Examples with LinkNode cbit.vcell.xml.gui.MiriamTreeModel.LinkNode used on opensource projects

Example 1 with LinkNode

use of cbit.vcell.xml.gui.MiriamTreeModel.LinkNode in project vcell by virtualcell.

the class AnnotationsPanel method getJTreeMIRIAM.

private JTree getJTreeMIRIAM() {
    if (jTreeMIRIAM == null) {
        try {
            DefaultTreeSelectionModel ivjLocalSelectionModel;
            ivjLocalSelectionModel = new DefaultTreeSelectionModel();
            ivjLocalSelectionModel.setSelectionMode(1);
            jTreeMIRIAM = new JTree();
            jTreeMIRIAM.setName("JTree1");
            jTreeMIRIAM.setToolTipText("");
            jTreeMIRIAM.setBounds(0, 0, 357, 405);
            jTreeMIRIAM.setMinimumSize(new java.awt.Dimension(100, 72));
            jTreeMIRIAM.setSelectionModel(ivjLocalSelectionModel);
            jTreeMIRIAM.setRowHeight(0);
            jTreeMIRIAM.setRootVisible(false);
            // Add cellRenderer
            DefaultTreeCellRenderer dtcr = new BioModelCellRenderer(null) {

                @Override
                public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
                    // default for LinkNode is in BioModelCellRenderer.java
                    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
                    // TODO: here
                    component.setIcon(null);
                    return component;
                }
            };
            jTreeMIRIAM.setCellRenderer(dtcr);
            MouseListener mouseListener = new MouseAdapter() {

                @Override
                public void mouseClicked(MouseEvent e) {
                    super.mouseClicked(e);
                // TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
                // showPopup(e, closestMousePath);
                }

                @Override
                public void mouseReleased(MouseEvent e) {
                    super.mouseReleased(e);
                // TreePath closestMousePath =jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
                // showPopup(e,closestMousePath);
                }

                public void mousePressed(MouseEvent e) {
                    TreePath closestMousePath = jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
                    jTreeMIRIAM.setSelectionPath(closestMousePath);
                    // showPopup(e,closestMousePath);
                    if (e.getClickCount() == 2) {
                        DefaultMutableTreeNode node = (DefaultMutableTreeNode) jTreeMIRIAM.getLastSelectedPathComponent();
                        if (node instanceof LinkNode) {
                            showBrowseToLink((LinkNode) node);
                        }
                    }
                }
            };
            jTreeMIRIAM.addMouseListener(mouseListener);
        } catch (java.lang.Throwable ivjExc) {
            ivjExc.printStackTrace(System.out);
        }
    }
    return jTreeMIRIAM;
}

Example 2 with LinkNode

use of cbit.vcell.xml.gui.MiriamTreeModel.LinkNode in project vcell by virtualcell.

the class MIRIAMAnnotationEditor method getJTreeMIRIAM.

private JTree getJTreeMIRIAM() {
    if (jTreeMIRIAM == null) {
        try {
            DefaultTreeSelectionModel ivjLocalSelectionModel;
            ivjLocalSelectionModel = new DefaultTreeSelectionModel();
            ivjLocalSelectionModel.setSelectionMode(1);
            jTreeMIRIAM = new JTree();
            jTreeMIRIAM.setName("JTree1");
            jTreeMIRIAM.setToolTipText("");
            jTreeMIRIAM.setBounds(0, 0, 357, 405);
            jTreeMIRIAM.setMinimumSize(new java.awt.Dimension(100, 72));
            jTreeMIRIAM.setSelectionModel(ivjLocalSelectionModel);
            jTreeMIRIAM.setRowHeight(0);
            // Add cellRenderer
            DefaultTreeCellRenderer dtcr = new BioModelCellRenderer(null) {

                @Override
                public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
                    // System.out.println(MIRIAMAnnotationEditor.this.getClass().getName()+".getJTreeMiriam():BioModelCellRenderer  "+value.getClass()+" "+
                    // (value instanceof cbit.vcell.desktop.BioModelNode?
                    // ((cbit.vcell.desktop.BioModelNode)value).getUserObject().getClass():""));
                    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
                    if (value instanceof BioModelNode && ((BioModelNode) value).getUserObject() instanceof Annotation) {
                        component.setToolTipText("(Double-click to edit notes)");
                        Annotation annotation = (Annotation) ((BioModelNode) value).getUserObject();
                        if (annotation.toString() == null || annotation.toString().length() == 0) {
                            component.setText("(Double-click to edit notes)");
                        }
                    }
                    return component;
                }
            };
            jTreeMIRIAM.setCellRenderer(dtcr);
            MouseListener mouseListener = new MouseAdapter() {

