Examples with BioModelEntityObject cbit.vcell.model.BioModelEntityObject used on opensource projects

Example 1 with BioModelEntityObject

use of cbit.vcell.model.BioModelEntityObject in project vcell by virtualcell.

the class BioPaxObjectPropertiesPanel method refreshInterface.

protected void refreshInterface() {
    if (bioPaxObject == null) {
        // sanity check
        return;
    }
    ArrayList<BioPaxObjectProperty> propertyList = new ArrayList<BioPaxObjectProperty>();
    if (!(bioPaxObject instanceof SBEntity)) {
        tableModel.setData(propertyList);
        return;
    }
    SBEntity sbEntity = (SBEntity) bioPaxObject;
    if (!(sbEntity instanceof Entity)) {
        tableModel.setData(propertyList);
        return;
    }
    Entity entity = (Entity) sbEntity;
    // entity::type
    propertyList.add(new BioPaxObjectProperty("Type", bioPaxObject.getTypeLabel()));
    if (lookupContains(entity)) {
        propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (looking...)"));
    } else if (entity.getFormalNames() != null && entity.getFormalNames().size() != 0) {
        propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (" + entity.getFormalNames().get(0) + ")"));
    } else if (entity.getName() != null && entity.getName().size() > 0) {
        String displayName = entity.getName().get(0);
        if (entity.getxRef() != null && entity.getxRef().size() > 0) {
            displayName = displayName + " (double-click lookup)";
        }
        // entity::name
        propertyList.add(new BioPaxObjectProperty("Name", displayName));
    }
    // entity::Link
    for (RelationshipObject rObject : bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject)) {
        BioModelEntityObject beObject = rObject.getBioModelEntityObject();
        propertyList.add(new BioPaxObjectProperty("Linked physiology object", beObject.getName(), beObject));
    }
    if (entity instanceof PhysicalEntity) {
        // ------------------------ PHYSICAL ENTITY -----------------------
        PhysicalEntity physicalEntity = (PhysicalEntity) entity;
        // physicalEntity::feature (***ignored***)
        // physicalEntity::memberPhysicalEntity (***ignored***)
        // physicalEntity::notFeature (***ignored***)
        // TODO:  extract the kinetic law, then the SBEntities, then the measurables, units, aso
        boolean isReactionParticipant = BioPAXUtil.isReactionParticipant(physicalEntity, bioModel.getPathwayModel());
        String role = "";
        if (BioPAXUtil.isController(physicalEntity, bioModel.getPathwayModel())) {
            role += "Controller";
            if (isReactionParticipant) {
                role += ", Participant";
            }
        } else if (isReactionParticipant) {
            role += "Participant";
        }
        if (!role.isEmpty()) {
            propertyList.add(new BioPaxObjectProperty("Role(s)", role));
        }
        if (!(physicalEntity instanceof SmallMolecule)) {
            // physicalEntity::cellular location
            CellularLocationVocabulary cellularLocation = physicalEntity.getCellularLocation();
            if (cellularLocation != null && cellularLocation.getTerm() != null && cellularLocation.getTerm().size() > 0) {
                propertyList.add(new BioPaxObjectProperty("Cellular Location", cellularLocation.getTerm().get(0), cellularLocation));
            } else if (entity.getName() != null && entity.getName().size() > 1) {
                String location = entity.getName().get(1);
                if (location.contains("[") && location.contains("]")) {
                    location = location.substring(location.indexOf("[") + 1, location.indexOf("]"));
                    propertyList.add(new BioPaxObjectProperty("Cellular Location", location));
                }
            }
        }
        if (physicalEntity instanceof Complex) {
            Complex complex = (Complex) physicalEntity;
            // complex::components
            for (PhysicalEntity pe : complex.getComponents()) {
                propertyList.add(new BioPaxObjectProperty("Component", getEntityName(pe), pe));
            }
        } else if (physicalEntity instanceof Protein) {
        // Protein protein = (Protein)entity;
        // protein::entity reference (***ignored***)
        } else if (physicalEntity instanceof SmallMolecule) {
            SmallMolecule sm = (SmallMolecule) physicalEntity;
            EntityReference er = sm.getEntityReference();
            if (er != null && !er.getName().isEmpty() && er.getName().get(0) != null && !er.getName().get(0).isEmpty()) {
