private void mergeTables(
final CyTable source, final CyTable target, final Class<? extends CyIdentifiable> type) {
CyColumn sourceKey = source.getPrimaryKey();
CyColumn targetKey = target.getPrimaryKey();
String keyName = sourceKey.getName();
// Make sure keys match
if (keyName.equals(targetKey.getName())) {
// Merge columns first, because even if the source table has no rows to merge,
// the columns have to be restored
mergeColumns(keyName, source, target);
for (CyRow sourceRow : source.getAllRows()) {
if (cancelled) return;
Long key = sourceRow.get(keyName, Long.class);
CyIdentifiable entry = cache.getObjectById(key, type);
Long mappedKey = entry != null ? entry.getSUID() : null;
if (mappedKey == null) mappedKey = key;
CyRow targetRow = target.getRow(mappedKey);
mergeRow(keyName, sourceRow, targetRow);
}
}
}
private List<String> getAttributeList(
CyNetwork network,
Set<Class<?>> allowedNodeAttributeTypes,
Set<Class<?>> allowedEdgeAttributeTypes) {
List<String> attributes = new ArrayList<String>();
Set<Class<?>> allowedTypes;
CyTable table;
if (allowedNodeAttributeTypes.size() > 0) {
allowedTypes = allowedNodeAttributeTypes;
table = network.getDefaultNodeTable();
} else if (allowedEdgeAttributeTypes.size() > 0) {
allowedTypes = allowedEdgeAttributeTypes;
table = network.getDefaultEdgeTable();
} else {
return attributes;
}
for (final CyColumn column : table.getColumns()) {
if (allowedTypes.contains(column.getType())) {
attributes.add(column.getName());
}
}
if (attributes.size() > 0) attributes.add(0, UNWEIGHTED);
return attributes;
}
private List<String> getSupportedAttributes(Set<Class<?>> types, CyTable table) {
List<String> attributes = new ArrayList<String>();
attributes.add(UNWEIGHTED);
for (CyColumn column : table.getColumns()) {
for (Class<?> type : types) {
if (column.getType().equals(type)) {
attributes.add(column.getName());
break;
}
}
}
if (attributes.size() > 1) return attributes;
return null;
}
boolean getSetData() {
inputKeyColName = new TreeMap<String, String>();
aimKeyColName = new TreeMap<String, String>();
Collection<CyColumn> columnList = wgs.net.getDefaultNodeTable().getColumns();
CyColumn col = null;
Iterator<CyColumn> iter = columnList.iterator();
while (iter.hasNext()) {
col = iter.next();
String colName;
if (col.getType() != Double.class) continue;
else colName = col.getName();
if (colName.length() > lengthID) {
if (colName.substring(0, lengthID).equals(inputSetID))
inputKeyColName.put(colName.substring(lengthID), colName);
if (colName.substring(0, lengthID).equals(outputAimID))
aimKeyColName.put(colName.substring(lengthID), colName);
}
}
if (inputKeyColName.isEmpty()) return false;
Iterator<String> setIt = inputKeyColName.keySet().iterator();
Iterator<String> aimIt = aimKeyColName.keySet().iterator();
while (setIt.hasNext() & aimIt.hasNext()) if (!setIt.next().equals(aimIt.next())) return false;
activIn = new double[inputKeyColName.keySet().size()][];
activAim = new double[aimKeyColName.keySet().size()][];
int set = 0;
for (String key : inputKeyColName.keySet()) {
activIn[set] = new double[wgs.nodes.size()];
for (int n = 0; n < wgs.nodes.size(); n++) {
Double d = wgs.net.getRow(wgs.nodes.get(n)).get(inputKeyColName.get(key), Double.class);
if (d != null) {
activIn[set][n] = d;
if (d != 0.0) menuUtils.srcDialog.add(n);
} else activIn[set][n] = 0.0;
}
activAim[set] = new double[wgs.nodes.size()];
for (int n = 0; n < wgs.nodes.size(); n++) {
Double d = wgs.net.getRow(wgs.nodes.get(n)).get(aimKeyColName.get(key), Double.class);
if (d != null) activAim[set][n] = d;
else activAim[set][n] = 0.0;
}
set++;
}
activOk = new int[inputKeyColName.keySet().size()];
activNo = new int[inputKeyColName.keySet().size()];
inhibOk = new int[inputKeyColName.keySet().size()];
inhibNo = new int[inputKeyColName.keySet().size()];
return true;
}
public ListSingleSelection<String> getTargetColumns(CyNetwork network) {
