Examples with ParameterMappingSpec cbit.vcell.modelopt.ParameterMappingSpec used on opensource projects

Example 1 with ParameterMappingSpec

use of cbit.vcell.modelopt.ParameterMappingSpec in project vcell by virtualcell.

the class ParameterMappingPanel method deleteParameter.

public void deleteParameter() {
    ArrayList<ParameterMappingSpec> list = new ArrayList<ParameterMappingSpec>();
    for (int row : getScrollPaneTable().getSelectedRows()) {
        ParameterMappingSpec pms = parameterMappingTableModel.getValueAt(row);
        list.add(pms);
    }
    for (ParameterMappingSpec pms : list) {
        pms.setSelected(false);
    }
}

Example 2 with ParameterMappingSpec

use of cbit.vcell.modelopt.ParameterMappingSpec in project vcell by virtualcell.

the class ParameterMappingPanel method addParameter.

public void addParameter() {
    JPanel panel = new JPanel(new BorderLayout());
    ArrayList<ParameterMappingSpec> dataList = new ArrayList<ParameterMappingSpec>();
    if (getParameterEstimationTask() != null) {
        for (ParameterMappingSpec pms : getParameterEstimationTask().getModelOptimizationSpec().getParameterMappingSpecs()) {
            if (!pms.isSelected()) {
                dataList.add(pms);
            }
        }
    }
    ScrollTable table = new ScrollTable();
    SelectParameterTableModel model = new SelectParameterTableModel(table, getParameterEstimationTask());
    table.setModel(model);
    model.refreshData();
    panel.add(new JScrollPane(table), BorderLayout.CENTER);
    panel.setPreferredSize(new Dimension(400, 300));
    int returnCode = DialogUtils.showComponentOKCancelDialog(this, panel, "Select Parameters");
    if (returnCode == JOptionPane.OK_OPTION) {
        for (int row : table.getSelectedRows()) {
            ParameterMappingSpec pms = model.getValueAt(row);
            pms.setSelected(true);
        }
    }
}

Example 3 with ParameterMappingSpec

use of cbit.vcell.modelopt.ParameterMappingSpec in project vcell by virtualcell.

the class ParameterMappingPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
    java.util.Vector<Expression> newExpressionsV = new java.util.Vector<Expression>();
    java.util.Vector<ParameterMappingSpec> changedParametersV = new java.util.Vector<ParameterMappingSpec>();
    try {
        if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
            Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
            SimulationContext sc = getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext();
            MathSymbolMapping msm = null;
            Exception mathMappingException = null;
            try {
                MathMapping mm = sc.createNewMathMapping();
                msm = mm.getMathSymbolMapping();
            } catch (Exception e) {
                mathMappingException = e;
                e.printStackTrace(System.out);
            }
            // if(msm == null){
            // try{
            // getParameterEstimationTask().refreshMappings();
            // msm = getParameterEstimationTask().getMathSymbolMapping();
            // }catch(Exception e){
            // e.printStackTrace();
            // }
            // }
            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) {
                ParameterMappingSpec pms = parameterMappingTableModel.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) {
                            ParameterMappingSpec pasteDestination = null;
                            Parameter clipboardBiologicalParameter = null;
                            if (rvs.getPrimarySymbolTableEntries()[j] instanceof Parameter) {
                                clipboardBiologicalParameter = (Parameter) rvs.getPrimarySymbolTableEntries()[j];
                            } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Parameter) {
                                clipboardBiologicalParameter = (Parameter) 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) {
                                        SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
                                        for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
                                            if (localBiologicalSymbolArr[k] == pms.getModelParameter()) {
                                                pasteDestination = pms;
                                                break;
                                            }
                                        }
                                    }
                                }
                            } else {
                                if (pms.getModelParameter().getName().equals(clipboardBiologicalParameter.getName()) && pms.getModelParameter().getClass().equals(clipboardBiologicalParameter.getClass()) && pms.getModelParameter().getNameScope().getName().equals(clipboardBiologicalParameter.getNameScope().getName())) {
                                    pasteDestination = pms;
                                }
                            }
                            if (pasteDestination != null) {
                                changedParametersV.add(pasteDestination);
                                newExpressionsV.add(rvs.getExpressionValues()[j]);
                                pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(pms.getModelParameter().getNameScope().getName(), pms.getModelParameter().getName(), pasteDestination.getCurrent() + "", rvs.getExpressionValues()[j].infix()));
                            }
                        }
                    }
                } catch (Throwable e) {
                    if (errors == null) {
                        errors = new StringBuffer();
                    }
                    errors.append(pms.getModelParameter().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n");
                }
            }
            if (errors != null) {
                throw new Exception(errors.toString());
            }
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getMessage(), e);
        return;
    }
    // Do paste
    try {
        if (pasteDescriptionsV.size() > 0) {
            String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
            pasteDescriptionsV.copyInto(pasteDescriptionArr);
            ParameterMappingSpec[] changedParametersArr = new ParameterMappingSpec[changedParametersV.size()];
            changedParametersV.copyInto(changedParametersArr);
            Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
            newExpressionsV.copyInto(newExpressionsArr);
            VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
        } else {
            PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getMessage(), e);
    }
}