                @Override
                public void mouseClicked(MouseEvent e) {
                    // TODO Auto-generated method stub
                    super.mouseClicked(e);
                    TreePath closestMousePath = jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
                    showPopup(e, closestMousePath);
                }

                @Override
                public void mouseReleased(MouseEvent e) {
                    // TODO Auto-generated method stub
                    super.mouseReleased(e);
                    TreePath closestMousePath = jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
                    showPopup(e, closestMousePath);
                }

                public void mousePressed(MouseEvent e) {
                    TreePath closestMousePath = jTreeMIRIAM.getClosestPathForLocation(e.getPoint().x, e.getPoint().y);
                    jTreeMIRIAM.setSelectionPath(closestMousePath);
                    showPopup(e, closestMousePath);
                    if (e.getClickCount() == 2) {
                        DefaultMutableTreeNode node = (DefaultMutableTreeNode) jTreeMIRIAM.getLastSelectedPathComponent();
                        if (node instanceof LinkNode) {
                            showBrowseToLink((LinkNode) node);
                        } else if (isNodeFreeHandTextEditable(node)) {
                            showEditFreehandText(node);
                        }
                    }
                }
            };
            jTreeMIRIAM.addMouseListener(mouseListener);
        } catch (java.lang.Throwable ivjExc) {
            ivjExc.printStackTrace(System.out);
        }
    }
    return jTreeMIRIAM;
}

Example 3 with LinkNode

use of cbit.vcell.xml.gui.MiriamTreeModel.LinkNode in project vcell by virtualcell.

the class BioModelEditorTreeCellRenderer method getTreeCellRendererComponent.

