Examples with ReactionSpec cbit.vcell.mapping.ReactionSpec used on opensource projects

Example 11 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class ModelProcessSpecsTableModel method setSimulationContext.

/**
 * Sets the simulationContext property (cbit.vcell.mapping.SimulationContext) value.
 * @param simulationContext The new value for the property.
 * @see #getSimulationContext
 */
public void setSimulationContext(SimulationContext simulationContext) {
    SimulationContext oldValue = fieldSimulationContext;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        ReactionContext reactionContext = oldValue.getReactionContext();
        reactionContext.removePropertyChangeListener(this);
        ReactionSpec[] oldReactionSpecs = reactionContext.getReactionSpecs();
        for (int i = 0; i < oldReactionSpecs.length; i++) {
            oldReactionSpecs[i].getReactionStep().removePropertyChangeListener(this);
            oldReactionSpecs[i].removePropertyChangeListener(this);
        }
        ReactionRuleSpec[] oldReactionRuleSpecs = reactionContext.getReactionRuleSpecs();
        for (int i = 0; i < oldReactionRuleSpecs.length; i++) {
            oldReactionRuleSpecs[i].getReactionRule().removePropertyChangeListener(this);
            oldReactionRuleSpecs[i].removePropertyChangeListener(this);
        }
    }
    fieldSimulationContext = simulationContext;
    refreshColumns();
    if (simulationContext != null) {
        simulationContext.addPropertyChangeListener(this);
        ReactionContext reactionContext = fieldSimulationContext.getReactionContext();
        reactionContext.addPropertyChangeListener(this);
        ReactionSpec[] newReactionSpecs = reactionContext.getReactionSpecs();
        for (int i = 0; i < newReactionSpecs.length; i++) {
            newReactionSpecs[i].getReactionStep().addPropertyChangeListener(this);
            newReactionSpecs[i].addPropertyChangeListener(this);
        }
        ReactionRuleSpec[] newReactionRuleSpecs = reactionContext.getReactionRuleSpecs();
        for (int i = 0; i < newReactionRuleSpecs.length; i++) {
            newReactionRuleSpecs[i].getReactionRule().addPropertyChangeListener(this);
            newReactionRuleSpecs[i].addPropertyChangeListener(this);
        }
    }
    firePropertyChange("simulationContext", oldValue, simulationContext);
}

Example 12 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class SimulationContextDbDriver method assignReactionSpecsSQL.

/**
 * This method was created in VisualAge.
 * @param simContextKey cbit.sql.KeyValue
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
private void assignReactionSpecsSQL(Connection con, KeyValue simContextKey, SimulationContext simContext) throws SQLException, DataAccessException {
    String sql;
    sql = " SELECT " + "*" + " FROM " + reactionSpecTable.getTableName() + " WHERE " + reactionSpecTable.simContextRef + " = " + simContextKey + " ORDER BY " + reactionSpecTable.id;
    // System.out.println("SimulationContextDbDriver.assignReactionSpecsSQL(), sql = "+sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue reactionStepRef = new KeyValue(rset.getBigDecimal(reactionSpecTable.reactionStepRef.toString()));
            int mapping = rset.getInt(reactionSpecTable.mapping.toString());
            // 
            ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
            for (int i = 0; i < reactionSpecs.length; i++) {
                if (reactionSpecs[i].getReactionStep().getKey().compareEqual(reactionStepRef)) {
                    try {
                        reactionSpecs[i].setReactionMapping(mapping);
                    } catch (Exception e) {
                        throw new DataAccessException("Error setting ReactionSpec 'mapping' for SimulationContext:" + simContext.getVersion().getName() + " id=" + simContextKey);
                    }
                    break;
                }
            }
        }
    } finally {
        stmt.close();
    }
}

Example 13 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class SimulationContextDbDriver method insertReactionSpecsSQL.

/**
 * This method was created in VisualAge.
 */
private void insertReactionSpecsSQL(Connection con, KeyValue simContextKey, SimulationContext simContext, Model updatedModel) throws SQLException, DataAccessException {
    String sql;
    ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
    for (int i = 0; i < reactionSpecs.length; i++) {
        // 
        KeyValue newReactionSpecKey = keyFactory.getNewKey(con);
        KeyValue reactionStepKey = updatedModel.getReactionStep(reactionSpecs[i].getReactionStep().getName()).getKey();
        // 
        sql = "INSERT INTO " + reactionSpecTable.getTableName() + " " + reactionSpecTable.getSQLColumnList() + " VALUES " + reactionSpecTable.getSQLValueList(newReactionSpecKey, simContextKey, reactionSpecs[i], reactionStepKey);
        // System.out.println("SimulationContextDbDriver.insertReactionSpecsSQL(), sql = "+sql);
        updateCleanSQL(con, sql);
    }
}

Example 14 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class ModelProcessSpecsTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    ModelProcessSpec modelProcessSpec = getValueAt(rowIndex);
    ColumnType columnType = columns.get(columnIndex);
    try {
        switch(columnType) {
            case COLUMN_ENABLED:
                {
                    boolean bEnabled = ((Boolean) aValue).booleanValue();
                    if (modelProcessSpec instanceof ReactionSpec) {
                        ReactionSpec reactionSpec = (ReactionSpec) modelProcessSpec;
                        if (bEnabled) {
                            reactionSpec.setReactionMapping(ReactionSpec.INCLUDED);
                        } else {
                            reactionSpec.setReactionMapping(ReactionSpec.EXCLUDED);
                        }
                    } else if (modelProcessSpec instanceof ReactionRuleSpec) {
                        ReactionRuleSpec reactionRuleSpec = (ReactionRuleSpec) modelProcessSpec;
                        if (bEnabled) {
                            reactionRuleSpec.setReactionRuleMapping(ReactionRuleMappingType.INCLUDED);
                        } else {
                            reactionRuleSpec.setReactionRuleMapping(ReactionRuleMappingType.EXCLUDED);
                        }
                    }
                    fireTableRowsUpdated(rowIndex, rowIndex);
                    break;
                }
            case COLUMN_FAST:
                {
                    boolean bFast = ((Boolean) aValue).booleanValue();
                    if (modelProcessSpec instanceof ReactionSpec) {
                        ReactionSpec reactionSpec = (ReactionSpec) modelProcessSpec;
                        if (bFast) {
                            reactionSpec.setReactionMapping(ReactionSpec.FAST);
                        } else {
                            reactionSpec.setReactionMapping(ReactionSpec.INCLUDED);
                        }
                    }
                    fireTableRowsUpdated(rowIndex, rowIndex);
                    break;
                }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
    }
}

Example 15 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class KineticsTypeTemplatePanel method onSelectedObjectsChange.

@Override
protected void onSelectedObjectsChange(Object[] selectedObjects) {
    if (selectedObjects == null || selectedObjects.length != 1) {
        return;
    }
    if (selectedObjects[0] instanceof ReactionStep) {
        setReactionStep((ReactionStep) selectedObjects[0]);
    } else if (selectedObjects[0] instanceof ReactionSpec) {
        setReactionStep(((ReactionSpec) selectedObjects[0]).getReactionStep());
    } else if (selectedObjects[0] instanceof KineticsParameter) {
        KineticsParameter kineticsParameter = (KineticsParameter) selectedObjects[0];
        setReactionStep(kineticsParameter.getKinetics().getReactionStep());
        for (int i = 0; i < getParameterTableModel().getRowCount(); i++) {
            if (kineticsParameter == getParameterTableModel().getValueAt(i)) {
                getScrollPaneTable().setRowSelectionInterval(i, i);
                break;
            }
        }
    } else {
        setReactionStep(null);
    }
}