Example usage for javax.swing JScrollPane setPreferredSize

List of usage examples for javax.swing JScrollPane setPreferredSize

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  4. javax.swing.*
  5. JScrollPane
  6. setPreferredSize

Introduction

In this page you can find the example usage for javax.swing JScrollPane setPreferredSize.

Prototype

@BeanProperty(preferred = true, description = "The preferred size of the component.")
public void setPreferredSize(Dimension preferredSize)

Source Link

Document

Sets the preferred size of this component.

Usage

From source file:org.p_vcd.ui.LicenseDialog.java

public LicenseDialog(String libName, String libHomepage, String licenseName, String licenseFilename) {
    setSize(680, 480);/*from  www .ja va2s.c  o  m*/
    setTitle(libName);
    getContentPane().setLayout(new BorderLayout());
    {
        JPanel panel = new JPanel();
        getContentPane().add(panel, BorderLayout.NORTH);
        panel.setLayout(new MigLayout("", "[grow,trailing][grow]", "[20px][][]"));
        {
            JLabel lblSoft = new JLabel(libName);
            lblSoft.setFont(new Font("Tahoma", Font.BOLD, 16));
            panel.add(lblSoft, "center,cell 0 0 2 1");
        }
        {
            JLabel lblHomePage = new JLabel("Home page:");
            lblHomePage.setFont(new Font("Tahoma", Font.BOLD, 14));
            panel.add(lblHomePage, "cell 0 1");
        }
        {
            JLabel lblHome = SwingUtil.createLink(libHomepage, libHomepage);
            lblHome.setFont(new Font("Tahoma", Font.PLAIN, 14));
            panel.add(lblHome, "cell 1 1");
        }
        {
            JLabel lblNewLabel = new JLabel("License:");
            lblNewLabel.setFont(new Font("Tahoma", Font.BOLD, 14));
            panel.add(lblNewLabel, "cell 0 2");
        }
        {
            JLabel lblLicense = new JLabel(licenseName);
            lblLicense.setFont(new Font("Tahoma", Font.PLAIN, 14));
            panel.add(lblLicense, "cell 1 2");
        }
    }
    {
        JPanel panel = new JPanel();
        getContentPane().add(panel, BorderLayout.CENTER);
        panel.setLayout(new FlowLayout());
        panel.setBorder(new EmptyBorder(5, 5, 5, 5));
        JScrollPane scrollPane = new JScrollPane();
        scrollPane.setPreferredSize(new Dimension(600, 300));
        scrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
        panel.add(scrollPane);
        {
            JTextArea txtLicense = new JTextArea();
            txtLicense.setEditable(false);
            txtLicense.setFont(new Font("Monospaced", Font.PLAIN, 11));
            txtLicense.setWrapStyleWord(true);
            txtLicense.setLineWrap(true);
            try {
                InputStream is = Thread.currentThread().getContextClassLoader()
                        .getResourceAsStream("org/p_vcd/licenses/" + licenseFilename);
                String text = IOUtils.toString(is, "UTF-8");
                IOUtils.closeQuietly(is);
                txtLicense.setText(text);
                txtLicense.setCaretPosition(0);
            } catch (Exception e) {
                e.printStackTrace();
            }
            scrollPane.setViewportView(txtLicense);
        }
    }
    {
        JPanel panel = new JPanel();
        getContentPane().add(panel, BorderLayout.SOUTH);
        panel.setLayout(new FlowLayout(FlowLayout.CENTER));
        JButton okButton = new JButton("OK");
        okButton.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                LicenseDialog.this.dispose();
            }
        });
        okButton.setActionCommand("OK");
        panel.add(okButton);
        getRootPane().setDefaultButton(okButton);
    }
}

From source file:org.rdv.ui.ConsoleDialog.java

public ConsoleDialog(JDialog owner) {
    super(owner);

    setName("consoleDialog");

    setDefaultCloseOperation(AboutDialog.DISPOSE_ON_CLOSE);

    JPanel container = new JPanel();
    container.setLayout(new BorderLayout());
    container.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
    setContentPane(container);/*  w  w w.  j  a v  a 2  s .co  m*/

    InputMap inputMap = container.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
    ActionMap actionMap = container.getActionMap();

    Action disposeAction = new AbstractAction() {
        /** serialized version identifier */
        private static final long serialVersionUID = 4380189911762232261L;

        public void actionPerformed(ActionEvent ae) {
            dispose();
        }
    };

