Examples with CyNetwork org.cytoscape.model.CyNetwork used on opensource projects

Example 51 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class FilterMainPanel method updateCMBAttributes.

/*
	 * Update the attribute list in the attribute combobox based on the settings in the 
	 * current selected filter
	 */
private void updateCMBAttributes() {
    DefaultComboBoxModel cbm;
    cbm = ((DefaultComboBoxModel) cmbAttributes.getModel());
    cbm.removeAllElements();
    cbm.addElement(attributesSeperator);
    CompositeFilter selectedFilter = (CompositeFilter) cmbFilters.getSelectedItem();
    if (selectedFilter == null) {
        return;
    }
    CyNetwork network = selectedFilter.getNetwork();
    if (network == null) {
        return;
    }
    List<String> av;
    av = getCyAttributesList(network, "node");
    for (int i = 0; i < av.size(); i++) {
        cbm.addElement(av.get(i));
    }
    av = getCyAttributesList(network, "edge");
    for (int i = 0; i < av.size(); i++) {
        cbm.addElement(av.get(i));
    }
    cbm.addElement(filtersSeparator);
    Vector<CompositeFilter> allFilters = modelLocator.getFilters();
    if (allFilters != null) {
        for (int i = 0; i < allFilters.size(); i++) {
            Object fi;
            fi = allFilters.elementAt(i);
            if (fi != selectedFilter) {
                cbm.addElement(fi);
            }
        }
    }
}

Example 52 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class FilterMainPanel method actionPerformed.

