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

Example 61 with ReactionStep

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

the class BioModelEditorReactionTableModel method computeData.

protected ArrayList<ModelProcess> computeData() {
    ArrayList<ModelProcess> processList = new ArrayList<ModelProcess>();
    if (getModel() != null) {
        ModelProcess[] modelProcesses = getModel().getModelProcesses();
        if (searchText == null || searchText.length() == 0) {
            processList.addAll(Arrays.asList(modelProcesses));
        } else {
            String lowerCaseSearchText = searchText.toLowerCase();
            for (ModelProcess process : modelProcesses) {
                boolean bMatchRelationshipObj = false;
                if (process instanceof ReactionStep) {
                    ReactionStep reactionStep = (ReactionStep) process;
                    HashSet<RelationshipObject> relObjsHash = bioModel.getRelationshipModel().getRelationshipObjects(reactionStep);
                    for (RelationshipObject relObj : relObjsHash) {
                        if (relObj.getBioPaxObject() instanceof Entity) {
                            if (((Entity) relObj.getBioPaxObject()).getName().get(0).toLowerCase().contains(lowerCaseSearchText)) {
                                bMatchRelationshipObj = true;
                                break;
                            }
                        }
                    }
                }
                if (bMatchRelationshipObj || process.containsSearchText(lowerCaseSearchText)) {
                    if (!processList.contains(process)) {
                        processList.add(process);
                    }
                }
                if (process instanceof ReactionStep) {
                    // we also search in reaction step expression, for strings like "s1 + s2" or s1 -> s2
                    ModelProcessEquation mpe = new ModelProcessEquation(process, bioModel.getModel());
                    if (mpe.toString().toLowerCase().contains(lowerCaseSearchText)) {
                        if (!processList.contains(process)) {
                            processList.add(process);
                        }
                    }
                }
            }
        }
    }
    return processList;
}

Example 62 with ReactionStep

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

the class BioModelParametersTableModel method bioModelChange.

@Override
protected void bioModelChange(PropertyChangeEvent evt) {
    super.bioModelChange(evt);
    BioModel oldValue = (BioModel) evt.getOldValue();
    if (oldValue != null) {
        for (EditableSymbolTableEntry parameter : oldValue.getModel().getModelParameters()) {
            parameter.removePropertyChangeListener(this);
        }
        for (SpeciesContext sc : oldValue.getModel().getSpeciesContexts()) {
            sc.removePropertyChangeListener(this);
        }
        for (ReactionStep reactionStep : oldValue.getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            Kinetics kinetics = reactionStep.getKinetics();
            kinetics.removePropertyChangeListener(this);
            for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
                kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
            for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
                proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
            for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
                unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
        }
        for (SimulationContext simulationContext : oldValue.getSimulationContexts()) {
            simulationContext.removePropertyChangeListener(this);
            simulationContext.getGeometryContext().removePropertyChangeListener(this);
            for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                mapping.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            simulationContext.getReactionContext().removePropertyChangeListener(this);
            for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                spec.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                elect.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                spatialObject.removePropertyChangeListener(this);
            }
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                spatialProcess.removePropertyChangeListener(this);
                for (LocalParameter p : spatialProcess.getParameters()) {
                    p.removePropertyChangeListener(this);
                }
            }
            for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                p.removePropertyChangeListener(this);
            }
        }
    }
    BioModel newValue = (BioModel) evt.getNewValue();
    if (newValue != null) {
        for (ModelParameter modelEditableSymbolTableEntry : newValue.getModel().getModelParameters()) {
            modelEditableSymbolTableEntry.addPropertyChangeListener(this);
        }
        for (SpeciesContext sc : newValue.getModel().getSpeciesContexts()) {
            sc.addPropertyChangeListener(this);
        }
        for (ReactionStep reactionStep : newValue.getModel().getReactionSteps()) {
            reactionStep.addPropertyChangeListener(this);
            Kinetics kinetics = reactionStep.getKinetics();
            kinetics.addPropertyChangeListener(this);
            for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
                kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
            for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
                proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
            for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
                unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
        }
        for (SimulationContext simulationContext : newValue.getSimulationContexts()) {
            simulationContext.addPropertyChangeListener(this);
            simulationContext.getGeometryContext().addPropertyChangeListener(this);
            for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                mapping.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            simulationContext.getReactionContext().addPropertyChangeListener(this);
            for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                spec.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                elect.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                spatialObject.addPropertyChangeListener(this);
            }
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                spatialProcess.addPropertyChangeListener(this);
                for (LocalParameter p : spatialProcess.getParameters()) {
                    p.addPropertyChangeListener(this);
                }
            }
            for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                p.addPropertyChangeListener(this);
            }
        }
    }
}

