Examples with SpatialProcess cbit.vcell.mapping.spatial.processes.SpatialProcess used on opensource projects

Example 11 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class SpatialProcessDisplayPanel method getFreeSurfaceRegionObject.

private SurfaceRegionObject getFreeSurfaceRegionObject() {
    for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
        if (spatialObject instanceof SurfaceRegionObject) {
            SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) spatialObject;
            boolean bSurfaceRegionObjectFree = true;
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                if (spatialProcess.getSpatialObjects().contains(surfaceRegionObject)) {
                    bSurfaceRegionObjectFree = false;
                    break;
                }
            }
            if (bSurfaceRegionObjectFree) {
                return surfaceRegionObject;
            }
        }
    }
    return null;
}

Example 12 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class SpatialProcessDisplayPanel method getOrCreateNextPointObject.

private PointObject getOrCreateNextPointObject() {
    for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
        if (spatialObject instanceof PointObject) {
            PointObject pointObject = (PointObject) spatialObject;
            boolean bPointObjectFree = true;
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                if (spatialProcess.getSpatialObjects().contains(pointObject)) {
                    bPointObjectFree = false;
                    break;
                }
            }
            if (bPointObjectFree) {
                return pointObject;
            }
        }
    }
    return simulationContext.createPointObject();
}

Example 13 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class SpatialProcessDisplayPanel method getFreeVolumeRegionObject.

private VolumeRegionObject getFreeVolumeRegionObject() {
    for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
        if (spatialObject instanceof VolumeRegionObject) {
            VolumeRegionObject volumeRegionObject = (VolumeRegionObject) spatialObject;
            boolean bVolumeRegionObjectFree = true;
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                if (spatialProcess.getSpatialObjects().contains(volumeRegionObject)) {
                    bVolumeRegionObjectFree = false;
                    break;
                }
            }
            if (bVolumeRegionObjectFree) {
                return volumeRegionObject;
            }
        }
    }
    return null;
}

Example 14 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    JComponent bottomComponent = rightBottomEmptyPanel;
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        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 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 || 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;
            }
        }
    }
    if (bShowPathway) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            if (rightBottomTabbedPane.getComponentAt(destComponentIndex) == 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);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightSplitPane.repaint();
    }
    if (rightBottomTabbedPane.getSelectedComponent() != bottomComponent) {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 15 with SpatialProcess

use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.

the class SpatialProcessParameterTableModel method setSpatialProcess.

/**
 * Sets the speciesContextSpec property (cbit.vcell.mapping.SpeciesContextSpec) value.
 * @param speciesContextSpec The new value for the property.
 * @see #getSpeciesContextSpec
 */
public void setSpatialProcess(SpatialProcess spatialProcess) {
    SpatialProcess oldValue = this.spatialProcess;
    this.spatialProcess = spatialProcess;
    firePropertyChange(PROPERTY_NAME_SPATIALPROCESS, oldValue, spatialProcess);
}