Examples with BioPaxObject org.vcell.pathway.BioPaxObject used on opensource projects

Example 31 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method groupBioPaxObjects.

private void groupBioPaxObjects() {
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
    selected.addAll(getSelectedBioPaxObjects());
    if (selected.size() == 0)
        return;
    if (bioModel == null || bioModel.getPathwayModel() == null)
        return;
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    ArrayList<String> names = new ArrayList<String>();
    String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
    String newName = null;
    try {
        newName = DialogUtils.showInputDialog0(this, "Name of the GroupObject", id);
    } catch (UtilCancelException ex) {
    // user canceled; it's ok
    }
    if (newName != null) {
        if (newName.length() == 0) {
            PopupGenerator.showErrorDialog(this, "The Name of the GroupObject should be provided.");
        } else {
            names.add(newName);
            GroupObject groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), names, id, selected, GroupObject.Type.GROUPEDBIOPAXOBJECTS);
            if (groupObject == null) {
                // error message
                DialogUtils.showErrorDialog(this, "The set of selected objects is a subset of one group object in the model. They will not be grouped together again.");
            } else {
                bioModel.getPathwayModel().add(groupObject);
                bioModel.getPathwayModel().refreshGroupMap();
                // set the grouped object to be selected
                graphCartoonTool.getGraphModel().setSelectedObjects(new GroupObject[] { groupObject });
            }
        }
    }
    pathwayGraphModel.refreshAll();
}

Example 32 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method showPhysiologyLinks.

private void showPhysiologyLinks() {
    BioPaxObject selectedBioPaxObject = getSelectedBioPaxObject();
    if (selectedBioPaxObject != null) {
        Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(selectedBioPaxObject);
        if (relationshipSet.size() > 0) {
            ArrayList<BioModelEntityObject> selectedBioModelEntityObjects = new ArrayList<BioModelEntityObject>();
            for (RelationshipObject re : relationshipSet) {
                BioModelEntityObject bioModelEntityObject = re.getBioModelEntityObject();
                selectedBioModelEntityObjects.add(bioModelEntityObject);
            }
            // if (selectedBioPaxObjects.get(0) instanceof ReactionStep) {
            // selectionManager.setActiveView(new ActiveView(null,DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions));
            // } else if (selectedBioPaxObjects.get(0) instanceof SpeciesContext) {
            // selectionManager.setActiveView(new ActiveView(null,DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species));
            // }
            selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram), selectedBioModelEntityObjects.toArray(new BioModelEntityObject[0]));
        }
    }
}

Example 33 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class BioPaxObjectPropertiesPanel method initialize.

private void initialize() {
    try {
        table = new ScrollTable();
        tableModel = new BioPaxObjectPropertiesTableModel(table);
        table.setModel(tableModel);
        details = new JTextPane();
        details.setContentType("text/html");
        details.setEditable(false);
        JScrollPane scrl = new JScrollPane(details);
        table.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

            @Override
            public void valueChanged(ListSelectionEvent e) {
                if (!e.getValueIsAdjusting()) {
                    BioPaxObjectProperty property = tableModel.getValueAt(table.getSelectedRow());
                    if (property != null) {
                        final String htmlStart = "<html><font face = \"Arial\"><font size =\"-2\">";
                        final String htmlEnd = "</font></font></html>";
                        if (!property.getDetails().isEmpty()) {
                            details.setText(htmlStart + property.getDetails() + htmlEnd);
                        } else if ((property.value != null) && !property.value.isEmpty()) {
                            String text = FormatDetails(property);
                            details.setText(htmlStart + text + htmlEnd);
                        } else {
                            details.setText(htmlStart + "row: " + table.getSelectedRow() + ", col: " + table.getSelectedColumn() + htmlEnd);
                        }
                    }
                }
            }
        });
        splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, table.getEnclosingScrollPane(), scrl);
        splitPane.setOneTouchExpandable(true);
        splitPane.setDividerLocation(150);
        // provide minimum sizes for the two components in the split pane
        Dimension minimumSize = new Dimension(100, 50);
        table.getEnclosingScrollPane().setMinimumSize(minimumSize);
        scrl.setMinimumSize(minimumSize);
        setLayout(new BorderLayout());
        // add(table.getEnclosingScrollPane(), BorderLayout.CENTER);
        // add(details, BorderLayout.CENTER);
        add(splitPane, BorderLayout.CENTER);
        setBackground(Color.white);
        table.addMouseListener(new MouseAdapter() {