                propertyList.add(new BioPaxObjectProperty("Entity Reference", er.getName().get(0)));
                ArrayList<Xref> xrefList = er.getxRef();
                for (Xref xref : xrefList) {
                    propertyList.add(new BioPaxObjectProperty("   Xref", xref.getDb() + ":" + xref.getId(), xref));
                }
            }
        } else if (physicalEntity instanceof Dna) {
        // dna::entityReference (***ignored***)
        } else if (physicalEntity instanceof DnaRegion) {
        // dnaRegion::entityReference (***ignored***)
        } else if (physicalEntity instanceof Rna) {
        // rna::entityReference (***ignored***)
        } else if (physicalEntity instanceof RnaRegion) {
        // rnaRegion::entityReference (***ignored***)
        }
    } else if (entity instanceof Interaction) {
        // --------------------------- INTERACTION -------------------
        Interaction interaction = (Interaction) entity;
        // interaction::interactionType
        for (InteractionVocabulary interactionVocabulary : interaction.getInteractionTypes()) {
            if (interactionVocabulary.getTerm().size() > 0) {
                propertyList.add(new BioPaxObjectProperty("Interaction Type", interactionVocabulary.getTerm().get(0), interactionVocabulary));
            }
        }
        // interaction::participants
        for (InteractionParticipant interactionParticipant : interaction.getParticipants()) {
            PhysicalEntity physicalEntity = interactionParticipant.getPhysicalEntity();
            String physicalEntityName = physicalEntity.getName().size() > 0 ? physicalEntity.getName().get(0) : physicalEntity.getIDShort();
            String cellularLocation = "";
            if (physicalEntity.getCellularLocation() != null) {
                cellularLocation = physicalEntity.getCellularLocation().getTerm().size() > 0 ? " [" + physicalEntity.getCellularLocation().getTerm().get(0) + "]" : "";
            }
            propertyList.add(new BioPaxObjectProperty(interactionParticipant.getLevel3PropertyName(), physicalEntityName + cellularLocation, physicalEntity));
        }
        // get the controllers for interactions
        // we always need this because there's no guarantee we'll have kinetic laws
        // for instance pathway commons doesn't have quantitative information
        Set<String> controllersNames = getControllersNames(interaction);
        if (controllersNames.size() > 0) {
            for (String str : controllersNames) {
                // String tooltip = "<html>how many of these 12 M <br>average size  1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
                String tooltip = "";
                propertyList.add(new BioPaxObjectProperty("Controlled by", str, interaction, tooltip));
            }
        }
        // get the kinetic laws (if any)
        Set<Control> controls = BioPAXUtil.getControlsOfInteraction(interaction, bioModel.getPathwayModel());
        for (Control control : controls) {
            ArrayList<SBEntity> sbEntities = control.getSBSubEntity();
            for (SBEntity sbE : sbEntities) {
                // the only SBSubEntities allowed in a control are kinetic laws
                if (sbE.getID().contains("kineticLaw")) {
                    String str = new String();
                    if (control.getPhysicalControllers() != null) {
                        str += " for Controller(s): ";
                        for (PhysicalEntity ep : control.getPhysicalControllers()) {
                            if (ep.getName().size() > 0) {
                                str += ep.getName().get(0);
                            } else {
                                str += ep.getIDShort();
                            }
                            str += " ";
                        }
                    }
                    String sDetails = "";
                    ArrayList<SBVocabulary> sbTerms = sbE.getSBTerm();
                    for (SBVocabulary sbv : sbTerms) {
                        // type of kinetic law
                        String str1 = sbv.getID();
                        str1 = str1.substring(str1.lastIndexOf('#') + 1);
                        System.out.println(str1);
                        SBOTerm sboT = SBOListEx.sboMap.get(str1);
                        sDetails += "<font color=\"#660000\"><b>" + sboT.getName() + "</b></font>" + "  " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
                        sDetails += "<br>";
                    }
                    ArrayList<SBEntity> klProperties = sbE.getSBSubEntity();
