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

Example 11 with Species

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

the class BioCartoonTool method getNewSpecies.

private static Species getNewSpecies(IdentityHashMap<Species, Species> speciesHash, Species copyFromSpecies, Model pasteToModel, boolean bNew, /* boolean bUseDBSpecies,*/
Structure pasteToStruct, HashMap<Structure, Species> userPreferredToTarget) {
    Species newSpecies = speciesHash.get(copyFromSpecies);
    if (newSpecies != null) {
        return newSpecies;
    }
    Species preferredToSpecies = (userPreferredToTarget != null ? userPreferredToTarget.values().iterator().next() : null);
    try {
        if (bNew || (userPreferredToTarget != null && preferredToSpecies == null)) {
            String newName = copyFromSpecies.getCommonName();
            while (pasteToModel.getSpecies(newName) != null) {
                newName = org.vcell.util.TokenMangler.getNextEnumeratedToken(newName);
            }
            newSpecies = new Species(newName, copyFromSpecies.getAnnotation(), copyFromSpecies.getDBSpecies());
            pasteToModel.addSpecies(newSpecies);
            speciesHash.put(copyFromSpecies, newSpecies);
        } else {
            // Find a matching existing species if possible
            if (preferredToSpecies != null) {
                return preferredToSpecies;
            }
            if (!pasteToModel.contains(copyFromSpecies)) {
                // Doesn't have Species (==)
                // see if we have a species with DBSpecies that matches
                // Species[] speciesFromDBSpeciesArr = (copyFromSpecies.getDBSpecies() != null ? pasteToModel.getSpecies(copyFromSpecies.getDBSpecies()) : null);
                // if(/*bUseDBSpecies && */speciesFromDBSpeciesArr != null && speciesFromDBSpeciesArr.length > 0){//DBSpecies match
                // //Choose the species in struct if exists
                // newSpecies = speciesFromDBSpeciesArr[0];
                // for(int i=0;i<speciesFromDBSpeciesArr.length;i+= 1){
                // if(pasteToModel.getSpeciesContext(speciesFromDBSpeciesArr[i], pasteToStruct) != null){
                // newSpecies = speciesFromDBSpeciesArr[i];
                // break;
                // }
                // }
                // }else{// No DBSpecies match
                // See if there is a species with same name
                newSpecies = pasteToModel.getSpecies(copyFromSpecies.getCommonName());
                if (newSpecies == null) {
                    // No name matches
                    String newName = copyFromSpecies.getCommonName();
                    newSpecies = new Species(newName, copyFromSpecies.getAnnotation(), copyFromSpecies.getDBSpecies());
                    pasteToModel.addSpecies(newSpecies);
                    speciesHash.put(copyFromSpecies, newSpecies);
                }
            // }
            } else {
                // Has species (==)
                newSpecies = copyFromSpecies;
            }
        }
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Could not add species to model : " + e.getMessage());
    }
    return newSpecies;
}

Example 12 with Species

use of cbit.vcell.model.Species 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 13 with Species

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

the class ModelDbDriver method getSpeciesContext.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.SpeciesContext
 * @param rset java.sql.ResultSet
 */
private SpeciesContext getSpeciesContext(QueryHashtable dbc, Connection con, ResultSet rset) throws SQLException, DataAccessException {
    // 
    // if in object cache, no need to create it
    // 
    KeyValue scKey = new KeyValue(rset.getBigDecimal(SpeciesContextModelTable.table.id.toString()));
    SpeciesContext speciesContext = (SpeciesContext) dbc.get(scKey);
    if (speciesContext != null) {
        return speciesContext;
    }
    // 
    // get foreign keys
    // 
    KeyValue structKey = new KeyValue(rset.getBigDecimal(SpeciesContextModelTable.table.structRef.toString()));
    KeyValue speciesKey = new KeyValue(rset.getBigDecimal(SpeciesContextModelTable.table.speciesRef.toString()));
    // 
    // get object (ignoring foreign keys)
    // 
    speciesContext = speciesContextModelTable.getSpeciesContext(rset, scKey);
    String speciesPatternString = speciesContext.getSpeciesPatternString();
    // 
    // add objects corresponding to foreign keys
    // 
    Structure structure = reactStepDB.getStructure(dbc, con, structKey);
    Species species = reactStepDB.getSpecies(dbc, con, speciesKey);
    speciesContext = new SpeciesContext(scKey, speciesContext.getName(), species, structure);
    speciesContext.setSpeciesPatternString(speciesPatternString);
    // 
    // put SpeciesContext into object cache
    // 
    dbc.put(scKey, speciesContext);
    return speciesContext;
}

