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

Example 76 with Structure

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

the class BioCartoonTool method pasteReactionsAndRules.

public static final void pasteReactionsAndRules(Component requester, ReactionSpeciesCopy rsCopy, Model pasteModel, Structure structTo, RXPasteInterface rxPasteInterface) {
    PasteHelper[] pasteHelper = new PasteHelper[1];
    AsynchClientTask issueTask = new AsynchClientTask("Checking Issues...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Model clonedModel = (Model) org.vcell.util.BeanUtils.cloneSerializable(pasteModel);
            clonedModel.refreshDependencies();
            // Model clonedModel = pasteModel;
            IssueContext issueContext = new IssueContext(ContextType.Model, clonedModel, null);
            Vector<Issue> issues = new Vector<>();
            checkStructuresCompatibility(rsCopy, clonedModel, structTo, issues, issueContext);
            Set<MolecularType> mtFromListStrict = getMoleculesFromStrict(rsCopy, clonedModel, issues, issueContext);
            if (issues.size() != 0) {
                // at this point we can only have fatal error issues or no issues at all
                if (!printIssues(issues, requester)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            // map all the structures of the reactions, rules and their participants to existing structures, at need make new structures
            // key is the "from" structure, value is the name of the equivalent "to" structure
            // on the first position we have the struct from where we copy (key) and the struct where we paste (value)
            Map<Structure, String> structuresMap;
            if (rsCopy.getStructuresArr().length > 1) {
                // throws CANCEL_GENERIC if the user cancels
                structuresMap = mapStructures(requester, rsCopy, clonedModel, structTo, issueContext);
            } else {
                // if length == 1 it's just structFrom which automatically maps to structTo
                structuresMap = new LinkedHashMap<>();
                structuresMap.put(rsCopy.getFromStructure(), structTo.getName());
            }
            pasteMolecules(mtFromListStrict, clonedModel, structuresMap);
            List<ReactionRule> rulesTo = pasteRules(rsCopy, clonedModel, structTo, issues, issueContext, structuresMap);
            // for(ReactionRule rr : rulesTo) {
            // clonedModel.getRbmModelContainer().addReactionRule(rr);
            // }
            clonedModel.getRbmModelContainer().addReactionRules(rulesTo);
            // TODO: make any final verifications in the cloned model here
            // if anything is wrong exit here with some helpful message
            // .....
            // otherwise go directly to populating the real model
            mapStructures(structuresMap, pasteModel);
            pasteMolecules(mtFromListStrict, pasteModel, structuresMap);
            // we repeat all the steps to paste the rules in the real model instead of the clone
            rulesTo = pasteRules(rsCopy, pasteModel, structTo, issues, issueContext, structuresMap);
            // for(ReactionRule rr : rulesTo) {
            // pasteModel.getRbmModelContainer().addReactionRule(rr);
            // }
            pasteModel.getRbmModelContainer().addReactionRules(rulesTo);
            System.out.println("done");
        }
    };
    AsynchClientTask pasteRXTask = new AsynchClientTask("Pasting Reaction...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            IssueContext issueContext = new IssueContext(ContextType.Model, pasteModel, null);
        // if (pasteHelper[0].issues.size() != 0) {
        // printIssues(pasteHelper[0].issues, requester);
        // }
        // if(rxPasteInterface != null){
        // for(BioModelEntityObject newBioModelEntityObject:pasteHelper[0].reactionsAndSpeciesContexts.keySet()) {
        // ReactionCartoonTool.copyRelativePosition(rxPasteInterface.getGraphPane().getGraphModel(), pasteHelper[0].reactionsAndSpeciesContexts.get(newBioModelEntityObject), newBioModelEntityObject);
        // }
        // ReactionCartoonTool.selectAndSaveDiagram(rxPasteInterface, new ArrayList<BioModelEntityObject>(pasteHelper[0].reactionsAndSpeciesContexts.keySet()));
        // //					//Setup to allow dispatcher to set focus on a specified component after it closes the ProgressPopup
        // setFinalWindow(hashTable, rxPasteInterface.getGraphPane());
        // }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<>(), new AsynchClientTask[] { issueTask, pasteRXTask }, false);
}

Example 77 with Structure

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

the class BioCartoonTool method pasteReactionSteps.

