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

Example 11 with ReactionStep

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

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    // TODO: here
    JComponent bottomComponent = rightBottomEmptyPanel;
    JComponent annotationComponent = rightBottomEmptyAnnotationsPanel;
    // properties panel
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    // annotations panel
    int annComponentIndex = DocumentEditorTabID.annotations.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        annotationComponent = getAnnotationsPanel();
        Object singleSelection = selections[0];
        if (singleSelection instanceof ReactionStep) {
            bottomComponent = getReactionPropertiesPanel();
        } else if (singleSelection instanceof ReactionRule) {
            bottomComponent = getReactionRulePropertiesPanel();
        } else if (singleSelection instanceof SpeciesContext) {
            bottomComponent = getSpeciesPropertiesPanel();
        } else if (singleSelection instanceof MolecularType) {
            bottomComponent = getMolecularTypePropertiesPanel();
        } else if (singleSelection instanceof RbmObservable) {
            bottomComponent = getObservablePropertiesPanel();
        } else if (singleSelection instanceof Structure) {
            bottomComponent = getStructurePropertiesPanel();
            getStructurePropertiesPanel().setModel(bioModel.getModel());
        } else if (singleSelection instanceof Parameter) {
            bottomComponent = getParameterPropertiesPanel();
        } else if (singleSelection instanceof SimulationContext) {
            bottomComponent = getApplicationPropertiesPanel();
        } else if (singleSelection instanceof ParameterEstimationTask) {
            bottomComponent = parameterEstimationTaskPropertiesPanel;
        } else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
            bottomComponent = getReactionParticipantPropertiesPanel();
        } else if (singleSelection instanceof BioModelNode.PublicationInfoNode) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof BioModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof MathModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = mathModelMetaDataPanel;
        } else if (singleSelection instanceof GeometryInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = geometryMetaDataPanel;
        } else if (singleSelection instanceof SpeciesContextSpec) {
            bottomComponent = getSpeciesContextSpecPanel();
        } else if (singleSelection instanceof ReactionSpec) {
            bottomComponent = getKineticsTypeTemplatePanel();
        } else if (singleSelection instanceof ReactionRuleSpec) {
            // 
            bottomComponent = getReactionRuleSpecPropertiesPanel();
        } else if (singleSelection instanceof BioModelsNetModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = getBioModelsNetPropertiesPanel();
        } else if (singleSelection instanceof Simulation) {
            bottomComponent = getSimulationSummaryPanel();
        } else if (singleSelection instanceof DataSymbol) {
            bottomComponent = getDataSymbolsSpecPanel();
        } else if (singleSelection instanceof BioEvent) {
            bottomComponent = getEventPanel();
        } else if (singleSelection instanceof SpatialObject) {
            bottomComponent = getSpatialObjectPropertyPanel();
        } else if (singleSelection instanceof SpatialProcess) {
            bottomComponent = getSpatialProcessPropertyPanel();
        } else if (singleSelection instanceof BioPaxObject) {
            bottomComponent = bioPaxObjectPropertiesPanel;
        } else if (singleSelection instanceof BioModel) {
            // only contains Notes, is displayed in the Object Properties Panel
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof VCMetaData) {
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof PathwayData) {
            bShowPathway = true;
            bottomComponent = getBioModelEditorPathwayPanel();
        } else if (singleSelection instanceof Model) {
        } else if (singleSelection instanceof RuleParticipantSignature) {
            bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
        } else if (singleSelection instanceof CSGObject) {
            bottomComponent = csgObjectPropertiesPanel;
            csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
        } else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
            DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
            if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionPropertiesPanel();
            } else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionRulePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
                bottomComponent = getStructurePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
                bottomComponent = getObservablePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bottomComponent = getApplicationsPropertiesPanel();
                getApplicationsPropertiesPanel().setBioModel(bioModel);
            } else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
                bottomComponent = parameterEstimationTaskPropertiesPanel;
            }
        } else if (singleSelection instanceof SelectionManager.AnnotationNavigator) {
            Object entity = ((SelectionManager.AnnotationNavigator) singleSelection).getEntity();
            if (entity instanceof ReactionStep) {
                bottomComponent = getReactionPropertiesPanel();
            } else if (entity instanceof SpeciesContext) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (entity instanceof Structure) {
                // Observables. MolecularType, Structures
                bottomComponent = getStructurePropertiesPanel();
            } else if (entity instanceof MolecularType) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (entity instanceof RbmObservable) {
                bottomComponent = getObservablePropertiesPanel();
            } else {
                bottomComponent = bioModelEditorAnnotationPanel;
            }
        }
    }
    if (bShowPathway) {
        int numTabs = rightBottomTabbedPane.getTabCount();
        for (destComponentIndex = 0; destComponentIndex < numTabs; destComponentIndex++) {
            Component current = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (current == bottomComponent) {
                break;
            }
        }
        String tabTitle = "Pathway Preview";
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
        }
    } else if (bShowInDatabaseProperties) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
                break;
            }
        }
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
        }
    }
    if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
        bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        annotationComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightBottomTabbedPane.setComponentAt(annComponentIndex, annotationComponent);
        rightSplitPane.repaint();
    }
    Component selectedComponent = rightBottomTabbedPane.getSelectedComponent();
    if (selections.length == 1 && selections[0] instanceof BioModel && bottomComponent instanceof BioModelEditorAnnotationPanel) {
        // if the biomodel name is selected in the upper left tree, we select the Annotations tab
        rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    } else if (selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && selections[0] instanceof SelectionManager.AnnotationNavigator) {
        // we want to navigate to the AnnotationPanel
        rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    // } else if(selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && bottomComponent instanceof BioModelEditorAnnotationPanel) {
    // // we want to navigate to the AnnotationPanel (old way)
    // rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    } else if (selectedComponent != bottomComponent) /* && rightBottomTabbedPane.getSelectedComponent() != annotationComponent */
    {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 12 with ReactionStep

