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

Example 26 with ReactionParticipant

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

the class ReactStepDbDriver method getReactionParticipant.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 * @exception java.sql.SQLException The exception description.
 */
private ReactionParticipant getReactionParticipant(QueryHashtable dbc, Connection con, ResultSet rset, ReactionStep rs) throws SQLException, DataAccessException {
    // 
    // try to get ReactionParticipant from object cache
    // 
    KeyValue rpKey = new KeyValue(rset.getBigDecimal(ReactPartTable.table.id.toString()));
    ReactionParticipant rp = (ReactionParticipant) dbc.get(rpKey);
    if (rp != null) {
        return rp;
    }
    // 
    // get foreign keys
    // 
    KeyValue speciesContextKey = new KeyValue(rset.getBigDecimal(ReactPartTable.table.scRef.toString()));
    // 
    // get ReactionParticipant
    // 
    rp = reactPartTable.getReactionParticipant(rpKey, rset);
    // 
    // get referenced Objects (Species and Structure)
    // 
    SpeciesContext speciesContext = modelDB.getSpeciesContext(dbc, con, speciesContextKey);
    try {
        rp.setSpeciesContext(speciesContext);
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("PropertyVetoException: " + e.getMessage());
    }
    rp.setReactionStep(rs);
    // ========== Since there is no flux carrier in fluxReaction, this is not required?? ===========
    // if (rp instanceof Flux && rs instanceof FluxReaction) {
    // try {
    // ((FluxReaction) rs).setFluxCarrier(speciesContext.getSpecies(), null);
    // }catch (ModelException e){
    // e.printStackTrace(System.out);
    // throw new DataAccessException("ModelException: "+e.getMessage());
    // }catch (PropertyVetoException e){
    // e.printStackTrace(System.out);
    // throw new DataAccessException("PropertyVetoException: "+e.getMessage());
    // }
    // }
    // 
    // stick ReactionParticipant in object cache
    // 
    dbc.put(rpKey, rp);
    return rp;
}

Example 27 with ReactionParticipant

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

the class ReactStepDbDriver method getReactionParticipants.

/**
 * getModel method comment.
 */
private ReactionParticipant[] getReactionParticipants(QueryHashtable dbc, Connection con, KeyValue reactStepID, ReactionStep rs) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (reactStepID == null) {
        throw new IllegalArgumentException("Improper parameters for getReactionParticipants");
    }
    // log.print("ModelDbDriver.getReactionParticipants(reactStepID=" + reactStepID + ")");
    String sql;
    sql = " SELECT * " + " FROM " + reactPartTable.getTableName() + " WHERE " + reactPartTable.reactStepRef + " = " + reactStepID;
    // System.out.println(sql);
    java.util.Vector rpList = new java.util.Vector();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        // 
        while (rset.next()) {
            ReactionParticipant rp = getReactionParticipant(dbc, con, rset, rs);
            rpList.addElement(rp);
        }
        // 
        if (rpList.size() == 0) {
            System.out.println("WARNING:::::ReactionParticipants for reactionStep(id=" + reactStepID + ") not found");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    ReactionParticipant[] reactionParticipants = new ReactionParticipant[rpList.size()];
    rpList.copyInto(reactionParticipants);
    return reactionParticipants;
}

Example 28 with ReactionParticipant

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

the class ReactionCartoonTool method getLineTypeFromDirection.

