarClienteDialogo = new JButton("Cancelar"); panelDialogo.add(botonCerrarClienteDialogo, c); dialogoEditar.add(panelDialogo); dialogoEditar.setVisible(true); botonCerrarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { dialogoEditar.dispose(); } }); botonGuardarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int row = tablaDialogo.getSelectedRow(); if (row == -1) { JOptionPane.showMessageDialog(dialogoEditar, "Por favor seleccione una fila"); } else { Object identificacionCliente = tablaDialogo.getValueAt(row, 0); mostrarIdentificacionCliente.setText(String.valueOf(identificacionCliente)); String nombreClientePago = String.valueOf(tablaDialogo.getValueAt(row, 1)); //Limitar a 15 caracteres if (nombreClientePago.length() >= 15) { nombreClientePago = nombreClientePago.substring(0, 12); } textoPersonaSaldo.setText(nombreClientePago); DefaultTableModel modeloClientes = (DefaultTableModel) TablaDeSaldoClientes.getModel(); for (int i = 0; i < modeloClientes.getRowCount(); i++) { modeloClientes.removeRow(i); } modeloClientes.setRowCount(0); ControladorFlujoFactura controladorFlujoFactura = new ControladorFlujoFactura(); //SELECT * FROM Flujo_Factura where factura_id in (select factura_id from Factura where cliente_id = 1130614506); ArrayList<String[]> flujosCliente = controladorFlujoFactura.getTodosFlujo_Factura( " where factura_id in (select factura_id from Factura where cliente_id = " + String.valueOf(identificacionCliente) + " and estado=\"fiado\") order by factura_id"); double pago = 0.0; for (int i = 0; i < flujosCliente.size(); i++) { String[] datos = flujosCliente.get(i); TablaDeSaldoClientes.setModel(modeloClientes); NumberFormat formatter = new DecimalFormat("#0"); String valorMovimiento = String.valueOf(formatter.format(Double.parseDouble(datos[4]))); Object[] rowData = { datos[1], datos[2], datos[3], valorMovimiento }; if (datos[2].equals("deuda")) { pago += Double.parseDouble(datos[4]); } else { pago -= Double.parseDouble(datos[4]); } modeloClientes.addRow(rowData); } TablaDeSaldoClientes.setModel(modeloClientes); NumberFormat formatter = new DecimalFormat("#0"); textoTotalDebe.setText(String.valueOf(formatter.format(pago))); dialogoEditar.dispose(); //Mostrar en table de clientes los datos botonRegistrarAbono.setEnabled(true); } } }); }
From source file:interfaces.InterfazPrincipal.java
private void jButton7ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton7ActionPerformed String nombreCliente = nombreClienteReporteCliente.getText(); String identificacion = identificacionClienteCliente.getText(); try {// w w w . j a v a 2s . c o m //08-11-2014 listar clientes por nombre ControladorCliente controladorCliente = new ControladorCliente(); ArrayList<Cliente> listaClientes = new ArrayList<Cliente>(); if (nombreCliente.equals("") && identificacion.equals("")) { listaClientes = controladorCliente.obtenerClientes(); } else { int identificacionNumerico = 0; if (!identificacion.equals("")) { identificacionNumerico = Integer.parseInt(identificacion); } listaClientes = controladorCliente.obtenerClientes(nombreCliente, identificacionNumerico); } //08-11-2014 Crear dialogo de bsqueda final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Buscar clientes"); dialogoEditar.setSize(300, 300); dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel ediitarTextoPrincipalDialogo = new JLabel("Buscar cliente"); c.gridx = 0; c.gridy = 0; c.gridwidth = 2; c.insets = new Insets(10, 60, 10, 10); Font textoGrande = new Font("Arial", 1, 16); ediitarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(ediitarTextoPrincipalDialogo, c); c.gridx = 0; c.gridy = 1; c.gridwidth = 2; c.insets = new Insets(10, 10, 10, 10); final JTable