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

the class BioModelEditorReactionTableModel method setValueAt.

public void setValueAt(Object value, int row, int column) {
    if (getModel() == null || value == null) {
        return;
    }
    try {
        ModelProcess modelProcess = getValueAt(row);
        if (modelProcess != null) {
            switch(column) {
                case COLUMN_NAME:
                    {
                        String inputValue = ((String) value);
                        inputValue = inputValue.trim();
                        modelProcess.setName(inputValue);
                        break;
                    }
                case COLUMN_EQUATION:
                    {
                        String inputValue = (String) value;
                        inputValue = inputValue.trim();
                        if (modelProcess instanceof ReactionStep) {
                            ReactionStep reactionStep = (ReactionStep) modelProcess;
                            ReactionParticipant[] rpArray = ModelProcessEquation.parseReaction(reactionStep, getModel(), inputValue);
                            for (ReactionParticipant rp : rpArray) {
                                SpeciesContext speciesContext = rp.getSpeciesContext();
                                if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
                                    bioModel.getModel().addSpecies(speciesContext.getSpecies());
                                    bioModel.getModel().addSpeciesContext(speciesContext);
                                }
                            }
                            reactionStep.setReactionParticipants(rpArray);
                        } else if (modelProcess instanceof ReactionRule) {
                            ReactionRule oldReactionRule = (ReactionRule) modelProcess;
                            // when editing an existing reaction rule
                            ReactionRule newReactionRule = (ReactionRule) RbmUtils.parseReactionRule(inputValue, oldReactionRule.getStructure(), bioModel);
                            if (newReactionRule != null) {
                                oldReactionRule.setProductPatterns(newReactionRule.getProductPatterns(), false, false);
                                oldReactionRule.setReactantPatterns(newReactionRule.getReactantPatterns(), false, false);
                            // String name = oldReactionRule.getName();
                            // RbmKineticLaw kl = oldReactionRule.getKineticLaw();
                            // Structure st = oldReactionRule.getStructure();
                            // getModel().getRbmModelContainer().removeReactionRule(oldReactionRule);
                            // newReactionRule.setName(name);
                            // newReactionRule.setKineticLaw(kl);
                            // newReactionRule.setStructure(st);
                            // getModel().getRbmModelContainer().addReactionRule(newReactionRule);
                            }
                        }
                        break;
                    }
                case COLUMN_STRUCTURE:
                    {
                        Structure s = (Structure) value;
                        modelProcess.setStructure(s);
                        break;
                    }
            }
        } else {
            switch(column) {
                case COLUMN_EQUATION:
                    {
                        if (getModel().getNumStructures() == 1) {
                            String inputValue = ((String) value);
                            inputValue = inputValue.trim();
                            if (inputValue.contains("(") && inputValue.contains(")")) {
                                ReactionRule reactionRule = (ReactionRule) RbmUtils.parseReactionRule(inputValue, getModel().getStructure(0), bioModel);
                                getModel().getRbmModelContainer().addReactionRule(reactionRule);
                            } else {
                                if (BioModelEditorRightSideTableModel.ADD_NEW_HERE_REACTION_TEXT.equals(inputValue)) {
                                    return;
                                }
                                ReactionStep reactionStep = getModel().createSimpleReaction(getModel().getStructure(0));
                                ReactionParticipant[] rpArray = ModelProcessEquation.parseReaction(reactionStep, getModel(), inputValue);
                                for (ReactionParticipant rp : rpArray) {
                                    SpeciesContext speciesContext = rp.getSpeciesContext();
                                    if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
                                        bioModel.getModel().addSpecies(speciesContext.getSpecies());
                                        bioModel.getModel().addSpeciesContext(speciesContext);
                                    }
                                }
                                reactionStep.setReactionParticipants(rpArray);
                            }
                        }
                        break;
                    }
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(ownerTable, e.getMessage(), e);
    }
}