private LineType getLineTypeFromDirection(Shape startingShape, Point worldPoint) throws Exception {
    Shape mouseOverShape = getReactionCartoon().pickWorld(worldPoint);
    if (mouseOverShape instanceof ReactionStepShape) {
        if (startingShape instanceof SpeciesContextShape) {
            SpeciesContext speciesContext = (SpeciesContext) startingShape.getModelObject();
            // check if the ReactionStep already has a Product for this SpeciesContext
            ReactionStep reactionStep = (ReactionStep) mouseOverShape.getModelObject();
            ReactionParticipant[] rps = reactionStep.getReactionParticipants();
            if ((mouseOverShape instanceof SimpleReactionShape) || (mouseOverShape instanceof FluxReactionShape)) {
                for (int i = 0; i < rps.length; i++) {
                    if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                        return LineType.NULL;
                    }
                }
                return LineType.REACTANT;
            }
        // else if (mouseOverShape instanceof FluxReactionShape){
        // for (int i = 0; i < rps.length; i++){
        // if ((rps[i] instanceof Reactant || rps[i] instanceof Product) && rps[i].getSpeciesContext() == speciesContext) {
        // return LineType.NULL;
        // }
        // }
        // return LineType.FLUX;
        // }
        }
    } else if (mouseOverShape instanceof SpeciesContextShape) {
        SpeciesContext speciesContext = (SpeciesContext) mouseOverShape.getModelObject();
        if (startingShape instanceof SpeciesContextShape) {
            // straight from one species to another ... will create a reaction upon release
            return LineType.PRODUCT;
        } else if (startingShape instanceof ReactionStepShape) {
            ReactionStep reactionStep = (ReactionStep) startingShape.getModelObject();
            ReactionParticipant[] rps = reactionStep.getReactionParticipants();
            // } else
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                for (int i = 0; i < rps.length; i++) {
                    if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                        return LineType.NULL;
                    }
                }
                return LineType.REACTANT;
            }
        }
    }
    return LineType.NULL;
}

Example 29 with ReactionParticipant

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

the class ReactionCartoonTool method lineAction.

private void lineAction(SpeciesContext speciesContextStart, ReactionStep reactionEnd) throws Exception {
    Structure endStructure = reactionEnd.getStructure();
    Structure startStructure = speciesContextStart.getStructure();
    if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, startStructure)) {
        int stoichiometry = 1;
        Reactant reactant = null;
        for (ReactionParticipant participant : reactionEnd.getReactionParticipants()) {
            if (participant instanceof Reactant && participant.getSpeciesContext().equals(speciesContextStart)) {
                reactant = (Reactant) participant;
            }
        }
        if (reactant != null) {
            // only increase stoichiometry if reaction is SimpleReaction
            if (reactionEnd instanceof SimpleReaction) {
                reactant.setStoichiometry(reactant.getStoichiometry() + 1);
            }
            Shape shape = getReactionCartoon().getShapeFromModelObject(reactant);
            if (shape != null) {
                shape.refreshLabel();
            }
        } else {
            // add speciesContextEnd as pdt to reactionStart only if reactionStart is a SimpleRxn or if it is a FluxRxn and doesn't have a pdt.
            if (reactionEnd instanceof SimpleReaction || ((reactionEnd instanceof FluxReaction) && !(reactionEnd.hasReactant()))) {
                reactionEnd.addReactant(speciesContextStart, stoichiometry);
            }
        }
        if (((startStructure instanceof Feature && endStructure instanceof Feature) || (startStructure instanceof Membrane && endStructure instanceof Membrane)) && startStructure != endStructure) {
        // ============ change kinetics to lumped or warn user ?????????
        // simpleReactionEnd.setKinetics(new GeneralLumpedKinetics(simpleReactionEnd));
        }
        getReactionCartoon().notifyChangeEvent();
    }
}

Example 30 with ReactionParticipant

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

the class ReactionCartoonTool method deleteReactionsAndSpecies.