    Action copyAction = new AbstractAction() {

        /** serialized version identifier */
        private static final long serialVersionUID = 2596081241883913660L;

        public void actionPerformed(ActionEvent e) {
            textArea.selectAll();
            textArea.copy();
        }
    };

    //    Action scrollLockAction = new AbstractAction() {
    //      /** serialized version identifier */
    //      private static final long serialVersionUID = -8089076016097529064L;
    //
    //      public void actionPerformed(ActionEvent e) {
    //        //toggle scroll lock
    //        scrollLock_=!scrollLock_;
    //      }
    //    };

    disposeAction.putValue(Action.NAME, "OK");
    inputMap.put(KeyStroke.getKeyStroke("ENTER"), "dispose");
    inputMap.put(KeyStroke.getKeyStroke("ESCAPE"), "dispose");
    actionMap.put("dispose", disposeAction);
    copyAction.putValue(Action.NAME, "Copy");
    actionMap.put("copy", copyAction);
    //    actionMap.put("scroll lock", scrollLockAction);
    //    scrollLockAction.putValue(Action.NAME, "Scroll Lock");

    textArea = new JTextArea();
    textArea.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    textArea.setBackground(Color.WHITE);
    textArea.setForeground(Color.BLACK);
    textArea.setEditable(false);
    textArea.setLineWrap(false);

    Iterator<String> msgIt = messageBuffer.getMessages().iterator();

    //add all the messages in the buffer to this point
    while (msgIt.hasNext()) {
        addMessage(msgIt.next());
    }

    JScrollPane scrollPane = new JScrollPane(textArea, ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS,
            ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
    scrollPane.setPreferredSize(new Dimension(640, 480));
    container.add(scrollPane, BorderLayout.CENTER);

    JPanel buttonPanel = new JPanel();
    buttonPanel.setLayout(new BorderLayout());
    buttonPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));

    JButton okButton = new JButton(disposeAction);
    buttonPanel.add(okButton, BorderLayout.EAST);

    JPanel leftBtnsPanel = new JPanel();
    leftBtnsPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
    buttonPanel.add(leftBtnsPanel, BorderLayout.WEST);

    JButton copyButton = new JButton(copyAction);
    leftBtnsPanel.add(copyButton);

    //    JButton scrollLockButton = new JButton(scrollLockAction);
    //    leftBtnsPanel.add(scrollLockButton);

    container.add(buttonPanel, BorderLayout.SOUTH);

    // inject resources from the properties for this component
    ResourceMap resourceMap = RDV.getInstance().getContext().getResourceMap(getClass());
    resourceMap.injectComponents(this);

    pack();
    okButton.requestFocusInWindow();
    setLocationByPlatform(true);
    setVisible(true);

    messageBuffer.addObserver(this);
}

From source file:org.rimudb.editor.DescriptorEditor.java

/**
 * Build the panel//from   ww w. j  a  v  a2  s  .  c o  m
 */
private JPanel createColumnTablePanel() {
    JPanel columnPanel = new JPanel();
    columnPanel.setLayout(new BoxLayout(columnPanel, BoxLayout.Y_AXIS));

    // Create the property table panel
    propertyModel = new PropertyTableModel();

    // Add a listener to set the changed state
    propertyModel.addTableModelListener(new TableModelListener() {
        public void tableChanged(TableModelEvent e) {
            markChanged();

            if (e instanceof PropertyTableModelEvent) {
                PropertyTableModelEvent ptme = (PropertyTableModelEvent) e;

                // If the columnName column was changed then check it isn't
                // a PK
                if (ptme.getColumn() == 1) {

                    String beforeColumnName = (String) ptme.getBeforeValue();
                    String afterColumnName = (String) ptme.getAfterValue();

                    // Is the field entry in the list of primary keys?
                    for (int i = 0; i < pkListModel.getSize(); i++) {
                        String pkColumnName = (String) pkListModel.get(i);
                        // If it's found then remove it
                        if (beforeColumnName.equals(pkColumnName)) {
                            pkListModel.set(i, afterColumnName);
                            break;
                        }
                    }

