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Example 1 with SBEntity

use of org.vcell.pathway.sbpax.SBEntity in project vcell by virtualcell.

the class BioModelEditorSabioPanel method treeSelectionChanged.

public void treeSelectionChanged() {
    System.out.println("treeSelectionChanged");
    final SBEntity kineticLaw = computeSelectedKineticLaw();
    if (kineticLaw == null) {
        return;
    }
    String kineticLawID = kineticLaw.getID();
    final String kls = new String("kineticLaw");
    if (!kineticLawID.contains(kls)) {
        return;
    }
    kineticLawID = kineticLawID.substring(kineticLawID.lastIndexOf(kls) + kls.length());
    command = "EntryID:" + kineticLawID;
    AsynchClientTask task1 = new AsynchClientTask("Importing Kinetic Laws", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            final URL url = new URL(BeanUtils.getDynamicClientProperties().getProperty(PropertyLoader.SABIO_SRCH_KINETIC_URL) + command);
            // final URL url = new URL("http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax?q=EntryID:33107");
            System.out.println(url.toString());
            String ERROR_CODE_TAG = "error_code";
            Document jdomDocument = XmlUtil.getJDOMDocument(url, getClientTaskStatusSupport());
            Element rootElement = jdomDocument.getRootElement();
            String errorCode = rootElement.getChildText(ERROR_CODE_TAG);
            if (errorCode != null) {
                throw new RuntimeException("Failed to access " + url + " \n\nPlease try again.");
            }
            PathwayModel pathwayModel = PathwayIOUtil.extractPathwayFromJDOM(jdomDocument, new RDFXMLContext(), getClientTaskStatusSupport());
            PathwayData pathwayData = new PathwayData("Sabio Kinetic Laws", pathwayModel);
            hashTable.put("pathwayData", pathwayData);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("showing", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            PathwayData pathwayData = (PathwayData) hashTable.get("pathwayData");
            if (pathwayData != null) {
                setSelectedObjects(new Object[] { pathwayData });
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, true, true, null);
}
Also used : AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) RDFXMLContext(org.vcell.pathway.persistence.RDFXMLContext) Hashtable(java.util.Hashtable) Element(org.jdom.Element) PathwayData(cbit.vcell.client.desktop.biomodel.BioModelEditorPathwayCommonsPanel.PathwayData) Document(org.jdom.Document) PathwayModel(org.vcell.pathway.PathwayModel) SBEntity(org.vcell.pathway.sbpax.SBEntity) URL(java.net.URL) PathwayStringObject(cbit.vcell.client.desktop.biomodel.BioModelEditorPathwayCommonsPanel.PathwayStringObject)

Example 2 with SBEntity

use of org.vcell.pathway.sbpax.SBEntity in project vcell by virtualcell.

the class PathwayTableModel method hasMeasuredData.

private boolean hasMeasuredData(Interaction interaction) {
    Set<SBEntity> subEntities = new HashSet<SBEntity>();
    subEntities.add(interaction);
    Set<Control> controls = BioPAXUtil.findAllControls(interaction, pathwayModel);
    subEntities.addAll(controls);
    subEntities = SBPAX3Util.extractAllEntities(subEntities);
    for (SBEntity subEntity : subEntities) {
        if (subEntity instanceof SBMeasurable) {
            return true;
        }
    }
    return false;
}
Also used : Control(org.vcell.pathway.Control) SBEntity(org.vcell.pathway.sbpax.SBEntity) HashSet(java.util.HashSet) SBMeasurable(org.vcell.pathway.sbpax.SBMeasurable)

