/** Constructor */
@SuppressWarnings("serial")
public SubnetExtraction(Frame aFrame, GenericElement item) {
super(aFrame);
item_ = item;
// Set model of "subnet size" spinner
SpinnerNumberModel model = new SpinnerNumberModel();
model.setMinimum(1);
model.setStepSize(1);
int maxSize =
(item instanceof StructureElement)
? ((StructureElement) item).getNetwork().getSize()
: ((DynamicalModelElement) item).getGeneNetwork().getSize();
model.setMaximum(maxSize);
int effectiveSize = (10 <= maxSize) ? 10 : maxSize;
model.setValue(effectiveSize);
subnetSize_.setModel(model);
// Set model of "number of subnets" spinner
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum(20);
model.setStepSize(1);
model.setValue(10);
numberSubnets_.setModel(model);
// Set model of "random among top" spinner
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum(100);
model.setStepSize(1);
model.setValue(20);
randomAmongTopSpinner_.setModel(model);
// Set model of "From strongly connected components"
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum(maxSize);
model.setStepSize(1);
model.setValue(10);
numStronglyConnected_.setModel(model);
// Set model of "From strongly connected components"
model = new SpinnerNumberModel();
model.setMinimum(1);
model.setMaximum((Integer) subnetSize_.getModel().getValue());
model.setStepSize(1);
model.setValue(10);
numRegulators_.setModel(model);
// add tooltips for all elements of the window
addTooltips();
String title1, title2;
title1 = title2 = "";
if (item_ instanceof StructureElement) {
ImodNetwork network = ((StructureElement) item_).getNetwork();
title1 = item_.getLabel();
title2 = network.getSize() + " nodes, " + network.getNumEdges() + " edges";
} else if (item_ instanceof DynamicalModelElement) {
GeneNetwork geneNetwork = ((DynamicalModelElement) item_).getGeneNetwork();
title1 = item_.getLabel();
title2 = geneNetwork.getSize() + " genes, " + geneNetwork.getNumEdges() + " interactions";
}
setGeneralInformation(title1 + " (" + title2 + ")");
/** ACTIONS */
subnetRootNameDocument_ = subnetRootName_.getDocument();
subnetRootNameDocument_.addDocumentListener(
new DocumentListener() {
public void changedUpdate(DocumentEvent arg0) {
runButton_.setEnabled(!subnetRootName_.getText().equals(""));
}
public void insertUpdate(DocumentEvent arg0) {
runButton_.setEnabled(!subnetRootName_.getText().equals(""));
}
public void removeUpdate(DocumentEvent arg0) {
runButton_.setEnabled(!subnetRootName_.getText().equals(""));
}
});
extractAllRegulators_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
disableExtractionOptions();
}
});
randomVertex_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateSeedControls();
}
});
selectionFromList_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateSeedControls();
}
});
greedy_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateNeighborSelectionControls();
}
});
randomAmongTop_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateNeighborSelectionControls();
}
});
stronglyConnected_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
updateSeedControls();
}
});
cancelButton.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
GnwSettings.getInstance().stopSubnetExtraction(true);
escapeAction();
}
});
runButton_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
run();
}
});
subnetSize_.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent arg0) {
updateRegulatorsOptions();
}
});
numRegulators_.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent arg0) {
updateRegulatorsOptions();
}
});
useNumRegulators_.addActionListener(
new ActionListener() {
public void actionPerformed(final ActionEvent arg0) {
numRegulators_.setEnabled(useNumRegulators_.isSelected());
}
});
// useNumRegulators_.addChangeListener(new ChangeListener() {
// public void stateChanged(ChangeEvent arg0) {
// numRegulators_.setEnabled(useNumRegulators_.isSelected());
// }
// });
subnetIdProposal();
setListVerticesID();
updateSeedControls();
updateNeighborSelectionControls();
useNumRegulators_.setSelected(false);
numRegulators_.setEnabled(false);
}
private void createDataTable(GeneNetwork grn) {
int numRxns = grn.getSize();
DefaultTableModel modelTable =
new DefaultTableModel(numRxns, columnName.length) {
public boolean isCellEditable(int row, int column) {
if (column == 0) return false;
if (column == 1) return false;
if (column == 2) return false;
if (column == 3) return false;
// if(column == 4)
// return true;
return true;
}
};
modelTable.setColumnIdentifiers(columnName);
table.setModel(modelTable);
// set content
List<RxnButtonRender> editors = new ArrayList<RxnButtonRender>(numRxns);
// set content
for (int i = 0; i < numRxns; i++) {
Gene targetGene = (Gene) grn.getNode(i);
String inputs = "";
ArrayList<Gene> inputGenes = ((Gene) targetGene).getInputGenes();
if (inputGenes != null && inputGenes.size() > 0) {
for (int j = 0; j < inputGenes.size() - 1; j++)
inputs += inputGenes.get(j).getLabel() + ",";
inputs += inputGenes.get(inputGenes.size() - 1).getLabel();
}
String reactantString = "";
ArrayList<Gene> reactants = ((Gene) targetGene).getReactants_();
if (reactants != null && reactants.size() > 0) {
for (int j = 0; j < reactants.size() - 1; j++)
reactantString += reactants.get(j).getLabel() + ",";
reactantString += reactants.get(reactants.size() - 1).getLabel();
}
// //third column
// String inputsActive = "";
// ArrayList<Gene> inputActivatorGenes = ((Gene) targetGene).getActivators();
// if( inputActivatorGenes != null && inputActivatorGenes.size()>0 ){
// for(int j=0;j<inputActivatorGenes.size()-1;j++)
// inputsActive += inputActivatorGenes.get(j).getLabel() + ",";
// inputsActive += inputActivatorGenes.get(inputActivatorGenes.size()-1).getLabel();
// }
//
// //fourth column
// String inputsInhibit = "";
// ArrayList<Gene> inputInhibitorGenes = ((Gene) targetGene).getInhibitors();
// if( inputInhibitorGenes != null && inputInhibitorGenes.size()>0 ){
// for(int j=0;j<inputInhibitorGenes.size()-1;j++)
// inputsInhibit += inputInhibitorGenes.get(j).getLabel() + ",";
// inputsInhibit += inputInhibitorGenes.get(inputInhibitorGenes.size()-1).getLabel();
// }
// fifth column
// String combination = ((Gene) targetGene).getCombination();
// String disEquation = ((Gene) targetGene).getDisEquation();
editors.add(
new RxnButtonRender(
table, targetGene.getLabel(), targetGene.getRnID(), element, targetGene, c));
// //content
// String[] tmp = {"R"+(i+1), targetGene.getLabel(), inputs, fourthContent};
// content
modelTable.setValueAt(targetGene.getRnID(), i, 0); // 1st
modelTable.setValueAt(targetGene.getLabel(), i, 1); // 2nd
modelTable.setValueAt(reactantString, i, 2); // 2nd
modelTable.setValueAt(inputs, i, 3); // 3rd
// modelTable.setValueAt(inputsInhibit, i, 3); //4rd
// modelTable.setValueAt(fourthContent, i, 3); //5th
} // end of for
table.setEditors(editors);
table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
JScrollPane scrollPane = new JScrollPane(table);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
// set column width
int[] width = {20, 20, 30, 30, 30};
table.setColumnModel(getColumn(table, width));
table.setRowHeight(20);
tablePanel.setLayout(new BoxLayout(tablePanel, BoxLayout.Y_AXIS));
tablePanel.add(Box.createVerticalStrut(10));
tablePanel.add(scrollPane);
}