                    for (SBEntity klProperty : klProperties) {
                        if (klProperty instanceof SBMeasurable) {
                            SBMeasurable m = (SBMeasurable) klProperty;
                            String str1 = "";
                            String str2 = "";
                            String str3 = "";
                            if (m.hasTerm()) {
                                str1 += m.extractSBOTermAsString();
                            }
                            if (m.hasNumber()) {
                                str2 += m.getNumber().get(0);
                            }
                            if (m.hasUnit()) {
                                str3 += m.extractSBOUnitAsString();
                            }
                            // str1 is an SBO id, for example "SBO:0000064"
                            SBOTerm sboT = SBOListEx.sboMap.get(str1);
                            sDetails += sboT.getSymbol() + "   (" + sboT.getName() + ")" + "<font color=\"#660000\"><b>" + str2 + str3 + "</b></font>" + "  " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
                        } else {
                            sDetails = klProperty.getIDShort() + "  " + klProperty.getTypeLabel();
                        }
                        sDetails += "<br>";
                    }
                    // String tooltip = "<html>how many of these 12 M <br>average size  1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
                    String tooltip = "";
                    BioPaxObjectProperty bpop = new BioPaxObjectProperty("Kinetic Law" + str, sbE.getID(), sbE, tooltip);
                    bpop.setDetails(sDetails);
                    propertyList.add(bpop);
                }
            }
        }
        if (interaction instanceof Control) {
            // TODO: is this ever being called?
            Control c = (Control) interaction;
            // catalysis::controlled
            Interaction controlledInteraction = c.getControlledInteraction();
            if (controlledInteraction != null) {
                String controlledName = controlledInteraction.getIDShort();
                if (controlledInteraction.getName().size() > 0) {
                    controlledName = controlledInteraction.getName().get(0);
                }
                propertyList.add(new BioPaxObjectProperty("Controlled Interaction", controlledName, controlledInteraction));
            }
        }
    } else if (entity instanceof GroupObject) {
        // ---------------------- GROUP OBJECT ------------------
        GroupObject groupObject = (GroupObject) entity;
        for (BioPaxObject bpo : groupObject.getGroupedObjects()) {
            propertyList.add(new BioPaxObjectProperty("Element::" + bpo.getTypeLabel(), getEntityName((Entity) bpo), bpo));
        }
    }
    // entity::comments
    for (String comment : entity.getComments()) {
        propertyList.add(new BioPaxObjectProperty("Comment", comment));
    }
    // entity::xRef
    ArrayList<Xref> xrefList = ((Entity) bioPaxObject).getxRef();
    for (Xref xref : xrefList) {
        if (xref instanceof UnificationXref) {
            propertyList.add(new BioPaxObjectProperty("Xref", xref.getDb() + ":" + xref.getId(), xref));
        }
    }
    for (Xref xref : xrefList) {
        if (xref instanceof RelationshipXref) {
            propertyList.add(new BioPaxObjectProperty("Xref (related)", xref.getDb() + ":" + xref.getId(), xref));
        }
    }
    for (Xref xref : xrefList) {
        if (xref instanceof PublicationXref) {
            propertyList.add(new BioPaxObjectProperty("Publication", xref.getDb() + ":" + xref.getId(), xref));
        }
    }
    // for(SBVocabulary sbVocab : sbEntity.getSBTerm()) {
    // propertyList.add(new BioPaxObjectProperty("SBO Term", SBPAXLabelUtil.makeLabel(sbVocab)));
    // }
    // if(sbEntity instanceof Interaction) {
    // // TODO: this goes away
    // Interaction interaction = (Interaction) sbEntity;
    // Set<SBEntity> subEntities = new HashSet<SBEntity>();
    // subEntities.add(interaction);
    // Set<Control> controls = BioPAXUtil.findAllControls(interaction, bioModel.getPathwayModel());
    // subEntities.addAll(controls);
    // subEntities = SBPAX3Util.extractAllEntities(subEntities);
    // for(SBEntity subEntity : subEntities) {
    // if(subEntity instanceof SBMeasurable) {
    // propertyList.add(new BioPaxObjectProperty("Measured quantity", SBPAXLabelUtil.makeLabel(subEntity)));
    // }
    // }
    // }
    tableModel.setData(propertyList);
}