Example 3 with SBEntity

use of org.vcell.pathway.sbpax.SBEntity 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();
        String sType = beObject.getDisplayType();
        propertyList.add(new BioPaxObjectProperty("Linked physiology object (" + sType + ")", 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);
}
Also used : SBVocabulary(org.vcell.pathway.sbpax.SBVocabulary) SBEntity(org.vcell.pathway.sbpax.SBEntity) PhysicalEntity(org.vcell.pathway.PhysicalEntity) Entity(org.vcell.pathway.Entity) Set(java.util.Set) TreeSet(java.util.TreeSet) HashSet(java.util.HashSet) Rna(org.vcell.pathway.Rna) PublicationXref(org.vcell.pathway.PublicationXref) InteractionVocabulary(org.vcell.pathway.InteractionVocabulary) BioPaxObject(org.vcell.pathway.BioPaxObject) ArrayList(java.util.ArrayList) CellularLocationVocabulary(org.vcell.pathway.CellularLocationVocabulary) SBEntity(org.vcell.pathway.sbpax.SBEntity) RelationshipObject(org.vcell.relationship.RelationshipObject) Complex(org.vcell.pathway.Complex) RnaRegion(org.vcell.pathway.RnaRegion) SBMeasurable(org.vcell.pathway.sbpax.SBMeasurable) Xref(org.vcell.pathway.Xref) UnificationXref(org.vcell.pathway.UnificationXref) RelationshipXref(org.vcell.pathway.RelationshipXref) PublicationXref(org.vcell.pathway.PublicationXref) Control(org.vcell.pathway.Control) DnaRegion(org.vcell.pathway.DnaRegion) EntityReference(org.vcell.pathway.EntityReference) Interaction(org.vcell.pathway.Interaction) UnificationXref(org.vcell.pathway.UnificationXref) GroupObject(org.vcell.pathway.GroupObject) SBOTerm(org.vcell.pathway.sbo.SBOTerm) BioModelEntityObject(cbit.vcell.model.BioModelEntityObject) Protein(org.vcell.pathway.Protein) RelationshipXref(org.vcell.pathway.RelationshipXref) PhysicalEntity(org.vcell.pathway.PhysicalEntity) SmallMolecule(org.vcell.pathway.SmallMolecule) Dna(org.vcell.pathway.Dna) InteractionParticipant(org.vcell.pathway.InteractionParticipant)

Example 4 with SBEntity

use of org.vcell.pathway.sbpax.SBEntity in project vcell by virtualcell.

the class SBPAXKineticsExtractor method extractKineticsExactMatch.

