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

Example 81 with SpeciesContext

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

the class InitialConditionsPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(final java.awt.event.ActionEvent actionEvent) {
    final Vector<String> pasteDescriptionsV = new Vector<String>();
    final Vector<Expression> newExpressionsV = new Vector<Expression>();
    final Vector<SpeciesContextSpec.SpeciesContextSpecParameter> changedParametersV = new Vector<SpeciesContextSpec.SpeciesContextSpecParameter>();
    AsynchClientTask task1 = new AsynchClientTask("validating", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
                Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
                MathSymbolMapping msm = null;
                Exception mathMappingException = null;
                try {
                    MathMapping mm = null;
                    mm = getSimulationContext().createNewMathMapping();
                    msm = mm.getMathSymbolMapping();
                } catch (Exception e) {
                    mathMappingException = e;
                    e.printStackTrace(System.out);
                }
                int[] rows = null;
                if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                    rows = new int[getScrollPaneTable().getRowCount()];
                    for (int i = 0; i < rows.length; i += 1) {
                        rows[i] = i;
                    }
                } else {
                    rows = getScrollPaneTable().getSelectedRows();
                }
                // 
                // Check paste
                // 
                StringBuffer errors = null;
                for (int i = 0; i < rows.length; i += 1) {
                    SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
                    try {
                        if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                            VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                            for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                                SpeciesContextSpec.SpeciesContextSpecParameter pasteDestination = null;
                                SpeciesContextSpec.SpeciesContextSpecParameter clipboardBiologicalParameter = null;
                                if (rvs.getPrimarySymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getPrimarySymbolTableEntries()[j];
                                } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getAlternateSymbolTableEntries()[j];
                                }
                                if (clipboardBiologicalParameter == null) {
                                    Variable pastedMathVariable = null;
                                    if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
                                    } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
                                    }
                                    if (pastedMathVariable != null) {
                                        if (msm == null) {
                                            throw mathMappingException;
                                        }
                                        Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
                                        if (localMathVariable == null) {
                                            // try if localMathVariable is a speciesContext init parameter
                                            String initSuffix = DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scs.getInitialConcentrationParameter().getUnitDefinition().getSymbol());
                                            localMathVariable = msm.findVariableByName(pastedMathVariable.getName() + initSuffix);
                                        }
                                        if (localMathVariable != null) {
                                            SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
                                            for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
                                                if (localBiologicalSymbolArr[k] instanceof SpeciesContext && scs.getSpeciesContext() == localBiologicalSymbolArr[k]) {
                                                    // need to change
                                                    pasteDestination = scs.getInitialConditionParameter();
                                                } else if (localBiologicalSymbolArr[k] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                                    for (int l = 0; l < scs.getParameters().length; l += 1) {
                                                        if (scs.getParameters()[l] == localBiologicalSymbolArr[k]) {
                                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) localBiologicalSymbolArr[k];
                                                            break;
                                                        }
                                                    }
                                                }
                                                if (pasteDestination != null) {
                                                    break;
                                                }
                                            }
                                        }
                                    }
                                } else {
                                    for (int k = 0; k < scs.getParameters().length; k += 1) {
                                        SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[k];
                                        if (scsp.getRole() == clipboardBiologicalParameter.getRole() && scs.getSpeciesContext().compareEqual(((SpeciesContextSpec) clipboardBiologicalParameter.getNameScope().getScopedSymbolTable()).getSpeciesContext())) {
                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) scsp;
                                        }
                                    }
                                }
                                if (pasteDestination != null) {
                                    changedParametersV.add(pasteDestination);
                                    newExpressionsV.add(rvs.getExpressionValues()[j]);
                                    pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(scs.getSpeciesContext().getName(), pasteDestination.getName(), pasteDestination.getExpression().infix(), rvs.getExpressionValues()[j].infix()));
                                }
                            }
                        }
                    } catch (Throwable e) {
                        if (errors == null) {
                            errors = new StringBuffer();
                        }
                        errors.append(scs.getSpeciesContext().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n\n");
                    }
                }
                if (errors != null) {
                    throw new Exception(errors.toString());
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("pasting", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Do paste
            if (pasteDescriptionsV.size() > 0) {
                String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
                pasteDescriptionsV.copyInto(pasteDescriptionArr);
                SpeciesContextSpec.SpeciesContextSpecParameter[] changedParametersArr = new SpeciesContextSpec.SpeciesContextSpecParameter[changedParametersV.size()];
                changedParametersV.copyInto(changedParametersArr);
                Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
                newExpressionsV.copyInto(newExpressionsArr);
                VCellCopyPasteHelper.chooseApplyPaste(InitialConditionsPanel.this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
            } else {
                PopupGenerator.showInfoDialog(InitialConditionsPanel.this, "No paste items match the destination (no changes made).");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 82 with SpeciesContext

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

the class SpeciesContextSpecsTableModel method getComparator.

public Comparator<SpeciesContextSpec> getComparator(final int col, final boolean ascending) {
    return new Comparator<SpeciesContextSpec>() {