Example 2 with BioModelEntityObject

use of cbit.vcell.model.BioModelEntityObject in project vcell by virtualcell.

the class BioPaxRelationshipTableModel method getValueAt.

public Object getValueAt(int iRow, int iCol) {
    BioPaxRelationshipTableRow entitySelectionTableRow = getValueAt(iRow);
    BioModelEntityObject bmObject = entitySelectionTableRow.getBioModelEntityObject();
    switch(iCol) {
        case iColSelected:
            {
                return entitySelectionTableRow.selected();
            }
        case iColEntity:
            {
                return bmObject.getName();
            }
        case iColType:
            {
                return bmObject.getTypeLabel();
            }
        default:
            {
                return null;
            }
    }
}

Example 3 with BioModelEntityObject

use of cbit.vcell.model.BioModelEntityObject in project vcell by virtualcell.

the class BioPaxRelationshipTableModel method refreshData.

private void refreshData() {
    ArrayList<BioPaxRelationshipTableRow> entityRows = new ArrayList<BioPaxRelationshipTableRow>();
    if (bioModel != null) {
        HashSet<RelationshipObject> relationshipObjects = null;
        if (bioPaxObject != null) {
            relationshipObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject);
        }
        List<BioPaxRelationshipTableRow> allEntityRows = new ArrayList<BioPaxRelationshipTableRow>();
        if (bioPaxObject instanceof Conversion) {
            for (ReactionStep rs : bioModel.getModel().getReactionSteps()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
            for (ReactionRule rr : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rr);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rr) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        } else if (bioPaxObject instanceof PhysicalEntity) {
            for (SpeciesContext rs : bioModel.getModel().getSpeciesContexts()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        }
        if (searchText == null || searchText.length() == 0) {
            entityRows.addAll(allEntityRows);
        } else {
            for (BioPaxRelationshipTableRow rs : allEntityRows) {
                BioModelEntityObject object = rs.getBioModelEntityObject();
                String lowerCaseSearchText = searchText.toLowerCase();
                if (object.getName().toLowerCase().contains(lowerCaseSearchText) || object.getTypeLabel().toLowerCase().contains(lowerCaseSearchText)) {
                    entityRows.add(rs);
                }
            }
        }
    }
    setData(entityRows);
    GuiUtils.flexResizeTableColumns(ownerTable);
}

Example 4 with BioModelEntityObject

use of cbit.vcell.model.BioModelEntityObject in project vcell by virtualcell.

the class BioModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    // 
    if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals("mathDescription") && evt.getNewValue() != null) {
        if (fieldSimulations != null) {
            for (int i = 0; i < fieldSimulations.length; i++) {
                if (fieldSimulations[i].getMathDescription() == evt.getOldValue()) {
                    try {
                        fieldSimulations[i].setMathDescription((MathDescription) evt.getNewValue());
                    } catch (PropertyVetoException e) {
                        System.out.println("error propagating math from SimulationContext '" + ((SimulationContext) evt.getSource()).getName() + "' to Simulation '" + fieldSimulations[i].getName());
                        e.printStackTrace(System.out);
                    }
                }
            }
        }
    }
    // 
    if (evt.getSource() == this && evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_SIMULATIONS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getOldValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].removeVetoableChangeListener(this);
                simulations[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getNewValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].addVetoableChangeListener(this);
                simulations[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_NAME_SIMULATION_CONTEXTS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getOldValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].removeVetoableChangeListener(this);
                simulationContexts[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getNewValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].addVetoableChangeListener(this);
                simulationContexts[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS) || evt.getPropertyName().equals(Model.PROPERTY_NAME_REACTION_STEPS))) {
        // remove the relationship objects if the biomodelEntity objects were removed
        Set<BioModelEntityObject> removedObjects = relationshipModel.getBioModelEntityObjects();
        for (SpeciesContext sc : fieldModel.getSpeciesContexts()) {
            removedObjects.remove(sc);
        }
        for (ReactionStep rs : fieldModel.getReactionSteps()) {
            removedObjects.remove(rs);
        }
        for (MolecularType mt : fieldModel.getRbmModelContainer().getMolecularTypeList()) {
            removedObjects.remove(mt);
        }
        for (ReactionRule rr : fieldModel.getRbmModelContainer().getReactionRuleList()) {
            removedObjects.remove(rr);
        }
        relationshipModel.removeRelationshipObjects(removedObjects);
    }
    // adjust the relationship model when a molecule gets deleted
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST))) {
        @SuppressWarnings("unchecked") List<MolecularType> oldListCopy = new ArrayList<MolecularType>((List<MolecularType>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<MolecularType> newList = (List<MolecularType>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (MolecularType removedMt : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedMt);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST))) {
        @SuppressWarnings("unchecked") List<ReactionRule> oldListCopy = new ArrayList<ReactionRule>((List<ReactionRule>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<ReactionRule> newList = (List<ReactionRule>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (ReactionRule removedRr : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedRr);
            }
        }
    }
}

Example 5 with BioModelEntityObject

use of cbit.vcell.model.BioModelEntityObject in project vcell by virtualcell.

the class ModelCartoon method refreshRelationshipInfo.

public final void refreshRelationshipInfo(RelationshipModel relationshipModel) {
    for (RelationshipObject relationship : relationshipModel.getRelationshipObjects()) {
        BioModelEntityObject bioModelEntity = relationship.getBioModelEntityObject();
        Shape shape = getShapeFromModelObject(bioModelEntity);
        if (shape instanceof SpeciesContextShape) {
            SpeciesContextShape scShape = (SpeciesContextShape) shape;
            scShape.setLinkText("L");
        } else if (shape instanceof SimpleReactionShape) {
            SimpleReactionShape srShape = (SimpleReactionShape) shape;
            srShape.setLinkText("L");
        } else if (shape instanceof ReactionRuleDiagramShape) {
            ReactionRuleDiagramShape srShape = (ReactionRuleDiagramShape) shape;
            srShape.setLinkText("L");
        }
    }
}