Beispiel #1
0
class NodeStatusTableModel extends AbstractTableModel implements NodeListener, RequestListener {
  private JTable table;
  private SpauldingApp spauldingApp;
  // We want fast lookup by index (row) and by nodeID
  private Vector<Node> nodes;
  private Map<Integer, Integer> nodeIDToRow; // Map<nodeID, rowIndex>
  private Map<Integer, Request> nodeIDToRequest =
      Collections.synchronizedMap(new HashMap<Integer, Request>());

  private String[] columnNames = {
    "NodeID", "State", "Tail", "Head", "Local time", "Global time", "Time synched", "Last request",
  };

  private void initColumnWidths(final JTable table) {
    javax.swing.SwingUtilities.invokeLater(
        new Runnable() {
          public void run() {
            table.getColumnModel().getColumn(0).setMaxWidth(100);
            table.getColumnModel().getColumn(1).setPreferredWidth(150);
            //                table.getColumnModel().getColumn(2).setPreferredWidth(5);
            //                table.getColumnModel().getColumn(3).setPreferredWidth(5);
            //                table.getColumnModel().getColumn(4).setPreferredWidth(5);
            //                table.getColumnModel().getColumn(5).setPreferredWidth(5);
            table.getColumnModel().getColumn(7).setPreferredWidth(175);
          }
        });
  }

  // ----------- Custom Renderers ----------------------------------------------------------------
  class LastRequestCellRendererClass {} // wrapper class

  class LastRequestCellRenderer extends JProgressBar implements TableCellRenderer {
    LastRequestCellRenderer() {
      super(0, 100);
      this.setBorderPainted(true);
      this.setStringPainted(true);
      // this.setForeground(new Color(0, 0, 150));
    }

    public Component getTableCellRendererComponent(
        JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
      if (isSelected) this.setBackground(table.getSelectionBackground());
      else this.setBackground(table.getBackground());

      Node node = nodes.get(row);
      Request request = nodeIDToRequest.get(node.getNodeID());
      if (request == null) {
        this.setString("NONE");
        this.setValue(0);
      } else {
        int percent = (int) Math.round(request.getPercentDone());
        this.setString(request.getType().toString() + "  " + percent + "%");
        this.setValue(percent);
      }
      return this;
    }
  }
  // ---------------------------------------------------------------------------------------------

  NodeStatusTableModel(SpauldingApp spauldingGUI, JTable table) {
    assert (spauldingGUI != null && table != null);
    this.table = table;
    this.spauldingApp = spauldingGUI;

    // set custom renderers
    table.setDefaultRenderer(
        new LastRequestCellRendererClass().getClass(), new LastRequestCellRenderer());

    this.initColumnWidths(table);
    updateNodes();
  }

  private void updateNodes() {
    nodes = spauldingApp.getNodesSorted();
    nodeIDToRow = Collections.synchronizedMap(new HashMap<Integer, Integer>());

    for (int r = 0; r < nodes.size(); ++r) nodeIDToRow.put(nodes.get(r).getNodeID(), r);
  }

  public Node getNode(int row) {
    return nodes.get(row);
  }

  public int getColumnCount() {
    return columnNames.length;
  }

  public int getRowCount() {
    return nodes.size();
  }

  public String getColumnName(int col) {
    return columnNames[col];
  }

  public synchronized Object getValueAt(int row, int col) {
    Node node = nodes.get(row);

    switch (col) {
      case 0:
        return node.getNodeID();
      case 1:
        return node.getCurrState();
      case 2:
        return node.getTailBlockID();
      case 3:
        return node.getHeadBlockID();
      case 4:
        return node.getLocalTime();
      case 5:
        return node.getGlobalTime();
      case 6:
        return node.getIsTimeSynchronized();
      case 7:
        return new LastRequestCellRendererClass();
      default:
        return "UNKNOWN";
    }
  }

  /*
   * JTable uses this method to determine the default renderer/
   * editor for each cell.  If we didn't implement this method,
   * then the last column would contain text ("true"/"false"),
   * rather than a check box.
   */
  public Class getColumnClass(int c) {
    return getValueAt(0, c).getClass();
  }

  public void updateNodeID(int nodeID) {
    Integer rowIndex = nodeIDToRow.get(nodeID);
    if (rowIndex == null) updateAll();
    else fireTableRowsUpdated(rowIndex, rowIndex);
  }

  public synchronized void updateAll() {
    updateNodes();
    fireTableDataChanged();
  }