tablaDialogo = new JTable(); DefaultTableModel modeloTabla = new DefaultTableModel() { @Override public boolean isCellEditable(int row, int column) { //all cells false return false; } }; ; modeloTabla.addColumn("Identificacin"); modeloTabla.addColumn("Nombre"); //LLenar tabla for (int i = 0; i < listaClientes.size(); i++) { Object[] data = { "1", "2" }; data[0] = listaClientes.get(i).getCliente_id(); data[1] = listaClientes.get(i).getNombre(); modeloTabla.addRow(data); } tablaDialogo.setModel(modeloTabla); tablaDialogo.getColumn("Identificacin").setMinWidth(110); tablaDialogo.getColumn("Nombre").setMinWidth(110); tablaDialogo.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); JScrollPane scroll = new JScrollPane(tablaDialogo); scroll.setPreferredSize(new Dimension(220, 150)); panelDialogo.add(scroll, c); c.insets = new Insets(0, 0, 0, 10); c.gridx = 0; c.gridy = 2; c.gridwidth = 1; JButton botonGuardarClienteDialogo = new JButton("Elegir"); panelDialogo.add(botonGuardarClienteDialogo, c); c.gridx = 1; c.gridy = 2; c.gridwidth = 1; JButton botonCerrarClienteDialogo = new JButton("Cancelar"); panelDialogo.add(botonCerrarClienteDialogo, c); dialogoEditar.add(panelDialogo); dialogoEditar.setVisible(true); botonCerrarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { dialogoEditar.dispose(); } }); botonGuardarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int row = tablaDialogo.getSelectedRow(); if (row == -1) { JOptionPane.showMessageDialog(dialogoEditar, "Por favor seleccione una fila"); } else { Object identificacionCliente = tablaDialogo.getValueAt(row, 0); jTextFieldIdentificacionClienteReporte.setText(String.valueOf(identificacionCliente)); botonGenerarReporteCliente.setEnabled(true); dialogoEditar.dispose(); } } }); // TODO add your handling code here: } catch (Exception e) { JOptionPane.showMessageDialog(this, "El valor de la identificacin de ser numrico"); } }
From source file:interfaces.InterfazPrincipal.java
private void tablaUsuariosDelSistemaMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_tablaUsuariosDelSistemaMouseClicked // TODO add your handling code here: String opcionHabilitar = "Habilitar"; String nombreUsuario = String .valueOf(tablaUsuariosDelSistema.getValueAt(tablaUsuariosDelSistema.getSelectedRow(), 0)); String estado = String .valueOf(tablaUsuariosDelSistema.getValueAt(tablaUsuariosDelSistema.getSelectedRow(), 2)); if (estado.equals("Habilitado")) { opcionHabilitar = "Deshabilitar"; }//from w w w.jav a2 s . c o m Object[] opciones = { "Cancelar", "Editar", opcionHabilitar }; final ControladorUsuarios controladorUsuarios = new ControladorUsuarios(); final Usuarios usuarioSelecionado = controladorUsuarios.obtenerUsuario(nombreUsuario); if (nombreUsuario.equals("admin") || nombreUsuario.equals(JTextFieldnombreDeUsuario.getText())) { JOptionPane.showMessageDialog(this, "No se puede editarse a si mismo o el usuario administrador del sistema", "Mensaje del sistema", JOptionPane.WARNING_MESSAGE); } else { int opcionElegida = JOptionPane.showOptionDialog(this, "Por favor elija una opcin", "Editar cliente", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.INFORMATION_MESSAGE, null, opciones, null); switch (opcionElegida) { case 1: final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Editar usuario"); dialogoEditar.setSize(400, 310); dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel editarTextoPrincipalDialogo = new JLabel("Editar clientes"); c.gridx = 0; c.gridy = 0; c.gridwidth = 2; c.insets = new Insets(15, 10, 40, 0); c.ipadx = 0; Font textoGrande = new Font("Arial", 1, 18); editarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(editarTextoPrincipalDialogo, c); c.insets = new