List of usage examples for javax.swing JCheckBox JCheckBox
public JCheckBox(Action a)
From source file:de.atomfrede.tools.evalutation.options.ui.OptionsDialog.java
private JCheckBox getAllSolenoidValveCheckBox() { if (allSolenoidValvesCheckbox == null) { allSolenoidValvesCheckbox = new JCheckBox(Messages.getString("OptionsDialog.6")); //$NON-NLS-1$ allSolenoidValvesCheckbox.addActionListener(new ActionListener() { @Override//from www. ja va 2s. co m public void actionPerformed(ActionEvent e) { selectAllCheckBox(); } }); } return allSolenoidValvesCheckbox; }
From source file:TexBug.java
JPanel texture2DPanel() {
JPanel panel = new JPanel();
panel.setLayout(new GridLayout(1, 0)); // horizontal
JPanel leftPanel = new JPanel();
leftPanel.setLayout(new GridLayout(0, 1)); // vertical
panel.add(leftPanel);//from w ww .j ava2 s. co m
JPanel rightPanel = new JPanel();
rightPanel.setLayout(new GridLayout(0, 1)); // vertical
panel.add(rightPanel);
texEnableCheckBox = new JCheckBox(texEnableString);
// set up the action commands
texEnableCheckBox.setActionCommand(texEnableString);
// register the applet as the listener for the buttons
texEnableCheckBox.addActionListener(this);
// set the initial value
texEnableCheckBox.setSelected(texEnable);
// add the checkbox to the panel
leftPanel.add(texEnableCheckBox);
// texture boundary S
leftPanel.add(new JLabel("Boundary S Mode:"));
// create the buttons
JRadioButton texBoundarySWrapButton = new JRadioButton(wrapString);
JRadioButton texBoundarySClampButton = new JRadioButton(clampString);
// set up the action commands
texBoundarySWrapButton.setActionCommand(texBoundarySWrapString);
texBoundarySClampButton.setActionCommand(texBoundarySClampString);
// add the buttons to a group so that only one can be selected
ButtonGroup boundSButtonGroup = new ButtonGroup();
boundSButtonGroup.add(texBoundarySWrapButton);
boundSButtonGroup.add(texBoundarySClampButton);
// register the applet as the listener for the buttons
texBoundarySWrapButton.addActionListener(this);
texBoundarySClampButton.addActionListener(this);
// add the buttons to the panel
leftPanel.add(texBoundarySWrapButton);
leftPanel.add(texBoundarySClampButton);
// set the default
texBoundarySWrapButton.setSelected(true);
// texture boundary T
leftPanel.add(new JLabel("Boundary T Mode:"));
// create the buttons
JRadioButton texBoundaryTWrapButton = new JRadioButton(wrapString);
JRadioButton texBoundaryTClampButton = new JRadioButton(clampString);
// set up the action commands
texBoundaryTWrapButton.setActionCommand(texBoundaryTWrapString);
texBoundaryTClampButton.setActionCommand(texBoundaryTClampString);
// add the buttons to a group so that only one can be selected
ButtonGroup boundTButtonGroup = new ButtonGroup();
boundTButtonGroup.add(texBoundaryTWrapButton);
boundTButtonGroup.add(texBoundaryTClampButton);
// register the applet as the listener for the buttons
texBoundaryTWrapButton.addActionListener(this);
texBoundaryTClampButton.addActionListener(this);
// add the buttons to the panel
leftPanel.add(texBoundaryTWrapButton);
leftPanel.add(texBoundaryTClampButton);
// set the default
texBoundaryTWrapButton.setSelected(true);
// texture min filter
rightPanel.add(new JLabel("Min Filter:"));
// create the buttons
JRadioButton texMinFilterBasePointButton = new JRadioButton(texFilterBasePointString);
JRadioButton texMinFilterBaseLinearButton = new JRadioButton(texFilterBaseLinearString);
JRadioButton texMinFilterMultiPointButton = new JRadioButton(texFilterMultiPointString);
JRadioButton texMinFilterMultiLinearButton = new JRadioButton(texFilterMultiLinearString);
JRadioButton texMinFilterNicestButton = new JRadioButton(nicestString);
JRadioButton texMinFilterFastestButton = new JRadioButton(fastestString);
// set up the action commands
texMinFilterBasePointButton.setActionCommand(texMinFilterBasePointString);
texMinFilterBaseLinearButton.setActionCommand(texMinFilterBaseLinearString);
texMinFilterMultiPointButton.setActionCommand(texMinFilterMultiPointString);
texMinFilterMultiLinearButton.setActionCommand(texMinFilterMultiLinearString);
texMinFilterNicestButton.setActionCommand(texMinFilterNicestString);
texMinFilterFastestButton.setActionCommand(texMinFilterFastestString);
// add the buttons to a group so that only one can be selected
ButtonGroup minFilterButtonGroup = new ButtonGroup();
minFilterButtonGroup.add(texMinFilterBasePointButton);
minFilterButtonGroup.add(texMinFilterBaseLinearButton);
minFilterButtonGroup.add(texMinFilterMultiPointButton);
minFilterButtonGroup.add(texMinFilterMultiLinearButton);
minFilterButtonGroup.add(texMinFilterNicestButton);
minFilterButtonGroup.add(texMinFilterFastestButton);
// register the applet as the listener for the buttons
texMinFilterBasePointButton.addActionListener(this);
texMinFilterBaseLinearButton.addActionListener(this);
texMinFilterMultiPointButton.addActionListener(this);
texMinFilterMultiLinearButton.addActionListener(this);
texMinFilterNicestButton.addActionListener(this);
texMinFilterFastestButton.addActionListener(this);
// add the buttons to the panel
rightPanel.add(texMinFilterBasePointButton);
rightPanel.add(texMinFilterBaseLinearButton);
rightPanel.add(texMinFilterMultiPointButton);
rightPanel.add(texMinFilterMultiLinearButton);
rightPanel.add(texMinFilterNicestButton);
rightPanel.add(texMinFilterFastestButton);
// set the default
texMinFilterBasePointButton.setSelected(true);
// texture max filter
rightPanel.add(new JLabel("Mag Filter:"));
// create the buttons
JRadioButton texMagFilterBasePointButton = new JRadioButton(texFilterBasePointString);
JRadioButton texMagFilterBaseLinearButton = new JRadioButton(texFilterBaseLinearString);
JRadioButton texMagFilterNicestButton = new JRadioButton(nicestString);
JRadioButton texMagFilterFastestButton = new JRadioButton(fastestString);
// set up the action commands
texMagFilterBasePointButton.setActionCommand(texMagFilterBasePointString);
texMagFilterBaseLinearButton.setActionCommand(texMagFilterBaseLinearString);
texMagFilterNicestButton.setActionCommand(texMagFilterNicestString);
texMagFilterFastestButton.setActionCommand(texMagFilterFastestString);
// add the buttons to a group so that only one can be selected
ButtonGroup magFilterButtonGroup = new ButtonGroup();
magFilterButtonGroup.add(texMagFilterBasePointButton);
magFilterButtonGroup.add(texMagFilterBaseLinearButton);
magFilterButtonGroup.add(texMagFilterNicestButton);
magFilterButtonGroup.add(texMagFilterFastestButton);
// register the applet as the listener for the buttons
texMagFilterBasePointButton.addActionListener(this);
texMagFilterBaseLinearButton.addActionListener(this);
texMagFilterNicestButton.addActionListener(this);
texMagFilterFastestButton.addActionListener(this);
// add the buttons to the panel
rightPanel.add(texMagFilterBasePointButton);
rightPanel.add(texMagFilterBaseLinearButton);
rightPanel.add(texMagFilterNicestButton);
rightPanel.add(texMagFilterFastestButton);
// set the default
texMagFilterBasePointButton.setSelected(true);
// MipMap Mode
leftPanel.add(new JLabel("MipMap Mode:"));
// create the buttons
JRadioButton texMipMapBaseButton = new JRadioButton(texMipMapBaseString);
JRadioButton texMipMapMultiButton = new JRadioButton(texMipMapMultiString);
// set up the action commands
texMipMapBaseButton.setActionCommand(texMipMapBaseString);
texMipMapMultiButton.setActionCommand(texMipMapMultiString);
// add the buttons to a group so that only one can be selected
ButtonGroup texMipMapButtonGroup = new ButtonGroup();
texMipMapButtonGroup.add(texMipMapBaseButton);
texMipMapButtonGroup.add(texMipMapMultiButton);
