Examples with DataSymbolMetadata cbit.vcell.solver.DataSymbolMetadata used on opensource projects

Example 1 with DataSymbolMetadata

use of cbit.vcell.solver.DataSymbolMetadata in project vcell by virtualcell.

the class ODESolverPlotSpecificationPanel method updateChoices.

/**
 * Insert the method's description here.
 * Creation date: (2/8/2001 4:56:15 PM)
 * @param cbit.vcell.solver.ode.ODESolverResultSet
 */
private synchronized void updateChoices(ODEDataInterface odedi) throws ExpressionException, ObjectNotFoundException {
    if (odedi == null) {
        return;
    }
    Object xAxisSelection = getXAxisComboBox_frm().getSelectedItem();
    Object[] yAxisSelections = getYAxisChoice().getSelectedValues();
    ArrayList<ColumnDescription> variableColumnDescriptions = new ArrayList<ColumnDescription>();
    ArrayList<ColumnDescription> sensitivityColumnDescriptions = new ArrayList<ColumnDescription>();
    ColumnDescription timeColumnDescription = null;
    // find TIME columnDescription
    ColumnDescription[] columnDescriptions = odedi.getAllColumnDescriptions();
    for (int i = 0; i < columnDescriptions.length; i++) {
        if (columnDescriptions[i].getName().equals(ReservedVariable.TIME.getName())) {
            timeColumnDescription = columnDescriptions[i];
        }
    }
    // find filtered columnDescriptions
    columnDescriptions = odedi.getFilteredColumnDescriptions();
    DataSymbolMetadataResolver damdr = odedi.getDataSymbolMetadataResolver();
    for (int i = 0; i < columnDescriptions.length; i++) {
        ColumnDescription cd = columnDescriptions[i];
        // If the column is "_initConnt" generated when using concentration as initial condition, we dont' put the function in list. amended again in August, 2008.
        if (cd.getParameterName() == null) {
            String name = cd.getName();
            DataSymbolMetadata damd = damdr.getDataSymbolMetadata(name);
            // filter entities measured as count vs concentration, based on the checkbox settings
            ModelCategoryType filterCategory = null;
            if (damd != null) {
                filterCategory = damd.filterCategory;
            }
            if (countCheckBox != null && concentrationCheckBox != null) {
                if (filterCategory instanceof BioModelCategoryType && filterCategory == BioModelCategoryType.Species && cd.getName().endsWith(AbstractMathMapping.MATH_VAR_SUFFIX_SPECIES_COUNT) && !countCheckBox.isSelected()) {
                    continue;
                } else if (filterCategory instanceof BioModelCategoryType && filterCategory == BioModelCategoryType.Species && !cd.getName().endsWith(AbstractMathMapping.MATH_VAR_SUFFIX_SPECIES_COUNT) && !concentrationCheckBox.isSelected()) {
                    continue;
                }
            }
            // filter out entities starting with "UnitFactor_" prefix
            if (filterCategory instanceof BioModelCategoryType && filterCategory == BioModelCategoryType.Other && cd.getName().startsWith(AbstractMathMapping.PARAMETER_K_UNITFACTOR_PREFIX)) {
                continue;
            }
            if (!cd.getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME) && !cd.getName().contains(DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT)) {
                variableColumnDescriptions.add(cd);
            }
        } else {
            sensitivityColumnDescriptions.add(cd);
        }
    }
    sortColumnDescriptions(variableColumnDescriptions);
    sortColumnDescriptions(sensitivityColumnDescriptions);
    // Hack this here, Later we can use an array utility...
    ArrayList<ColumnDescription> sortedColumndDescriptions = new ArrayList<ColumnDescription>();
    if (timeColumnDescription != null) {
        // add time first
        sortedColumndDescriptions.add(timeColumnDescription);
    }
    boolean bMultiTrialData = odedi.isMultiTrialData();
    sortedColumndDescriptions.addAll(variableColumnDescriptions);
    if (!bMultiTrialData) {
        sortedColumndDescriptions.addAll(sensitivityColumnDescriptions);
    }
    // finally, update widgets
    try {
        getXAxisComboBox_frm().removeItemListener(ivjEventHandler);
        getYAxisChoice().removeListSelectionListener(ivjEventHandler);
        getComboBoxModelX_frm().removeAllElements();
        if (!bMultiTrialData) {
            // Don't put anything in X Axis, if the results of multiple trials are being displayed.
            ArrayList<ColumnDescription> xColumnDescriptions = new ArrayList<ColumnDescription>(Arrays.asList(odedi.getAllColumnDescriptions()));
            sortColumnDescriptions(xColumnDescriptions);
            if (timeColumnDescription != null) {
                getComboBoxModelX_frm().addElement(timeColumnDescription.getName());
            }
            for (ColumnDescription columnDescription : xColumnDescriptions) {
                if (!columnDescription.getName().equals((timeColumnDescription == null ? null : timeColumnDescription.getName()))) {
                    getComboBoxModelX_frm().addElement(columnDescription.getName());
                }
            }
        }
        getDefaultListModelY().removeAllElements();
        for (int i = 0; i < sortedColumndDescriptions.size(); i++) {
            if (sortedColumndDescriptions.get(i).getName().equals(ReservedVariable.TIME.getName())) {
                continue;
            }
            getDefaultListModelY().addElement(sortedColumndDescriptions.get(i).getName());
        }
        if (sortedColumndDescriptions.size() > 0) {
            // Don't put anything in X Axis, if the results of multifple trials are being displayed.
            if (!bMultiTrialData) {
                getXAxisComboBox_frm().setSelectedItem(xAxisSelection);
                if (getXAxisComboBox_frm().getSelectedIndex() == -1) {
                    getXAxisComboBox_frm().setSelectedIndex(0);
                }
            }
            if (yAxisSelections != null && yAxisSelections.length > 0) {
                ArrayList<Integer> carryoverSelections = new ArrayList<Integer>();
                for (int i = 0; i < getYAxisChoice().getModel().getSize(); i++) {
                    for (int j = 0; j < yAxisSelections.length; j++) {
                        if (getYAxisChoice().getModel().getElementAt(i).equals(yAxisSelections[j])) {
                            carryoverSelections.add(i);
                            break;
                        }
                    }
                }
                if (carryoverSelections.size() > 0) {
                    int[] carryoverInts = new int[carryoverSelections.size()];
                    for (int i = 0; i < carryoverInts.length; i++) {
                        carryoverInts[i] = carryoverSelections.get(i);
                    }
                    getYAxisChoice().setSelectedIndices(carryoverInts);
                } else {
                    getYAxisChoice().setSelectedIndex((getYAxisChoice().getModel().getSize() > 1 ? 1 : 0));
                }
            } else {
                getYAxisChoice().setSelectedIndex(sortedColumndDescriptions.size() > 1 ? 1 : 0);
            }
        }
    } finally {
        getXAxisComboBox_frm().addItemListener(ivjEventHandler);
        getYAxisChoice().addListSelectionListener(ivjEventHandler);
    }
    regeneratePlot2D();
}