Example 14 with Species

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

the class ModelDbDriver method getModel.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Model
 * @param rset java.sql.ResultSet
 */
private Model getModel(QueryHashtable dbc, ResultSet rset, Connection con, User user) throws SQLException, DataAccessException {
    // User owner = new User(ownerName, ownerRef);
    try {
        Model model = modelTable.getModel(rset, con);
        // model.setOwner(owner);
        KeyValue modelKey = model.getVersion().getVersionKey();
        // 
        // set structures for this model
        // 
        StructureTopology structureTopology = model.getStructureTopology();
        Structure[] structures = reactStepDB.getStructuresFromModel(dbc, con, modelKey);
        if (structures != null && structures.length > 0) {
            model.setStructures(structures);
        }
        HashMap<KeyValue, StructureKeys> structureKeysMap = reactStepDB.getStructureParentMapByModel(dbc, con, modelKey);
        ReactStepDbDriver.populateStructureAndElectricalTopology(model, structureKeysMap);
        // 
        // set species for this model
        // 
        SpeciesContext[] speciesContexts = getSpeciesContextFromModel(dbc, con, user, modelKey, structureTopology);
        if (speciesContexts != null) {
            Vector<Species> speciesList = new Vector<Species>();
            for (int i = 0; i < speciesContexts.length; i++) {
                if (!speciesList.contains(speciesContexts[i].getSpecies())) {
                    speciesList.addElement(speciesContexts[i].getSpecies());
                }
            }
            Species[] speciesArray = new Species[speciesList.size()];
            speciesList.copyInto(speciesArray);
            model.setSpecies(speciesArray);
        }
        // 
        if (speciesContexts != null) {
            model.setSpeciesContexts(speciesContexts);
        }
        // 
        // Add global parameters to the model
        // 
        GlobalModelParameterTable.table.setModelParameters(con, model);
        // 
        // add reactionSteps for this model
        // 
        ReactionStep[] reactSteps = reactStepDB.getReactionStepsFromModel(dbc, con, model, modelKey);
        if (reactSteps != null) {
            model.setReactionSteps(reactSteps);
            for (int i = 0; i < reactSteps.length; i++) {
                try {
                    // 
                    // fix any improperly defined reactionSteps (which have parameters that should be catalysts)
                    // name space of kinetic parameters should be unique with respect to SpeciesContexts (so if they overlap, should be a catalyst).
                    // 
                    Kinetics.KineticsParameter[] params = reactSteps[i].getKinetics().getKineticsParameters();
                    for (int j = 0; j < params.length; j++) {
                        SpeciesContext speciesContext = model.getSpeciesContext(params[j].getName());
                        if (speciesContext != null) {
                            reactSteps[i].addCatalyst(speciesContext);
                            if (lg.isWarnEnabled())
                                lg.warn("ModelDbDriver.getModel(), Parameter '" + params[j].getName() + "' in Reaction " + reactSteps[i].getName() + " in Model(" + model.getKey() + ") conflicts with SpeciesContext, added as a catalyst");
                        }
                    }
                } catch (Throwable e) {
                    lg.error(e.getMessage(), e);
                }
                try {
                    reactSteps[i].rebindAllToModel(model);
                } catch (cbit.vcell.parser.ExpressionBindingException e) {
                    throw new DataAccessException("bindingException: " + e.getMessage());
                } catch (cbit.vcell.parser.ExpressionException e) {
                    throw new DataAccessException(e.getMessage());
                } catch (PropertyVetoException e) {
                    throw new DataAccessException("PropertyVetoException: " + e.getMessage());
                } catch (cbit.vcell.model.ModelException e) {
                    throw new DataAccessException(e.getMessage());
                }
            }
        }
        // 
        // add diagrams for this model
        // 
        Diagram[] diagrams = getDiagramsFromModel(dbc, con, modelKey, structureTopology, dbSyntax);
        model.setDiagrams(diagrams);
        // 
        // add rbm
        // 
        ModelTable.readRbmElement(con, model, dbSyntax);
        if (!model.getRbmModelContainer().isEmpty()) {
            for (SpeciesContext sc : model.getSpeciesContexts()) {
                sc.parseSpeciesPatternString(model);
            }
        }
        return model;
    } catch (PropertyVetoException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 15 with Species

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

the class ReactStepDbDriver method getSpecies.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Species
 * @param rset java.sql.ResultSet
 * @exception java.sql.SQLException The exception description.
 */
private Species getSpecies(QueryHashtable dbc, ResultSet rset, Connection con) throws SQLException, DataAccessException {
    // 
    // look in object cache (don't instantiate a new one if possible)
    // 
    KeyValue speciesKey = new KeyValue(rset.getBigDecimal(speciesTable.id.toString()));
    Species species = (Species) dbc.get(speciesKey);
    if (species != null) {
        return species;
    } else {
        DBSpecies dbSpeciesRef = null;
        KeyValue dbSpeciesKey = null;
        java.math.BigDecimal dbSpeciesKeyS = rset.getBigDecimal(speciesTable.dbSpeciesRef.toString());
        if (dbSpeciesKeyS != null) {
            dbSpeciesKey = new KeyValue(dbSpeciesKeyS);
        }
        if (dbSpeciesKey != null) {
            dbSpeciesRef = (DBSpecies) dbc.get(dbSpeciesKey);
            if (dbSpeciesRef == null) {
                dbSpeciesRef = dictDB.getDBSpeciesFromKeyValue(dbc, con, dbSpeciesKey);
            }
        }
        species = speciesTable.getSpecies(rset, dbSpeciesRef);
        // 
        // stick new one in cache
        // 
        dbc.put(speciesKey, species);
        return species;
    }
}