// register the applet as the listener for the buttons
texMipMapBaseButton.addActionListener(this);
texMipMapMultiButton.addActionListener(this);
// add the buttons to the panel
leftPanel.add(texMipMapBaseButton);
leftPanel.add(texMipMapMultiButton);
// set the default
texMipMapBaseButton.setSelected(true);
return panel;
}
From source file:net.sf.taverna.t2.activities.wsdlsir.views.WSDLActivityConfigurationView.java
private void initComponents() { this.setModalityType(Dialog.ModalityType.DOCUMENT_MODAL); int gridy = 0; // title panel JPanel titlePanel = new JPanel(new BorderLayout()); titlePanel.setBackground(Color.WHITE); JLabel titleLabel = new JLabel("Security configuration"); titleLabel.setFont(titleLabel.getFont().deriveFont(Font.BOLD, 13.5f)); titleLabel.setBorder(new EmptyBorder(10, 10, 0, 10)); DialogTextArea titleMessage = new DialogTextArea("Select a security profile for the service"); titleMessage.setMargin(new Insets(5, 20, 10, 10)); titleMessage.setFont(titleMessage.getFont().deriveFont(11f)); titleMessage.setEditable(false);/* w w w. j av a 2 s. com*/ titleMessage.setFocusable(false); titlePanel.setBorder(new EmptyBorder(10, 10, 0, 10)); titlePanel.add(titleLabel, BorderLayout.NORTH); titlePanel.add(titleMessage, BorderLayout.CENTER); addDivider(titlePanel, SwingConstants.BOTTOM, true); // Main panel JPanel mainPanel = new JPanel(); mainPanel.setLayout(new GridBagLayout()); mainPanel.setBorder(new EmptyBorder(10, 10, 10, 10)); //Create the radio buttons noSecurityRadioButton = new JRadioButton("None"); noSecurityRadioButton.addItemListener(this); wsSecurityAuthNRadioButton = new JRadioButton("WS-Security username and password authentication"); wsSecurityAuthNRadioButton.addItemListener(this); httpSecurityAuthNRadioButton = new JRadioButton("HTTP username and password authentication"); httpSecurityAuthNRadioButton.addItemListener(this); SAMLSecurityAuthNRadioButton = new JRadioButton("SAML WEB SSO profile authentication"); SAMLSecurityAuthNRadioButton.addItemListener(this); //Group the radio buttons buttonGroup = new ButtonGroup(); buttonGroup.add(noSecurityRadioButton); buttonGroup.add(wsSecurityAuthNRadioButton); buttonGroup.add(httpSecurityAuthNRadioButton); buttonGroup.add(SAMLSecurityAuthNRadioButton); GridBagConstraints gbc = new GridBagConstraints(); gbc.weightx = 1.0; gbc.weighty = 0.0; gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(5, 10, 0, 0); mainPanel.add(noSecurityRadioButton, gbc); noSecurityLabel = new JLabel("Service requires no security"); noSecurityLabel.setFont(noSecurityLabel.getFont().deriveFont(11f)); // addDivider(noSecurityLabel, SwingConstants.BOTTOM, false); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.HORIZONTAL; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(0, 40, 10, 10); mainPanel.add(noSecurityLabel, gbc); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(5, 10, 0, 0); mainPanel.add(httpSecurityAuthNRadioButton, gbc); ActionListener usernamePasswordListener = new ActionListener() { public void actionPerformed(ActionEvent e) { // Get Credential Manager UI to get the username and password for the service CredentialManagerUI credManagerUI = CredentialManagerUI.getInstance(); if (credManagerUI != null) credManagerUI.newPasswordForService(oldBean.getWsdl()); } }; httpSecurityAuthNLabel = new JLabel( "Service requires HTTP username and password in order to authenticate the user"); httpSecurityAuthNLabel.setFont(httpSecurityAuthNLabel.getFont().deriveFont(11f)); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.HORIZONTAL; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(0, 40, 10, 10); mainPanel.add(httpSecurityAuthNLabel, gbc); // Set username and password button; setHttpUsernamePasswordButton = new JButton("Set username and password"); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.EAST; gbc.insets = new Insets(0, 40, 10, 10); gbc.weightx = 1.0; gbc.weighty = 1.0; // add any vertical space to this component mainPanel.add(setHttpUsernamePasswordButton, gbc); setHttpUsernamePasswordButton.addActionListener(usernamePasswordListener); /////SAML gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(5, 10, 0, 0); mainPanel.add(SAMLSecurityAuthNRadioButton, gbc); ActionListener getCookieListener = new ActionListener() { /** * This listener will use the CallPreparator to obtain the cookies (included shibsession_XXX cookie) and * save it in the Credential Manager (as the password for user "nomatter") */ public void actionPerformed(ActionEvent e) { try { WSDLParser parser = new WSDLParser(newBean.getWsdl()); List<String> endpoints = parser.getOperationEndpointLocations(newBean.getOperation()); for (String endpoint : endpoints) //Actually i am only expecting one endpoint { if (debug) System.out .println("Obtaining a SAML cookies to save in credential manager:" + endpoint); Cookie[] cookies = CallPreparator.createCookieForCallToEndpoint(endpoint); // Uncomment for just the shibsession cookie // Cookie[] cookiessession = new Cookie[1]; // for (Cookie cook : cookies) // if (cook.getName().contains("shibsession")) // cookiessession[0]=cook; // cookies=cookiessession; CredentialManager credman = CredentialManager.getInstance(); credman.saveUsernameAndPasswordForService( new UsernamePassword("nomatter", serializetoString(cookies)), new URI(endpoint)); } } catch (WSDLException ex) { System.err.println( "Problem getting or saving SAML cookie: " + newBean.getWsdl() + ". " + ex.getMessage()); ex.printStackTrace(); } catch (ParserConfigurationException ex) { System.err.println( "Problem getting or saving SAML cookie: " + newBean.getWsdl() + ". " + ex.getMessage()); ex.printStackTrace(); } catch (Exception ex) { System.err.println( "Problem getting or saving SAML cookie: " + newBean.getWsdl() + ". " + ex.getMessage()); ex.printStackTrace(); } } }; SAMLSecurityAuthNLabel = new JLabel("<html>" + "Service requires SAML Web SSO profile to be perfomed in order to authenticate the user. " + "A cookie will be saved in your Credential Manger. " + "In the case that it stops working, please delete the entry in your Credential Manager or re-authenticate" + "</html>"); SAMLSecurityAuthNLabel.setFont(SAMLSecurityAuthNLabel.getFont().deriveFont(11f)); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.HORIZONTAL; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(3, 40, 10, 10); mainPanel.add(SAMLSecurityAuthNLabel, gbc); // Set username and password button; setSAMLGETCookieButton = new JButton("Authenticate and save Authentication data in Credential Manger"); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.EAST; gbc.insets = new Insets(0, 40, 10, 10); gbc.weightx = 1.0; gbc.weighty = 1.0; // add any vertical space to this component mainPanel.add(setSAMLGETCookieButton, gbc); setSAMLGETCookieButton.addActionListener(getCookieListener); //END SAML gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(5, 10, 0, 0); mainPanel.add(wsSecurityAuthNRadioButton, gbc); wsSecurityAuthNLabel = new JLabel( "Service requires WS-Security username and password in order to authenticate the user"); wsSecurityAuthNLabel.setFont(wsSecurityAuthNLabel.getFont().deriveFont(11f)); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.HORIZONTAL; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(0, 40, 0, 0); mainPanel.add(wsSecurityAuthNLabel, gbc); // Password type list passwordTypeComboBox = new JComboBox(passwordTypes); passwordTypeComboBox.setRenderer(new ComboBoxTooltipRenderer()); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(10, 40, 0, 0); mainPanel.add(passwordTypeComboBox, gbc); // 'Add timestamp' checkbox addTimestampCheckBox = new JCheckBox("Add a timestamp