@Override
public void actionPerformed(ActionEvent e) {
    Object _actionObject = e.getSource();
    // handle Button events
    if (_actionObject instanceof JButton) {
        JButton _btn = (JButton) _actionObject;
        if (_btn == btnApplyFilter) {
            CompositeFilter theFilterToApply = (CompositeFilter) cmbFilters.getSelectedItem();
            final CyNetwork currentNetwork = applicationManager.getCurrentNetwork();
            if (currentNetwork == null)
                return;
            theFilterToApply.setNetwork(currentNetwork);
            FilterUtil.doSelection(theFilterToApply, applicationManager);
        }
        if (_btn == btnAddFilterWidget) {
            // btnAddFilterWidget is clicked!
            CompositeFilter selectedFilter = (CompositeFilter) cmbFilters.getSelectedItem();
            FilterSettingPanel theSettingPanel = filter2SettingPanelMap.get(selectedFilter);
            if (cmbAttributes.getSelectedItem() instanceof String) {
                String selectItem = (String) cmbAttributes.getSelectedItem();
                if (selectItem.equalsIgnoreCase(filtersSeparator) || selectItem.equalsIgnoreCase(attributesSeperator)) {
                    return;
                }
            }
            if (cmbAttributes.getSelectedItem().toString().startsWith("node.") || cmbAttributes.getSelectedItem().toString().startsWith("edge.")) {
                // "node" or "edge"
                String attributeType = cmbAttributes.getSelectedItem().toString().substring(0, 4);
                String attributeName = cmbAttributes.getSelectedItem().toString().substring(5);
                if (CyAttributesUtil.isNullAttribute(applicationManager.getCurrentNetwork(), attributeType, attributeName)) {
                    JOptionPane.showMessageDialog(this, "All the values for this column are NULL.", "Can not create filter", JOptionPane.ERROR_MESSAGE);
                    return;
                }
            }
            theSettingPanel.addNewWidget(cmbAttributes.getSelectedItem());
        }
        if (_btn == btnSelectAll) {
            CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
            SelectUtil.selectAllNodes(cyNetwork);
            SelectUtil.selectAllEdges(cyNetwork);
        }
        if (_btn == btnDeSelect) {
            CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
            SelectUtil.unselectAllNodes(cyNetwork);
            SelectUtil.unselectAllEdges(cyNetwork);
        }
    }
    if (_actionObject instanceof JMenuItem) {
        CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
        JMenuItem _menuItem = (JMenuItem) _actionObject;
        if (_menuItem == newFilterMenuItem || _menuItem == newTopologyFilterMenuItem || _menuItem == newNodeInteractionFilterMenuItem || _menuItem == newEdgeInteractionFilterMenuItem) {
            String filterType = "Composite";
            if (_menuItem == newTopologyFilterMenuItem) {
                filterType = "Topology";
                if (cyNetwork != null) {
                    SelectUtil.unselectAllNodes(cyNetwork);
                }
            }
            if (_menuItem == newNodeInteractionFilterMenuItem) {
                filterType = "NodeInteraction";
                if (cyNetwork != null) {
                    SelectUtil.unselectAllNodes(cyNetwork);
                }
            }
            if (_menuItem == newEdgeInteractionFilterMenuItem) {
                filterType = "EdgeInteraction";
                if (cyNetwork != null) {
                    SelectUtil.unselectAllNodes(cyNetwork);
                }
            }
            String newFilterName = "";
            while (true) {
                newFilterName = JOptionPane.showInputDialog(this, "New filter name", "New Filter Name", JOptionPane.INFORMATION_MESSAGE);
                if (newFilterName == null) {
                    // user clicked "cancel"
                    break;
                }
                if (newFilterName.trim().equals("")) {
                    Object[] options = { "OK" };
                    JOptionPane.showOptionDialog(this, "Filter name is empty.", "Warning", JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
                    continue;
                }
                if (org.cytoscape.filter.internal.filters.util.FilterUtil.isFilterNameDuplicated(modelLocator.getFilters(), newFilterName)) {
                    Object[] options = { "OK" };
                    JOptionPane.showOptionDialog(this, "Filter name already existed.", "Warning", JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
                    continue;
                }
                break;
            }
            if ((newFilterName != null) && (!newFilterName.trim().equals(""))) {
                createNewFilter(newFilterName, filterType);
            // pcs.firePropertyChange("NEW_FILTER_CREATED", "", "");
            // // TODO: Port this
            // if (FilterPlugin.shouldFireFilterEvent) {
            // PropertyChangeEvent evt = new PropertyChangeEvent(this, "NEW_FILTER_CREATED", null, null);
            // Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
            // }
            }
        } else if (_menuItem == deleteFilterMenuItem) {
            CompositeFilter theSelectedFilter = (CompositeFilter) cmbFilters.getSelectedItem();
            if (theSelectedFilter == null) {
                return;
            }
            Object[] options = { "YES", "CANCEL" };
            int userChoice = JOptionPane.showOptionDialog(this, "Are you sure you want to delete " + theSelectedFilter.getName() + "?", "Warning", JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
            if (userChoice == 1) {
                // user clicked CANCEL
                return;
            }
            deleteFilter(theSelectedFilter);
        // // TODO: Port this?  No one listens for these events
        // if (FilterPlugin.shouldFireFilterEvent) {
        // PropertyChangeEvent evt = new PropertyChangeEvent(this, "FILTER_DELETED", null, null);
        // Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
        // }
        } else if (_menuItem == renameFilterMenuItem) {
            CompositeFilter theSelectedFilter = (CompositeFilter) cmbFilters.getSelectedItem();
            if (theSelectedFilter == null) {
                return;
            }
            renameFilter();
        // // TODO: Port this?  No one listens for these events
        // if (FilterPlugin.shouldFireFilterEvent) {
        // PropertyChangeEvent evt = new PropertyChangeEvent(this, "FILTER_RENAMED", null, null);
        // Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
        // }
        } else if (_menuItem == duplicateFilterMenuItem) {
            CompositeFilter theSelectedFilter = (CompositeFilter) cmbFilters.getSelectedItem();
            if (theSelectedFilter == null) {
                return;
            }
            duplicateFilter();
        // // TODO: Port this?  No one listens for these events
        // if (FilterPlugin.shouldFireFilterEvent) {
        // PropertyChangeEvent evt = new PropertyChangeEvent(this, "FILTER_DUPLICATED", null, null);
        // Cytoscape.getPropertyChangeSupport().firePropertyChange(evt);
        // }
        }
    }
    // JMenuItem event
    updateInteractionMenuItemStatus();
    updateView();
}