/**
 * pasteReactionSteps : this method clones the model argument and calls the private pasteReationSteps0 method with the cloned model to see if
 * there are any issues with the paste operation. If so, the issue list is popped up in a warning dialog, and user is given the option of proceeding
 * with the paste or cancelling the operation.
 *
 * @param reactionStepsArr : reactions to be pasted
 * @param model : model where reactions are to be pasted
 * @param struct : strucure in 'model' where the reactions should be pasted
 * @param bNew : is it 'paste' or 'paste new' reaction (new reaction Participants are created if 'bNew' is <true>).
 * @param guiRequestComponent : the parent component for the warning dialog that pops up the issues, if any, encountered in the pasting process
 * @throws Exception
 */
public static final void pasteReactionSteps(Component requester, ReactionStep[] reactionStepsArrOrig, Model pasteModel, Structure struct, boolean bNew, /*boolean bUseDBSpecies,*/
UserResolvedRxElements userResolvedRxElements, RXPasteInterface rxPasteInterface) {
    PasteHelper[] pasteHelper = new PasteHelper[1];
    AsynchClientTask issueTask = new AsynchClientTask("Checking Issues...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Model clonedModel = (Model) org.vcell.util.BeanUtils.cloneSerializable(pasteModel);
            clonedModel.refreshDependencies();
            IssueContext issueContext = new IssueContext(ContextType.Model, clonedModel, null);
            pasteHelper[0] = pasteReactionSteps0(null, requester, issueContext, reactionStepsArrOrig, clonedModel, clonedModel.getStructure(struct.getName()), bNew, /*bUseDBSpecies,*/
            UserResolvedRxElements.createCompatibleUserResolvedRxElements(userResolvedRxElements, clonedModel));
            if (pasteHelper[0].issues.size() != 0) {
                if (!printIssues(pasteHelper[0].issues, requester)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            if (pasteHelper[0].rxPartMapStruct != null) {
                // Convert rxPartMapStruct instances from cloned to pasteModel
                HashMap<String, HashMap<ReactionParticipant, Structure>> new_rxPartMapStruct = new HashMap<>();
                for (int i = 0; reactionStepsArrOrig != null && i < reactionStepsArrOrig.length; i++) {
                    new_rxPartMapStruct.put(reactionStepsArrOrig[i].getName(), new HashMap<ReactionParticipant, Structure>());
                    for (ReactionParticipant rxPart : pasteHelper[0].rxPartMapStruct.get(reactionStepsArrOrig[i].getName()).keySet()) {
                        ReactionParticipant[] origRXParts = reactionStepsArrOrig[i].getReactionParticipants();
                        for (int j = 0; j < origRXParts.length; j++) {
                            if (origRXParts[j].getName().equals(rxPart.getName())) {
                                new_rxPartMapStruct.get(reactionStepsArrOrig[i].getName()).put(origRXParts[j], pasteModel.getStructure(pasteHelper[0].rxPartMapStruct.get(reactionStepsArrOrig[i].getName()).get(rxPart).getName()));
                            }
                        }
                    }
                }
                pasteHelper[0].rxPartMapStruct = new_rxPartMapStruct;
            }
        }
    };
    AsynchClientTask pasteRXTask = new AsynchClientTask("Pasting Reaction...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            IssueContext issueContext = new IssueContext(ContextType.Model, pasteModel, null);
            pasteHelper[0] = pasteReactionSteps0(pasteHelper[0].rxPartMapStruct, requester, issueContext, reactionStepsArrOrig, pasteModel, struct, bNew, /*bUseDBSpecies,*/
            userResolvedRxElements);
            if (pasteHelper[0].issues.size() != 0) {
                printIssues(pasteHelper[0].issues, requester);
            }
            if (rxPasteInterface != null) {
                for (BioModelEntityObject newBioModelEntityObject : pasteHelper[0].reactionsAndSpeciesContexts.keySet()) {
                    ReactionCartoonTool.copyRelativePosition(rxPasteInterface.getGraphPane().getGraphModel(), pasteHelper[0].reactionsAndSpeciesContexts.get(newBioModelEntityObject), newBioModelEntityObject);
                }
                ReactionCartoonTool.selectAndSaveDiagram(rxPasteInterface, new ArrayList<BioModelEntityObject>(pasteHelper[0].reactionsAndSpeciesContexts.keySet()));
                // //Setup to allow dispatcher to set focus on a specified component after it closes the ProgressPopup
                setFinalWindow(hashTable, rxPasteInterface.getGraphPane());
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<>(), new AsynchClientTask[] { issueTask, pasteRXTask }, false);
}

