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

Example 1 with ReactionStepInfo

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

the class DictionaryDbDriver method getReactionStepInfos.

/**
 * Insert the method's description here.
 * Creation date: (4/18/2003 10:23:37 AM)
 */
public ReactionStepInfo[] getReactionStepInfos(Connection con, User user, KeyValue[] reactionStepKeys) throws SQLException {
    String sql = ReactStepTable.table.getSQLReactionStepInfosQuery(reactionStepKeys, user, dbSyntax);
    Statement stmt = con.createStatement();
    Vector<ReactionStepInfo> reactionStepInfoList = new Vector<ReactionStepInfo>();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            java.math.BigDecimal rxID = rset.getBigDecimal(ReactStepTable.table.id.toString());
            KeyValue rxKey = new KeyValue(rxID);
            String modelOwnerName = rset.getString(UserTable.table.userid.toString());
            java.math.BigDecimal modelOwnerID = rset.getBigDecimal(BioModelTable.table.ownerRef.toString());
            User owner = new User(modelOwnerName, new KeyValue(modelOwnerID));
            String bioModelName = rset.getString(ReactStepTable.RXIDDN_BIOMODEL_NAME_INDEX);
            String rxName = rset.getString(ReactStepTable.RXIDDN_REACTSTEP_NAME_INDEX);
            java.sql.Date bioModelDate = rset.getDate(BioModelTable.table.versionDate.toString());
            String structType = rset.getString(StructTable.table.structType.getUnqualifiedColName());
            ReactionStepInfo reactionStepInfo = new ReactionStepInfo(rxKey, owner, bioModelName, rxName, bioModelDate, structType);
            reactionStepInfoList.add(reactionStepInfo);
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    if (reactionStepInfoList.size() == 0) {
        return null;
    }
    return (ReactionStepInfo[]) BeanUtils.getArray(reactionStepInfoList, ReactionStepInfo.class);
}

Example 2 with ReactionStepInfo

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

the class DBReactionWizardPanel method configureRXParameterList.

/**
 * Comment
 */
private void configureRXParameterList(javax.swing.event.ListSelectionEvent listSelectionEvent) {
    // 
    final DefaultListModel<MapStringToObject> pndlm = (DefaultListModel<MapStringToObject>) getParameterNamesJList().getModel();
    // 
    if (lastReactionSelection == null || !lastReactionSelection.equals(getReactionsJList().getSelectedValue())) {
        lastReactionSelection = getReactionsJList().getSelectedValue();
        setReactionStep(null);
        setReactionDescription(null);
        // 
        pndlm.removeAllElements();
        // 
        if (getReactionsJList().getSelectedValue() instanceof String) {
            // User Reactions
            Vector<String> rxIDV = mapRXStringtoRXIDs.get(getReactionsJList().getSelectedValue());
            // String[] rxIDArr = (String[])rxIDV.toArray(new String[rxIDV.size()]);
            final KeyValue[] rxKeys = new KeyValue[rxIDV.size()];
            for (int i = 0; i < rxKeys.length; i++) {
                rxKeys[i] = new KeyValue(rxIDV.elementAt(i));
            }
            AsynchClientTask task1 = new AsynchClientTask("getting user reaction step infos", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    ReactionStepInfo[] reactionStepInfos = getDocumentManager().getUserReactionStepInfos(rxKeys);
                    hashTable.put("reactionStepInfos", reactionStepInfos);
                }
            };
            AsynchClientTask task2 = new AsynchClientTask("getting user reaction step infos", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                public void run(Hashtable<String, Object> hashTable) {
                    ReactionStepInfo[] reactionStepInfos = (ReactionStepInfo[]) hashTable.get("reactionStepInfos");
                    for (int i = 0; reactionStepInfos != null && i < reactionStepInfos.length; i++) {
                        String structTypeName = (reactionStepInfos[i].getStructType().equals("feature") ? Structure.TYPE_NAME_FEATURE : (reactionStepInfos[i].getStructType().equals("membrane") ? Structure.TYPE_NAME_MEMBRANE : reactionStepInfos[i].getStructType()));
                        String descriptiveText = structTypeName + " " + reactionStepInfos[i].getOwner().getName() + " - " + "  " + reactionStepInfos[i].getBioModelName() + "  " + "(" + reactionStepInfos[i].getReactionName() + ")" + " " + reactionStepInfos[i].getBioModelVersionDate();
                        pndlm.addElement(new MapStringToObject(descriptiveText, /*reactionStepInfos[i].getDescriptiveText()*/
                        reactionStepInfos[i], getStructure().getTypeName().equals(structTypeName)));
                    }
                }
            };
            Hashtable<String, Object> hash = new Hashtable<String, Object>();
            AsynchClientTask[] taskArray = new AsynchClientTask[] { task1, task2 };
            ClientTaskDispatcher.dispatch(this, hash, taskArray);
        } else {
            // Dictionary ReactionDescription
            ReactionDescription dbfr = (ReactionDescription) getReactionsJList().getSelectedValue();
            getRXParticipantResolverPanel().setupRX(dbfr, getModel(), getStructure());
        }
    }
// if(pndlm.size() == 0){
// //Skip parameters if there are none
// ((java.awt.CardLayout)getCardLayoutJPanel().getLayout()).next(getCardLayoutJPanel());
// }
}

