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());
}
}
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);
}
/** @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);
}
}