                }

            }
        }
    });

    table = new ATable(getPropertyModel());
    table.setName("ColumnTable");
    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
    table.getSelectionModel().addListSelectionListener(new ListSelectionListener() {
        public void valueChanged(ListSelectionEvent e) {
            int selectedRowCount = table.getSelectedRowCount();
            removeColumnBtn.setEnabled(selectedRowCount > 0);
            moveUpBtn.setEnabled(selectedRowCount > 0);
            moveDownBtn.setEnabled(selectedRowCount > 0);
        }
    });
    table.setTransferHandler(new TransferHandler() {

        public int getSourceActions(JComponent c) {
            return COPY;
        }

        protected Transferable createTransferable(JComponent c) {
            ATable columnTable = (ATable) c;
            int row = columnTable.getSelectedRow();
            String columnName = getPropertyModel().getRow(row).getColumnName();
            return new StringSelection(columnName);
        }
    });
    table.setDragEnabled(true);

    JScrollPane sp = new JScrollPane(table);
    sp.setMaximumSize(new Dimension(Short.MAX_VALUE, 325));
    sp.setPreferredSize(new Dimension(Short.MAX_VALUE, 325));
    sp.setMinimumSize(new Dimension(Short.MAX_VALUE, 325));

    JComboBox typeCB = new JComboBox(DatabaseTypes.getAllTypes());
    typeCB.setEditable(false);

    javax.swing.table.TableColumn typeColumn = table.getColumnModel().getColumn(2);
    typeColumn.setCellEditor(new DefaultCellEditor(typeCB));

    // Create the popup menu and set it on the table
    propertyPopup = new TablePopupMenu(this, table);
    table.addMouseListener(propertyPopup);
    sp.addMouseListener(propertyPopup);
    sp.setAlignmentX(LEFT_ALIGNMENT);

    columnPanel.add(sp);

    columnPanel.add(Box.createVerticalStrut(10));

    JLabel pkLabel = new JLabel("Primary Key Columns", SwingConstants.LEFT);
    pkLabel.setAlignmentX(LEFT_ALIGNMENT);
    columnPanel.add(pkLabel);

    pkListModel = new DefaultListModel();
    pkListModel.addListDataListener(new ListDataListener() {
        public void intervalRemoved(ListDataEvent e) {
            markChanged();
        }

        public void intervalAdded(ListDataEvent e) {
            markChanged();
        }

        public void contentsChanged(ListDataEvent e) {
            markChanged();
        }
    });

    pkList = new JList(pkListModel);
    pkList.setName("pkList");
    pkList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
    pkList.addListSelectionListener(new ListSelectionListener() {
        public void valueChanged(ListSelectionEvent e) {
            int selectedRowCount = pkList.getSelectedIndex();
            removePkBtn.setEnabled(selectedRowCount > -1);
        }
    });
    pkList.setTransferHandler(new TransferHandler() {

        public boolean canImport(TransferHandler.TransferSupport info) {
            // we only import Strings
            if (!info.isDataFlavorSupported(DataFlavor.stringFlavor)) {
                return false;
            }

            JList.DropLocation dl = (JList.DropLocation) info.getDropLocation();
            if (dl.getIndex() == -1) {
                return false;
            }
            return true;
        }

        public boolean importData(TransferHandler.TransferSupport info) {
            if (!info.isDrop()) {
                return false;
            }

            // Check for String flavor
            if (!info.isDataFlavorSupported(DataFlavor.stringFlavor)) {
                displayDropLocation("List doesn't accept a drop of this type.");
                return false;
            }

            JList.DropLocation dl = (JList.DropLocation) info.getDropLocation();
            DefaultListModel listModel = (DefaultListModel) pkList.getModel();
            int index = dl.getIndex();

            // Get the string that is being dropped.
            Transferable t = info.getTransferable();
            String data;
            try {
                data = (String) t.getTransferData(DataFlavor.stringFlavor);
            } catch (Exception e) {
                return false;
            }

            // If this is a copy action then check we don't already have that String
            if (info.getDropAction() == COPY && listModel.indexOf(data) > -1) {
                displayDropLocation("The column " + data + " is already a primary key");
                return false;
            }

            // Perform the actual import. 
            if (dl.isInsert()) {
                int oldIndex = listModel.indexOf(data);
                if (oldIndex < index) {
                    listModel.add(index, data);
                    listModel.remove(oldIndex);
                } else {
                    listModel.remove(oldIndex);
                    listModel.add(index, data);
                }
            } else {
                // Don't handle replacements
            }
            return true;
        }

        public int getSourceActions(JComponent c) {
            return MOVE;
        }

        protected Transferable createTransferable(JComponent c) {
            JList list = (JList) c;
            Object[] values = list.getSelectedValues();