Example 2 with DataSymbolMetadata

use of cbit.vcell.solver.DataSymbolMetadata in project vcell by virtualcell.

the class PDEPlotControlPanel method initConnections.

/**
 * Initializes connections
 * @exception java.lang.Exception The exception description.
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initConnections() throws java.lang.Exception {
    // user code begin {1}
    // user code end
    getJTextField1().addActionListener(ivjEventHandler);
    getJTextField1().addFocusListener(ivjEventHandler);
    getDefaultListModelCivilized1().addListDataListener(ivjEventHandler);
    getViewFunctionButton().addActionListener(ivjEventHandler);
    getPlotVariableJList().setModel(getDefaultListModelCivilized1());
    getJSliderTime().getModel().addChangeListener(ivjEventHandler);
    getPlotVariableJList().addListSelectionListener(ivjEventHandler);
    getPlotVariableJList().setCellRenderer(new DefaultListCellRenderer() {

        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
            JLabel c = (JLabel) super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
            if (dataInfoProvider == null) {
                if (value instanceof DataIdentifier) {
                    DataIdentifier var = (DataIdentifier) value;
                    if (var.getVariableType() == VariableType.POSTPROCESSING) {
                        setToolTipText(getText());
                        setText(var.getName());
                    }
                }
                return this;
            }
            // System.out.println("rendering object "+value+" of type "+value.getClass());
            DataIdentifier var = (DataIdentifier) value;
            c.setText(var.getName());
            c.setToolTipText("dataInfoProvier not found");
            DataSymbolMetadataResolver dataSymbolMetadataResolver = dataInfoProvider.getSimulationModelInfo().getDataSymbolMetadataResolver();
            if (dataSymbolMetadataResolver != null && dataSymbolMetadataResolver.getDataSymbolMetadata(var.getName()) != null) {
                DataSymbolMetadata dsm = dataSymbolMetadataResolver.getDataSymbolMetadata(var.getName());
                String tooltipString = "dataInfoProvider found, but identifier " + var.getName() + " not found";
                if (dsm == null) {
                    tooltipString = "did not find info on variable " + var.getDisplayName();
                } else {
                    c.setText(var.getName() + " [" + dsm.unit + "]");
                    tooltipString = dsm.tooltipString;
                }
                c.setToolTipText(tooltipString);
            }
            return this;
        }
    });
}

Example 3 with DataSymbolMetadata

use of cbit.vcell.solver.DataSymbolMetadata in project vcell by virtualcell.

the class ODESolverPlotSpecificationPanel method initConnections.