        /**
         * Compares its two arguments for order.  Returns a negative integer,
         * zero, or a positive integer as the first argument is less than, equal
         * to, or greater than the second.<p>
         */
        public int compare(SpeciesContextSpec speciesContextSpec1, SpeciesContextSpec speciesContextSpec2) {
            SpeciesContext speciesContext1 = speciesContextSpec1.getSpeciesContext();
            SpeciesContext speciesContext2 = speciesContextSpec2.getSpeciesContext();
            ColumnType columnType = columns.get(col);
            switch(columnType) {
                case COLUMN_SPECIESCONTEXT:
                    {
                        String name1 = speciesContext1.getName();
                        String name2 = speciesContext2.getName();
                        if (ascending) {
                            return name1.compareToIgnoreCase(name2);
                        } else {
                            return name2.compareToIgnoreCase(name1);
                        }
                    }
                case COLUMN_STRUCTURE:
                    {
                        String name1 = speciesContext1.getStructure().getName();
                        String name2 = speciesContext2.getStructure().getName();
                        if (ascending) {
                            return name1.compareToIgnoreCase(name2);
                        } else {
                            return name2.compareToIgnoreCase(name1);
                        }
                    }
                case COLUMN_CLAMPED:
                    {
                        Boolean bClamped1 = new Boolean(speciesContextSpec1.isConstant());
                        Boolean bClamped2 = new Boolean(speciesContextSpec2.isConstant());
                        if (ascending) {
                            return bClamped1.compareTo(bClamped2);
                        } else {
                            return bClamped2.compareTo(bClamped1);
                        }
                    }
                case COLUMN_FORCECONTINUOUS:
                    {
                        Boolean bForceContinuous1 = new Boolean(speciesContextSpec1.isForceContinuous());
                        Boolean bForceContinuous2 = new Boolean(speciesContextSpec2.isForceContinuous());
                        if (ascending) {
                            return bForceContinuous1.compareTo(bForceContinuous2);
                        } else {
                            return bForceContinuous2.compareTo(bForceContinuous1);
                        }
                    }
                case COLUMN_WELLMIXED:
                    {
                        Boolean bWellMixed1 = new Boolean(speciesContextSpec1.isWellMixed());
                        Boolean bWellMixed2 = new Boolean(speciesContextSpec2.isWellMixed());
                        if (ascending) {
                            return bWellMixed1.compareTo(bWellMixed2);
                        } else {
                            return bWellMixed2.compareTo(bWellMixed1);
                        }
                    }
                case COLUMN_INITIAL:
                    {
                        Expression initExp1 = speciesContextSpec1.getInitialConditionParameter().getExpression();
                        Expression initExp2 = speciesContextSpec2.getInitialConditionParameter().getExpression();
                        return TableUtil.expressionCompare(initExp1, initExp2, ascending);
                    }
                case COLUMN_DIFFUSION:
                    {
                        Expression diffExp1 = speciesContextSpec1.getDiffusionParameter().getExpression();
                        Expression diffExp2 = speciesContextSpec2.getDiffusionParameter().getExpression();
                        return TableUtil.expressionCompare(diffExp1, diffExp2, ascending);
                    }
            }
            return 1;
        }
    };
}

