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

Example 6 with Xref

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

the class AnnotationMapping method annotation2BioPaxObject.

public String annotation2BioPaxObject(BioModel bioModel, Identifiable identifiable) {
    String name = "";
    String type = "";
    ArrayList<String> componentInfo = getComponentInfo(bioModel, identifiable);
    if (componentInfo.size() > 0) {
        name = componentInfo.get(0);
        type = componentInfo.get(1);
    }
    String info = type + " : " + name;
    HashMap<String, String> refInfo = getRefInfo(bioModel, identifiable);
    // otherwise, create object and add link
    if (type.equals(VCID.CLASS_SPECIES)) {
        // lookup name by speciesContext
        ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>(Arrays.asList(new SpeciesContext[] { bioModel.getModel().getSpeciesContext(name) }));
        if (speciesContextArrList.get(0) == null) {
            speciesContextArrList.clear();
            // lookup name by species
            for (int i = 0; i < bioModel.getModel().getSpeciesContexts().length; i++) {
                if (bioModel.getModel().getSpeciesContexts()[i].getSpecies().getCommonName().equals(name)) {
                    speciesContextArrList.add(bioModel.getModel().getSpeciesContexts()[i]);
                }
            }
        }
        for (int i = 0; i < speciesContextArrList.size(); i++) {
            SpeciesContext speciesContext = speciesContextArrList.get(i);
            if (bioModel.getRelationshipModel().getRelationshipObjects(speciesContext).size() == 0) {
                ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
                ArrayList<String> refName = getNameRef(xRef, name);
                BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_PHYSICALENTITY);
            // 
            // Commenting out legacy code from the times when we didn't have proper annotation visualization
            // What we were doing below was to create a bioPax object, link it to the species and create
            // copies of the annotations in order to be able to navigate to external databases through XRef
            // Commenting out this code since we can now navigate to external databases from the annotation panel
            // 
            // if(bpObject == null){
            // bpObject = createPhysicalEntity(xRef, refName, name);
            // bioModel.getPathwayModel().add(bpObject);
            // }
            // if(bpObject != null && !isLinked(bioModel, bpObject, speciesContext)) {
            // // create linkage
            // RelationshipObject newRelationship = new RelationshipObject(speciesContext, bpObject);
            // bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
            // return info;
            // }
            }
        }
    } else if (type.equals(VCID.CLASS_BIOMODEL)) {
    // BioPaxObject bpObject = bioModel.getPathwayModel().findFromName(refName.get(0), "Pathway");
    // if(bpObject == null){
    // bpObject = createPathway(componentInfo, refInfo);
    // bioModel.getPathwayModel().add(bpObject);
    // return info;
    // }
    } else if (type.equals(VCID.CLASS_REACTION_STEP)) {
        ReactionStep reactionStep = bioModel.getModel().getReactionStep(name);
        ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
        ArrayList<String> refName = getNameRef(xRef, name);
        if (bioModel.getRelationshipModel().getRelationshipObjects(reactionStep).size() == 0) {
            BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_INTERACTION);
        // 
        // We are eliminating some obsolete code, see above the species context comment
        // 
        // if(bpObject == null){
        // bpObject = createInteraction(reactionStep, xRef, refName);
        // bioModel.getPathwayModel().add(bpObject);
        // }
        // if(bpObject != null && !isLinked(bioModel, bpObject, reactionStep)) {
        // // create linkage
        // RelationshipObject newRelationship = new RelationshipObject(reactionStep, bpObject);
        // bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
        // return info;
        // }
        }
    }
    return null;
}

Example 7 with Xref

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

the class AnnotationMapping method isSmallMolecule.

// private Pathway createPathway(ArrayList<String> componentInfo, HashMap<String, String> refInfo){
// Pathway pathway = new Pathway();
// ArrayList<String> name = getName(componentInfo);
// pathway.setName(name);
// pathway.setxRef(getXrefs(refInfo));
// pathway.setID(name.get(0));
// return pathway;
// }
private boolean isSmallMolecule(ArrayList<Xref> xRef) {
    HashSet<String> refDB = new HashSet<String>();
    for (Xref xref : xRef) {
        String ref = xref.getDb().toLowerCase();
        if (ref.contains("chebi"))
            ref = "chebi";
        refDB.add(ref);
    }
    if (refDB.contains("chebi") && !refDB.contains("uniprot"))
        return true;
    return false;
}

Example 8 with Xref

use of org.vcell.pathway.Xref 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 (bioModelEntityObject instanceof SimpleReaction) {
                                    selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram), 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 = BeanUtils.getDynamicClientProperties().getProperty(PropertyLoader.SABIO_DIRECT_IFRAME_URL) + 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 9 with Xref

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

the class PathwayProducerBiopax3 method addContentControlledVocabulary.

// term	String		multiple
// xref	Xref		multiple
private Element addContentControlledVocabulary(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    ControlledVocabulary ob = (ControlledVocabulary) bpObject;
    Element tmpElement = null;
    if (ob.getxRef() != null && ob.getxRef().size() > 0) {
        List<Xref> list = ob.getxRef();
        for (Xref item : list) {
            tmpElement = new Element("xref", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getTerm() != null && ob.getTerm().size() > 0) {
        List<String> list = ob.getTerm();
        for (String item : list) {
            tmpElement = new Element("term", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}

Example 10 with Xref

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

the class PathwayProducerBiopax3 method addContentEntityReference.

// memberEntityReference	EntityReference					multiple
// entityReferenceType		EntityReferenceTypeVocabulary	single
// entityFeature			EntityFeature					multiple
// name					String							multiple
// xref					Xref							multiple
// evidence				Evidence						multiple
private Element addContentEntityReference(BioPaxObject bpObject, Element element) {
    element = addContentUtilityClass(bpObject, element);
    EntityReference ob = (EntityReference) bpObject;
    Element tmpElement = null;
    if (ob.getMemberEntityReference() != null && ob.getMemberEntityReference().size() > 0) {
        List<EntityReference> list = ob.getMemberEntityReference();
        for (EntityReference item : list) {
            tmpElement = new Element("memberEntityReference", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEntityReferenceType() != null) {
        tmpElement = new Element("entityReferenceType", bp);
        addIDToProperty(tmpElement, ob.getEntityReferenceType());
        mustPrintObject(ob.getEntityReferenceType());
        element.addContent(tmpElement);
    }
    if (ob.getEntityFeature() != null && ob.getEntityFeature().size() > 0) {
        List<EntityFeature> list = ob.getEntityFeature();
        for (EntityFeature item : list) {
            tmpElement = new Element("entityFeature", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getName() != null && ob.getName().size() > 0) {
        List<String> list = ob.getName();
        for (String item : list) {
            tmpElement = new Element("name", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getxRef() != null && ob.getxRef().size() > 0) {
        List<Xref> list = ob.getxRef();
        for (Xref item : list) {
            tmpElement = new Element("xref", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        List<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}