            StringBuffer buff = new StringBuffer();

            for (int i = 0; i < values.length; i++) {
                Object val = values[i];
                buff.append(val == null ? "" : val.toString());
                if (i != values.length - 1) {
                    buff.append("\n");
                }
            }
            return new StringSelection(buff.toString());
        }
    });
    pkList.setDropMode(DropMode.INSERT);
    pkList.setDragEnabled(true);

    JScrollPane pkScrollPanel = new JScrollPane(pkList);
    pkScrollPanel.setMaximumSize(new Dimension(Short.MAX_VALUE, 100));
    pkScrollPanel.setAlignmentX(LEFT_ALIGNMENT);

    columnPanel.add(pkScrollPanel);

    return columnPanel;
}

From source file:org.simmi.GeneSetHead.java

License:asdf

public void blastn(boolean show) {
    String dbname = null;/*from w  w  w  .j  a v  a  2 s .  c o  m*/

    final JTextArea ta = new JTextArea();
    JScrollPane sp = new JScrollPane(ta);
    Dimension dim = new Dimension(400, 300);
    sp.setSize(dim);
    sp.setPreferredSize(dim);
    JTextField tf = new JTextField();
    tf.setText("0.00001");
    Object[] objs = new Object[] { sp, tf };
    JOptionPane.showMessageDialog(GeneSetHead.this, objs);

    doBlastn(ta.getText(), tf.getText(), false, null, show);
}

From source file:org.simmi.GeneSetHead.java

License:asdf

public void blast(boolean x) {
    //String dbname = null;

    /*try {/*from ww  w. j  a  v a  2  s. c  om*/
       Map<String,String> env = new HashMap<String,String>();
       Path path = zipfile.toPath();
       String uristr = "jar:" + path.toUri();
       geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")* );
       geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env );
               
       final PathMatcher pm = geneset.zipfilesystem.getPathMatcher("*.p??");
       for( Path p : zipfilesystem.getRootDirectories() ) {
    Files.walkFileTree( p, new SimpleFileVisitor<Path>() {
       @Override
       public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
          if( pm.matches( file ) ) {
             ByteArrayOutputStream baos = new ByteArrayOutputStream();
             byte[] bb = new byte[1024];
             int r = zipm.read( bb );
             while( r > 0 ) {
                baos.write(bb, 0, r);
                r = zipm.read( bb );
             }
             Files.write( new File("c:/"+file.getFileName().).toPath(), baos.toByteArray(), StandardOpenOption.CREATE);
             //unresolvedmap = loadunresolvedmap( new InputStreamReader( zipm ) );
                     
             dbname = zname.substring(0, zname.length()-4);
          }
          return null;*
       }
    });
       }*/
    //Path nf = zipfilesystem.getPath("/unresolved.blastout");
    //unresolvedmap = loadunresolvedmap( new InputStreamReader( Files.newInputStream(nf, StandardOpenOption.READ) ) );

    /*ZipInputStream zipm = new ZipInputStream( new ByteArrayInputStream( zipf ) );
    ZipEntry ze = zipm.getNextEntry();
    while( ze != null ) {
    String zname = ze.getName();
    if( zname.endsWith(".phr") || zname.endsWith(".pin") || zname.endsWith(".psq") ) {
       ByteArrayOutputStream baos = new ByteArrayOutputStream();
       byte[] bb = new byte[1024];
       int r = zipm.read( bb );
       while( r > 0 ) {
          baos.write(bb, 0, r);
          r = zipm.read( bb );
       }
       Files.write( new File("c:/"+zname).toPath(), baos.toByteArray(), StandardOpenOption.CREATE);
       //unresolvedmap = loadunresolvedmap( new InputStreamReader( zipm ) );
               
       dbname = zname.substring(0, zname.length()-4);
    }
    ze = zipm.getNextEntry();
    }*
    } catch (IOException e1) {
    e1.printStackTrace();
    }*/