Insets(0, 5, 10, 0); c.gridx = 0; c.gridy = 1; c.gridwidth = 1; c.ipadx = 0; JLabel editarNombreClienteDialogo = new JLabel("Login:"); panelDialogo.add(editarNombreClienteDialogo, c); final JTextField valorEditarNombreClienteDialogo = new JTextField(); c.gridx = 1; c.gridy = 1; c.gridwidth = 1; c.ipadx = 0; c.insets = new Insets(0, 5, 10, 0); valorEditarNombreClienteDialogo.setText(usuarioSelecionado.getLogin()); panelDialogo.add(valorEditarNombreClienteDialogo, c); c.gridx = 0; c.gridy = 2; c.gridwidth = 1; c.ipadx = 0; c.insets = new Insets(0, 5, 10, 0); JLabel editarPasswordClienteDialogo = new JLabel("Contrasea:"); panelDialogo.add(editarPasswordClienteDialogo, c); final JTextField valoreditarPasswordClienteDialogo = new JTextField(); c.gridx = 1; c.gridy = 2; c.gridwidth = 1; c.ipadx = 0; c.insets = new Insets(0, 5, 10, 0); panelDialogo.add(valoreditarPasswordClienteDialogo, c); c.gridx = 0; c.gridy = 3; c.gridwidth = 2; c.ipadx = 0; c.insets = new Insets(0, 5, 10, 0); JLabel mensajeEditarPassword = new JLabel( "Si no desea editar la contrasea deje este espacio en blanco:"); panelDialogo.add(mensajeEditarPassword, c); c.gridx = 0; c.gridy = 4; c.gridwidth = 1; c.ipadx = 0; c.insets = new Insets(0, 15, 10, 15); JButton botonGuardarClienteDialogo = new JButton("Guardar"); panelDialogo.add(botonGuardarClienteDialogo, c); c.gridx = 1; c.gridy = 4; c.gridwidth = 1; c.insets = new Insets(0, 15, 10, 15); c.ipadx = 0; JButton botonCerrarClienteDialogo = new JButton("Cancelar"); panelDialogo.add(botonCerrarClienteDialogo, c); botonCerrarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { dialogoEditar.dispose(); } }); botonGuardarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String nombreUsuario = valorEditarNombreClienteDialogo.getText(); usuarioSelecionado.setLogin(nombreUsuario); if (!valoreditarPasswordClienteDialogo.getText().equals("")) { usuarioSelecionado.setPassword(valoreditarPasswordClienteDialogo.getText()); } controladorUsuarios.modificarUsuario(usuarioSelecionado.getUser_id(), usuarioSelecionado.getLogin(), usuarioSelecionado.getPassword()); JOptionPane.showMessageDialog(dialogoEditar, "Se ha modificado el usuario con xito", "Mensaje del sistema", JOptionPane.INFORMATION_MESSAGE); generarTablaUsuarios(); dialogoEditar.dispose(); } }); dialogoEditar.add(panelDialogo); dialogoEditar.setVisible(true); break; case 2: if (estado.equals("Habilitado")) { usuarioSelecionado.setStatus('i'); } else { usuarioSelecionado.setStatus('e'); } controladorUsuarios.modificarEstadoUsuario(usuarioSelecionado); JOptionPane.showMessageDialog(this, "Se ha cambiado el estado del usuario", "Mensaje del sistema", JOptionPane.INFORMATION_MESSAGE); generarTablaUsuarios(); break; default: break; } } // TODO add your handling code here: }
From source file:interfaces.InterfazPrincipal.java
private void jButton9ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton9ActionPerformed // TODO add your handling code here: String nombre = jTextFieldNombreSaldoProveedores.getText(); ControladorProveedores controladorProveedores = new ControladorProveedores(); ArrayList<Proveedores> listaProveedores = controladorProveedores.obtenerProveedores("", nombre); final JDialog dialogoEditar = new JDialog(this); dialogoEditar.setTitle("Buscar proveedores"); dialogoEditar.setSize(500, 300);/*from ww w . j av a2s . c o m*/ dialogoEditar.setResizable(false); JPanel panelDialogo = new JPanel(); panelDialogo.setLayout(new GridBagLayout()); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.HORIZONTAL; JLabel ediitarTextoPrincipalDialogo = new JLabel("Buscar Proveedores"); c.gridx = 0; c.gridy = 0; c.gridwidth = 3; c.insets = new Insets(10, 60, 10, 10); Font