to SOAP message"); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; gbc.insets = new Insets(5, 40, 10, 10); mainPanel.add(addTimestampCheckBox, gbc); // Set username and password button; setWsdlUsernamePasswordButton = new JButton("Set username and password"); gbc.gridx = 0; gbc.gridy = gridy++; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.EAST; gbc.insets = new Insets(0, 40, 10, 10); gbc.weightx = 1.0; gbc.weighty = 1.0; // add any vertical space to this component mainPanel.add(setWsdlUsernamePasswordButton, gbc); setWsdlUsernamePasswordButton.addActionListener(usernamePasswordListener); addDivider(mainPanel, SwingConstants.BOTTOM, true); // OK/Cancel button panel JPanel okCancelPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT)); JButton okButton = new JButton("OK"); okButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { okPressed(); } }); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { cancelPressed(); } }); okCancelPanel.add(cancelButton); okCancelPanel.add(okButton); // Enable/disable controls based on what is the current security profiles String securityProfile = oldBean.getSecurityProfile(); if (securityProfile == null) { noSecurityRadioButton.setSelected(true); } else { if (securityProfile.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD) || securityProfile.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD) || securityProfile.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD) || securityProfile.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)) { wsSecurityAuthNRadioButton.setSelected(true); } if (securityProfile.equals(SecurityProfiles.HTTP_BASIC_AUTHN) || securityProfile.equals(SecurityProfiles.HTTP_DIGEST_AUTHN)) { httpSecurityAuthNRadioButton.setSelected(true); } if (securityProfile.equals(SecurityProfiles.SAMLWEBSSOAUTH)) { SAMLSecurityAuthNRadioButton.setSelected(true); } if (securityProfile.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD) || securityProfile .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)) { passwordTypeComboBox.setSelectedItem(PLAINTEXT_PASSWORD); } else if (securityProfile.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD) || securityProfile.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)) { passwordTypeComboBox.setSelectedItem(DIGEST_PASSWORD); } if (securityProfile.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD) || securityProfile .equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)) { addTimestampCheckBox.setSelected(true); } else { addTimestampCheckBox.setSelected(false); } } // Put everything together JPanel layoutPanel = new JPanel(new BorderLayout()); layoutPanel.add(titlePanel, BorderLayout.NORTH); layoutPanel.add(mainPanel, BorderLayout.CENTER); layoutPanel.add(okCancelPanel, BorderLayout.SOUTH); layoutPanel.setPreferredSize(new Dimension(550, 490)); this.getContentPane().add(layoutPanel); this.pack(); }
From source file:de.atomfrede.tools.evalutation.options.ui.OptionsDialog.java
private JCheckBox getSolenoidValveZeroCheckBox() { if (solenoidValveZeroCheckbox == null) { solenoidValveZeroCheckbox = new JCheckBox("0.0"); solenoidValveZeroCheckbox.addActionListener(new ActionListener() { @Override/*from ww w .ja va 2 s. c o m*/ public void actionPerformed(ActionEvent e) { if (solenoidValveZeroCheckbox.isSelected()) solenoidValvesOfInterest.add(Double.valueOf(0.0)); else solenoidValvesOfInterest.remove(Double.valueOf(0.0)); } }); } return solenoidValveZeroCheckbox; }
From source file:cellularAutomata.analysis.PricingDistributionAnalysis.java
/** * Create the panel used to display the pricing statistics. *//*from w ww . j a v a 2 s . com*/ private void createDisplayPanel() { int displayWidth = CAFrame.tabbedPaneDimension.width; int displayHeight = 600 + (100 * numberOfStates); // create the display panel if (displayPanel == null) { displayPanel = new JPanel(new GridBagLayout()); displayPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5)); displayPanel.setPreferredSize(new Dimension(displayWidth, displayHeight)); } else { displayPanel.removeAll(); } if (isCompatibleRule && (numberOfStates <= MAX_NUMBER_OF_STATES)) { // create a panel that displays messages JPanel messagePanel = createMessagePanel(); // create the labels for the display createDataDisplayLabels(); JLabel generationLabel = new JLabel("Generation: "); JLabel stateLabel = new JLabel("State:"); JLabel numStateLabel = new JLabel("Number:"); JLabel percentOccupiedLabel = new JLabel("Kurtosis:"); // create boxes for each column of the display (a Box uses the // BoxLayout, so it is handy for laying out components) Box boxOfStateLabels = Box.createVerticalBox(); Box boxOfNumberLabels = Box.createVerticalBox(); Box boxOfPercentLabels = Box.createVerticalBox(); // the amount of vertical space to put between components int verticalSpace = 5; // add the states to the first vertical box boxOfStateLabels.add(stateLabel); boxOfStateLabels.add(Box.createVerticalStrut(verticalSpace)); for (int state = 0; state < numberOfStates; state++) { boxOfStateLabels.add(new JLabel("" + state)); boxOfStateLabels.add(Box.createVerticalStrut(verticalSpace)); } // add the numbers (in each state) to the second vertical box boxOfNumberLabels.add(numStateLabel); boxOfNumberLabels.add(Box.createVerticalStrut(verticalSpace)); for (int i = 0; i < numberOfStates; i++) { boxOfNumberLabels.add(numberOccupiedByStateDataLabel[i]); boxOfNumberLabels.add(Box.createVerticalStrut(verticalSpace)); } // add the percents (in each state) to the third vertical box boxOfPercentLabels.add(percentOccupiedLabel); boxOfPercentLabels.add(Box.createVerticalStrut(verticalSpace)); for (int i = 0; i < numberOfStates; i++) { boxOfPercentLabels.add(percentOccupiedByStateDataLabel[i]); boxOfPercentLabels.add(Box.createVerticalStrut(verticalSpace)); } // create another box that holds all of the label boxes Box boxOfLabels = Box.createHorizontalBox(); boxOfLabels.add(boxOfStateLabels); boxOfLabels.add(boxOfNumberLabels); boxOfLabels.add(boxOfPercentLabels); boxOfLabels.setBorder(BorderFactory.createEmptyBorder(7, 7, 7, 7)); // put the boxOfLabels in a scrollPane -- with many states, will get // very large JScrollPane stateScroller = new JScrollPane(boxOfLabels); int scrollPaneWidth = (int) (displayWidth * 0.8); int scrollPaneHeight = displayHeight / 4; stateScroller.setPreferredSize(new Dimension(scrollPaneWidth, scrollPaneHeight)); stateScroller.setMinimumSize(new Dimension(scrollPaneWidth, scrollPaneHeight)); stateScroller.setMaximumSize(new Dimension(scrollPaneWidth, scrollPaneHeight)); stateScroller.