Example 83 with SpeciesContext

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

the class ParameterTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Parameter parameter = getValueAt(rowIndex);
    // try {
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            if (parameter instanceof Kinetics.KineticsParameter) {
                                reactionStep.getKinetics().renameParameter(parameter.getName(), newName);
                            } else if (parameter instanceof Kinetics.KineticsProxyParameter) {
                                parameter.setName(newName);
                            }
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_IS_GLOBAL:
            {
                if (aValue.equals(Boolean.FALSE)) {
                    // check box has been <unset> (<true> to <false>) : change param from global to local
                    if ((parameter instanceof KineticsProxyParameter) && ((((KineticsProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((KineticsProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((KineticsProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((KineticsProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
                    } else {
                        try {
                            reactionStep.getKinetics().convertParameterType(parameter, false);
                        } catch (PropertyVetoException pve) {
                            pve.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + pve.getMessage());
                        } catch (ExpressionBindingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + e.getMessage());
                        }
                    }
                } else {
                    // check box has been <set> (<false> to <true>) : change param from local to global
                    if ((parameter instanceof KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_UserDefined)) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a pre-defined kinetics parameter (not user-defined); cannot convert it to a model level (global) parameter.");
                    } else {
                        ModelParameter mp = reactionStep.getKinetics().getReactionStep().getModel().getModelParameter(parameter.getName());
                        // model already had the model parameter 'param', but check if 'param' value is different from
                        // model parameter with same name. If it is, the local value will be overridden by global (model) param
                        // value, and user should be warned.
                        String choice = "Ok";
                        if (mp != null && !(mp.getExpression().compareEqual(parameter.getExpression()))) {
                            String msgStr = "Model already has a global parameter named : \'" + parameter.getName() + "\'; with value = \'" + mp.getExpression().infix() + "\'; This local parameter \'" + parameter.getName() + "\' with value = \'" + parameter.getExpression().infix() + "\' will be overridden by the global value. \nPress \'Ok' to override " + "local value with global value of \'" + parameter.getName() + "\'. \nPress \'Cancel\' to retain new local value.";
                            choice = PopupGenerator.showWarningDialog(ownerTable, msgStr, new String[] { "Ok", "Cancel" }, "Ok");
                        }
                        if (choice.equals("Ok")) {
                            try {
                                // Now 'parameter' is a local kinetic parameter. If it is not numeric, and if its expression
                                // contains other local kinetic parameters, warn user that 'parameter' cannot be promoted because
                                // of its expression containing other local parameters.
                                boolean bPromoteable = true;
                                if (!parameter.getExpression().isNumeric()) {
                                    String[] symbols = parameter.getExpression().getSymbols();
                                    for (int i = 0; i < symbols.length; i++) {
                                        if (reactionStep.getKinetics().getKineticsParameter(symbols[i]) != null) {
                                            PopupGenerator.showErrorDialog(ownerTable, "Parameter \'" + parameter.getName() + "\' contains other local kinetic parameters; Cannot convert it to global until the referenced parameters are global.");
                                            bPromoteable = false;
                                        }
                                    }
                                }
                                if (bPromoteable) {
                                    reactionStep.getKinetics().convertParameterType(parameter, true);
                                }
                            } catch (PropertyVetoException pve) {
                                pve.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + pve.getMessage());
                            } catch (ExpressionBindingException e) {
                                e.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + e.getMessage());
                            }
                        }
                    }
                }
                fireTableRowsUpdated(rowIndex, rowIndex);
                break;
            }
        case COLUMN_VALUE:
            {
                try {
                    if (aValue instanceof ScopedExpression) {
                        // }
                        throw new RuntimeException("unexpected value type ScopedExpression");
                    } else if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        if (parameter instanceof Kinetics.KineticsParameter) {
                            reactionStep.getKinetics().setParameterValue((Kinetics.KineticsParameter) parameter, new Expression(newExpressionString));
                        } else if (parameter instanceof Kinetics.KineticsProxyParameter) {
                            parameter.setExpression(new Expression(newExpressionString));
                        }
                    }
                    reactionStep.getKinetics().resolveUndefinedUnits();
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error:\n" + e.getMessage());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_UNITS:
            {
                try {
                    if (aValue instanceof String && parameter instanceof Kinetics.KineticsParameter && ((Kinetics.KineticsParameter) parameter).getRole() == Kinetics.ROLE_UserDefined) {
                        String newUnitString = (String) aValue;
                        Kinetics.KineticsParameter kineticsParm = (Kinetics.KineticsParameter) parameter;
                        ModelUnitSystem modelUnitSystem = reactionStep.getModel().getUnitSystem();
                        if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
                            kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
                            reactionStep.getKinetics().resolveUndefinedUnits();
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (VCUnitException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter unit:\n" + e.getMessage());
                }
                break;
            }
    }
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}

Example 84 with SpeciesContext

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

the class GeneratedSpeciesTableRow method deriveSpecies.

private void deriveSpecies(String inputString, Model tempModel) {
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                tempModel.addFeature(strStructure);
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        // System.out.println(sp.toString());
        species = new SpeciesContext(new Species("a", ""), structure, sp);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
    }
}

Example 85 with SpeciesContext

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

the class NetworkFreePanel method refreshInterface.

public void refreshInterface() {
    int s1 = 0;
    int s2 = 0;
    for (SpeciesContext sc : fieldSimulationContext.getModel().getSpeciesContexts()) {
        if (sc.hasSpeciesPattern()) {
            s1++;
        } else {
            s2++;
        }
    }
    int s3 = fieldSimulationContext.getModel().getNumSpeciesContexts();
    int r1 = fieldSimulationContext.getModel().getNumReactions();
    int r2 = fieldSimulationContext.getModel().getRbmModelContainer().getReactionRuleList().size();
    int m1 = fieldSimulationContext.getModel().getRbmModelContainer().getMolecularTypeList().size();
    int o1 = fieldSimulationContext.getModel().getRbmModelContainer().getObservableList().size();
    speciesLabel.setText(s2 + "");
    speciesMoleculesLabel.setText(s1 + "");
    futureSpeciesLabel.setText(s1 + s2 + "");
    reactionsLabel.setText(r1 + "");
    rulesLabel.setText(r2 + "");
    futureRulesLabel.setText((r1 + r2) + "");
    molecularTypesLabel.setText(m1 + "");
    observablesLabel.setText(o1 + "");
    futureMolecularTypesLabel.setText((m1 + s2) + "");
    futureObservablesLabel.setText((o1 + s2) + "");
    // if(s1 > 0) {
    rateWarningLabel.setText("<html><font color=#8C001A>" + SimulationContext.rateWarning + "</font></html>");
    // } else {
    // rateWarningLabel.setText("");
    // }
    createModelButton.setEnabled(true);
}