support for local field data and SBML I/O in libvcell

vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java

@@ -633,7 +633,7 @@ public XmlTreeDiff compareWithSaved(VCDocument document) {
 	public XmlTreeDiff compareApplications(BioModel bioModel, String appName1, String appName2) throws Exception {
 
 		// clone BioModel as bioModel1 and remove all but appName1
-		BioModel bioModel1 = (BioModel) BeanUtils.cloneSerializable(bioModel);
+		BioModel bioModel1 = XmlHelper.cloneBioModel(bioModel);
 		bioModel1.refreshDependencies();
 		SimulationContext[] allSimContexts1 = bioModel1.getSimulationContexts();
 		for (SimulationContext sc : allSimContexts1) {
@@ -643,7 +643,7 @@ public XmlTreeDiff compareApplications(BioModel bioModel, String appName1, Strin
 		}
 
 		// clone BioModel as bioModel2 and remove all but appName2
-		BioModel bioModel2 = (BioModel) BeanUtils.cloneSerializable(bioModel);
+		BioModel bioModel2 = XmlHelper.cloneBioModel(bioModel);
 		bioModel2.refreshDependencies();
 		SimulationContext[] allSimContexts2 = bioModel2.getSimulationContexts();
 		for (SimulationContext sc : allSimContexts2) {

vcell-client/src/main/java/cbit/vcell/client/task/RunSims.java

@@ -14,6 +14,7 @@
 import java.util.Vector;
 
 import cbit.vcell.solver.*;
+import cbit.vcell.xml.XmlHelper;
 import org.vcell.util.*;
 import org.vcell.util.document.VCDocument;
 import org.vcell.util.gui.DialogUtils;
@@ -197,7 +198,7 @@ public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception
 						int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
 						int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
 						if (defaultTotalVolumeElements > newTotalVolumeElements) { // coarser
-							Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
+							Geometry resampledGeometry = XmlHelper.cloneGeometry(mathGeometry);
 							GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
 							geoSurfaceDesc.setVolumeSampleSize(newSize);
 							geoSurfaceDesc.updateAll();

vcell-client/src/main/java/cbit/vcell/geometry/gui/SurfaceViewer.java

@@ -550,7 +550,7 @@ private cbit.vcell.geometry.surface.SurfaceCollection getCentroidSurface(cbit.vc
 		cbit.vcell.geometry.surface.OrigSurface quadSurface = (cbit.vcell.geometry.surface.OrigSurface)quadSurfaceCollection.getSurfaces(0);
 		cbit.vcell.geometry.surface.OrigSurface quadSurfaceCopy = null;
 		try {
-			quadSurfaceCopy = (cbit.vcell.geometry.surface.OrigSurface)org.vcell.util.BeanUtils.cloneSerializable(quadSurface);
+			quadSurfaceCopy = quadSurface.deepClone();
 		}catch (Throwable e){
 			e.printStackTrace(System.out);
 			throw new RuntimeException(e.getMessage());

vcell-client/src/main/java/cbit/vcell/graph/gui/BioCartoonTool.java

@@ -9,78 +9,38 @@
  */
 
 package cbit.vcell.graph.gui;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Window;
-import java.beans.PropertyVetoException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JComboBox;
-import javax.swing.JOptionPane;
-import javax.swing.JTextField;
-
-import org.vcell.model.rbm.MolecularType;
-import org.vcell.model.rbm.RbmNetworkGenerator.CompartmentMode;
-import org.vcell.model.rbm.RbmUtils;
-import org.vcell.model.rbm.SpeciesPattern;
-import org.vcell.util.BeanUtils;
-import org.vcell.util.CommentStringTokenizer;
-import org.vcell.util.Compare;
-import org.vcell.util.Issue;
-import org.vcell.util.Issue.IssueCategory;
-import org.vcell.util.IssueContext;
-import org.vcell.util.IssueContext.ContextType;
-import org.vcell.util.document.KeyValue;
-import org.vcell.util.TokenMangler;
-import org.vcell.util.UserCancelException;
-import org.vcell.util.gui.DialogUtils;
 