            @Override
            public void mouseClicked(MouseEvent e) {
                if (e.getClickCount() == 2) {
                    // launch the browser when double click on hyperlinks
                    Point pt = e.getPoint();
                    int crow = table.rowAtPoint(pt);
                    int ccol = table.columnAtPoint(pt);
                    if (table.convertColumnIndexToModel(ccol) == BioPaxObjectPropertiesTableModel.Column_Value) {
                        BioPaxObjectProperty property = tableModel.getValueAt(crow);
                        BioPaxObject bioPaxObject = property.bioPaxObject;
                        if (bioPaxObject == null) {
                            BioModelEntityObject bioModelEntityObject = property.bioModelEntityObject;
                            if (bioModelEntityObject != null) {
                                if (bioModelEntityObject instanceof SpeciesContext) {
                                    selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram), new Object[] { bioModelEntityObject });
                                } else if (bioModelEntityObject instanceof MolecularType) {
                                    selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE, ActiveViewID.species_definitions), new Object[] { bioModelEntityObject });
                                }
                            } else if (((Entity) BioPaxObjectPropertiesPanel.this.bioPaxObject).getFormalNames() == null || ((Entity) BioPaxObjectPropertiesPanel.this.bioPaxObject).getFormalNames().size() == 0) {
                                lookupFormalName(crow);
                            }
                        } else if (bioPaxObject instanceof Xref) {
                            // if xRef, get url
                            String url = ((Xref) bioPaxObject).getURL();
                            DialogUtils.browserLauncher(BioPaxObjectPropertiesPanel.this, url, "Wrong URL.");
                        } else if (bioPaxObject instanceof SBEntity) {
                            // TODO: kineticLaw
                            SBEntity sbE = (SBEntity) bioPaxObject;
                            if (sbE.getID().contains("kineticLaw")) {
                                // String url = "http://sabio.h-its.org/sabioRestWebServices/kineticLaws/" + sbE.getID().substring(sbE.getID().indexOf("kineticLaw") + 10);
                                String url = "http://sabiork.h-its.org/kindatadirectiframe.jsp?kinlawid=" + sbE.getID().substring(sbE.getID().indexOf("kineticLaw") + 10);
                                DialogUtils.browserLauncher(BioPaxObjectPropertiesPanel.this, url, "Wrong URL.");
                            }
                        }
                    }
                }
            }
        });
        // --- end of addMouseListener()
        table.getColumnModel().getColumn(BioPaxObjectPropertiesTableModel.Column_Value).setCellRenderer(new DefaultScrollTableCellRenderer() {

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (column == BioPaxObjectPropertiesTableModel.Column_Value) {
                    BioPaxObjectProperty property = tableModel.getValueAt(row);
                    BioPaxObject bpObject = property.bioPaxObject;
                    String text = property.value;
                    // colorize BLUE and add surround text with <html></html> tags
                    if (bpObject == null) {
                        BioModelEntityObject bioModelEntityObject = property.bioModelEntityObject;
                        if (bioModelEntityObject != null) {
                            if (!isSelected) {
                                setForeground(Color.blue);
                            }
                            setText("<html><u>" + text + "</u></html>");
                        }
                    } else {
                        if (bpObject instanceof Xref) {
                            String url = ((Xref) bpObject).getURL();
                            if (url != null) {
                                setToolTipText(url);
                                if (!isSelected) {
                                    setForeground(Color.blue);
                                }
                                setText("<html><u>" + text + "</u></html>");
                            }
                        } else if (bpObject instanceof SBEntity) {
                            String url = ((SBEntity) bpObject).getID();
                            if (url.contains("kineticLaw")) {
                                setToolTipText(url);
                                if (!isSelected) {
                                    setForeground(Color.blue);
                                }
                                if (url.contains("http")) {
                                    setText("<html><u>" + text + "</u></html>");
                                }
                            }
                        }
                    }
                }
                BioPaxObjectProperty property = tableModel.getValueAt(row);
                if (!property.tooltip.isEmpty()) {
                    setToolTipText(property.tooltip);
                }
                return this;
            }
        });
    // --- end of setCellRenderer()
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 34 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class BioModelEditorConversionTableModel method getValueAt.

public Object getValueAt(int iRow, int iCol) {
    ConversionTableRow conversionTableRow = getValueAt(iRow);
    BioPaxObject bpObject = conversionTableRow.getBioPaxObject();
    switch(iCol) {
        case iColInteraction:
            {
                return conversionTableRow.interactionLabel();
            }
        case iColParticipant:
            {
                return conversionTableRow.participantType();
            }
        case iColEntity:
            {
                return getLabel(bpObject);
            }
        case iColType:
            {
                return getType(bpObject);
            }
        case iColStoich:
            {
                return conversionTableRow.stoich();
            }
        case iColID:
            {
                return conversionTableRow.id();
            }
        case iColLocation:
            {
                return conversionTableRow.location();
            }
        default:
            {
                return null;
            }
    }
}

Example 35 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class BioModelEditorConversionTableModel method refreshData.