    final JTextArea ta = new JTextArea();
    JScrollPane sp = new JScrollPane(ta);
    Dimension dim = new Dimension(400, 300);
    sp.setSize(dim);
    sp.setPreferredSize(dim);
    JTextField tf = new JTextField();
    tf.setText("0.00001");
    Object[] objs = new Object[] { sp, tf };
    JOptionPane.showMessageDialog(GeneSetHead.this, objs);

    doBlast(ta.getText(), tf.getText(), true, null, x);
}

From source file:org.ut.biolab.medsavant.client.project.ProjectWizard.java

private AbstractWizardPage getPatientFieldsPage() {

    //setup page//from w w  w.  j a va2 s  .c o  m
    final DefaultWizardPage page = new DefaultWizardPage(PAGENAME_PATIENTS) {
        @Override
        public void setupWizardButtons() {
            fireButtonEvent(ButtonEvent.SHOW_BUTTON, ButtonNames.BACK);
            fireButtonEvent(ButtonEvent.ENABLE_BUTTON, ButtonNames.BACK);
            fireButtonEvent(ButtonEvent.HIDE_BUTTON, ButtonNames.FINISH);
            fireButtonEvent(ButtonEvent.ENABLE_BUTTON, ButtonNames.NEXT);
        }
    };

    page.addText("Add relevant fields for patients. ");

    JScrollPane scrollpane = new JScrollPane();
    scrollpane.setPreferredSize(new Dimension(300, 250));
    scrollpane.getViewport().setBackground(Color.white);

    final JTable table = new JTable() {
        @Override
        public Class<?> getColumnClass(int column) {
            if (column == 2) {
                return Boolean.class;
            } else {
                return String.class;
            }
        }
    };

    patientFormatModel = new DefaultTableModel() {
        @Override
        public boolean isCellEditable(int row, int col) {
            return row >= 8;
        }
    };

    patientFormatModel.addColumn("Name");
    patientFormatModel.addColumn("Type");
    patientFormatModel.addColumn("Filterable");
    patientFormatModel.addColumn("Alias");
    patientFormatModel.addColumn("Description");

    patientFormatModel.addRow(new Object[] { FAMILY_ID.getColumnName(), FAMILY_ID.getTypeString(), true,
            FAMILY_ID.getAlias(), "" });
    patientFormatModel.addRow(new Object[] { HOSPITAL_ID.getColumnName(), HOSPITAL_ID.getTypeString(), true,
            HOSPITAL_ID.getAlias(), "" });
    patientFormatModel.addRow(
            new Object[] { IDBIOMOM.getColumnName(), IDBIOMOM.getTypeString(), true, IDBIOMOM.getAlias(), "" });
    patientFormatModel.addRow(
            new Object[] { IDBIODAD.getColumnName(), IDBIODAD.getTypeString(), true, IDBIODAD.getAlias(), "" });
    patientFormatModel.addRow(
            new Object[] { GENDER.getColumnName(), GENDER.getTypeString(), true, GENDER.getAlias(), "" });
    patientFormatModel.addRow(
            new Object[] { AFFECTED.getColumnName(), AFFECTED.getTypeString(), true, AFFECTED.getAlias(), "" });
    patientFormatModel.addRow(
            new Object[] { DNA_IDS.getColumnName(), DNA_IDS.getTypeString(), true, DNA_IDS.getAlias(), "" });
    patientFormatModel.addRow(
            new Object[] { BAM_URL.getColumnName(), BAM_URL.getTypeString(), true, BAM_URL.getAlias(), "" });
    patientFormatModel.addRow(new Object[] { PHENOTYPES.getColumnName(), PHENOTYPES.getTypeString(), true,
            PHENOTYPES.getAlias(), "" });

    if (modify) {
        for (CustomField f : customFields) {
            patientFormatModel.addRow(new Object[] { f.getColumnName(), f.getTypeString(), f.isFilterable(),
                    f.getAlias(), f.getDescription() });
        }
    }

    table.setModel(patientFormatModel);
    table.putClientProperty("terminateEditOnFocusLost", Boolean.TRUE);
    scrollpane.getViewport().add(table);
    page.addComponent(scrollpane);

    JButton addFieldButton = new JButton("Add Field");
    addFieldButton.addMouseListener(new MouseAdapter() {
        @Override
        public void mouseReleased(MouseEvent e) {
            patientFormatModel.addRow(new Object[5]);
            table.setModel(patientFormatModel);
        }
    });
    page.addComponent(addFieldButton);