 import cbit.gui.graph.gui.GraphPane;
 import cbit.vcell.client.task.AsynchClientTask;
 import cbit.vcell.client.task.ClientTaskDispatcher;
 import cbit.vcell.clientdb.DocumentManager;
-import cbit.vcell.model.BioModelEntityObject;
-import cbit.vcell.model.Catalyst;
-import cbit.vcell.model.Feature;
-import cbit.vcell.model.FluxReaction;
-import cbit.vcell.model.Kinetics;
+import cbit.vcell.model.*;
 import cbit.vcell.model.Kinetics.KineticsParameter;
 import cbit.vcell.model.Kinetics.KineticsProxyParameter;
-import cbit.vcell.model.KineticsDescription;
-import cbit.vcell.model.Membrane;
 import cbit.vcell.model.Membrane.MembraneVoltage;
-import cbit.vcell.model.Model;
 import cbit.vcell.model.Model.ModelParameter;
 import cbit.vcell.model.Model.RbmModelContainer;
 import cbit.vcell.model.Model.StructureTopology;
-import cbit.vcell.model.ModelException;
-import cbit.vcell.model.Product;
-import cbit.vcell.model.Reactant;
-import cbit.vcell.model.ReactionDescription;
-import cbit.vcell.model.ReactionParticipant;
-import cbit.vcell.model.ReactionRule;
-import cbit.vcell.model.ReactionSpeciesCopy;
-import cbit.vcell.model.ReactionStep;
-import cbit.vcell.model.SimpleReaction;
-import cbit.vcell.model.Species;
-import cbit.vcell.model.SpeciesContext;
-import cbit.vcell.model.Structure;
 import cbit.vcell.model.Structure.StructureSize;
 import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionBindingException;
 import cbit.vcell.parser.SymbolTableEntry;
+import cbit.vcell.xml.XmlHelper;
+import org.vcell.model.rbm.MolecularType;
+import org.vcell.model.rbm.RbmNetworkGenerator.CompartmentMode;
+import org.vcell.model.rbm.RbmUtils;
+import org.vcell.model.rbm.SpeciesPattern;
+import org.vcell.util.*;
+import org.vcell.util.Issue.IssueCategory;
+import org.vcell.util.IssueContext.ContextType;
+import org.vcell.util.gui.DialogUtils;
+
+import javax.swing.*;
+import java.awt.*;
+import java.beans.PropertyVetoException;
+import java.util.*;
+import java.util.List;
+import java.util.Map.Entry;
 
 public abstract class BioCartoonTool extends cbit.gui.graph.gui.CartoonTool {
 	private DocumentManager documentManager = null;
@@ -338,7 +298,7 @@ public static final void pasteReactionsAndRules(Component requester, ReactionSpe
 		AsynchClientTask issueTask = new AsynchClientTask("Checking Issues...",AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
 			@Override
 			public void run(Hashtable<String, Object> hashTable) throws Exception {
-				Model clonedModel = (Model)org.vcell.util.BeanUtils.cloneSerializable(pasteModel);
+				Model clonedModel = XmlHelper.cloneModel(pasteModel);
 				clonedModel.refreshDependencies();
 //				Model clonedModel = pasteModel;
 				IssueContext issueContext = new IssueContext(ContextType.Model, clonedModel, null);
@@ -549,7 +509,7 @@ public void run(Hashtable<String, Object> hashTable) throws Exception {
 			public void run(Hashtable<String, Object> hashTable) throws Exception {
 				ReactionStep[] reactionStepsArrOrig = new ReactionStep[] {(ReactionStep)hashTable.get("fromRXStep")};
 				UserResolvedRxElements userResolvedRxElements = (UserResolvedRxElements)hashTable.get("userResolvedRxElements");
-				Model clonedModel = (Model)org.vcell.util.BeanUtils.cloneSerializable(pasteToModel);
+				Model clonedModel = XmlHelper.cloneModel(pasteToModel);
 				clonedModel.refreshDependencies();
 				IssueContext issueContext = new IssueContext(ContextType.Model, clonedModel, null);
 				HashMap<String,HashMap<ReactionParticipant,Structure>> userResolved_rxPartMapStruct = null;

vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java

@@ -10,19 +10,24 @@
 
 package cbit.vcell.biomodel;
 
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.beans.VetoableChangeSupport;
-import java.util.*;
-import java.util.function.Consumer;
-import java.util.stream.Collectors;
-
+import cbit.image.ImageException;
 import cbit.image.VCImage;
+import cbit.vcell.biomodel.meta.IdentifiableProvider;
+import cbit.vcell.biomodel.meta.VCID;
+import cbit.vcell.biomodel.meta.VCMetaData;
+import cbit.vcell.geometry.*;
+import cbit.vcell.geometry.surface.GeometrySurfaceDescription;
 import cbit.vcell.mapping.*;
 import cbit.vcell.mapping.SimulationContext.Application;
+import cbit.vcell.math.MathDescription;
 import cbit.vcell.model.*;
+import cbit.vcell.model.Model.RbmModelContainer;
+import cbit.vcell.model.Structure.SpringStructureEnum;
+import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.parser.NameScope;
+import cbit.vcell.parser.SymbolTableEntry;
+import cbit.vcell.solver.Simulation;
+import cbit.vcell.xml.XmlHelper;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.model.rbm.MolecularType;
@@ -38,24 +43,10 @@
 import org.vcell.util.document.*;
 import org.vcell.util.document.BioModelChildSummary.MathType;
 