Example 53 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class FilterMainPanel method updateFeedbackTableModel.

private void updateFeedbackTableModel() {
    String netName = null;
    String nodeCount = null;
    String edgeCount = null;
    final CyNetwork net = applicationManager.getCurrentNetwork();
    if (net != null) {
        netName = net.getRow(net).get(CyNetwork.NAME, String.class);
        nodeCount = net.getNodeCount() + "(" + net.getDefaultNodeTable().countMatchingRows(CyNetwork.SELECTED, true) + ")";
        edgeCount = net.getEdgeCount() + "(" + net.getDefaultEdgeTable().countMatchingRows(CyNetwork.SELECTED, true) + ")";
    }
    tblFeedBack.getModel().setValueAt(netName, 0, 0);
    tblFeedBack.getModel().setValueAt(nodeCount, 0, 1);
    tblFeedBack.getModel().setValueAt(edgeCount, 0, 2);
}

Example 54 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class FilterMainPanel method enableForNetwork.

/**
 * Enable select/deselect buttons if the current network exists and is not null.
 */
private void enableForNetwork() {
    CyNetwork n = applicationManager.getCurrentNetwork();
    if (n == null) {
        this.btnSelectAll.setEnabled(false);
        this.btnDeSelect.setEnabled(false);
        btnApplyFilter.setVisible(false);
    } else {
        this.btnSelectAll.setEnabled(true);
        this.btnDeSelect.setEnabled(true);
        btnApplyFilter.setVisible(true);
    }
}

Example 55 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-impl by cytoscape.

the class FilterMainPanel method itemStateChanged.

@Override
public void itemStateChanged(ItemEvent e) {
    Object source = e.getSource();
    if (source instanceof JComboBox) {
        JComboBox cmb = (JComboBox) source;
        if (cmb == cmbFilters) {
            CompositeFilter selectedFilter = (CompositeFilter) cmbFilters.getSelectedItem();
            if (selectedFilter == null) {
                this.btnApplyFilter.setEnabled(false);
                this.btnAddFilterWidget.setEnabled(false);
                return;
            } else {
                this.btnAddFilterWidget.setEnabled(true);
                this.btnApplyFilter.setEnabled(true);
            }
            CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
            selectedFilter.setNetwork(cyNetwork);
            replaceFilterSettingPanel(selectedFilter);
            if (cyNetwork != null) {
                SelectUtil.unselectAllNodes(cyNetwork);
            }
            if (cmbFilters.getSelectedItem() instanceof TopologyFilter || cmbFilters.getSelectedItem() instanceof InteractionFilter) {
                // do not apply TopologyFilter or InteractionFilter automatically
                return;
            }
            // If network size is greater than pre-defined threshold, don't apply it automatically
            if (FilterUtil.isDynamicFilter(selectedFilter)) {
                FilterUtil.doSelection(selectedFilter, applicationManager);
            }
            updateView();
            refreshAttributeCMB();
        } else if (cmb == cmbAttributes) {
            Object selectObject = cmbAttributes.getSelectedItem();
            if (selectObject != null) {
                String selectItem = selectObject.toString();
                // Disable the Add button if "--Table Column--" or "-- Filter ---" is selected
                if (selectItem.equalsIgnoreCase(filtersSeparator) || selectItem.equalsIgnoreCase(attributesSeperator)) {
                    btnAddFilterWidget.setEnabled(false);
                } else {
                    btnAddFilterWidget.setEnabled(true);
                }
            }
        }
    }
}