    JButton removeFieldButton = new JButton("Remove Field");
    removeFieldButton.setEnabled(false);
    removeFieldButton.addMouseListener(new MouseAdapter() {
        @Override
        public void mouseReleased(MouseEvent e) {
            int row = table.getSelectedRow();
            // Minus one because patient_id isn't in the table.
            if (row >= BasicPatientColumns.REQUIRED_PATIENT_FIELDS.length - 1) {
                patientFormatModel.removeRow(row);
            }
            table.setModel(patientFormatModel);
        }
    });
    table.getSelectionModel().addListSelectionListener(
            new RemovalEnabler(BasicPatientColumns.REQUIRED_PATIENT_FIELDS.length - 1, removeFieldButton));
    page.addComponent(removeFieldButton);

    return page;
}

From source file:org.ut.biolab.medsavant.client.project.ProjectWizard.java

private AbstractWizardPage getVCFFieldsPage() {

    //setup page/*from   w ww  . j a  v a 2s .c om*/
    final DefaultWizardPage page = new DefaultWizardPage(PAGENAME_VCF) {
        @Override
        public void setupWizardButtons() {
            fireButtonEvent(ButtonEvent.SHOW_BUTTON, ButtonNames.BACK);
            fireButtonEvent(ButtonEvent.ENABLE_BUTTON, ButtonNames.BACK);
            fireButtonEvent(ButtonEvent.HIDE_BUTTON, ButtonNames.FINISH);
            fireButtonEvent(ButtonEvent.ENABLE_BUTTON, ButtonNames.NEXT);
        }
    };

    page.addText("Add extra fields to parse from INFO text in VCF files. ");

    JScrollPane scrollpane = new JScrollPane();
    scrollpane.setPreferredSize(new Dimension(300, 250));
    scrollpane.getViewport().setBackground(Color.white);

    final JTable table = new JTable() {
        @Override
        public Class<?> getColumnClass(int column) {
            if (column == 2) {
                return Boolean.class;
            } else {
                return String.class;
            }
        }
    };

    variantFormatModel = new DefaultTableModel();

    variantFormatModel.addColumn("Key");
    variantFormatModel.addColumn("Type");
    variantFormatModel.addColumn("Filterable");
    variantFormatModel.addColumn("Alias");
    variantFormatModel.addColumn("Description");

    if (modify) {
        try {
            int firstRef = manager.getReferenceIDsForProject(LoginController.getSessionID(), projectID)[0];
            CustomField[] fields = manager.getCustomVariantFields(LoginController.getSessionID(), projectID,
                    firstRef,
                    manager.getNewestUpdateID(LoginController.getSessionID(), projectID, firstRef, false));
            for (CustomField f : fields) {
                //casing of f.getColumnName should match database.
                variantFormatModel.addRow(new Object[] { f.getColumnName(), f.getTypeString(), f.isFilterable(),
                        f.getAlias(), f.getDescription() });
            }
        } catch (Exception ex) {
            LOG.error("Error getting reference IDs for project.", ex);
        }
    } else {
        variantFormatModel
                .addRow(new Object[] { AA.getColumnName(), AA.getTypeString(), true, AA.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { AC.getColumnName(), AC.getTypeString(), true, AC.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { AF.getColumnName(), AF.getTypeString(), true, AF.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { AN.getColumnName(), AN.getTypeString(), true, AN.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { BQ.getColumnName(), BQ.getTypeString(), true, BQ.getAlias(), "" });
        variantFormatModel.addRow(
                new Object[] { CIGAR.getColumnName(), CIGAR.getTypeString(), true, CIGAR.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { DB.getColumnName(), DB.getTypeString(), true, DB.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { DP.getColumnName(), DP.getTypeString(), true, DP.getAlias(), "" });
        //variantFormatModel.addRow(new Object[]{END.getColumnName(), END.getTypeString(), true, END.getAlias(), ""});
        variantFormatModel
                .addRow(new Object[] { H2.getColumnName(), H2.getTypeString(), true, H2.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { MQ.getColumnName(), MQ.getTypeString(), true, MQ.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { MQ0.getColumnName(), MQ0.getTypeString(), true, MQ0.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { NS.getColumnName(), NS.getTypeString(), true, NS.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { SB.getColumnName(), SB.getTypeString(), true, SB.getAlias(), "" });
        variantFormatModel.addRow(new Object[] { SOMATIC.getColumnName(), SOMATIC.getTypeString(), true,
                SOMATIC.getAlias(), "" });
        variantFormatModel.addRow(new Object[] { VALIDATED.getColumnName(), VALIDATED.getTypeString(), true,
                VALIDATED.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { JANNOVAR_EFFECT.getColumnName(), JANNOVAR_EFFECT.getTypeString(),
                        JANNOVAR_EFFECT.isFilterable(), JANNOVAR_EFFECT.getAlias(), "" });
        variantFormatModel
                .addRow(new Object[] { JANNOVAR_SYMBOL.getColumnName(), JANNOVAR_SYMBOL.getTypeString(),
                        JANNOVAR_SYMBOL.isFilterable(), JANNOVAR_SYMBOL.getAlias(), "" });
        variantFormatModel.addRow(new Object[] { FORMAT.getColumnName(), FORMAT.getTypeString(),
                FORMAT.isFilterable(), FORMAT.getAlias(), "" });
        variantFormatModel.addRow(new Object[] { SAMPLE_INFO.getColumnName(), SAMPLE_INFO.getTypeString(),
                SAMPLE_INFO.isFilterable(), SAMPLE_INFO.getAlias(), "" });
    }