-import cbit.image.ImageException;
-import cbit.vcell.biomodel.meta.IdentifiableProvider;
-import cbit.vcell.biomodel.meta.VCID;
-import cbit.vcell.biomodel.meta.VCMetaData;
-import cbit.vcell.geometry.AnalyticSubVolume;
-import cbit.vcell.geometry.Geometry;
-import cbit.vcell.geometry.GeometryException;
-import cbit.vcell.geometry.GeometrySpec;
-import cbit.vcell.geometry.SubVolume;
-import cbit.vcell.geometry.SurfaceClass;
-import cbit.vcell.geometry.surface.GeometrySurfaceDescription;
-import cbit.vcell.math.MathDescription;
-import cbit.vcell.model.Model.RbmModelContainer;
-import cbit.vcell.model.Structure.SpringStructureEnum;
-import cbit.vcell.parser.ExpressionException;
-import cbit.vcell.parser.NameScope;
-import cbit.vcell.parser.SymbolTableEntry;
-import cbit.vcell.solver.Simulation;
+import java.beans.*;
+import java.util.*;
+import java.util.function.Consumer;
+import java.util.stream.Collectors;
 
 /**
  * Insert the type's description here.
@@ -114,7 +105,7 @@ public void transformLumpedToDistributed(){
                     Kinetics origKinetics = reactionStep.getKinetics();
                     // clone it for backup purposes
                     origKinetics.setReactionStep(null);
-                    Kinetics clonedKinetics = (Kinetics) BeanUtils.cloneSerializable(origKinetics);
+                    Kinetics clonedKinetics = XmlHelper.cloneReactionStep(reactionStep).getKinetics();
                     origKinetics.setReactionStep(reactionStep);
                     try {
                         DistributedKinetics.toDistributedKinetics((LumpedKinetics) origKinetics, false);

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGMolecule.java

@@ -117,4 +117,15 @@ public void setComponentsStates(){
     public String toString(){
         return getName();
     }
+
+    public BNGMolecule deepClone() {
+        BNGMolecule bngMoleculeClone = new BNGMolecule(getName());
+        if (molComponents != null) {
+            bngMoleculeClone.molComponents = new BNGSpeciesComponent[molComponents.length];
+            for (int i = 0; i < molComponents.length; i++) {
+                bngMoleculeClone.molComponents[i] = molComponents[i].deepClone();
+            }
+        }
+        return bngMoleculeClone;
+    }
 }

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGOutputSpec.java

@@ -49,6 +49,51 @@ public BNGOutputSpec(BNGParameter[] argParams, BNGMolecule[] argMols, BNGSpecies
 	}
 }
 
+public BNGOutputSpec deepClone() {
+	BNGParameter[] bngParamsClone = null;
+	if (bngParams != null) {
+		bngParamsClone = new BNGParameter[bngParams.length];
+		for (int i = 0; i < bngParams.length; i++) {
+			bngParamsClone[i] = bngParams[i].deepClone();
+		}
+	}
+	BNGMolecule[] bngMoleculeTypesClone = null;
+	if (bngMoleculeTypes != null){
+		bngMoleculeTypesClone = new BNGMolecule[bngMoleculeTypes.length];
+		for (int i = 0; i < bngMoleculeTypes.length; i++) {
+			bngMoleculeTypesClone[i] = bngMoleculeTypes[i].deepClone();
+		}
+	}
+	BNGSpecies[] bngSpeciesClone = null;
+	if (bngSpecies != null){
+		bngSpeciesClone = new BNGSpecies[bngSpecies.length];
+		for (int i = 0; i < bngSpecies.length; i++) {
+			bngSpeciesClone[i] = bngSpecies[i].deepClone();
+		}
+	}
+	BNGReactionRule[] bngReactionRulesClone = null;
+	if (bngReactionRules != null){
+		bngReactionRulesClone = new BNGReactionRule[bngReactionRules.length];
+		for (int i = 0; i < bngReactionRules.length; i++) {
+			bngReactionRulesClone[i] = bngReactionRules[i].deepClone();
+		}
+	}
+	BNGReaction[] bngReactionsClone = null;
+	if (bngReactions != null) {
+		bngReactionsClone = new BNGReaction[bngReactions.length];
+		for (int i = 0; i < bngReactions.length; i++) {
+			bngReactionsClone[i] = bngReactions[i].deepClone();
+		}
+	}
+	ObservableGroup[] bngObservableGroupsClone = null;
+	if (bngObservableGroups != null){
+		bngObservableGroupsClone = new ObservableGroup[bngObservableGroups.length];
+		for (int i = 0; i < bngObservableGroups.length; i++) {
+			bngObservableGroupsClone[i] = bngObservableGroups[i].deepClone();
+		}
+	}
+	return new BNGOutputSpec(bngParamsClone, bngMoleculeTypesClone, bngSpeciesClone, bngReactionRulesClone, bngReactionsClone, bngObservableGroupsClone);
+}
 public BNGMolecule[] getBNGMolecules() {
 	return	bngMoleculeTypes;
 }

