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

Example 1 with ModelProcessSpec

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

the class ModelProcessSpecsPanel 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
    this.addPropertyChangeListener(ivjEventHandler);
    getScrollPaneTable().setModel(getModelProcessSpecsTableModel());
    getScrollPaneTable().setDefaultRenderer(ModelProcess.class, new DefaultScrollTableCellRenderer() {

        public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
            super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
            defaultToolTipText = null;
            if (value instanceof ModelProcess) {
                setText(((ModelProcess) value).getName());
                defaultToolTipText = getText();
                setToolTipText(defaultToolTipText);
            }
            TableModel tableModel = table.getModel();
            if (tableModel instanceof SortTableModel) {
                DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
            }
            return this;
        }
    });
    DefaultScrollTableCellRenderer rbmReactionShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

        List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();

        SpeciesPatternSmallShape spss = null;

        @Override
        public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
            super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
            if (table.getModel() instanceof VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == ivjModelProcessSpecsTableModel) {
                    selectedObject = ivjModelProcessSpecsTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ModelProcessSpec) {
                        ModelProcessSpec mps = (ModelProcessSpec) selectedObject;
                        ModelProcess mp = (ModelProcess) mps.getModelProcess();
                        if (mp instanceof ReactionRule) {
                            ReactionRule rr = (ReactionRule) mp;
                            Graphics panelContext = table.getGraphics();
                            spssList.clear();
                            List<ReactantPattern> rpList = rr.getReactantPatterns();
                            int xPos = 4;
                            for (int i = 0; i < rpList.size(); i++) {
                                SpeciesPattern sp = rr.getReactantPattern(i).getSpeciesPattern();
                                spss = new SpeciesPatternSmallShape(xPos, 2, sp, shapeManager, panelContext, rr, isSelected, issueManager);
                                if (i < rpList.size() - 1) {
                                    spss.addEndText("+");
                                } else {
                                    if (rr.isReversible()) {
                                        spss.addEndText("<->");
                                        xPos += 7;
                                    } else {
                                        spss.addEndText("->");
                                    }
                                }
                                xPos += spss.getWidth() + 15;
                                spssList.add(spss);
                            }
                            List<ProductPattern> ppList = rr.getProductPatterns();
                            xPos += 7;
                            for (int i = 0; i < ppList.size(); i++) {
                                SpeciesPattern sp = rr.getProductPattern(i).getSpeciesPattern();
                                spss = new SpeciesPatternSmallShape(xPos, 2, sp, shapeManager, panelContext, rr, isSelected, issueManager);
                                if (i < ppList.size() - 1) {
                                    spss.addEndText("+");
                                }
                                xPos += spss.getWidth() + 15;
                                spssList.add(spss);
                            }
                        } else {
                            ReactionStep rs = (ReactionStep) mp;
                            Graphics panelContext = table.getGraphics();
                            spssList.clear();
                            int xPos = 4;
                            int extraSpace = 0;
                            for (int i = 0; i < rs.getNumReactants(); i++) {
                                SpeciesPattern sp = rs.getReactant(i).getSpeciesContext().getSpeciesPattern();
                                spss = new SpeciesPatternSmallShape(xPos, 2, sp, shapeManager, panelContext, rs, isSelected, issueManager);
                                if (i < rs.getNumReactants() - 1) {
                                    spss.addEndText("+");
                                } else {
                                    if (rs.isReversible()) {
                                        spss.addEndText("<->");
                                        extraSpace += 7;
                                    } else {
                                        spss.addEndText("->");
                                    }
                                }
                                int offset = sp == null ? 17 : 15;
                                offset += extraSpace;
                                int w = spss.getWidth();
                                xPos += w + offset;
                                spssList.add(spss);
                            }
                            xPos += 8;
                            for (int i = 0; i < rs.getNumProducts(); i++) {
                                SpeciesPattern sp = rs.getProduct(i).getSpeciesContext().getSpeciesPattern();
                                if (i == 0 && rs.getNumReactants() == 0) {
                                    xPos += 14;
                                }
                                spss = new SpeciesPatternSmallShape(xPos, 2, sp, shapeManager, panelContext, rs, isSelected, issueManager);
                                if (i == 0 && rs.getNumReactants() == 0) {
                                    spss.addStartText("->");
                                }
                                if (i < rs.getNumProducts() - 1) {
                                    spss.addEndText("+");
                                }
                                int offset = sp == null ? 17 : 15;
                                int w = spss.getWidth();
                                xPos += w + offset;
                                spssList.add(spss);
                            }
                        }
                    }
                } else {
                    spssList.clear();
                }
            }
            setText("");
            return this;
        }