Example 78 with Structure

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

the class BioCartoonTool method pasteSpecies.

/**
 * Insert the method's description here.
 * Creation date: (5/10/2003 3:55:25 PM)
 * @param pasteToModel cbit.vcell.model.Model
 * @param pasteToStruct cbit.vcell.model.Structure
 * @param bNew boolean
 */
protected static final SpeciesContext pasteSpecies(Component parent, Species copyFromSpecies, String useThisSpeciesContextRootName, Model pasteToModel, Structure pasteToStruct0, boolean bNew, /*boolean bUseDBSpecies, */
IdentityHashMap<Species, Species> speciesHash, HashMap<Structure, Species> userPreferredToTarget) {
    Structure preferredToStructure = (userPreferredToTarget != null ? userPreferredToTarget.keySet().iterator().next() : pasteToStruct0);
    if (!pasteToModel.contains(preferredToStructure)) {
        throw new IllegalArgumentException("CartoonTool.pasteSpecies model '" + pasteToModel.getName() + "' does not contain structure " + (preferredToStructure == null ? null : "'" + preferredToStructure.getName() + "'"));
    }
    Species newSpecies = null;
    if (copyFromSpecies != null) {
        try {
            newSpecies = getNewSpecies(speciesHash, copyFromSpecies, pasteToModel, bNew, preferredToStructure, userPreferredToTarget);
            // see if we have SpeciesContext
            SpeciesContext speciesContext = pasteToModel.getSpeciesContext(newSpecies, preferredToStructure);
            if (speciesContext == null) {
                // Has Species but not SpeciesContext
                speciesContext = pasteToModel.addSpeciesContext(newSpecies, preferredToStructure);
                String newSpeciesContextName = newSpecies.getCommonName();
                if (useThisSpeciesContextRootName != null) {
                    newSpeciesContextName = useThisSpeciesContextRootName + "_" + speciesContext.getStructure().getName();
                    while (pasteToModel.getSpeciesContext(newSpeciesContextName) != null) {
                        newSpeciesContextName = TokenMangler.getNextEnumeratedToken(newSpeciesContextName);
                    }
                }
                speciesContext.setName(newSpeciesContextName);
            }
        } catch (Exception e) {
            DialogUtils.showErrorDialog(parent, e.getMessage(), e);
        }
    }
    return pasteToModel.getSpeciesContext(newSpecies, preferredToStructure);
}

Example 79 with Structure

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

the class BioCartoonTool method checkStructuresCompatibility.