Example 4 with ParameterMappingSpec

use of cbit.vcell.modelopt.ParameterMappingSpec in project vcell by virtualcell.

the class ParameterMappingTableModel method refreshData.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2003 1:24:52 PM)
 * @return cbit.vcell.model.Parameter
 * @param row int
 */
private void refreshData() {
    ArrayList<ParameterMappingSpec> list = new ArrayList<ParameterMappingSpec>();
    if (getParameterEstimationTask() != null) {
        for (ParameterMappingSpec pms : getParameterEstimationTask().getModelOptimizationSpec().getParameterMappingSpecs()) {
            if (pms.isSelected()) {
                list.add(pms);
            }
        }
    }
    setData(list);
}

Example 5 with ParameterMappingSpec

use of cbit.vcell.modelopt.ParameterMappingSpec in project vcell by virtualcell.

the class ParameterMappingPanel method jMenuItemCopy_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemCopy_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    if (actionEvent.getSource() == getJMenuItemCopy() || actionEvent.getSource() == getJMenuItemCopyAll()) {
        try {
            // 
            // Copy Optimization Parameters (Initial Guess or Solution)
            // 
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemCopyAll()) {
                rows = new int[getScrollPaneTable().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getScrollPaneTable().getSelectedRows();
            }
            SimulationContext sc = getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext();
            MathSymbolMapping msm = null;
            try {
                MathMapping mm = sc.createNewMathMapping();
                msm = mm.getMathSymbolMapping();
            } catch (Exception e) {
                e.printStackTrace(System.out);
                DialogUtils.showWarningDialog(this, "current math not valid, some paste operations will be limited\n\nreason: " + e.getMessage());
            }
            boolean bInitialGuess = (getScrollPaneTable().getSelectedColumn() == ParameterMappingTableModel.COLUMN_CURRENTVALUE);
            ParameterMappingSpec[] parameterMappingSpecs = new ParameterMappingSpec[rows.length];
            java.util.Vector<SymbolTableEntry> primarySymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<SymbolTableEntry> alternateSymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<Expression> resolvedValuesV = new java.util.Vector<Expression>();
            // 
            // Create formatted string for text/spreadsheet pasting.
            // 
            StringBuffer sb = new StringBuffer();
            sb.append("\"Parameters for (Optimization Task)" + getParameterEstimationTask().getName() + " -> " + "(BioModel)" + getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext().getBioModel().getName() + " -> " + "(App)" + getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext().getName() + "\"\n");
            sb.append("\"Parameter Name\"\t\"" + (bInitialGuess ? "Initial Guess" : "Solution") + "\"\n");
            for (int i = 0; i < rows.length; i += 1) {
                ParameterMappingSpec pms = parameterMappingTableModel.getValueAt(rows[i]);
                parameterMappingSpecs[i] = pms;
                primarySymbolTableEntriesV.add(pms.getModelParameter());
                if (msm != null) {
                    alternateSymbolTableEntriesV.add(msm.getVariable(pms.getModelParameter()));
                } else {
                    alternateSymbolTableEntriesV.add(null);
                }
                Double resolvedValue = null;
                if (!bInitialGuess) {
                    resolvedValue = getParameterEstimationTask().getCurrentSolution(pms);
                }
                if (resolvedValue == null) {
                    resolvedValue = new Double(pms.getCurrent());
                }
                resolvedValuesV.add(new Expression(resolvedValue.doubleValue()));
                sb.append("\"" + parameterMappingSpecs[i].getModelParameter().getName() + "\"\t" + resolvedValue + "\n");
            }
            // 
            // Send to clipboard
            // 
            VCellTransferable.ResolvedValuesSelection rvs = new VCellTransferable.ResolvedValuesSelection((SymbolTableEntry[]) BeanUtils.getArray(primarySymbolTableEntriesV, SymbolTableEntry.class), (SymbolTableEntry[]) BeanUtils.getArray(alternateSymbolTableEntriesV, SymbolTableEntry.class), (Expression[]) BeanUtils.getArray(resolvedValuesV, Expression.class), sb.toString());
            VCellTransferable.sendToClipboard(rvs);
        } catch (Throwable e) {
            PopupGenerator.showErrorDialog(this, "ParameterMappingPanel copy failed.  " + e.getMessage(), e);
        }
    }
}