public static boolean extractKineticsExactMatch(ReactionStep reaction, Process process) throws ExpressionException, PropertyVetoException {
    // we try a perfect match first based on the existence of a SBOTerm in the kinetic law
    if (process.getControl() == null) {
        // no control means no kinetic law - nothing more to do
        return true;
    }
    Control control = process.getControl();
    ArrayList<SBEntity> sbEntities = control.getSBSubEntity();
    for (SBEntity sbE : sbEntities) {
        // the only SBSubEntities allowed in a control are kinetic laws
        if (sbE.getID().contains("kineticLaw")) {
            // build list of the parameters of this kinetic law in sboParams
            // params of this kinetic law
            ArrayList<SBOParam> sboParams = new ArrayList<SBOParam>();
            ArrayList<SBEntity> subEntities = sbE.getSBSubEntity();
            for (SBEntity subEntity : subEntities) {
                if (subEntity instanceof SBMeasurable) {
                    SBMeasurable m = (SBMeasurable) subEntity;
                    if (!m.hasTerm()) {
                        // we don't know what to do with a measurable with no SBTerm
                        break;
                    }
                    String termName = m.extractSBOTermAsString();
                    SBOTerm sboT = SBOListEx.sboMap.get(termName);
                    System.out.println("    " + sboT.getIndex() + "  " + sboT.getName());
                    SBOParam sboParam = matchSBOParam(sboT);
                    if (m.hasNumber()) {
                        double number = m.getNumber().get(0);
                        sboParam.setNumber(number);
                    }
                    if (m.hasUnit()) {
                        String unit = m.extractSBOUnitAsString();
                        sboParam.setUnit(unit);
                    }
                    sboParams.add(sboParam);
                }
            }
            // find if a kinetic law type exists and if not guesstimate one based on parameters
            // simple rule: if we have a Km param it's MM, otherwise it's mass action
            ArrayList<SBVocabulary> sbTerms = sbE.getSBTerm();
            if (sbTerms.isEmpty()) {
                // return false;
                SBVocabulary sbTerm = new SBVocabulary();
                ArrayList<String> termNames = new ArrayList<String>();
                String id;
                SBOParam kMichaelis = extractMichaelisForwardParam(sboParams);
                if (kMichaelis == null) {
                    // mass action rate law
                    id = new String("SBO:0000012");
                } else {
                    // irreversible Henri-Michaelis-Menten rate law
                    id = new String("SBO:0000029");
                }
                // termNames.add(id);
                // sbTerm.setTerm(termNames);
                sbTerm.setID(id);
                sbTerms.add(sbTerm);
            }
            System.out.println(" kinetic law ID: " + sbTerms.get(0).getID());
            // identify the kinetic law type (mass action, michaelis menten, etc) and bring it in vCell
            for (SBVocabulary sbv : sbTerms) {
                // use for loop even though we only expect 1 SBTerm
                // SBVocabulary id, used to retrieve the kinetic law type
                String vocabularyID = sbv.getID();
                SBOTerm sboT = SBOUtil.getSBOTermFromVocabularyId(vocabularyID);
                System.out.println(vocabularyID + "   " + sboT.getName());
                SBOParam kForward;
                SBOParam kCat;
                SBOParam vM;
                SBOParam kReverse;
                SBOParam kMichaelis;
                Kinetics kinetics;
                MappedKinetics current = matchSBOKineticLaw(sboT);
                switch(current) {
                    case SBO_0000069:
                    case SBO_0000432:
                        // some kinetic laws unknown to vCell will fall through to this category
                        // honestly i don't know what to do with them
                        System.out.println("GeneralKinetics");
                        // TODO: what to do here?
                        return true;
                    case SBO_0000012:
                    case SBO_0000078:
                        System.out.println("MassActionKinetics - reversible");
                        kForward = extractKForwardParam(sboParams);
                        kReverse = extractKReverseParam(sboParams);
                        kinetics = new MassActionKinetics(reaction);
                        reaction.setKinetics(kinetics);
                        setKForwardParam(reaction, kForward, kinetics);
                        setKReverseParam(reaction, kReverse, kinetics);
                        return true;
                    case SBO_0000043:
                        System.out.println("MassActionKinetics - zeroth order irreversible, Kr <- 0  ");
                        kForward = extractKForwardParam(sboParams);
                        kinetics = new MassActionKinetics(reaction);
                        // TODO: what to do here?
                        return true;
                    case SBO_0000044:
                        System.out.println("MassActionKinetics - first order irreversible, Kr <- 0  ");
                        kForward = extractKForwardParam(sboParams);
                        kinetics = new MassActionKinetics(reaction);
                        reaction.setKinetics(kinetics);
                        setKForwardParam(reaction, kForward, kinetics);
                        return true;
                    case SBO_0000028:
                    case SBO_0000029:
                        System.out.println("HMM_IRRKinetics");
                        // TODO: make kCat global variable, set its number and unit in annotation
                        // TODO: make vM global variable, set its number and unit in annotation
                        // get the numbers, if present (may be null)
                        kMichaelis = extractMichaelisForwardParam(sboParams);
                        vM = extractVMForwardParam(sboParams, process);
                        kCat = extractKCatForwardParam(sboParams);
                        kinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
                        try {
                            // TODO: create expression only if kCat != null, otherwise use vM directly (if != null) otherwise ???
                            kinetics.reading(true);
                            setVMForwardParamAsExpression(reaction, kCat, kinetics);
                        } finally {
                            kinetics.reading(false);
                        }
                        reaction.setKinetics(kinetics);
                        setMichaelisForwardParam(reaction, kMichaelis, kinetics);
                        return true;
                    case SBO_0000438:
                        System.out.println("HMMREVKinetics");
                        kinetics = new HMM_REVKinetics((SimpleReaction) reaction);
                        return true;
                    default:
                        // TODO: guessing happens above - if we have nothing by now we need to raise runtime exception
                        // change the code below !!!
                        System.out.println("Unable to match the SBOTerm with any compatible kinetic law.");
                        // found unmapped kinetic law, we'll try to guess a match
                        return false;
                }
            }
        }
    }
    // no SBTerm found so we cannot know for sure the kinetic law, we'll have to guess it
    return false;
}
Also used : SBVocabulary(org.vcell.pathway.sbpax.SBVocabulary) SimpleReaction(cbit.vcell.model.SimpleReaction) HMM_IRRKinetics(cbit.vcell.model.HMM_IRRKinetics) ArrayList(java.util.ArrayList) SBOTerm(org.vcell.pathway.sbo.SBOTerm) HMM_REVKinetics(cbit.vcell.model.HMM_REVKinetics) SBEntity(org.vcell.pathway.sbpax.SBEntity) SBOParam(org.vcell.pathway.sbo.SBOParam) SBMeasurable(org.vcell.pathway.sbpax.SBMeasurable) Control(org.vcell.pathway.Control) MassActionKinetics(cbit.vcell.model.MassActionKinetics) HMM_IRRKinetics(cbit.vcell.model.HMM_IRRKinetics) Kinetics(cbit.vcell.model.Kinetics) HMM_REVKinetics(cbit.vcell.model.HMM_REVKinetics) MassActionKinetics(cbit.vcell.model.MassActionKinetics)