public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    if (regularFont == null) {
        regularFont = getFont();
        boldFont = regularFont.deriveFont(Font.BOLD);
    }
    Font font = regularFont;
    Icon icon = null;
    String labelText = null;
    String toolTipPrefix = "";
    String toolTipSuffix = "";
    if (value instanceof LinkNode) {
        LinkNode ln = (LinkNode) value;
        String link = ln.getLink();
        String text = ln.getText();
        String qualifier = ln.getMiriamQualifier().getDescription();
        if (link != null) {
            String colorString = (sel) ? "white" : "blue";
            toolTipPrefix = "double-click to open link " + link;
            labelText = "<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\"><a href=" + link + ">" + text + "</a></font></html>";
        } else {
            String colorString = (sel) ? "white" : "black";
            labelText = "<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\">" + text + "</font></html>";
        }
    } else if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObj = node.getUserObject();
        if (userObj instanceof BioModel) {
            font = boldFont;
            icon = VCellIcons.documentIcon;
            labelText = ((BioModel) userObj).getName();
            toolTipPrefix = "BioModel: ";
        } else if (userObj instanceof SimulationContext) {
            // --- root: application name
            font = boldFont;
            // icon = VCellIcons.applicationIcon;
            SimulationContext simContext = (SimulationContext) userObj;
            if (simContext.isRuleBased()) {
                if (simContext.getGeometry().getDimension() == 0) {
                    icon = VCellIcons.appRbmNonspIcon;
                    toolTipSuffix = "Rule Based / Non spatial";
                }
            } else if (simContext.isStoch()) {
                if (simContext.getGeometry().getDimension() == 0) {
                    icon = VCellIcons.appStoNonspIcon;
                    toolTipSuffix = "Stochastic / Non spatial";
                } else {
                    icon = VCellIcons.appStoSpatialIcon;
                    toolTipSuffix = "Stochastic / Spatial";
                }
            } else {
                // deterministic
                if (simContext.getGeometry().getDimension() == 0) {
                    icon = VCellIcons.appDetNonspIcon;
                    toolTipSuffix = "Deterministic / Non spatial";
                } else {
                    icon = VCellIcons.appDetSpatialIcon;
                    toolTipSuffix = "Deterministic / Spatial";
                }
            }
            labelText = /*"Application: " + */
            ((SimulationContext) userObj).getName();
            toolTipPrefix = "Application: ";
        } else if (userObj instanceof DocumentEditorTreeFolderNode) {
            // --- 1st level folders
            DocumentEditorTreeFolderNode folder = (DocumentEditorTreeFolderNode) userObj;
            labelText = folder.getName();
            if (folder.isBold()) {
                font = boldFont;
            }
            DocumentEditorTreeFolderClass folderClass = folder.getFolderClass();
            switch(folderClass) {
                // break;
                case REACTIONS_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        int numReactions = bioModel.getModel().getNumReactions();
                        if (bioModel.getModel().getRbmModelContainer() != null) {
                            numReactions += bioModel.getModel().getRbmModelContainer().getReactionRuleList().size();
                        }
                        labelText = folder.getName() + " (" + numReactions + ")";
                    }
                    break;
                case STRUCTURES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getModel().getNumStructures() + ")";
                    }
                    break;
                case SPECIES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getModel().getNumSpeciesContexts() + ")";
                    }
                    break;
                case MOLECULAR_TYPES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        if (rbmModelContainer == null) {
                            labelText = folder.getName() + "(00000)";
                        } else {
                            labelText = folder.getName() + " (" + rbmModelContainer.getMolecularTypeList().size() + ")";
                        }
                    }
                    break;
                case OBSERVABLES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        if (rbmModelContainer == null) {
                            labelText = folder.getName() + "(00000)";
                        } else {
                            labelText = folder.getName() + " (" + rbmModelContainer.getObservableList().size() + ")";
                        }
                    }
                    break;
                case APPLICATIONS_NODE:
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getNumSimulationContexts() + ")";
                    }
                    break;
                case REACTION_DIAGRAM_NODE:
                    icon = VCellIcons.diagramIcon;
                    break;
                // break;
                case GEOMETRY_NODE:
                    icon = VCellIcons.geometryIcon;
                    break;
                case SPECIFICATIONS_NODE:
                    icon = VCellIcons.settingsIcon;
                    break;
                case PROTOCOLS_NODE:
                    icon = VCellIcons.protocolsIcon;
                    TreeNode tn = node.getParent();
                    if (tn instanceof BioModelNode) {
                        BioModelNode applicationNode = (BioModelNode) tn;
                        Object uo = applicationNode.getUserObject();
                        if (uo instanceof SimulationContext) {
                            SimulationContext sc = (SimulationContext) uo;
                            int numProtocols = 0;
                            // }
                            if (sc.getRateRules() != null) {
                                numProtocols += sc.getRateRules().length;
                            }
                            if (sc.getAssignmentRules() != null) {
                                numProtocols += sc.getAssignmentRules().length;
                            }
                            if (numProtocols > 0) {
                                labelText += " (rules: " + numProtocols + ")";
                            }
                        }
                    }
                    break;
                case SIMULATIONS_NODE:
                    icon = VCellIcons.simulationIcon;
                    break;
                case PARAMETER_ESTIMATION_NODE:
                    icon = VCellIcons.fittingIcon;
                    break;
                case PATHWAY_DIAGRAM_NODE:
                    icon = VCellIcons.diagramIcon;
                    break;
                case PATHWAY_OBJECTS_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getPathwayModel().getBiopaxObjects().size() + ")";
                    }
                    break;
                case BIOPAX_SUMMARY_NODE:
                    icon = VCellIcons.textNotesIcon;
                    break;
                case BIOPAX_TREE_NODE:
                    icon = VCellIcons.tableIcon;
                    break;
            }
        }
    }
    setIcon(icon);
    setFont(font);
    setText(labelText);
    if (toolTipSuffix.length() == 0) {
        toolTipSuffix = labelText;
    }
    setToolTipText(toolTipPrefix + toolTipSuffix);
    return this;
}

Example 4 with LinkNode

use of cbit.vcell.xml.gui.MiriamTreeModel.LinkNode in project vcell by virtualcell.

the class BioModelPropertiesPanel method updateInterface.