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); // create a "plot zero state" check box plotZeroStateCheckBox = new JCheckBox(PLOT_ZERO_STATE); plotZeroStateCheckBox.setSelected(true); plotZeroStateCheckBox.setToolTipText(PLOT_ZERO_STATE_TOOLTIP); plotZeroStateCheckBox.setActionCommand(PLOT_ZERO_STATE); plotZeroStateCheckBox.addActionListener(this); JPanel plotZeroStatePanel = new JPanel(new BorderLayout()); plotZeroStatePanel.setBorder(BorderFactory.createEmptyBorder(7, 7, 7, 7)); plotZeroStatePanel.add(BorderLayout.CENTER, plotZeroStateCheckBox); // create a "save data" check box saveDataCheckBox = new JCheckBox(SAVE_DATA); saveDataCheckBox.setToolTipText(SAVE_DATA_TOOLTIP); saveDataCheckBox.setActionCommand(SAVE_DATA); saveDataCheckBox.addActionListener(this); JPanel saveDataPanel = new JPanel(new BorderLayout()); saveDataPanel.setBorder(BorderFactory.createEmptyBorder(7, 7, 7, 7)); saveDataPanel.add(BorderLayout.CENTER, saveDataCheckBox); // create a panel that plots the data plot = new SimplePlot(); // add all the components to the panel int row = 0; displayPanel.add(messagePanel, new GBC(1, row).setSpan(4, 1).setFill(GBC.BOTH).setWeight(1.0, 1.0) .setAnchor(GBC.WEST).setInsets(1)); row++; displayPanel.add(plot, new GBC(1, row).setSpan(4, 1).setFill(GBC.BOTH).setWeight(10.0, 10.0) .setAnchor(GBC.WEST).setInsets(1)); row++; for (int i = 0; i < numberOfStates; i++) { timeSeriesPlot[i] = new SimplePlot(); displayPanel.add(timeSeriesPlot[i], new GBC(1, row).setSpan(4, 1).setFill(GBC.BOTH) .setWeight(10.0, 10.0).setAnchor(GBC.WEST).setInsets(1)); row++; } displayPanel.add(plotZeroStatePanel, new GBC(1, row).setSpan(4, 1).setFill(GBC.NONE).setWeight(1.0, 1.0) .setAnchor(GBC.CENTER).setInsets(1)); row++; displayPanel.add(generationLabel, new GBC(1, row).setSpan(1, 1).setFill(GBC.NONE).setWeight(1.0, 1.0) .setAnchor(GBC.EAST).setInsets(1)); displayPanel.add(generationDataLabel, new GBC(2, row).setSpan(1, 1).setFill(GBC.NONE) .setWeight(1.0, 1.0).setAnchor(GBC.WEST).setInsets(1)); row++; displayPanel.add(stateScroller, new GBC(1, row).setSpan(4, 1).setFill(GBC.BOTH).setWeight(1.0, 1.0) .setAnchor(GBC.WEST).setInsets(1)); row++; displayPanel.add(saveDataPanel, new GBC(1, row).setSpan(4, 1).setFill(GBC.NONE).setWeight(1.0, 1.0) .setAnchor(GBC.CENTER).setInsets(1)); } else { int row = 0; displayPanel.add(createWarningMessagePanel(), new GBC(1, row).setSpan(4, 1).setFill(GBC.BOTH) .setWeight(1.0, 1.0).setAnchor(GBC.WEST).setInsets(1)); } }
From source file:eu.apenet.dpt.standalone.gui.ead2edm.EdmOptionsPanel.java
private void createOptionPanel() { labels = dataPreparationToolGUI.getLabels(); JPanel creativeCommonsPanel = new CreativeCommonsPanel(); JPanel europeanaRightsPanel = new EuropeanaRightsPanel(); JPanel emptyPanel = new JPanel(); JPanel formPanel = new JPanel(new GridLayout(14, 1)); JPanel extraLicenseCardLayoutPanel = new JPanel(new CardLayout()); extraLicenseCardLayoutPanel.add(creativeCommonsPanel, CREATIVE_COMMONS); extraLicenseCardLayoutPanel.add(europeanaRightsPanel, EUROPEANA_RIGHTS_STATEMENTS); extraLicenseCardLayoutPanel.add(emptyPanel, EMPTY_PANEL); CardLayout cardLayout = (CardLayout) extraLicenseCardLayoutPanel.getLayout(); cardLayout.show(extraLicenseCardLayoutPanel, EMPTY_PANEL); JPanel panel = new JPanel(new FlowLayout(FlowLayout.CENTER)); conversionModeGroup = new ButtonGroup(); JRadioButton radioButton;// ww w. j a v a 2 s .c o m panel.add(new Label(this.labels.getString("edm.panel.label.choose.mode"))); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.mode.minimal")); radioButton.setActionCommand(MINIMAL); radioButton.setSelected(true); radioButton.addActionListener(new ConversionModeListener()); conversionModeGroup.add(radioButton); panel.add(radioButton); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.mode.full")); radioButton.setActionCommand(FULL); radioButton.addActionListener(new ConversionModeListener()); conversionModeGroup.add(radioButton); panel.add(radioButton); formPanel.add(panel); panel = new JPanel(new FlowLayout(FlowLayout.CENTER)); cLevelIdSourceButtonGroup = new ButtonGroup(); panel.add(new Label(this.labels.getString("edm.generalOptionsForm.identifierSource.header"))); radioButton = new JRadioButton(this.labels.getString("edm.generalOptionsForm.identifierSource.unitid")); radioButton.setActionCommand(UNITID); if (retrieveFromDb.retrieveCIdentifierSource().equals(radioButton.getActionCommand())) { radioButton.setSelected(true); } cLevelIdSourceButtonGroup.add(radioButton); panel.add(radioButton); radioButton = new JRadioButton(this.labels.getString("edm.generalOptionsForm.identifierSource.cid")); radioButton.setActionCommand(CID); if (retrieveFromDb.retrieveCIdentifierSource().equals(radioButton.getActionCommand())) { radioButton.setSelected(true); } cLevelIdSourceButtonGroup.add(radioButton); panel.add(radioButton); formPanel.add(panel); panel = new JPanel(new FlowLayout(FlowLayout.CENTER)); sourceOfFondsTitleGroup = new ButtonGroup(); determineDaoInformation(); panel.add(new Label(this.labels.getString("edm.generalOptionsForm.sourceOfFondsTitle"))); if (!this.batch && StringUtils.isBlank(ead2EdmInformation.getArchdescUnittitle()) && StringUtils.isBlank(ead2EdmInformation.getTitlestmtTitleproper())) { panel.add(new Label( this.labels.getString("edm.generalOptionsForm.sourceOfFondsTitle.noSourceAvailable"))); } else { radioButton = new JRadioButton( this.labels.getString("edm.generalOptionsForm.sourceOfFondsTitle.archdescUnittitle")); radioButton.setActionCommand(ARCHDESC_UNITTITLE); radioButton.setSelected(true); radioButton.addActionListener(new ConversionModeListener()); sourceOfFondsTitleGroup.add(radioButton); panel.add(radioButton); radioButton = new JRadioButton( this.labels.getString("edm.generalOptionsForm.sourceOfFondsTitle.titlestmtTitleproper")); radioButton.setActionCommand(TITLESTMT_TITLEPROPER); radioButton.addActionListener(new ConversionModeListener()); sourceOfFondsTitleGroup.add(radioButton); panel.add(radioButton); } formPanel.add(panel); panel = new JPanel(new GridLayout(2, 2)); landingPageButtonGroup = new ButtonGroup(); panel.add(new Label(this.labels.getString("edm.generalOptionsForm.landingPages.header"))); radioButton = new JRadioButton(this.labels.getString("edm.generalOptionsForm.landingPages.ape")); radioButton.setActionCommand(APE); if (retrieveFromDb.retrieveLandingPageBase().equals(APE_BASE)) { radioButton.setSelected(true); } landingPageButtonGroup.add(radioButton); panel.add(radioButton); panel.add(new Label()); JPanel otherPanel = new JPanel(new GridLayout(1, 2)); radioButton = new JRadioButton(this.labels.getString("edm.generalOptionsForm.landingPages.other")); radioButton.setActionCommand(OTHER); landingPageButtonGroup.add(radioButton); otherPanel.add(radioButton); landingPageTextArea = new JTextArea(); landingPageTextArea.setLineWrap(true); landingPageTextArea.setWrapStyleWord(true); if (!retrieveFromDb.retrieveLandingPageBase().equals(APE_BASE)) { radioButton.setSelected(true); landingPageTextArea.setText(retrieveFromDb.retrieveLandingPageBase()); } JScrollPane lptaScrollPane = new JScrollPane(landingPageTextArea); lptaScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED); otherPanel.add(lptaScrollPane); panel.add(otherPanel); formPanel.add(panel); panel = new JPanel(new GridLayout(1, 1)); panel.add(new Label(labels.getString("ese.mandatoryFieldsInfo"))); panel.add(new Label("")); panel.setBorder(BLACK_LINE); formPanel.add(panel); panel = new JPanel(new GridLayout(1, 3)); panel.add(new Label(labels.getString("ese.dataProvider") + ":" + "*")); dataProviderTextArea = new JTextArea(); dataProviderTextArea.setLineWrap(true); dataProviderTextArea.setWrapStyleWord(true); JScrollPane dptaScrollPane = new JScrollPane(dataProviderTextArea); dptaScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED); panel.add(dptaScrollPane); useExistingRepoCheckbox = new JCheckBox(labels.getString("ese.takeFromFileRepository")); useExistingRepoCheckbox.setSelected(true); useExistingRepoCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { //empty method on purpose } }); JPanel panel2 = new JPanel(new GridLayout(1, 1)); panel2.add(useExistingRepoCheckbox); if (!batch) { String repository = ead2EdmInformation.getRepository(); if (repository != null && !repository.equals("")) { dataProviderTextArea.setText(repository); } else { if (archdescRepository != null) { dataProviderTextArea.setText(archdescRepository); } else { useExistingRepoCheckbox.setSelected(false); } } } panel.add(panel2); panel.setBorder(BLACK_LINE); formPanel.add(panel); /* panel = new JPanel(new GridLayout(1, 3)); panel.add(new Label(labels.getString("ese.provider") + ":" + "*")); providerTextArea = new JTextArea(); providerTextArea.setLineWrap(true); providerTextArea.setWrapStyleWord(true); JScrollPane ptaScrollPane = new JScrollPane(providerTextArea); ptaScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED); panel.add(ptaScrollPane); panel.add(new Label("")); panel.setBorder(BLACK_LINE); formPanel.add(panel); */ panel = new JPanel(new GridLayout(5, 3)); typeGroup = new ButtonGroup(); panel.add(new Label(labels.getString("ese.type") + ":" + "*")); String currentRoleType; if (batch) { currentRoleType = ""; } else { currentRoleType = ead2EdmInformation.getRoleType(); } radioButton = new JRadioButton(this.labels.getString("edm.panel.dao.role.text")); if (currentRoleType.equals(EdmOptionsPanel.TEXT)) { radioButton.setSelected(true); } radioButton.setActionCommand(TEXT); radioButton.addActionListener(new ConversionModeListener()); typeGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.dao.role.image")); if (currentRoleType.equals(EdmOptionsPanel.IMAGE)) { radioButton.setSelected(true); } radioButton.setActionCommand(IMAGE); radioButton.addActionListener(new ConversionModeListener()); typeGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.dao.role.video")); if (currentRoleType.equals(EdmOptionsPanel.VIDEO)) { radioButton.setSelected(true); } radioButton.setActionCommand(VIDEO); radioButton.addActionListener(new ConversionModeListener()); typeGroup.add(radioButton); panel.add(radioButton); useExistingDaoRoleCheckbox = new JCheckBox(labels.getString("ese.takeFromFileDaoRole")); useExistingDaoRoleCheckbox.setSelected(true); useExistingDaoRoleCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { } }); panel.add(useExistingDaoRoleCheckbox); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.dao.role.sound")); if (currentRoleType.equals(EdmOptionsPanel.SOUND)) { radioButton.setSelected(true); } radioButton.setActionCommand(SOUND); radioButton.addActionListener(new ConversionModeListener()); typeGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.dao.role.threed")); if (currentRoleType.equals(EdmOptionsPanel.THREE_D)) { radioButton.setSelected(true); } radioButton.setActionCommand(THREE_D); radioButton.addActionListener(new ConversionModeListener()); typeGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); panel.setBorder(GREY_LINE); formPanel.add(panel); if (this.batch) { panel = new JPanel(new GridLayout(1, 3)); panel.add(new Label(labels.getString("ese.selectLanguage") + ":" + "*")); panel.add(languageBoxPanel); useExistingLanguageCheckbox = new JCheckBox(labels.getString("ese.takeFromFileLanguage")); useExistingLanguageCheckbox.setSelected(true); useExistingLanguageCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { //empty method on purpose } }); panel.add(useExistingLanguageCheckbox); panel.setBorder(BLACK_LINE); formPanel.add(panel); } else { inheritLanguagePanel = new JPanel(new GridLayout(1, 3)); inheritLanguagePanel.add(new Label(labels.getString("ese.inheritLanguage") + ":" + "*")); JPanel rbPanel = new JPanel(new GridLayout(4, 1)); inheritLanguageGroup = new ButtonGroup(); inhLanYesRadioButton = new JRadioButton(labels.getString("ese.yes")); inhLanYesRadioButton.setActionCommand(YES); inhLanYesRadioButton.addActionListener(new ChangePanelActionListener(languageBoxPanel)); inheritLanguageGroup.add(inhLanYesRadioButton); rbPanel.add(inhLanYesRadioButton); inhLanNoRadioButton = new JRadioButton(labels.getString("ese.no"), true); inhLanNoRadioButton.setActionCommand(NO); inhLanNoRadioButton.addActionListener(new ChangePanelActionListener(languageBoxPanel)); inheritLanguageGroup.add(inhLanNoRadioButton); rbPanel.add(inhLanNoRadioButton); inhLanProvideRadioButton = new JRadioButton(labels.getString("ese.provide")); inhLanProvideRadioButton.setActionCommand(PROVIDE); inhLanProvideRadioButton.addActionListener(new ChangePanelActionListener(languageBoxPanel)); inheritLanguageGroup.add(inhLanProvideRadioButton); rbPanel.add(inhLanProvideRadioButton); useExistingLanguageCheckbox = new JCheckBox(labels.getString("ese.takeFromFileLanguage")); useExistingLanguageCheckbox.setSelected(true); useExistingLanguageCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { //empty method on purpose } }); rbPanel.add(useExistingLanguageCheckbox); inheritLanguagePanel.add(rbPanel, BorderLayout.WEST); languageBoxPanel.setVisible(true); inheritLanguagePanel.add(languageBoxPanel, BorderLayout.EAST); inheritLanguagePanel.setBorder(BLACK_LINE); inheritLanguagePanel.setVisible(true); formPanel.add(inheritLanguagePanel); } // if (this.batch) { panel = new JPanel(new GridLayout(1, 3)); panel.add(new JLabel(labels.getString("edm.panel.license.inheritLicense") + ":" + "*")); useExistingRightsInfoCheckbox = new JCheckBox(labels.getString("ese.takeFromFileLicense")); useExistingRightsInfoCheckbox.setSelected(true); useExistingRightsInfoCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { //empty method on purpose } }); panel.add(useExistingRightsInfoCheckbox); panel.add(new JLabel()); panel.setBorder(BLACK_LINE); panel.setVisible(true); formPanel.add(panel); // } else { // panel = new JPanel(new GridLayout(3, 3)); // inheritLicenseGroup = new ButtonGroup(); // // panel.add(new Label(labels.getString("edm.panel.license.inheritLicense") + ":" + "*")); // inhLicYesRadioButton = new JRadioButton(labels.getString("ese.yes")); // inhLicYesRadioButton.setActionCommand(YES); //// inhLicYesRadioButton.addActionListener(new ChangePanelActionListener(languageBoxPanel)); // inheritLicenseGroup.add(inhLicYesRadioButton); // panel.add(inhLicYesRadioButton); // panel.add(new JLabel()); // // panel.add(new JLabel()); // inhLicNoRadioButton = new JRadioButton(labels.getString("ese.no"), true); // inhLicNoRadioButton.setActionCommand(NO); //// inhLicNoRadioButton.addActionListener(new ChangePanelActionListener(languageBoxPanel)); // inheritLicenseGroup.add(inhLicNoRadioButton); // panel.add(inhLicNoRadioButton); // useExistingRightsInfoCheckbox = new JCheckBox(labels.getString("ese.takeFromFileLicense")); // useExistingRightsInfoCheckbox.setSelected(true); // useExistingRightsInfoCheckbox.addItemListener(new ItemListener() { // @Override // public void itemStateChanged(ItemEvent e) { // //empty method on purpose // } // }); // // panel.add(useExistingRightsInfoCheckbox); // // panel.add(new JLabel()); // inhLicProvideRadioButton = new JRadioButton(labels.getString("ese.provide")); // inhLicProvideRadioButton.setActionCommand(PROVIDE); //// inhLicProvideRadioButton.addActionListener(new ChangePanelActionListener(languageBoxPanel)); // inheritLicenseGroup.add(inhLicProvideRadioButton); // panel.add(inhLicProvideRadioButton); // panel.add(new JLabel()); // // panel.setBorder(BLACK_LINE); // panel.setVisible(true); // formPanel.add(panel); // } JPanel mainLicensePanel = new JPanel(new BorderLayout()); panel = new JPanel(new GridLayout(5, 2)); licenseGroup = new ButtonGroup(); // String currentRightsInformation; // if (batch) { // currentRightsInformation = ""; // } else { // currentRightsInformation = ead2EdmInformation.getArchdescLicenceType(); // } panel.add(new Label(labels.getString("ese.specifyLicense") + ":" + "*")); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.cc")); // if (currentRightsInformation.equals(EdmOptionsPanel.CREATIVE_COMMONS)) { // radioButton.setSelected(true); // } radioButton.setActionCommand(CREATIVE_COMMONS); radioButton.addActionListener(new ChangePanelActionListener(extraLicenseCardLayoutPanel)); licenseGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.cc.zero")); // if (currentRightsInformation.equals(EdmOptionsPanel.CREATIVE_COMMONS_CC0)) { // radioButton.setSelected(true); // } radioButton.setActionCommand(CREATIVE_COMMONS_CC0); radioButton.addActionListener(new ChangePanelActionListener(extraLicenseCardLayoutPanel)); licenseGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.cc.public")); // if (currentRightsInformation.equals(EdmOptionsPanel.CREATIVE_COMMONS_PUBLIC_DOMAIN_MARK)) { // radioButton.setSelected(true); // } radioButton.setActionCommand(CREATIVE_COMMONS_PUBLIC_DOMAIN_MARK); radioButton.addActionListener(new ChangePanelActionListener(extraLicenseCardLayoutPanel)); licenseGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.europeana.rights")); // if (currentRightsInformation.equals(EdmOptionsPanel.EUROPEANA_RIGHTS_STATEMENTS)) { // radioButton.setSelected(true); // } radioButton.setActionCommand(EUROPEANA_RIGHTS_STATEMENTS); radioButton.addActionListener(new ChangePanelActionListener(extraLicenseCardLayoutPanel)); licenseGroup.add(radioButton); panel.add(radioButton); panel.add(new JLabel("")); radioButton = new JRadioButton(this.labels.getString("edm.panel.label.out.copyright")); // if (currentRightsInformation.equals(EdmOptionsPanel.OUT_OF_COPYRIGHT)) { // radioButton.setSelected(true); // } radioButton.setActionCommand(EdmOptionsPanel.OUT_OF_COPYRIGHT); radioButton.addActionListener(new ChangePanelActionListener(extraLicenseCardLayoutPanel)); licenseGroup.add(radioButton); panel.add(radioButton); mainLicensePanel.add(panel, BorderLayout.WEST); mainLicensePanel.add(extraLicenseCardLayoutPanel, BorderLayout.EAST); // if (currentRightsInformation.equals(EdmOptionsPanel.EUROPEANA_RIGHTS_STATEMENTS) || currentRightsInformation.equals(EdmOptionsPanel.CREATIVE_COMMONS)) { // cardLayout.show(extraLicenseCardLayoutPanel, currentRightsInformation); // if (currentRightsInformation.equals(EdmOptionsPanel.EUROPEANA_RIGHTS_STATEMENTS)) { // if (ead2EdmInformation.getArchdescLicenceLink().endsWith("rr-f/")) { // europeanaRightsComboBox.setSelectedIndex(0); // } else if (ead2EdmInformation.getArchdescLicenceLink().endsWith("orphan-work-eu/")) { // europeanaRightsComboBox.setSelectedIndex(1); // } else if (ead2EdmInformation.getArchdescLicenceLink().endsWith("rr-p/")) { // europeanaRightsComboBox.setSelectedIndex(2); // } else { // europeanaRightsComboBox.setSelectedIndex(3); // } // } else if (currentRightsInformation.equals(EdmOptionsPanel.CREATIVE_COMMONS)) { // // get respective items from EAD2EDMInfo and set panel items appropriately // } // } mainLicensePanel.setBorder(BLACK_LINE); formPanel.add(mainLicensePanel); panel = new JPanel(new GridLayout(1, 1)); panel.add(new Label(labels.getString("ese.specifyAdditionalRightsInfo") + ":")); additionalRightsTextArea = new JTextArea(); additionalRightsTextArea.setLineWrap(true); additionalRightsTextArea.setWrapStyleWord(true); JScrollPane artaScrollPane = new JScrollPane(additionalRightsTextArea); artaScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED); panel.add(artaScrollPane); panel.setBorder(GREY_LINE); formPanel.add(panel); inheritParentPanel = new JPanel(new GridLayout(2, 3)); inheritParentCheckbox = new JCheckBox(labels.getString("ese.inheritParent") + ":" + "*"); inheritParentCheckbox.setSelected(true); inheritParentCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { inhParYesRadioButton.setEnabled(true); inhParNoRadioButton.setEnabled(true); } if (e.getStateChange() == ItemEvent.DESELECTED) { inhParYesRadioButton.setEnabled(false); inhParNoRadioButton.setEnabled(false); } } }); inheritParentPanel.add(inheritParentCheckbox); inheritParentGroup = new ButtonGroup(); inhParYesRadioButton = new JRadioButton(labels.getString("ese.yes")); inhParYesRadioButton.setActionCommand(YES); inheritParentGroup.add(inhParYesRadioButton); inheritParentPanel.add(inhParYesRadioButton); inheritParentPanel.add(new JLabel("")); inhParNoRadioButton = new JRadioButton(labels.getString("ese.no"), true); inhParNoRadioButton.setActionCommand(NO); inheritParentGroup.add(inhParNoRadioButton); inheritParentPanel.add(inhParNoRadioButton); inheritParentPanel.setBorder(GREY_LINE); inheritParentPanel.setVisible(false); formPanel.add(inheritParentPanel); inheritOriginationPanel = new JPanel(new GridLayout(2, 3)); inheritOriginationCheckbox = new JCheckBox(labels.getString("ese.inheritOrigination") + ":" + "*"); inheritOriginationCheckbox.setSelected(true); inheritOriginationCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { inhOriYesRadioButton.setEnabled(true); inhOriNoRadioButton.setEnabled(true); } if (e.getStateChange() == ItemEvent.DESELECTED) { inhOriYesRadioButton.setEnabled(false); inhOriNoRadioButton.setEnabled(false); } } }); inheritOriginationPanel.add(inheritOriginationCheckbox); inheritOriginationGroup = new ButtonGroup(); inhOriYesRadioButton = new JRadioButton(labels.getString("ese.yes")); inhOriYesRadioButton.setActionCommand(YES); inheritOriginationGroup.add(inhOriYesRadioButton); inheritOriginationPanel.add(inhOriYesRadioButton); inheritOriginationPanel.add(new JLabel("")); inhOriNoRadioButton = new JRadioButton(labels.getString("ese.no"), true); inhOriNoRadioButton.setActionCommand(NO); inheritOriginationGroup.add(inhOriNoRadioButton); inheritOriginationPanel.add(inhOriNoRadioButton); inheritOriginationPanel.setBorder(BLACK_LINE); inheritOriginationPanel.setVisible(false); formPanel.add(inheritOriginationPanel); inheritUnittitlePanel = new JPanel(new GridLayout(2, 3)); inheritUnittitleCheckbox = new JCheckBox(labels.getString("ese.inheritUnittitle") + ":" + "*"); inheritUnittitleCheckbox.setSelected(true); inheritUnittitleCheckbox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { inhTitleYesRadioButton.setEnabled(true); inhTitleNoRadioButton.setEnabled(true); } if (e.getStateChange() == ItemEvent.DESELECTED) { inhTitleYesRadioButton.setEnabled(false); inhTitleNoRadioButton.setEnabled(false); } } }); inheritUnittitlePanel.add(inheritUnittitleCheckbox); inheritUnittitleGroup = new ButtonGroup(); inhTitleYesRadioButton = new JRadioButton(labels.getString("ese.yes")); inhTitleYesRadioButton.setActionCommand(YES); inheritUnittitleGroup.add(inhTitleYesRadioButton); inheritUnittitlePanel.add(inhTitleYesRadioButton); inheritUnittitlePanel.add(new JLabel("")); inhTitleNoRadioButton = new JRadioButton(labels.getString("ese.no"), true); inhTitleNoRadioButton.setActionCommand(NO); inheritUnittitleGroup.add(inhTitleNoRadioButton); inheritUnittitlePanel.add(inhTitleNoRadioButton); inheritUnittitlePanel.setBorder(BLACK_LINE); inheritUnittitlePanel.setVisible(false); formPanel.add(inheritUnittitlePanel); JButton createEdmBtn = new JButton(labels.getString("ese.createEseBtn")); JButton cancelBtn = new JButton(labels.getString("ese.cancelBtn")); createEdmBtn.addActionListener(new CreateEdmActionListener()); cancelBtn.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { for (Map.Entry<String, FileInstance> entry : fileInstances.entrySet()) { FileInstance fileInstance = entry.getValue(); fileInstance.setEdm(false); } dataPreparationToolGUI.enableEdmConversionBtn(); if (batch) { dataPreparationToolGUI.enableAllBatchBtns(); } dataPreparationToolGUI.enableRadioButtons(); close(); } }); JPanel buttonPanel = new JPanel(new GridLayout(1, 5)); buttonPanel.add(new JLabel("")); buttonPanel.add(cancelBtn); buttonPanel.add(new JLabel("")); buttonPanel.add(createEdmBtn); buttonPanel.add(new JLabel("")); add(formPanel, BorderLayout.CENTER); add(buttonPanel, BorderLayout.SOUTH); }
From source file:com.att.aro.ui.view.menu.tools.RegexWizard.java