Example 5 with SBEntity

use of org.vcell.pathway.sbpax.SBEntity in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentEntity.

// dataSource		Provenance	multiple
// availability	String		multiple
// name			String		multiple
// xref			Xref		multiple
// evidence		Evidence	multiple
private Element addContentEntity(BioPaxObject bpObject, Element element) {
    element = addContentBioPaxObject(bpObject, element);
    Entity ob = (Entity) bpObject;
    Element tmpElement = null;
    if (ob.getDataSource() != null && ob.getDataSource().size() > 0) {
        ArrayList<Provenance> list = ob.getDataSource();
        for (Provenance item : list) {
            tmpElement = new Element("dataSource", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getAvailability() != null && ob.getAvailability().size() > 0) {
        ArrayList<String> list = ob.getAvailability();
        for (String item : list) {
            tmpElement = new Element("availability", bp);
            tmpElement.setAttribute("datatype", schemaString, rdf);
            tmpElement.setText(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getName() != null && ob.getName().size() > 0) {
        ArrayList<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) {
        ArrayList<Xref> list = ob.getxRef();
        for (Xref item : list) {
            String elementName = "xref";
            tmpElement = new Element(elementName, bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getEvidence() != null && ob.getEvidence().size() > 0) {
        ArrayList<Evidence> list = ob.getEvidence();
        for (Evidence item : list) {
            tmpElement = new Element("evidence", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getSBSubEntity() != null && ob.getSBSubEntity().size() > 0) {
        ArrayList<SBEntity> list = ob.getSBSubEntity();
        for (SBEntity item : list) {
            tmpElement = new Element("sbSubEntity", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    return element;
}
Also used : SBEntity(org.vcell.pathway.sbpax.SBEntity) PhysicalEntity(org.vcell.pathway.PhysicalEntity) Entity(org.vcell.pathway.Entity) Provenance(org.vcell.pathway.Provenance) Xref(org.vcell.pathway.Xref) RelationshipXref(org.vcell.pathway.RelationshipXref) PublicationXref(org.vcell.pathway.PublicationXref) Element(org.jdom.Element) Evidence(org.vcell.pathway.Evidence) PathwayXMLHelper.schemaString(org.vcell.pathway.PathwayXMLHelper.schemaString) SBEntity(org.vcell.pathway.sbpax.SBEntity)

Aggregations

SBEntity (org.vcell.pathway.sbpax.SBEntity)11 SBMeasurable (org.vcell.pathway.sbpax.SBMeasurable)5 HashSet (java.util.HashSet)4 ArrayList (java.util.ArrayList)3 Element (org.jdom.Element)3 BioPaxObject (org.vcell.pathway.BioPaxObject)3 Control (org.vcell.pathway.Control)3 Entity (org.vcell.pathway.Entity)3 GroupObject (org.vcell.pathway.GroupObject)3 PhysicalEntity (org.vcell.pathway.PhysicalEntity)3 PublicationXref (org.vcell.pathway.PublicationXref)3 RelationshipXref (org.vcell.pathway.RelationshipXref)3 Xref (org.vcell.pathway.Xref)3 SBOTerm (org.vcell.pathway.sbo.SBOTerm)3 SBVocabulary (org.vcell.pathway.sbpax.SBVocabulary)3 PathwayStringObject (cbit.vcell.client.desktop.biomodel.BioModelEditorPathwayCommonsPanel.PathwayStringObject)2 BioModelEntityObject (cbit.vcell.model.BioModelEntityObject)2 SimpleReaction (cbit.vcell.model.SimpleReaction)2 SBOParam (org.vcell.pathway.sbo.SBOParam)2 PathwayData (cbit.vcell.client.desktop.biomodel.BioModelEditorPathwayCommonsPanel.PathwayData)1