textoGrande = new Font("Arial", 1, 16); ediitarTextoPrincipalDialogo.setFont(textoGrande); panelDialogo.add(ediitarTextoPrincipalDialogo, c); c.gridx = 0; c.gridy = 1; c.gridwidth = 3; c.insets = new Insets(10, 10, 10, 10); final JTable tablaDialogo = new JTable(); DefaultTableModel modeloTabla = new DefaultTableModel() { @Override public boolean isCellEditable(int row, int column) { //all cells false return false; } }; ; modeloTabla.addColumn("ID"); modeloTabla.addColumn("Identificacin"); modeloTabla.addColumn("Nombre"); //LLenar tabla for (int i = 0; i < listaProveedores.size(); i++) { Object[] data = { "1", "2", "3" }; data[0] = listaProveedores.get(i).getID(); data[1] = listaProveedores.get(i).getIdentificacion(); data[2] = listaProveedores.get(i).getNombre(); System.out.println("Nombre!!" + data[2]); modeloTabla.addRow(data); } tablaDialogo.setModel(modeloTabla); tablaDialogo.getColumn("ID").setMinWidth(70); tablaDialogo.getColumn("Identificacin").setMinWidth(60); tablaDialogo.getColumn("Nombre").setMinWidth(150); tablaDialogo.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); JScrollPane scroll = new JScrollPane(tablaDialogo); scroll.setPreferredSize(new Dimension(220, 150)); panelDialogo.add(scroll, c); c.insets = new Insets(0, 0, 0, 10); c.gridx = 0; c.gridy = 2; c.gridwidth = 1; JButton botonGuardarClienteDialogo = new JButton("Elegir"); panelDialogo.add(botonGuardarClienteDialogo, c); c.gridx = 1; c.gridy = 2; c.gridwidth = 1; JButton botonCerrarClienteDialogo = new JButton("Cancelar"); panelDialogo.add(botonCerrarClienteDialogo, c); dialogoEditar.add(panelDialogo); dialogoEditar.setVisible(true); botonCerrarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { dialogoEditar.dispose(); } }); botonGuardarClienteDialogo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int row = tablaDialogo.getSelectedRow(); if (row == -1) { JOptionPane.showMessageDialog(dialogoEditar, "Por favor seleccione una fila"); } else { Object identificacionCliente = tablaDialogo.getValueAt(row, 0); Object idCliente = tablaDialogo.getValueAt(row, 1); mostrarIDProveedor.setText(String.valueOf(identificacionCliente)); String nombreClientePago = String.valueOf(tablaDialogo.getValueAt(row, 2)); //Limitar a 15 caracteres if (nombreClientePago.length() >= 15) { nombreClientePago = nombreClientePago.substring(0, 12); } textoNombreProveedor.setText(nombreClientePago); DefaultTableModel modeloClientes = (DefaultTableModel) TablaDeSaldoProveedor.getModel(); for (int i = 0; i < modeloClientes.getRowCount(); i++) { modeloClientes.removeRow(i); } modeloClientes.setRowCount(0); ControladorFlujoCompras controladorFlujoCompra = new ControladorFlujoCompras(); //SELECT * FROM Flujo_Factura where factura_id in (select factura_id from Factura where cliente_id = 1130614506); ArrayList<Flujo_Compra> flujosProveedor = controladorFlujoCompra.obtenerFlujosCompras( " where ID_CompraProveedor in (select ID_CompraProveedor from Compra_Proveedores where IDProveedor = " + String.valueOf(identificacionCliente) + ") order by ID_CompraProveedor"); double pago = 0.0; for (int i = 0; i < flujosProveedor.size(); i++) { Flujo_Compra datos = flujosProveedor.get(i); Object[] rowData = { datos.getID_CompraProveedor(), datos.getTipo_flujo(), datos.getFecha(), datos.getMonto() }; if (datos.getTipo_flujo().equals("deuda")) { pago += Double.parseDouble(datos.getMonto() + ""); } else { pago -= Double.parseDouble(datos.getMonto() + ""); } modeloClientes.addRow(rowData); } TablaDeSaldoProveedor.setModel(modeloClientes); deudaActualProveedor.setText(String.valueOf(pago)); dialogoEditar.dispose(); //Mostrar en table de clientes los datos botonRegistrarAbono.setEnabled(true); } } }); }