private JPanel getMatcherPanel() { if (matcherPanel == null) { matcherPanel = new JPanel(); matcherPanel.setLayout(new GridBagLayout()); Color bgColor = matcherPanel.getBackground(); matcherPanel.setBorder(new RoundedBorderPanel(bgColor)); GridBagConstraints constraint = new GridBagConstraints(); constraint.gridx = 0;/*from ww w. j av a2 s . c o m*/ constraint.gridy = 0; constraint.insets = new Insets(0, 0, 0, 0); constraint.anchor = GridBagConstraints.FIRST_LINE_START; constraint.weightx = 0.5; ignore = new JRadioButton(ResourceBundleHelper.getMessageString("videoTab.ignore")); match = new JRadioButton(ResourceBundleHelper.getMessageString("videoTab.match")); ButtonGroup groupBtn = new ButtonGroup(); groupBtn.add(ignore); groupBtn.add(match); keep = new JCheckBox(ResourceBundleHelper.getMessageString("videoTab.keep")); alpha = new JCheckBox(ResourceBundleHelper.getMessageString("videoTab.alpha")); characters = new JCheckBox(ResourceBundleHelper.getMessageString("videoTab.characters")); charField = new JTextField(20); numeric = new JCheckBox(ResourceBundleHelper.getMessageString("videoTab.numeric")); lengthMin = new JCheckBox(ResourceBundleHelper.getMessageString("videoTab.min.length")); lengthMax = new JCheckBox(ResourceBundleHelper.getMessageString("videoTab.max.length")); lengthMinField = new JTextField(10); lengthMaxField = new JTextField(10); matcherPanel.add(ignore, constraint); constraint.gridy = 1; constraint.anchor = GridBagConstraints.WEST; matcherPanel.add(match, constraint); constraint.anchor = GridBagConstraints.EAST; enterBtn = new JButton(ResourceBundleHelper.getMessageString("videoTab.enter")); enterBtn.setName(ResourceBundleHelper.getMessageString("videoTab.enter")); enterBtn.addActionListener(this); matcherPanel.add(enterBtn, constraint); constraint.anchor = GridBagConstraints.WEST; constraint.gridy = 2; matcherPanel.add(keep, constraint); constraint.gridy = 3; matcherPanel.add(alpha, constraint); constraint.gridy = 4; JPanel panelChar = new JPanel(new FlowLayout()); panelChar.add(characters); panelChar.add(charField); matcherPanel.add(panelChar, constraint); constraint.gridy = 5; matcherPanel.add(numeric, constraint); constraint.gridy = 6; JPanel panelNumericLength = new JPanel(); panelNumericLength.setLayout(new BoxLayout(panelNumericLength, BoxLayout.Y_AXIS)); JPanel panelMinLength = new JPanel(new FlowLayout()); panelMinLength.add(lengthMin); panelMinLength.add(lengthMinField); panelNumericLength.add(panelMinLength); JPanel panelMaxLength = new JPanel(new FlowLayout()); panelMaxLength.add(lengthMax); panelMaxLength.add(lengthMaxField); panelNumericLength.add(panelMaxLength); matcherPanel.add(panelNumericLength, constraint); constraint.weighty = 1; matcherPanel.add(new JPanel(), constraint); } return matcherPanel; }
From source file:de.atomfrede.tools.evalutation.options.ui.OptionsDialog.java
private JCheckBox getSolenoidValveOneCheckBox() { if (solenoidValveOneCheckBox == null) { solenoidValveOneCheckBox = new JCheckBox("1.0"); //$NON-NLS-1$ solenoidValveOneCheckBox.addActionListener(new ActionListener() { @Override//ww w. ja va 2 s.c om public void actionPerformed(ActionEvent e) { if (solenoidValveOneCheckBox.isSelected()) solenoidValvesOfInterest.add(Double.valueOf(1.0)); else solenoidValvesOfInterest.remove(Double.valueOf(1.0)); } }); } return solenoidValveOneCheckBox; }
From source file:org.fhaes.fhsamplesize.view.FHSampleSize.java
/** * Initialize GUI components./*ww w. jav a 2 s . co m*/ */ @SuppressWarnings({ "rawtypes", "unchecked" }) private void initGUI() { App.init(); // setBounds(100, 100, 972, 439); setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); setIconImage(Builder.getApplicationIcon()); setTitle("Sample Size Analysis"); getContentPane().setLayout(new MigLayout("", "[1136px,grow,fill]", "[30px][405px,grow]")); JToolBar toolBar = new JToolBar(); toolBar.setFloatable(false); getContentPane().add(toolBar, "cell 0 0,growx,aligny top"); JToolBarButton btnOpen = new JToolBarButton(actionBrowse); btnOpen.setIcon(Builder.getImageIcon("fileopen.png")); toolBar.add(btnOpen); JToolBarButton btnSave = new JToolBarButton(actionSaveTable); btnSave.setIcon(Builder.getImageIcon("save.png")); toolBar.add(btnSave); JToolBarButton btnExportPDF = new JToolBarButton(actionExportPDF); btnExportPDF.setIcon(Builder.getImageIcon("pdf.png")); toolBar.add(btnExportPDF); JToolBarButton btnExportPNG = new JToolBarButton(actionExportPNG); btnExportPNG.setIcon(Builder.getImageIcon("formatpng.png")); toolBar.add(btnExportPNG); toolBar.addSeparator(); JToolBarButton btnRun = new JToolBarButton(actionRun); btnRun.setIcon(Builder.getImageIcon("run.png")); toolBar.add(btnRun); JPanel panelMain = new JPanel(); getContentPane().add(panelMain, "cell 0 1,grow"); panelMain.setLayout(new BorderLayout(0, 0)); JSplitPane splitPaneMain = new JSplitPane(); splitPaneMain.setOneTouchExpandable(true); panelMain.add(splitPaneMain); JPanel panelParameters = new JPanel(); splitPaneMain.setLeftComponent(panelParameters); panelParameters.setLayout(new MigLayout("", "[grow,right]", "[][][][193.00,grow,fill][]")); JPanel panelInput = new JPanel(); panelInput.setBorder(new TitledBorder(null, "Input", TitledBorder.LEADING, TitledBorder.TOP, null, null)); panelParameters.add(panelInput, "cell 0 0,grow"); panelInput.setLayout(new MigLayout("", "[100px:100px:180px,right][grow,fill][]", "[]")); JLabel lblInputFile = new JLabel("Input file:"); panelInput.add(lblInputFile, "cell 0 0"); txtInputFile = new JTextField(); panelInput.add(txtInputFile, "cell 1 0,growx"); txtInputFile.setActionCommand("NewFileTyped"); txtInputFile.addActionListener(this); txtInputFile.setColumns(10); JButton btnBrowse = new JButton(""); panelInput.add(btnBrowse, "cell 2 0"); btnBrowse.setAction(actionBrowse); btnBrowse.setText(""); btnBrowse.setIcon(Builder.getImageIcon("fileopen16.png")); btnBrowse.setPreferredSize(new Dimension(25, 25)); btnBrowse.setMaximumSize(new Dimension(25, 25)); btnBrowse.putClientProperty("JButton.buttonType", "segmentedTextured"); btnBrowse.putClientProperty("JButton.segmentPosition", "middle"); JPanel panelAnalysisOptions = new JPanel(); panelAnalysisOptions.setBorder(new TitledBorder(null, "Analysis and filtering options", TitledBorder.LEADING, TitledBorder.TOP, null, null)); panelParameters.add(panelAnalysisOptions, "cell 0 1,grow"); panelAnalysisOptions.setLayout(new MigLayout("", "[100px:100px:180px,right][grow][][]", "[][][][][]")); JLabel lblEventTypes = new JLabel("Event type:"); panelAnalysisOptions.add(lblEventTypes, "cell 0 0"); cboEventType = new JComboBox(); panelAnalysisOptions.add(cboEventType, "cell 1 0 3 1"); cboEventType.setModel(new DefaultComboBoxModel(EventTypeToProcess.values())); new EventTypeWrapper(cboEventType, PrefKey.EVENT_TYPE_TO_PROCESS, EventTypeToProcess.FIRE_EVENT); chkCommonYears = new JCheckBox("<html>Only analyze years all series have in common"); chkCommonYears.setEnabled(false); new CheckBoxWrapper(chkCommonYears, PrefKey.SSIZ_CHK_COMMON_YEARS, false); panelAnalysisOptions.add(chkCommonYears, "cell 1 1 3 1"); chkExcludeSeriesWithNoEvents = new JCheckBox("<html>Exclude series/segments with no events"); chkExcludeSeriesWithNoEvents.setEnabled(false); new CheckBoxWrapper(chkExcludeSeriesWithNoEvents, PrefKey.SSIZ_CHK_EXCLUDE_SERIES_WITH_NO_EVENTS, false); panelAnalysisOptions.add(chkExcludeSeriesWithNoEvents, "cell 1 2 3 1"); JLabel lblThresholdType = new JLabel("Threshold:"); panelAnalysisOptions.add(lblThresholdType, "cell 0 3"); cboThresholdType = new JComboBox(); panelAnalysisOptions.add(cboThresholdType, "cell 1 3"); cboThresholdType.setModel(new DefaultComboBoxModel(FireFilterType.values())); new FireFilterTypeWrapper(cboThresholdType, PrefKey.COMPOSITE_FILTER_TYPE_WITH_ALL_TREES, FireFilterType.NUMBER_OF_EVENTS); JLabel