/**
 * Initializes connections
 * @exception java.lang.Exception The exception description.
 */
@SuppressWarnings({ "serial", "unchecked" })
private void initConnections() throws java.lang.Exception {
    // user code begin {1}
    // user code end
    getFilterPanel().addPropertyChangeListener(ivjEventHandler);
    getYAxisChoice().addListSelectionListener(ivjEventHandler);
    this.addPropertyChangeListener(ivjEventHandler);
    getXAxisComboBox_frm().addItemListener(ivjEventHandler);
    getLogSensCheckbox().addActionListener(ivjEventHandler);
    getSensitivityParameterSlider().addChangeListener(ivjEventHandler);
    connPtoP1SetTarget();
    connPtoP3SetTarget();
    getYAxisChoice().setCellRenderer(new DefaultListCellRenderer() {

        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
            super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
            ODEDataInterface mdi = getMyDataInterface();
            if (mdi == null) {
                return this;
            }
            String varName = (String) value;
            ColumnDescription cd = null;
            try {
                cd = mdi.getColumnDescription(varName);
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
            }
            if (cd instanceof FunctionColumnDescription && ((FunctionColumnDescription) cd).getIsUserDefined()) {
                if (function_icon == null) {
                    function_icon = new ImageIcon(getClass().getResource("/icons/function_icon.png"));
                }
                setIcon(function_icon);
            }
            if (mdi.getDataSymbolMetadataResolver() != null && mdi.getDataSymbolMetadataResolver().getDataSymbolMetadata(varName) != null) {
                DataSymbolMetadata dsm = mdi.getDataSymbolMetadataResolver().getDataSymbolMetadata(varName);
                String tooltipString = dsm.tooltipString;
                if (tooltipString == null) {
                    tooltipString = varName;
                }
                setToolTipText(tooltipString);
            }
            return this;
        }
    });
}

Example 4 with DataSymbolMetadata

use of cbit.vcell.solver.DataSymbolMetadata in project vcell by virtualcell.

the class ODEDataViewer method updateMetadata.

private void updateMetadata() {
    /* Set the target from the source */
    if (getOdeSolverResultSet() == null) {
        return;
    }
    final HashMap<String, DataSymbolMetadata> auxDataSymbolMap = new HashMap();
    for (ColumnDescription columnDescription : getOdeSolverResultSet().getColumnDescriptions()) {
        if (columnDescription.getName().startsWith("sens_") && columnDescription.getName().contains("_wrt_")) {
            DataSymbolMetadata dataSymbolMetadata = sensitivityMetaDataParser(columnDescription.getName());
            auxDataSymbolMap.put(columnDescription.getName(), dataSymbolMetadata);
        }
    }
    try {
        AsynchClientTask filterCategoriesTask = new AsynchClientTask("Calculating Filter...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                if (ODEDataViewer.this.getSimulationModelInfo() != null) {
                    SimulationModelInfo simulationModelInfo = ODEDataViewer.this.getSimulationModelInfo();
                    simulationModelInfo.getDataSymbolMetadataResolver().populateDataSymbolMetadata(auxDataSymbolMap);
                }
            }
        };
        AsynchClientTask firePropertyChangeTask = new AsynchClientTask("Fire Property Change...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                SimulationModelInfo simulationModelInfo = ODEDataViewer.this.getSimulationModelInfo();
                ODEDataInterfaceImpl oDEDataInterfaceImpl = new ODEDataInterfaceImpl(getVcDataIdentifier(), getOdeSolverResultSet(), simulationModelInfo);
                getODESolverPlotSpecificationPanel1().setMyDataInterface(oDEDataInterfaceImpl);
            // new Thread(new Runnable() {
            // @Override
            // public void run() {
            // while(ClientTaskDispatcher.isBusy()){
            // try{Thread.sleep(200);}catch(Exception e){e.printStackTrace();}
            // }
            // SwingUtilities.invokeLater(new Runnable() {
            // @Override
            // public void run() {
            // ((Window)BeanUtils.findTypeParentOfComponent(ODEDataViewer.this, Window.class)).toFront();
            // }
            // });
            // }
            // }).start();
            }
        };
        ClientTaskDispatcher.dispatch(ODEDataViewer.this, new Hashtable<String, Object>(), new AsynchClientTask[] { filterCategoriesTask, firePropertyChangeTask }, false, false, false, null, true);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 5 with DataSymbolMetadata

use of cbit.vcell.solver.DataSymbolMetadata in project vcell by virtualcell.

the class SimulationWorkspaceModelInfo method addAssignmentRuleParametersToMetaData.

private static void addAssignmentRuleParametersToMetaData(SimulationContext simulationContext, HashMap<String, DataSymbolMetadata> metaDataMap) {
    if (metaDataMap != null && simulationContext.getAssignmentRules() != null) {
        for (AssignmentRule ar : simulationContext.getAssignmentRules()) {
            if (ar.getAssignmentRuleVar() instanceof Model.ModelParameter) {
                Model.ModelParameter mp = (Model.ModelParameter) ar.getAssignmentRuleVar();
                VCUnitDefinition unit = mp.getUnitDefinition();
                String tooltip = "Assignment Rule Variable (ModelParameter), Function";
                DataSymbolMetadata dsmd = new DataSymbolMetadata(BioModelCategoryType.Other, unit, tooltip);
                metaDataMap.put(mp.getName(), dsmd);
            }
        }
    }
}