Example 13 with ReactionStep

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

the class BioModelEditorReactionTableModel method propertyChange.

// public boolean isCellEditable(int row, int column) {
// if (bioModel == null) {
// return false;
// }
// ModelProcess process = getValueAt(row);
// if (column == COLUMN_NAME && process != null) {
// return true;
// }
// if (column == COLUMN_EQUATION) {
// //			if(bioModel.getModel().getNumStructures() != 1) {
// //				return false;
// //			}
// Object o = getValueAt(row);
// if(o instanceof ReactionRule) {
// ReactionRule rr = (ReactionRule)o;
// final List<ReactantPattern> rpList = rr.getReactantPatterns();
// for(ReactantPattern rp : rpList) {
// final List<MolecularTypePattern> mtpList = rp.getSpeciesPattern().getMolecularTypePatterns();
// for(MolecularTypePattern mtp : mtpList) {
// MolecularType mt = mtp.getMolecularType();
// if(mt.getComponentList().size() != 0) {
// return false;
// }
// }
// }
// final List<ProductPattern> ppList = rr.getProductPatterns();
// for(ProductPattern pp : ppList) {
// final List<MolecularTypePattern> mtpList = pp.getSpeciesPattern().getMolecularTypePatterns();
// for(MolecularTypePattern mtp : mtpList) {
// MolecularType mt = mtp.getMolecularType();
// if(mt.getComponentList().size() != 0) {
// return false;
// }
// }
// }
// }
// return true;
// }
// return false;
// }
@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    super.propertyChange(evt);
    if (evt.getSource() == bioModel.getModel()) {
        if (evt.getPropertyName().equals(Model.PROPERTY_NAME_STRUCTURES)) {
        // updateStructureComboBox();
        } else if (evt.getPropertyName().equals(Model.PROPERTY_NAME_REACTION_STEPS)) {
            ReactionStep[] oldValue = (ReactionStep[]) evt.getOldValue();
            if (oldValue != null) {
                for (ReactionStep rs : oldValue) {
                    rs.removePropertyChangeListener(this);
                }
            }
            ReactionStep[] newValue = (ReactionStep[]) evt.getNewValue();
            if (newValue != null) {
                for (ReactionStep rs : newValue) {
                    rs.addPropertyChangeListener(this);
                }
            }
            refreshData();
        }
    } else if (evt.getSource() instanceof ReactionStep) {
        ReactionStep reactionStep = (ReactionStep) evt.getSource();
        int changeRow = getRowIndex(reactionStep);
        if (changeRow >= 0) {
            fireTableRowsUpdated(changeRow, changeRow);
        }
    }
    // if (evt.getSource() == bioModel.getModel().getRbmModelContainer()) {
    if (evt.getSource() == bioModel.getModel()) {
        if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST)) {
            List<ReactionRule> oldValue = (List<ReactionRule>) evt.getOldValue();
            if (oldValue != null) {
                for (ReactionRule rs : oldValue) {
                    rs.removePropertyChangeListener(this);
                }
            }
            List<ReactionRule> newValue = (List<ReactionRule>) evt.getNewValue();
            if (newValue != null) {
                for (ReactionRule rs : newValue) {
                    rs.addPropertyChangeListener(this);
                }
            }
            refreshData();
        }
    } else if (evt.getSource() instanceof ReactionRule) {
        ReactionRule reactionRule = (ReactionRule) evt.getSource();
        int changeRow = getRowIndex(reactionRule);
        if (changeRow >= 0) {
            fireTableRowsUpdated(changeRow, changeRow);
        }
    }
}

Example 14 with ReactionStep

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

the class AnnotationsPanel method addIdentifier.