Example 3 with ReactionStepInfo

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

the class DBReactionWizardPanel method parameterNameSelectionChanged.

/**
 * Comment
 */
private void parameterNameSelectionChanged() {
    try {
        // 
        if (getParameterNamesJList().getSelectedValue() != null) {
            // final cbit.vcell.clientdb.DocumentManager docManager = getDocumentManager();
            // final javax.swing.JList jlist = getReactionsJList();
            final MapStringToObject parameNameMSO = (MapStringToObject) getParameterNamesJList().getSelectedValue();
            final KeyValue reactionStepKey = ((ReactionStepInfo) parameNameMSO.getToObject()).getReactionKey();
            // 
            final String RXSTEP_HASH_VALUE_KEY = "rxStep";
            AsynchClientTask searchReactions = new AsynchClientTask("Getting Full Reaction", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                public void run(Hashtable<String, Object> hash) throws Exception {
                    Model reactionModel = getDocumentManager().getReactionStepAsModel(reactionStepKey);
                    ReactionStep rStep = reactionModel.getReactionStep(((ReactionStepInfo) parameNameMSO.getToObject()).getReactionName());
                    if (rStep != null) {
                        rStep.rebindAllToModel(reactionModel);
                        hash.put(RXSTEP_HASH_VALUE_KEY, rStep);
                    }
                }
            };
            // 
            AsynchClientTask updateRXParams = new AsynchClientTask("updateRXParams", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                public void run(Hashtable<String, Object> hash) throws DataAccessException {
                    ReactionStep rStep = (ReactionStep) hash.get(RXSTEP_HASH_VALUE_KEY);
                    if (rStep != null) {
                        Kinetics.KineticsParameter[] kpArr = rStep.getKinetics().getKineticsParameters();
                        ReactionParticipant[] rpArr = rStep.getReactionParticipants();
                        // 
                        DefaultListModel<String> pvdlm = (DefaultListModel<String>) getParameterValuesJList().getModel();
                        pvdlm.removeAllElements();
                        for (int i = 0; i < kpArr.length; i += 1) {
                            pvdlm.addElement("Parameter - " + kpArr[i].getName().toString() + " = " + kpArr[i].getExpression().infix());
                        }
                        pvdlm.addElement("PhysicsOption=" + rStep.getPhysicsOptions());
                        for (int i = 0; i < rpArr.length; i += 1) {
                            String role = "Unknown";
                            if (rpArr[i] instanceof Reactant) {
                                role = "Reactant";
                            } else if (rpArr[i] instanceof Product) {
                                role = "Product";
                            } else if (rpArr[i] instanceof Catalyst) {
                                role = "Catalyst";
                            }
                            String fluxFlag = "";
                            // if(rStep instanceof FluxReaction){
                            // Membrane rStepStruct = (Membrane)rStep.getStructure();
                            // if(rpArr[i] instanceof Flux){
                            // if(rpArr[i].getStructure().equals(getModel().getStructureTopology().getOutsideFeature(rStepStruct))){
                            // fluxFlag = "Outside";
                            // }else{
                            // fluxFlag = "Inside";
                            // }
                            // }
                            // }
                            pvdlm.addElement("RXParticipant(" + role + ") " + fluxFlag + " " + (rpArr[i].getSpecies().getDBSpecies() != null ? "*" : "-") + " " + rpArr[i].getSpeciesContext().getName());
                        }
                    }
                    setReactionStep(rStep);
                    configureBFN();
                }
            };
            // 
            Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
            ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXParams }, true);
        } else {
            setReactionStep(null);
        }
    } catch (Exception e) {
        PopupGenerator.showErrorDialog(this, e.getMessage(), e);
    }
    // 
    configureBFN();
}