label = new JLabel(">="); panelAnalysisOptions.add(label, "flowx,cell 2 3"); spnThresholdValueGT = new JSpinner(); panelAnalysisOptions.add(spnThresholdValueGT, "cell 3 3"); spnThresholdValueGT.setModel(new SpinnerNumberModel(1, 1, 999, 1)); new SpinnerWrapper(spnThresholdValueGT, PrefKey.COMPOSITE_FILTER_VALUE, 1); chkEnableLessThan = new JCheckBox(""); chkEnableLessThan.setActionCommand("LessThanThresholdStatus"); chkEnableLessThan.addActionListener(this); panelAnalysisOptions.add(chkEnableLessThan, "flowx,cell 1 4,alignx right"); lblLessThan = new JLabel("<="); lblLessThan.setEnabled(false); panelAnalysisOptions.add(lblLessThan, "cell 2 4"); spnThresholdValueLT = new JSpinner(); spnThresholdValueLT.setEnabled(false); spnThresholdValueLT.setModel(new SpinnerNumberModel(1, 1, 999, 1)); panelAnalysisOptions.add(spnThresholdValueLT, "cell 3 4"); lblAnd = new JLabel("and"); panelAnalysisOptions.add(lblAnd, "cell 1 4"); JPanel panelSimulations = new JPanel(); panelSimulations.setBorder( new TitledBorder(null, "Simulations", TitledBorder.LEADING, TitledBorder.TOP, null, null)); panelParameters.add(panelSimulations, "cell 0 2,grow"); panelSimulations.setLayout(new MigLayout("", "[100px:100px:180px,right][fill]", "[][][]")); JLabel lblSimulations = new JLabel("Simulations:"); panelSimulations.add(lblSimulations, "cell 0 0"); spnSimulations = new JSpinner(); panelSimulations.add(spnSimulations, "cell 1 0"); spnSimulations.setModel(new SpinnerNumberModel(new Integer(1000), new Integer(1), null, new Integer(1))); new SpinnerWrapper(spnSimulations, PrefKey.SSIZ_SIMULATION_COUNT, 1000); JLabel lblSeedNumber = new JLabel("Seed number:"); panelSimulations.add(lblSeedNumber, "cell 0 1"); spnSeed = new JSpinner(); panelSimulations.add(spnSeed, "cell 1 1"); spnSeed.setModel(new SpinnerNumberModel(new Integer(30188), null, null, new Integer(1))); new SpinnerWrapper(spnSeed, PrefKey.SSIZ_SEED_NUMBER, 30188); JLabel lblResampling = new JLabel("Resampling:"); panelSimulations.add(lblResampling, "cell 0 2"); cboResampling = new JComboBox(); panelSimulations.add(cboResampling, "cell 1 2"); cboResampling .setModel(new DefaultComboBoxModel(new String[] { "With replacement", "Without replacement" })); new ResamplingTypeWrapper(cboResampling, PrefKey.SSIZ_RESAMPLING_TYPE, ResamplingType.WITH_REPLACEMENT); segmentationPanel = new SegmentationPanel(); segmentationPanel.chkSegmentation.setText("Process subset or segments of dataset?"); segmentationPanel.chkSegmentation.setEnabled(false); panelParameters.add(segmentationPanel, "cell 0 3,growx"); JPanel panel_3 = new JPanel(); panelParameters.add(panel_3, "cell 0 4,grow"); panel_3.setLayout(new MigLayout("", "[left][grow][right]", "[]")); JButton btnReset = new JButton("Reset"); btnReset.setActionCommand("Reset"); btnReset.addActionListener(this); panel_3.add(btnReset, "cell 0 0,grow"); JButton btnRunAnalysis = new JButton("Run Analysis"); btnRunAnalysis.setAction(actionRun); panel_3.add(btnRunAnalysis, "cell 2 0,grow"); JPanel panelResults = new JPanel(); splitPaneMain.setRightComponent(panelResults); panelResults.setLayout(new BorderLayout(0, 0)); splitPaneResults = new JSplitPane(); splitPaneResults.setResizeWeight(0.5); splitPaneResults.setOneTouchExpandable(true); splitPaneResults.setDividerLocation(0.5d); panelResults.add(splitPaneResults, BorderLayout.CENTER); splitPaneResults.setOrientation(JSplitPane.VERTICAL_SPLIT); JPanel panelResultsTop = new JPanel(); splitPaneResults.setLeftComponent(panelResultsTop); panelResultsTop.setLayout(new BorderLayout(0, 0)); JPanel panelChartOptions = new JPanel(); panelChartOptions.setBackground(Color.WHITE); panelResultsTop.add(panelChartOptions, BorderLayout.SOUTH); panelChartOptions.setLayout(new MigLayout("", "[][][][][][grow][grow]", "[15px,center]")); JLabel lblNewLabel = new JLabel("Plot:"); panelChartOptions.add(lblNewLabel, "cell 0 0,alignx trailing,aligny center"); cboChartMetric = new JComboBox(); cboChartMetric.setEnabled(false); cboChartMetric.setModel(new DefaultComboBoxModel(MiddleMetric.values())); panelChartOptions.add(cboChartMetric, "cell 1 0,growx"); cboChartMetric.setBackground(Color.WHITE); JLabel lblOfSegment = new JLabel("of segment:"); panelChartOptions.add(lblOfSegment, "cell 2 0,alignx trailing"); cboSegment = new JComboBox(); cboSegment.setBackground(Color.WHITE); cboSegment.setActionCommand("UpdateChart"); cboSegment.addActionListener(this); panelChartOptions.add(cboSegment, "cell 3 0,growx"); cboChartMetric.setActionCommand("UpdateChart"); JLabel lblWithAsymptoteType = new JLabel("with asymptote type:"); panelChartOptions.add(lblWithAsymptoteType, "cell 4 0,alignx trailing"); JComboBox comboBox = new JComboBox(); comboBox.setEnabled(false); comboBox.setModel(new DefaultComboBoxModel(new String[] { "none", "Weibull", "Michaelis-Menten", "Modified Michaelis-Menten", "Logistic", "Modified exponential" })); comboBox.setBackground(Color.WHITE); panelChartOptions.add(comboBox, "cell 5 0,growx"); cboChartMetric.addActionListener(this); panelChart = new JPanel(); panelChart.setMinimumSize(new Dimension(200, 200)); panelResultsTop.add(panelChart, BorderLayout.CENTER); panelChart.setLayout(new BorderLayout(0, 0)); panelChart.setBackground(Color.WHITE); JTabbedPane panelResultsBottom = new JTabbedPane(JTabbedPane.BOTTOM); splitPaneResults.setRightComponent(panelResultsBottom); simulationsTable = new SSIZResultsTable(); simulationsTable.setEnabled(false); simulationsTable.addMouseListener(new TablePopClickListener()); simulationsTable.setVisibleRowCount(10); adapter = new JTableSpreadsheetByRowAdapter(simulationsTable); scrollPaneSimulations = new JScrollPane(); panelResultsBottom.addTab("Simulations", null, scrollPaneSimulations, null); scrollPaneSimulations.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED); scrollPaneSimulations.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS); scrollPaneSimulations.setViewportView(simulationsTable); JPanel panelAsymptote = new JPanel(); asymptoteTable = new AsymptoteTable(); asymptoteTable.setEnabled(false); // asymptoteTable.addMouseListener(new TablePopClickListener()); asymptoteTable.setVisibleRowCount(10); scrollPaneAsymptote = new JScrollPane(); scrollPaneAsymptote.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED); scrollPaneAsymptote.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS); scrollPaneAsymptote.setViewportView(asymptoteTable); panelAsymptote.setLayout(new BorderLayout()); panelAsymptote.add(scrollPaneAsymptote, BorderLayout.CENTER); panelResultsBottom.addTab("Asymptote", null, panelAsymptote, null); // Disable asymptote tab until it is implemented panelResultsBottom.setEnabledAt(1, false); panelProgressBar = new JPanel(); panelProgressBar.setLayout(new BorderLayout()); btnCancelAnalysis = new JButton("Cancel"); btnCancelAnalysis.setIcon(Builder.getImageIcon("delete.png")); btnCancelAnalysis.setVisible(false); btnCancelAnalysis.setActionCommand("CancelAnalysis"); btnCancelAnalysis.addActionListener(this); progressBar = new JProgressBar(); panelProgressBar.add(progressBar, BorderLayout.CENTER); panelProgressBar.add(btnCancelAnalysis, BorderLayout.EAST); progressBar.setStringPainted(true); fileDialogWasUsed = false; mouseListenersActive = false; this.setGUIForFHFileReader(); this.setGUIForThresholdStatus(); pack(); this.setExtendedState(this.getExtendedState() | JFrame.MAXIMIZED_BOTH); setVisible(true); }
From source file:MiGA.StatsSelection.java
public StatsSelection(final String[] organisms, final boolean flag) { setTitle("MiGA"); setSize(800, 600);//from w w w . j a v a 2 s. 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); }