public static void deleteReactionsAndSpecies(Component requester, ReactionStep[] reactionStepArr, SpeciesContext[] speciesContextArr) throws Exception, UserCancelException {
    if ((speciesContextArr == null && reactionStepArr == null) || (reactionStepArr == null && speciesContextArr != null && speciesContextArr.length == 0) || (speciesContextArr == null && reactionStepArr != null && reactionStepArr.length == 0) || (speciesContextArr != null && speciesContextArr.length == 0 && reactionStepArr != null && reactionStepArr.length == 0)) {
        return;
    }
    int rxCount = (reactionStepArr != null ? reactionStepArr.length : 0);
    int speciesCount = (speciesContextArr != null ? speciesContextArr.length : 0);
    boolean bHasBoth = speciesCount > 0 && rxCount > 0;
    ReactionCartoon rxCartoon = null;
    if (requester instanceof GraphPane && ((GraphPane) requester).getGraphModel() instanceof ReactionCartoon) {
        rxCartoon = (ReactionCartoon) (((GraphPane) requester).getGraphModel());
    } else if (requester instanceof ReactionCartoonEditorPanel) {
        rxCartoon = ((ReactionCartoonEditorPanel) requester).getReactionCartoon();
    } else {
        throw new IllegalArgumentException("ReactionCartoonTool.deleteSpeciesContext not implemented for type '" + requester.getClass().getName() + "'");
    }
    DeleteSpeciesInfo deleteSpeciesInfo = null;
    final String DETAILS = "Details...";
    while (true) {
        String response = DialogUtils.showWarningDialog(requester, RXSPECIES_DELETE + " " + (bHasBoth ? "Reactions and Species." : (rxCount > 0 ? "Reactions." : (speciesCount > 0 ? "Species." : ""))), RXSPECIES_DELETE + " " + (bHasBoth ? rxCount + " Reactions and " + speciesCount + " Species." : (rxCount > 0 ? rxCount + " Reactions." : (speciesCount > 0 ? speciesCount + " Species." : ""))), new String[] { RXSPECIES_DELETE, DETAILS, RXSPECIES_CANCEL }, RXSPECIES_DELETE);
        if (response == null || response.equals(RXSPECIES_CANCEL)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        deleteSpeciesInfo = (deleteSpeciesInfo == null ? detailsDeleteSpecies(requester, speciesContextArr, reactionStepArr, rxCartoon) : deleteSpeciesInfo);
        if (response.equals(DETAILS)) {
            TableListResult tableListResult = showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, false);
        // if(!tableListResult.selectedOption.equals(RXSPECIES_BACK)){
        // //if(!tableListResult.selectedOption.equals((bCut?RXSPECIES_CUT:RXSPECIES_DELETE))){
        // throw UserCancelException.CANCEL_GENERIC;
        // }
        } else {
            break;
        }
    }
    if (deleteSpeciesInfo != null) {
        for (Boolean errors : deleteSpeciesInfo.getbUnresolvableHashMap().values()) {
            if (errors) {
                while (true) {
                    String response = DialogUtils.showWarningDialog(requester, "Error warning.", "Warning: 1 or more SpeciesContexts have Model references that could cause Model corruption if " + RXSPECIES_DELETE + ".", new String[] { DETAILS, RXSPECIES_CANCEL }, DETAILS);
                    if (response == null || response.equals(RXSPECIES_CANCEL)) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, true);
                }
            }
        }
    }
    if (reactionStepArr != null) {
        for (int i = 0; i < reactionStepArr.length; i += 1) {
            rxCartoon.getModel().removeReactionStep(reactionStepArr[i]);
        }
    }
    if (deleteSpeciesInfo != null) {
        // remove all ReactionParticipants ("lines" between reaction and species in "Reaction Diagram") that have this speciesContext before deleting SpeciesContext
        for (SpeciesContext objSpeciesContext : deleteSpeciesInfo.getRxPartHashMap().keySet()) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(objSpeciesContext)) {
                continue;
            }
            Iterator<ReactionParticipant> iterRxPart = deleteSpeciesInfo.getRxPartHashMap().get(objSpeciesContext).iterator();
            while (iterRxPart.hasNext()) {
                ReactionParticipant objRxPart = iterRxPart.next();
                if (rxCartoon.getObjects().contains(objRxPart)) {
                    // Reaction delete may have already removed
                    objRxPart.getReactionStep().removeReactionParticipant(objRxPart);
                }
            }
        }
        // remove the SpeciesContext
        for (int i = 0; i < speciesContextArr.length; i++) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(speciesContextArr[i])) {
                continue;
            }
            if (rxCartoon.getObjects().contains(speciesContextArr[i])) {
                // Reaction delete may have already removed
                rxCartoon.getModel().removeSpeciesContext(speciesContextArr[i]);
            }
        }
    }
}