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGParameter.java

@@ -69,4 +69,8 @@ public void setValue(double argValue) {
 public String toString() {
 	return new String(getName() + ";\t" + getValue());
 }
+
+    public BNGParameter deepClone() {
+		return new BNGParameter(name, value);
+    }
 }

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGReaction.java

@@ -354,4 +354,22 @@ public String toStringShort() {
 	}
 	return reactionStr;
 }
+
+
+    public BNGReaction deepClone() {
+		BNGSpecies[] bngReactantsClone = new BNGSpecies[reactants.length];
+		for (int i = 0; i < reactants.length; i++) {
+			bngReactantsClone[i] = reactants[i].deepClone();
+		}
+		BNGSpecies[] bngProductsClone = new BNGSpecies[products.length];
+		for (int i = 0; i < products.length; i++) {
+			bngProductsClone[i] = products[i].deepClone();
+		}
+		Expression newParamExpression = paramExpression;
+		if (newParamExpression != null) {
+			newParamExpression = Expression.clone(paramExpression);
+		}
+		BNGReaction bngReactionClone = new BNGReaction(matchingKey, matchingKey, bngReactantsClone, bngProductsClone, newParamExpression, ruleName, bRuleReversed);
+		return bngReactionClone;
+    }
 }

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGReactionRule.java

@@ -186,4 +186,20 @@ public String writeReaction() {
 
 	return reactionStr;
 }
+
+    public BNGReactionRule deepClone() {
+		BNGParameter[] bngParamsClone = new BNGParameter[parameters.length];
+		for (int i = 0; i < parameters.length; i++) {
+			bngParamsClone[i] = parameters[i].deepClone();
+		}
+		BNGSpecies[] bngReactantsClone = new BNGSpecies[reactants.length];
+		for (int i = 0; i < reactants.length; i++) {
+			bngReactantsClone[i] = reactants[i].deepClone();
+		}
+		BNGSpecies[] bngProductsClone = new BNGSpecies[products.length];
+		for (int i = 0; i < products.length; i++) {
+			bngProductsClone[i] = products[i].deepClone();
+		}
+		return new BNGReactionRule(bngParamsClone, bngReactantsClone, bngProductsClone, isReversible());
+    }
 }

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGSpecies.java

@@ -122,7 +122,15 @@ public String toStringShort() {
 	return new String(getName());
 }
 
-public enum SignatureDetailLevel {
+    public BNGSpecies deepClone() {
+		Expression newConc = getConcentration();
+		if (newConc != null) {
+			newConc = Expression.clone(newConc);
+		}
+		return new BNGComplexSpecies(getName(), newConc, getNetworkFileIndex());
+    }
+
+    public enum SignatureDetailLevel {
 	MoleculesOnly,
 	ComponentsAndStates		// molecules and components with states, no bond
 }

vcell-core/src/main/java/cbit/vcell/bionetgen/BNGSpeciesComponent.java

@@ -88,4 +88,15 @@ public String extractComponentPatternSignature() {
 	}
 	return prefix;
 }
+
+    public BNGSpeciesComponent deepClone() {
+		String[] newStateNames = null;
+		if (stateNames != null) {
+			newStateNames = new String[stateNames.length];
+			for (int i = 0; i < stateNames.length; i++) {
+				newStateNames[i] = stateNames[i];
+			}
+		}
+		return new BNGSpeciesComponent(componentName, currentState, newStateNames);
+    }
 }