CyTable selectedTable = network.getTable(CyNode.class, CyRootNetwork.SHARED_ATTRS);
List<String> colNames = new ArrayList<String>();
for (CyColumn col : selectedTable.getColumns()) {
// Exclude SUID from the mapping key list
if (col.getName().equalsIgnoreCase("SUID")) {
continue;
}
colNames.add(col.getName());
}
ListSingleSelection<String> columns = new ListSingleSelection<String>(colNames);
// columns.setSelectedValue("shared name"); this does not work, why
return columns;
}
private void mergeColumns(final String keyName, final CyTable source, final CyTable target) {
for (CyColumn column : source.getColumns()) {
String columnName = column.getName();
if (columnName.equals(keyName)) continue;
if (target.getColumn(columnName) == null) {
Class<?> type = column.getType();
boolean immutable = column.isImmutable();
if (type.equals(List.class)) {
Class<?> elementType = column.getListElementType();
target.createListColumn(columnName, elementType, immutable);
} else {
target.createColumn(columnName, type, immutable);
}
}
}
}
private Double getMean(CyColumn c) {
Double x = 5d;
List<Double> values = c.getValues(Double.class);
Iterator<Double> it = values.iterator();
while (it.hasNext()) {
Double y = it.next();
x += y;
}
x = x / values.size();
return x;
}
private void mergeRow(String keyName, CyRow sourceRow, CyRow targetRow) {
for (CyColumn column : sourceRow.getTable().getColumns()) {
if (cancelled) return;
String columnName = column.getName();
if (columnName.equals(keyName)) continue;
Class<?> type = column.getType();
if (type.equals(List.class)) {
Class<?> elementType = column.getListElementType();
List<?> list = sourceRow.getList(columnName, elementType);
targetRow.set(columnName, list);
} else {
Object value = sourceRow.get(columnName, type);
targetRow.set(columnName, value);
}
}
}
private Collection<String> getAttributes(boolean node) {
CyNetwork network = applicationManager.getCurrentNetwork();
CyTable table = node ? network.getDefaultNodeTable() : network.getDefaultEdgeTable();
Collection<CyColumn> columns = table.getColumns();
Set<String> attributes =
new TreeSet<String>(
new Comparator<String>() {
public int compare(String s1, String s2) {
return s1.compareToIgnoreCase(s2);
}
});
for (CyColumn column : columns) {
if (!CyIdentifiable.SUID.equals(column.getName())
&& (node || Number.class.isAssignableFrom(column.getType()))) {
attributes.add(column.getName());
}
}
return attributes;
}
private Double getMinimum(CyColumn c) {
Double x = Double.MAX_VALUE;
List<Double> values = c.getValues(Double.class);
Iterator<Double> it = values.iterator();
while (it.hasNext()) {
Double y = it.next();
if (y < x) {
x = y;
}
}
return x;
}
@Override
public boolean handleIt(
final CyIdentifiable to,
final CyColumn toColumn,
final Map<CyIdentifiable, CyColumn> mapFromGOFromAttr) {
if (to == null || toColumn == null || mapFromGOFromAttr == null) {
throw new java.lang.NullPointerException("All parameters should not be null.");
}
final CyTable table = toColumn.getTable();
final CyRow row = table.getRow(to.getSUID());
final ColumnType type = ColumnType.getType(toColumn);
if (type == ColumnType.STRING) {
final String toValue = row.get(toColumn.getName(), String.class);
final Set<String> values = new TreeSet<String>();
values.add(toValue);
for (Map.Entry<CyIdentifiable, CyColumn> entry : mapFromGOFromAttr.entrySet()) {
final CyIdentifiable from = entry.getKey();
final CyColumn fromColumn = entry.getValue();
final CyRow fromRow = fromColumn.getTable().getRow(from.getSUID());
// TODO figure out which network to be using
String fromValue = fromRow.get(fromColumn.getName(), String.class);
if (fromValue != null) {
values.add(fromValue.toString());
}
}
StringBuilder str = new StringBuilder();
for (String v : values) {
str.append(v + ";");
}
str.deleteCharAt(str.length() - 1);
row.set(toColumn.getName(), str.toString());
return true;
}
// FIXME: how about Integer, Double, Boolean?