// --------------------------------------------------------------------------------------------------------------------------------------
private static void checkStructuresCompatibility(ReactionSpeciesCopy rsCopy, Model modelTo, Structure structTo, Vector<Issue> issueVector, IssueContext issueContext) {
    Structure fromStruct = rsCopy.getFromStructure();
    if (rsCopy.getFromStructure().getDimension() != structTo.getDimension()) {
        // the source and destination structures need to have the same dimension, can't paste from compartment to membrane or vice-versa
        String msg = "Unable to paste from a " + fromStruct.getTypeName() + " to a " + structTo.getTypeName();
        msg += ". Both source and destination Structures need to have the same dimension.";
        Issue issue = new Issue(fromStruct, issueContext, IssueCategory.CopyPaste, msg, Issue.Severity.ERROR);
        issueVector.add(issue);
    }
    for (Structure from : rsCopy.getStructuresArr()) {
        Structure to = modelTo.getStructure(from.getName());
        if (to != null && from.getDimension() != to.getDimension()) {
            String msg = "Unable to paste " + from.getTypeName() + " " + from.getName();
            msg += " because a " + to.getTypeName() + " with the same name already exists.";
            Issue issue = new Issue(from, issueContext, IssueCategory.CopyPaste, msg, Issue.Severity.ERROR);
            issueVector.add(issue);
        }
    }
}

Example 80 with Structure

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

the class BioCartoonTool method mapStructures.

// map the structures to be pasted to existing structures in the cloned model
// we may need to generate some name iteratively until we solve all naming conflicts
private static Map<Structure, String> mapStructures(Component requester, ReactionSpeciesCopy rsCopy, Model modelTo, Structure structTo, IssueContext issueContext) {
    // use internally only; we exit the dialog when there are no issues left
    Vector<Issue> issueVector = new Vector<>();
    Structure structFrom = rsCopy.getFromStructure();
    Map<Structure, String> fullyMappedStructures = new LinkedHashMap<>();
    fullyMappedStructures.put(structFrom, structTo.getName());
    StructurePasteMappingPanel structureMappingPanel = null;
    do {
        issueVector.clear();
        if (structureMappingPanel == null) {
            structureMappingPanel = new StructurePasteMappingPanel(rsCopy, modelTo, structTo, issueVector, issueContext);
            structureMappingPanel.setPreferredSize(new Dimension(400, 220));
        }
        int result = DialogUtils.showComponentOKCancelDialog(requester, structureMappingPanel, "Assign 'From' structures to 'To' structures");
        if (result != JOptionPane.OK_OPTION) {
            throw UserCancelException.CANCEL_GENERIC;
        }
    } while (structureMappingPanel.hasErrors());
    for (Map.Entry<Structure, JComboBox<String>> entry : structureMappingPanel.getStructureMap().entrySet()) {
        if (entry.getValue().getSelectedItem().equals(StructurePasteMappingPanel.MAKE_NEW)) {
            // we generate a "to" structure name based on the "from" name
            String newNameTo = entry.getKey().getName();
            while (modelTo.getStructure(newNameTo) != null) {
                newNameTo = org.vcell.util.TokenMangler.getNextEnumeratedToken(newNameTo);
                for (Structure sFrom : rsCopy.getStructuresArr()) {
                    if (newNameTo.equals(sFrom.getName())) {
                        // the new name must not match any existing "from" name either
                        newNameTo = org.vcell.util.TokenMangler.getNextEnumeratedToken(newNameTo);
                        break;
                    }
                }
            }
            try {
                // as to avoid risk of duplicates / conflicting names
                if (entry.getKey() instanceof Membrane) {
                    modelTo.addMembrane(newNameTo);
                } else {
                    modelTo.addFeature(newNameTo);
                }
            } catch (ModelException | PropertyVetoException e) {
                throw new RuntimeException("Failed to generate the missing 'from' Structures in the cloned model, " + e.getMessage());
            }
            fullyMappedStructures.put(entry.getKey(), newNameTo);
        } else {
            // name of an existing "to" structure
            fullyMappedStructures.put(entry.getKey(), (String) entry.getValue().getSelectedItem());
        }
    }
    return fullyMappedStructures;
}