  // ----------- Listening Interfaces ---------
  public void newSamplingMsg(
      SamplingMsg samplingMsg) { // Just ignore, we don't care about new samples
  }

  public void newReplyMsg(ReplyMsg replyMsg) {
    updateNodeID(replyMsg.get_srcAddr());
  }

  public void requestDone(Request request, boolean isSuccessful) {}

  public void percentCompletedChanged(Request request, double percentCompleted) {
    assert (request != null);
    this.nodeIDToRequest.put(request.getDestAddr(), request);
    updateNodeID(request.getDestAddr());
  }
}
Beispiel #2
0
  private void updateNodes() {
    nodes = spauldingApp.getNodesSorted();
    nodeIDToRow = Collections.synchronizedMap(new HashMap<Integer, Integer>());

    for (int r = 0; r < nodes.size(); ++r) nodeIDToRow.put(nodes.get(r).getNodeID(), r);
  }
Beispiel #3
0
/** @author Jim Robinson */
public class EncodeFileBrowser extends JDialog {

  private static Logger log = Logger.getLogger(EncodeFileBrowser.class);

  private static Map<String, EncodeFileBrowser> instanceMap =
      Collections.synchronizedMap(new HashMap<String, EncodeFileBrowser>());
  private static NumberFormatter numberFormatter = new NumberFormatter();

  private JButton cancelButton;
  private JPanel dialogPane;
  private JPanel contentPanel;
  private JScrollPane scrollPane1;
  private JTable table;
  private JPanel filterPanel;
  private JLabel filterLabel;
  private JTextField filterTextField;
  private JLabel rowCountLabel;
  private JPanel buttonBar;
  private JButton okButton;

  EncodeTableModel model;
  private boolean canceled;

  public static synchronized EncodeFileBrowser getInstance(String genomeId) throws IOException {

    String encodeGenomeId = getEncodeGenomeId(genomeId);
    EncodeFileBrowser instance = instanceMap.get(encodeGenomeId);
    if (instance == null) {
      Pair<String[], List<EncodeFileRecord>> records = getEncodeFileRecords(encodeGenomeId);
      if (records == null) {
        return null;
      }
      Frame parent = IGV.hasInstance() ? IGV.getMainFrame() : null;
      instance =
          new EncodeFileBrowser(
              parent, new EncodeTableModel(records.getFirst(), records.getSecond()));
      instanceMap.put(encodeGenomeId, instance);
    }

    return instance;
  }

  private static String getEncodeGenomeId(String genomeId) {
    if (genomeId.equals("b37") || genomeId.equals("1kg_v37")) return "hg19";
    else if (genomeId.equals("1kg_ref")) return "hg19";
    else return genomeId;
  }

  private static Pair<String[], List<EncodeFileRecord>> getEncodeFileRecords(String genomeId)
      throws IOException {

    InputStream is = null;

    try {

      is = EncodeFileBrowser.class.getResourceAsStream("encode." + genomeId + ".txt");
      if (is == null) {
        return null;
      }
      BufferedReader reader = new BufferedReader(new InputStreamReader(is));

      String[] headers = Globals.tabPattern.split(reader.readLine());

      List<EncodeFileRecord> records = new ArrayList<EncodeFileRecord>(20000);
      String nextLine;
      while ((nextLine = reader.readLine()) != null) {
        if (!nextLine.startsWith("#")) {

          String[] tokens = Globals.tabPattern.split(nextLine, -1);
          String path = tokens[0];

          Map<String, String> attributes = new HashMap<String, String>();
          for (int i = 0; i < headers.length; i++) {
            String value = i < tokens.length ? tokens[i] : "";
            if (value.length() > 0) {
              attributes.put(headers[i], value);
            }
          }
          records.add(new EncodeFileRecord(path, attributes));
        }
      }
      return new Pair(headers, records);
    } finally {
      if (is != null) is.close();
    }
  }

  private EncodeFileBrowser(Frame owner, EncodeTableModel model) {
    super(owner);
    this.model = model;
    setModal(true);
    initComponents();
    init(model);
  }

  private void init(final EncodeTableModel model) {
    setModal(true);
    setTitle("Encode Production Data");

    table.setAutoCreateRowSorter(true);
    table.setModel(model);
    table.setRowSorter(model.getSorter());
    try {
      rowCountLabel.setText(numberFormatter.valueToString(table.getRowCount()) + " rows");
    } catch (ParseException e) {