Example 63 with ReactionStep

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

the class AnnotationsPanel method changeTextAnnotation.

private void changeTextAnnotation() {
    try {
        if (bioModel == null || selectedObject == null) {
            return;
        }
        Identifiable entity = getIdentifiable(selectedObject);
        String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length() == 0 ? null : annotationTextArea.getText());
        String oldText = bioModel.getVCMetaData().getFreeTextAnnotation(entity);
        if (textAreaStr == null || textAreaStr.isEmpty() || emptyHtmlText.equals(textAreaStr)) {
            // no annotation now, the field is empty
            // delete, if there's something previously saved
            bioModel.getVCMetaData().deleteFreeTextAnnotation(entity);
            if (selectedObject instanceof ReactionStep) {
                // we tell ReactionPropertiesPanel to refresh the annotation icon
                ((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
            }
        } else if (!Compare.isEqualOrNull(oldText, textAreaStr)) {
            // some text annotation different from what's already saved
            // overwrite
            bioModel.getVCMetaData().setFreeTextAnnotation(entity, textAreaStr);
            if (selectedObject instanceof ReactionStep) {
                // we tell ReactionPropertiesPanel to refresh the text annotation icon
                ((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Annotation Error\n" + e.getMessage(), e);
    }
}

Example 64 with ReactionStep

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

the class AnnotationsPanel method removeIdentifier.

private void removeIdentifier() {
    Object treeNode = jTreeMIRIAM.getLastSelectedPathComponent();
    if (treeNode instanceof LinkNode) {
        LinkNode linkNode = (LinkNode) treeNode;
        MiriamResource resourceToDelete = linkNode.getMiriamResource();
        Identifiable entity = getIdentifiable(selectedObject);
        // Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = vcMetaData.getMiriamManager().getAllMiriamRefGroups(entity);
        MiriamManager mm = vcMetaData.getMiriamManager();
        Map<MiriamRefGroup, MIRIAMQualifier> refGroupsToRemove = mm.getMiriamTreeMap().get(entity);
        boolean found = false;
        for (MiriamRefGroup refGroup : refGroupsToRemove.keySet()) {
            MIRIAMQualifier qualifier = refGroupsToRemove.get(refGroup);
            for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
                if (!isEqual(miriamResource, resourceToDelete)) {
                    continue;
                }
                try {
                    // remove the ref group for this resource
                    mm.remove2(entity, qualifier, refGroup);
                    System.out.println(vcMetaData.printRdfStatements());
                    found = true;
                    break;
                } catch (URNParseFailureException e) {
                    e.printStackTrace(System.out);
                }
            }
            if (found == true) {
                updateInterface();
                if (selectedObject instanceof ReactionStep) {
                    ((ReactionStep) selectedObject).firePropertyChange("addIdentifier", true, false);
                }
                break;
            }
        }
    }
}

Example 65 with ReactionStep

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

the class AnnotationsPanel method removeText.

private void removeText() {
    if (bioModel == null || selectedObject == null) {
        return;
    }
    Identifiable entity = getIdentifiable(selectedObject);
    annotationTextArea.setText(null);
    // delete, if there's something previously saved
    bioModel.getVCMetaData().deleteFreeTextAnnotation(entity);
    if (selectedObject instanceof ReactionStep) {
        ((ReactionStep) selectedObject).firePropertyChange("addIdentifier", false, true);
    }
}