        @Override
        public void paintComponent(Graphics g) {
            super.paintComponent(g);
            for (SpeciesPatternSmallShape spss : spssList) {
                if (spss == null) {
                    continue;
                }
                spss.paintSelf(g);
            }
        }
    };
    getScrollPaneTable().setDefaultRenderer(SpeciesPattern.class, rbmReactionShapeDepictionCellRenderer);
    // ivjScrollPaneTable.getColumnModel().getColumn(ModelProcessSpecsTableModel.ColumnType.COLUMN_DEPICTION.ordinal()).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
    // ivjScrollPaneTable.getColumnModel().getColumn(ModelProcessSpecsTableModel.ColumnType.COLUMN_DEPICTION.ordinal()).setPreferredWidth(180);
    getScrollPaneTable().getSelectionModel().addListSelectionListener(ivjEventHandler);
}

Example 2 with ModelProcessSpec

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

the class ModelProcessSpecsTableModel method getValueAt.

/**
 * getValueAt method comment.
 */
public Object getValueAt(int row, int col) {
    ModelProcessSpec modelProcessSpec = getValueAt(row);
    ColumnType columnType = columns.get(col);
    switch(columnType) {
        case COLUMN_NAME:
            {
                return modelProcessSpec.getModelProcess();
            }
        case COLUMN_TYPE:
            {
                return modelProcessSpec.getModelProcess().getDisplayType();
            }
        case COLUMN_ENABLED:
            {
                return new Boolean(!modelProcessSpec.isExcluded());
            }
        case COLUMN_FAST:
            {
                if (!(modelProcessSpec.getModelProcess() instanceof SimpleReaction)) {
                    return new Boolean(false);
                } else {
                    return new Boolean(modelProcessSpec.isFast());
                }
            }
        default:
            {
                return null;
            }
    }
}

Example 3 with ModelProcessSpec

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

the class ModelProcessSpecsTableModel method computeData.

protected List<ModelProcessSpec> computeData() {
    ArrayList<ModelProcessSpec> allParameterList = new ArrayList<ModelProcessSpec>();
    if (getSimulationContext() != null) {
        allParameterList.addAll(Arrays.asList(getSimulationContext().getReactionContext().getReactionSpecs()));
        allParameterList.addAll(Arrays.asList(getSimulationContext().getReactionContext().getReactionRuleSpecs()));
    } else {
        return null;
    }
    boolean bSearchInactive = searchText == null || searchText.length() == 0;
    if (bSearchInactive) {
        return allParameterList;
    }
    String lowerCaseSearchText = bSearchInactive ? null : searchText.toLowerCase();
    ArrayList<ModelProcessSpec> parameterList = new ArrayList<ModelProcessSpec>();
    for (ModelProcessSpec parameter : allParameterList) {
        if (bSearchInactive || parameter.getModelProcess().getName().toLowerCase().contains(lowerCaseSearchText) || parameter.getModelProcess().getStructure().getName().toLowerCase().contains(lowerCaseSearchText)) /*|| parameter.getNameScope().getPathDescription().toLowerCase().contains(lowerCaseSearchText)
				|| parameter.getName().toLowerCase().contains(lowerCaseSearchText)
				|| parameter.getExpression() != null && parameter.getExpression().infix().toLowerCase().contains(lowerCaseSearchText)
				|| parameter.getDescription().toLowerCase().contains(lowerCaseSearchText)*/
        {
            parameterList.add(parameter);
        }
    }
    return parameterList;
}

Example 4 with ModelProcessSpec

use of cbit.vcell.mapping.ModelProcessSpec 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);
    }
}