private void refreshData() {
    if (bioModel == null || bioModel.getPathwayModel() == null || bioPaxObjects == null) {
        setData(null);
        return;
    }
    // function I :: get selected objects only
    // create ConversionTableRow objects
    allPathwayObjectList = new ArrayList<ConversionTableRow>();
    convertedBPObjects = new HashSet<BioPaxObject>();
    printObjects(bioPaxObjects);
    BioModel.printBpModelObjects(bioModel.getPathwayModel().getBiopaxObjects());
    // BioModel.printBpRelationshipObjects(bioModel.getRelationshipModel().getBioPaxObjects());	// derived; the bpObjects that are part of a relationship
    BioModel.printRelationships(bioModel.getRelationshipModel().getRelationshipObjects());
    System.out.println("----------------------------------------------------------------------");
    for (BioPaxObject bpo : bioPaxObjects) {
        if (bpo instanceof Conversion) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                Conversion conversion = (Conversion) bpo;
                ArrayList<String> nameList = conversion.getName();
                String interactionId = conversion.getID();
                String interactionLabel = nameList.isEmpty() ? conversion.getIDShort() : nameList.get(0);
                ConversionTableRow newConversionTableRow = createTableRow(conversion, interactionId, interactionLabel, "Conversion", 1.0, null);
                allPathwayObjectList.add(newConversionTableRow);
                convertedBPObjects.add(bpo);
                ArrayList<Stoichiometry> stoichiometryList = conversion.getParticipantStoichiometry();
                // stoichiometryMap problem:
                // how to deal with the case that the same object occurs on both left and right sides
                HashMap<PhysicalEntity, Double> stoichiometryMap = createStoichiometryMap(stoichiometryList);
                // reactant
                for (BioPaxObject bpObject1 : conversion.getLeft()) {
                    Double stoich = 1.0;
                    if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
                        stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
                    }
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
                    } else {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(bpObject1);
                }
                // product
                for (BioPaxObject bpObject1 : conversion.getRight()) {
                    Double stoich = 1.0;
                    if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
                        stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
                    }
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
                    } else {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(bpObject1);
                }
                // control
                for (BioPaxObject bpObject : bioModel.getPathwayModel().getBiopaxObjects()) {
                    if (bpObject instanceof Control) {
                        Control control = (Control) bpObject;
                        if (control instanceof Catalysis) {
                            // catalysis
                            if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
                                for (PhysicalEntity pe : ((Catalysis) control).getPhysicalControllers()) {
                                    ConversionTableRow conversionTableRow;
                                    if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, null);
                                    } else {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
                                    }
                                    allPathwayObjectList.add(conversionTableRow);
                                    convertedBPObjects.add(pe);
                                }
                            }
                        } else {
                            // other control types
                            if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
                                for (PhysicalEntity pe : control.getPhysicalControllers()) {
                                    ConversionTableRow conversionTableRow;
                                    if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, null);
                                    } else {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
                                    }
                                    allPathwayObjectList.add(conversionTableRow);
                                    convertedBPObjects.add(pe);
                                }
                            }
                        }
                    }
                }
            }
        } else if (bpo instanceof Catalysis) {
            for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
                if (!convertedBPObjects.contains(pe)) {
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
                        conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, null);
                    } else {
                        conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(pe);
                }
            }
            for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
            // TODO
            }
        } else if (bpo instanceof Control) {
            for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
                if (!convertedBPObjects.contains(pe)) {
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
                        conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, null);
                    } else {
                        conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(pe);
                }
            }
            for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
            // TODO
            }
        }
    }
    // 2nd pass - entities selected as themselves
    for (BioPaxObject bpo : bioPaxObjects) {
        if (bpo instanceof PhysicalEntity) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                PhysicalEntity physicalEntityObject = (PhysicalEntity) bpo;
                // we add standalone selected entities, only if they were not already added as part of any reaction
                if (!convertedBPObjects.contains(physicalEntityObject)) {
                    ConversionTableRow conversionTableRow = createTableRow(physicalEntityObject, "", "", "", 1.0, null);
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(physicalEntityObject);
                }
            }
        }
    }
    // apply text search function for particular columns
    ArrayList<ConversionTableRow> pathwayObjectList = new ArrayList<ConversionTableRow>();
    if (searchText == null || searchText.length() == 0) {
        pathwayObjectList.addAll(allPathwayObjectList);
    } else {
        String lowerCaseSearchText = searchText.toLowerCase();
        for (ConversionTableRow rs : allPathwayObjectList) {
            BioPaxObject bpObject = rs.getBioPaxObject();
            if (rs.interactionLabel().toLowerCase().contains(lowerCaseSearchText) || rs.participantType().toLowerCase().contains(lowerCaseSearchText) || getLabel(bpObject).toLowerCase().contains(lowerCaseSearchText) || getType(bpObject).toLowerCase().contains(lowerCaseSearchText)) {
                pathwayObjectList.add(rs);
            }
        }
    }
    setData(pathwayObjectList);
    GuiUtils.flexResizeTableColumns(ownerTable);
}