return false;
}
/** Create the dialog. */
@SuppressWarnings("serial")
private PortalImportDialog() {
setTitle("Load Data From cBio Portal");
setBounds(100, 100, 650, 500);
BorderLayout borderLayout = new BorderLayout();
borderLayout.setVgap(2);
borderLayout.setHgap(2);
getContentPane().setLayout(borderLayout);
contentPanel.setBorder(new EmptyBorder(5, 5, 5, 5));
getContentPane().add(contentPanel, BorderLayout.CENTER);
contentPanel.setLayout(new BorderLayout(5, 5));
{
JScrollPane scrollPane = new JScrollPane();
scrollPane.setViewportBorder(
new TitledBorder(
new LineBorder(new Color(184, 207, 229)),
"Select Genomic Profile(s)",
TitledBorder.LEADING,
TitledBorder.TOP,
null,
new Color(51, 51, 51)));
contentPanel.add(scrollPane, BorderLayout.CENTER);
{
profileList =
new JList() {
public String getToolTipText(MouseEvent event) { // tooltip for each profile
Point point = event.getPoint();
// Get the item in the list box at the mouse location
int index = this.locationToIndex(point);
// Get the value of the item in the list
return ((GeneticProfile) this.getModel().getElementAt(index)).getDescription();
}
};
scrollPane.setViewportView(profileList);
}
}
{
JPanel panel = new JPanel();
contentPanel.add(panel, BorderLayout.NORTH);
panel.setLayout(new GridLayout(2, 1, 0, 0));
{
JLabel lblNewLabel = new JLabel("Select a Cancer Study");
panel.add(lblNewLabel);
}
cancerStudyComboBox = new JComboBox();
panel.add(cancerStudyComboBox);
cancerStudyComboBox.setRenderer(
new BasicComboBoxRenderer() {
public Component getListCellRendererComponent(
JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
if (isSelected) {
setBackground(list.getSelectionBackground());
setForeground(list.getSelectionForeground());
if (-1 < index) {
list.setToolTipText(
"<html><body>"
+ ((CancerStudy) cancerStudyComboBox.getModel().getElementAt(index))
.getDescription()
+ "</body></html>");
}
} else {
setBackground(list.getBackground());
setForeground(list.getForeground());
}
setFont(list.getFont());
setText((value == null) ? "" : value.toString());
return this;
}
});
{
JPanel panel_1 = new JPanel();
contentPanel.add(panel_1, BorderLayout.SOUTH);
panel_1.setLayout(new GridLayout(4, 1, 0, 0));
{
JLabel lblNewLabel_1 = new JLabel("Select Patient/Case Set");
panel_1.add(lblNewLabel_1);
}
{
caseSetComboBox = new JComboBox();
panel_1.add(caseSetComboBox);
caseSetComboBox.setRenderer(
new BasicComboBoxRenderer() {
public Component getListCellRendererComponent(
JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
if (isSelected) {
setBackground(list.getSelectionBackground());
setForeground(list.getSelectionForeground());
if (-1 < index) {
list.setToolTipText(
"<html><body>"
+ ((CaseList) caseSetComboBox.getModel().getElementAt(index))
.getDescription()
+ "</body></html>");
}
} else {
setBackground(list.getBackground());
setForeground(list.getForeground());
}
setFont(list.getFont());
setText((value == null) ? "" : value.toString());
return this;
}
});
}
{
JLabel lblNewLabel_2 = new JLabel("Select Node Attribute for Gene Symbols");
panel_1.add(lblNewLabel_2);
}
{
geneSymbolComboBox = new JComboBox();
panel_1.add(geneSymbolComboBox);
// Get the node attributes from current network
Collection<CyColumn> cols =
MondrianApp.getInstance()
.getAppManager()
.getCurrentNetwork()
.getDefaultNodeTable()
.getColumns();
List<String> attrs = new ArrayList<String>();
final List<String> toolTips = new ArrayList<String>();
for (CyColumn col : cols) {
if (col.getType() != String.class) {
continue; // Looking for gene symbols, which should be String column
}
attrs.add(col.getName());
List<Object> values = col.getValues(col.getType());
String toolTip = "<html><body>";
for (int j = 0; j < Math.min(values.size(), 3); j++) {
toolTip += values.get(j).toString();
if (j < Math.min(values.size(), 3) - 1) toolTip += "<br/>";
}
if (values.size() > 3) toolTip += "<br/>...";
toolTip += "</body></html>";
toolTips.add(toolTip);
}
geneSymbolComboBox.setModel(
new DefaultComboBoxModel(attrs.toArray(new String[attrs.size()])));
geneSymbolComboBox.setRenderer(
new BasicComboBoxRenderer() {
public Component getListCellRendererComponent(
JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
if (isSelected) {
setBackground(list.getSelectionBackground());
setForeground(list.getSelectionForeground());
if (-1 < index) {
list.setToolTipText(toolTips.get(index));
}
} else {
setBackground(list.getBackground());
setForeground(list.getForeground());
}
setFont(list.getFont());
setText((value == null) ? "" : value.toString());
return this;
}
});
}
}
cancerStudyComboBox.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
CancerStudy study = (CancerStudy) cancerStudyComboBox.getSelectedItem();
if (!study.equals(portalClient.getCurrentCancerStudy())) {
DialogTaskManager taskManager = MondrianApp.getInstance().getTaskManager();
taskManager.execute(new TaskIterator(new LoadCancerStudyTask()));
}
}
});
}
{
JPanel buttonPane = new JPanel();
buttonPane.setLayout(new FlowLayout(FlowLayout.RIGHT));
getContentPane().add(buttonPane, BorderLayout.SOUTH);
{
JButton okButton = new JButton("OK");
okButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
PortalImportDialog.getInstance().setVisible(false);
DialogTaskManager taskManager = MondrianApp.getInstance().getTaskManager();
taskManager.execute(new TaskIterator(new ImportDataTask()));
}
});
okButton.setActionCommand("OK");
buttonPane.add(okButton);
getRootPane().setDefaultButton(okButton);
}
{
JButton cancelButton = new JButton("Cancel");
cancelButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
PortalImportDialog.getInstance().setVisible(false);
}
});
cancelButton.setActionCommand("Cancel");
buttonPane.add(cancelButton);
}
}
DialogTaskManager taskManager = MondrianApp.getInstance().getTaskManager();
taskManager.execute(new TaskIterator(new InitializeCancerStudyTask()));
}