// -------------------------------------------------------------------------------------------------------
private void addIdentifier() {
    if (PopupGenerator.showComponentOKCancelDialog(AnnotationsPanel.this, getJPanelNewIdentifier(), "Define New Formal Identifier") != JOptionPane.OK_OPTION) {
        return;
    }
    MIRIAMQualifier qualifier = (MIRIAMQualifier) getJComboBoxQualifier().getSelectedItem();
    MiriamManager.DataType objectNamespace = (MiriamManager.DataType) getJComboBoxURI().getSelectedItem();
    String objectID = getJTextFieldFormalID().getText();
    if (objectID.compareTo("NewID") == 0) {
        return;
    }
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    HashSet<MiriamResource> miriamResources = new HashSet<MiriamResource>();
    try {
        Identifiable entity = getIdentifiable(selectedObject);
        MiriamResource mr = miriamManager.createMiriamResource(objectNamespace.getBaseURN() + ":" + objectID);
        miriamResources.add(mr);
        miriamManager.addMiriamRefGroup(entity, qualifier, miriamResources);
        // System.out.println(vcMetaData.printRdfStatements());
        updateInterface();
        if (selectedObject instanceof ReactionStep) {
            // we tell ReactionPropertiesPanel to refresh the annotation icon
            ((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
        }
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, "Add Identifier failed:\n" + e.getMessage(), e);
    }
}

Example 15 with ReactionStep

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

the class VCellCopyPasteHelper method chooseApplyPaste.

/**
 * Insert the method's description here.
 * Creation date: (7/10/2006 11:05:19 AM)
 */
public static void chooseApplyPaste(Component requester, String[] pasteDetails, Parameter[] changingParamters, Expression[] newParameterExpression) {
    if (pasteDetails.length != changingParamters.length || changingParamters.length != newParameterExpression.length) {
        throw new IllegalArgumentException(VCellCopyPasteHelper.class.getName() + ".chooseApplyPaste(...) arguments must have unequal lengths");
    }
    // Only present things that will actually change
    boolean bAtLeatOneDifferent = false;
    boolean[] bEnableDisplay = new boolean[changingParamters.length];
    for (int i = 0; i < changingParamters.length; i += 1) {
        // bEnableDisplay[i] = !changingParamters[i].getExpression().equals(newParameterExpression[i]);
        bEnableDisplay[i] = !Compare.isEqualOrNull(changingParamters[i].getExpression(), newParameterExpression[i]);
        bAtLeatOneDifferent = bAtLeatOneDifferent || bEnableDisplay[i];
    }
    if (!bAtLeatOneDifferent) {
        PopupGenerator.showInfoDialog(requester, "All valid paste values are equal to the destination values.\nNo paste needed.");
        return;
    }
    boolean[] bChoices = showChoices(requester, pasteDetails, bEnableDisplay);
    if (bChoices != null) {
        StringBuffer statusMessages = new StringBuffer();
        boolean bFailure = false;
        for (int i = 0; i < changingParamters.length; i += 1) {
            try {
                if (bChoices[i]) {
                    if (changingParamters[i] instanceof Kinetics.KineticsParameter) {
                        Kinetics kinetics = ((ReactionStep) changingParamters[i].getNameScope().getScopedSymbolTable()).getKinetics();
                        kinetics.setParameterValue((Kinetics.KineticsParameter) changingParamters[i], newParameterExpression[i]);
                    } else {
                        throw new Exception("Changing " + changingParamters[i].getNameScope().getName() + " " + changingParamters[i].getName() + " not yet implemented");
                    }
                }
                statusMessages.append("(OK) " + pasteDetails + "\n");
            } catch (Exception e) {
                bFailure = true;
                statusMessages.append("(Failed) " + pasteDetails + " " + e.getMessage() + " " + e.getClass().getName() + "\n");
            }
        }
        if (bFailure) {
            PopupGenerator.showErrorDialog(requester, "Paste Results:\n" + statusMessages.toString());
        }
    }
}