    table.setModel(variantFormatModel);
    table.putClientProperty("terminateEditOnFocusLost", Boolean.TRUE);
    scrollpane.getViewport().add(table);
    page.addComponent(scrollpane);

    table.addKeyListener(new KeyListener() {
        @Override
        public void keyTyped(KeyEvent e) {
            variantFieldsChanged = true;
        }

        @Override
        public void keyPressed(KeyEvent e) {
            variantFieldsChanged = true;
        }

        @Override
        public void keyReleased(KeyEvent e) {
            variantFieldsChanged = true;
        }
    });

    JButton addFieldButton = new JButton("Add Field");
    addFieldButton.addMouseListener(new MouseAdapter() {
        @Override
        public void mouseReleased(MouseEvent e) {
            variantFormatModel.addRow(new Object[2]);
            table.setModel(variantFormatModel);
            variantFieldsChanged = true;
        }
    });
    page.addComponent(addFieldButton);

    JButton removeFieldButton = new JButton("Remove Field");
    removeFieldButton.setEnabled(false);
    removeFieldButton.addMouseListener(new MouseAdapter() {
        @Override
        public void mouseReleased(MouseEvent e) {
            int row = table.getSelectedRow();
            if (row >= 0) {
                variantFormatModel.removeRow(row);
                table.setModel(variantFormatModel);
                variantFieldsChanged = true;
            }
        }
    });
    table.getSelectionModel().addListSelectionListener(new RemovalEnabler(0, removeFieldButton));
    page.addComponent(removeFieldButton);

    return page;
}

From source file:org.ut.biolab.medsavant.client.project.ProjectWizard.java

private AbstractWizardPage getReferencePage() throws SQLException, RemoteException {
    //setup page/*from w  w  w  .ja  v  a  2s  .com*/
    final DefaultWizardPage page = new DefaultWizardPage(PAGENAME_REF) {
        @Override
        public void setupWizardButtons() {
            fireButtonEvent(ButtonEvent.ENABLE_BUTTON, ButtonNames.BACK);
            fireButtonEvent(ButtonEvent.HIDE_BUTTON, ButtonNames.FINISH);
            fireButtonEvent(ButtonEvent.ENABLE_BUTTON, ButtonNames.NEXT);
        }
    };
    page.addText("Choose reference genome(s) to add to this project, along\n"
            + "with corresponding annotations. Annotations will be\n"
            + "applied to all variants added to these tables.");

    //setup list
    JScrollPane scrollpane = new JScrollPane();
    scrollpane.setPreferredSize(new Dimension(300, 220));
    scrollpane.getViewport().setBackground(Color.white);

    final JPanel p = new JPanel();
    p.setBackground(Color.white);
    p.setLayout(new BoxLayout(p, BoxLayout.Y_AXIS));
    refreshReferencePanel(p);
    scrollpane.getViewport().add(p);

    page.addComponent(scrollpane);