    }

    table.setRowSelectionAllowed(false);
    table.setColumnSelectionAllowed(false);

    filterTextField
        .getDocument()
        .addDocumentListener(
            new DocumentListener() {
              public void changedUpdate(DocumentEvent e) {
                updateFilter();
              }

              public void insertUpdate(DocumentEvent e) {
                updateFilter();
              }

              public void removeUpdate(DocumentEvent e) {
                updateFilter();
              }
            });
  }

  /** Update the row filter regular expression from the expression in the text box. */
  private void updateFilter() {

    RowFilter<EncodeTableModel, Object> rf = null;
    // If current expression doesn't parse, don't update.
    try {
      rf = new RegexFilter(filterTextField.getText());
    } catch (java.util.regex.PatternSyntaxException e) {
      return;
    }
    model.getSorter().setRowFilter(rf);

    try {
      rowCountLabel.setText(numberFormatter.valueToString(table.getRowCount()) + " rows");
    } catch (ParseException e) {
      e
          .printStackTrace(); // To change body of catch statement use File | Settings | File
                              // Templates.
    }
  }

  private void loadButtonActionPerformed(ActionEvent e) {
    canceled = false;
    setVisible(false);
  }

  private void cancelButtonActionPerformed(ActionEvent e) {
    canceled = true;
    setVisible(false);
  }

  public boolean isCanceled() {
    return canceled;
  }

  private Set<String> getLoadedPaths() {

    if (!IGV.hasInstance()) return new HashSet<String>();

    Collection<ResourceLocator> locators = IGV.getInstance().getDataResourceLocators();
    HashSet<String> loadedPaths = new HashSet<String>(locators.size());
    for (ResourceLocator locator : locators) {
      loadedPaths.add(locator.getPath());
    }
    return loadedPaths;
  }

  /**
   * @return the list of VISIBLE selected records. Filtered records are not returned even if
   *     record.selected == true
   * @throws IOException
   */
  public List<EncodeFileRecord> getSelectedRecords() throws IOException {

    List<EncodeFileRecord> selectedRecords = new ArrayList<EncodeFileRecord>();
    List<EncodeFileRecord> allRecords = model.getRecords();

    int rowCount = table.getRowCount();
    for (int i = 0; i < rowCount; i++) {
      int modelIdx = table.convertRowIndexToModel(i);
      EncodeFileRecord record = allRecords.get(modelIdx);
      if (record.isSelected()) {
        selectedRecords.add(record);
      }
    }

    return selectedRecords;
  }

  private class RegexFilter extends RowFilter {

    List<Pair<String, Matcher>> matchers;

    RegexFilter(String text) {

      if (text == null) {
        throw new IllegalArgumentException("Pattern must be non-null");
      }
      matchers = new ArrayList<Pair<String, Matcher>>();
      String[] tokens = Globals.whitespacePattern.split(text);
      for (String t : tokens) {
        // If token contains an = sign apply to specified column only
        String column = "*";
        String value = t.trim();
        if (t.contains("=")) {
          String[] kv = Globals.equalPattern.split(t);
          if (kv.length > 1) {
            column = kv[0].trim();
            value = kv[1].trim();
          } else {
            value = kv[0]; // Value is column name until more input is entered
          }
        }

        matchers.add(new Pair(column, Pattern.compile("(?i)" + value).matcher("")));
      }
    }

    /**
     * Include row if each matcher succeeds in at least one column. In other words all the
     * conditions are combined with "and"
     *
     * @param value
     * @return
     */
    @Override
    public boolean include(Entry value) {

      for (Pair<String, Matcher> entry : matchers) {
        String column = entry.getFirst();
        Matcher matcher = entry.getSecond();

        // Search for a match in at least one column.  The first column is the checkbox.
        boolean found = false; // Pessimistic
        int nColumns = table.getColumnCount();
        for (int index = 1; index < nColumns; index++) {