/**
 * Comment
 */
private void updateInterface() {
    if (bioModel == null || bioModelWindowManager == null) {
        return;
    }
    nameLabel.setText("<html><b>" + bioModel.getName() + "</b></html>");
    Version version = bioModel.getVersion();
    if (version != null) {
        ownerLabel.setText(version.getOwner().getName());
        String text = "biomodel-" + version.getVersionKey().toString();
        idLabel.setText(text);
        lastModifiedLabel.setText(version.getDate().toString());
        try {
            // permissions
            BioModelInfo bioModelInfo = bioModelWindowManager.getRequestManager().getDocumentManager().getBioModelInfo(version.getVersionKey());
            String permissions = bioModelInfo.getVersion().getGroupAccess().getDescription();
            if (bioModelInfo.getPublicationInfos() != null && bioModelInfo.getPublicationInfos().length > 0) {
                if (bioModelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Published)) {
                    // must be Public
                    permissions = "Published";
                } else {
                    permissions = "Curated";
                }
            } else if (bioModelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Archived)) {
                permissions += "Archived";
            }
            permissionLabel.setText(permissions);
        } catch (DataAccessException e) {
            e.printStackTrace();
        }
        changePermissionButton.setEnabled(true);
    }
    // not in use anymore and unmaintained
    webLinksPanel.removeAll();
    webLinksPanel.setLayout(new GridLayout(0, 1));
    Set<MiriamRefGroup> resources = new HashSet<MiriamRefGroup>();
    Set<MiriamRefGroup> isDescribedByAnnotation = bioModel.getVCMetaData().getMiriamManager().getMiriamRefGroups(bioModel, MIRIAMQualifier.MODEL_isDescribedBy);
    Set<MiriamRefGroup> isAnnotation = bioModel.getVCMetaData().getMiriamManager().getMiriamRefGroups(bioModel, MIRIAMQualifier.MODEL_is);
    resources.addAll(isDescribedByAnnotation);
    resources.addAll(isAnnotation);
    for (MiriamRefGroup refGroup : resources) {
        for (MiriamResource miriamResources : refGroup.getMiriamRefs()) {
            LinkNode linkNode = new MiriamTreeModel.LinkNode(MIRIAMQualifier.MODEL_isDescribedBy, miriamResources);
            final String link = linkNode.getLink();
            String labelText = miriamResources.getDataType() == null ? "" : miriamResources.getDataType().getDataTypeName();
            String toolTip = null;
            if (link != null) {
                toolTip = "double-click to open link " + link;
                labelText = "<html><b>" + labelText + "</b>&nbsp;" + "<font color=blue><a href=" + link + ">" + link + "</a></font></html>";
            }
            JLabel label = new JLabel(labelText);
            label.addMouseListener(new MouseListener() {

                public void mouseReleased(MouseEvent e) {
                }

                public void mousePressed(MouseEvent e) {
                }

                public void mouseExited(MouseEvent e) {
                }

                public void mouseEntered(MouseEvent e) {
                }

                public void mouseClicked(MouseEvent e) {
                    if (e.getClickCount() == 2) {
                        DialogUtils.browserLauncher(BioModelPropertiesPanel.this, link, "failed to open " + link);
                    }
                }
            });
            label.setToolTipText(toolTip);
            webLinksPanel.add(label);
        }
    }
    applicationsPanel.updateInterface();
}

Example 5 with LinkNode

use of cbit.vcell.xml.gui.MiriamTreeModel.LinkNode in project vcell by virtualcell.

the class AnnotationsPanel method removeIdentifier.

private void removeIdentifier() {
    Object treeNode = jTreeMIRIAM.getLastSelectedPathComponent();
    if (treeNode instanceof LinkNode) {
        LinkNode linkNode = (LinkNode) treeNode;
        MiriamResource resourceToDelete = linkNode.getMiriamResource();
        Identifiable entity = getIdentifiable(selectedObject);
        // Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = vcMetaData.getMiriamManager().getAllMiriamRefGroups(entity);
        MiriamManager mm = vcMetaData.getMiriamManager();
        Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = mm.getMiriamTreeMap().get(entity);
        boolean found = false;
        for (MiriamRefGroup refGroup : refGroupsToRemove.keySet()) {
            MIRIAMQualifier qualifier = refGroupsToRemove.get(refGroup);
            for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
                if (!isEqual(miriamResource, resourceToDelete)) {
                    continue;
                }
                try {
                    // remove the ref group for this resource
                    mm.remove2(entity, qualifier, refGroup);
                    System.out.println(vcMetaData.printRdfStatements());
                    found = true;
                    break;
                } catch (URNParseFailureException e) {
                    e.printStackTrace(System.out);
                }
            }
            if (found == true) {
                updateInterface();
                if (selectedObject instanceof ReactionStep) {
                    ((ReactionStep) selectedObject).firePropertyChange("addIdentifier", true, false);
                }
                break;
            }
        }
    }
}