    JButton addRefButton = new JButton("New Reference");
    addRefButton.addMouseListener(new MouseAdapter() {
        @Override
        public void mouseReleased(MouseEvent e) {
            try {
                new NewReferenceDialog().setVisible(true);
                refreshReferencePanel(p);
            } catch (Exception ex) {
                ClientMiscUtils.reportError("Unable to retrieve references and annotations: %s", ex);
            }
        }
    });
    page.addComponent(addRefButton);

    return page;
}

From source file:org.ut.biolab.medsavant.client.view.genetics.charts.SummaryChart.java

private synchronized void drawScatterChart(ScatterChartMap entries) {

    Chart chart = new Chart(new Dimension(200, 200));
    Legend legend = new Legend(chart);

    //Create x axis
    int max = 0;//w  ww.  j  a  v a2 s. c o  m
    CategoryRange<String> range = new CategoryRange<String>();
    for (int i = 0; i < entries.getNumX(); i++) {
        range.add(new ChartCategory(entries.getXValueAt(i)));
    }

    //create models
    DefaultChartModel[] models = new DefaultChartModel[entries.getNumY()];
    for (int i = 0; i < entries.getNumY(); i++) {
        models[i] = new DefaultChartModel();
    }

    for (int i = 0; i < entries.getNumX(); i++) {
        //ScatterChartEntry[] x = entries[i];
        for (int j = 0; j < entries.getNumY(); j++) {
            ScatterChartEntry entry = entries.getValueAt(i, j);
            if (entry != null) {
                max = Math.max(max, entry.getFrequency());
                models[j].addPoint(new ChartPoint(range.getCategoryValues().get(i), entry.getFrequency()));
                models[j].setName(entry.getYRange());
            } else {
                models[j].addPoint(new ChartPoint(range.getCategoryValues().get(i), 0));
            }
        }
    }

    //add models
    for (int i = 0; i < models.length; i++) {
        Color translucentGreen = ViewUtil.getColor(i, models.length);
        ChartStyle style = new ChartStyle(translucentGreen, PointShape.DISC);
        style.setPointSize(10);
        chart.addModel(models[i], style);
    }

    //add axes
    CategoryAxis xaxis = new CategoryAxis(range, mapGenerator.getName());
    chart.setXAxis(xaxis);
    chart.setYAxis(new Axis(new NumericRange(0, max * 1.1), "Frequency"));

    //add chart
    add(chart, c, JLayeredPane.DEFAULT_LAYER);

    //add legend in scrollpane
    JScrollPane scroll = new JScrollPane(legend);
    scroll.setPreferredSize(new Dimension(150, 100));
    c.gridx = 1;
    c.weightx = 0;
    add(scroll, c, JLayeredPane.DEFAULT_LAYER);
    c.weightx = 1;
    c.gridx = 0;

}

From source file:org.ut.biolab.medsavant.client.view.genetics.variantinfo.OtherIndividualsSubInspector.java

protected final void init(VariantFrequencyAggregatePane ap) {
    this.aggregatePane = ap;
    ap.setSplitScreenPanel(splitScreenPanel);

    infoPanel = new JPanel();
    infoPanel.setLayout(new BoxLayout(infoPanel, BoxLayout.Y_AXIS));
    innerPanel = new JPanel();
    innerPanel.setLayout(new BoxLayout(innerPanel, BoxLayout.Y_AXIS));
    initHierarchicalTable();//from  w  ww .j  ava  2s.  c  om
    JScrollPane jsp = new JScrollPane(hTable);
    jsp.setPreferredSize(PREFERRED_SIZE);
    innerPanel.add(jsp);
    innerPanel.setPreferredSize(PREFERRED_SIZE);

    JPanel buttonPanel = new JPanel();
    buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.Y_AXIS));

    JButton cohortButton = new JButton("? " + aggregatePane.getTitle("Cohort"));
    cohortButton.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ae) {
            openAggregatePane("Cohort");
        }
    });

    JButton familyButton = new JButton(
            "? " + aggregatePane.getTitle(BasicPatientColumns.FAMILY_ID.getAlias()));
    familyButton.addActionListener(new ActionListener() {
        @Override
        public void actionPerformed(ActionEvent ae) {
            openAggregatePane(BasicPatientColumns.FAMILY_ID.getAlias());
        }
    });
    buttonPanel.add(cohortButton);
    buttonPanel.add(familyButton);
    innerPanel.add(buttonPanel);
    firstCol = "Cohort";

}