          // Include column headings in search.  This is to prevent premature filtering when
          // entering a
          // specific column condition (e.g. cataType=ChipSeq)
          matcher.reset(table.getColumnName(index).toLowerCase());
          if (matcher.find()) {
            found = true;
            break;
          }

          boolean wildcard = column.equals("*");
          if (wildcard || column.equalsIgnoreCase(table.getColumnName(index))) {
            matcher.reset(value.getStringValue(index));
            if (matcher.find()) {
              found = true;
              break;
            }
          }
        }
        if (!found) return false;
      }
      return true; // If we get here we matched them all
    }
  }

  private void initComponents() {

    dialogPane = new JPanel();
    contentPanel = new JPanel();
    scrollPane1 = new JScrollPane();
    table = new JTable();
    filterPanel = new JPanel();
    filterLabel = new JLabel();
    filterTextField = new JTextField();
    rowCountLabel = new JLabel();
    buttonBar = new JPanel();
    okButton = new JButton();
    cancelButton = new JButton();

    getRootPane().setDefaultButton(okButton);

    final String filterToolTip =
        "Enter multiple filter strings separated by commas.  e.g.  GM12878, ChipSeq";
    filterLabel.setToolTipText(filterToolTip);
    filterTextField.setToolTipText(filterToolTip);

    // ======== this ========
    Container contentPane = getContentPane();
    contentPane.setLayout(new BorderLayout());

    // ======== dialogPane ========

    dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
    dialogPane.setLayout(new BorderLayout());

    // ======== contentPanel ========

    contentPanel.setLayout(new BorderLayout(0, 10));

    // ======== scrollPane1 ========

    scrollPane1.setViewportView(table);

    contentPanel.add(scrollPane1, BorderLayout.CENTER);

    // ======== panel1 ========

    filterPanel.setLayout(new JideBoxLayout(filterPanel, JideBoxLayout.X_AXIS, 5));

    // ---- label1 ----
    filterLabel.setText("Filter:");
    filterPanel.add(filterLabel, JideBoxLayout.FIX);

    // ---- filterTextField ----
    filterPanel.add(filterTextField, JideBoxLayout.VARY);

    rowCountLabel.setHorizontalAlignment(JLabel.RIGHT);
    JPanel sillyPanel = new JPanel();
    sillyPanel.setLayout(new JideBoxLayout(sillyPanel, JideBoxLayout.X_AXIS, 0));
    sillyPanel.setPreferredSize(new Dimension(100, 28));
    sillyPanel.add(rowCountLabel, JideBoxLayout.VARY);

    filterPanel.add(sillyPanel, JideBoxLayout.FIX);

    contentPanel.add(filterPanel, BorderLayout.NORTH);

    dialogPane.add(contentPanel, BorderLayout.CENTER);

    // ======== buttonBar ========

    buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
    buttonBar.setLayout(new GridBagLayout());
    ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[] {0, 85, 80};
    ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[] {1.0, 0.0, 0.0};

    // ---- okButton ----
    okButton.setText("Load");
    okButton.addActionListener(
        new ActionListener() {
          @Override
          public void actionPerformed(ActionEvent e) {
            loadButtonActionPerformed(e);
          }
        });
    buttonBar.add(
        okButton,
        new GridBagConstraints(
            1,
            0,
            1,
            1,
            0.0,
            0.0,
            GridBagConstraints.CENTER,
            GridBagConstraints.BOTH,
            new Insets(0, 0, 0, 5),
            0,
            0));

    // ---- cancelButton ----
    cancelButton.setText("Cancel");
    cancelButton.addActionListener(
        new ActionListener() {
          @Override
          public void actionPerformed(ActionEvent e) {
            cancelButtonActionPerformed(e);
          }
        });
    buttonBar.add(
        cancelButton,
        new GridBagConstraints(
            2,
            0,
            1,
            1,
            0.0,
            0.0,
            GridBagConstraints.CENTER,
            GridBagConstraints.BOTH,
            new Insets(0, 0, 0, 0),
            0,
            0));

    dialogPane.add(buttonBar, BorderLayout.SOUTH);

    contentPane.add(dialogPane, BorderLayout.CENTER);
    setSize(700, 620);
    setLocationRelativeTo(getOwner());
  }

  public static void main(String[] args) throws IOException {
    getInstance("hg19").setVisible(true);
  }
}