Merge pull request #1108 from virtualcell/dan-ss-is2D-flag

Added is2D flag, domain name bug fixed in the math

vcell-client/src/main/java/cbit/vcell/mapping/gui/MolecularTypeSpecsTableModel.java

@@ -52,15 +52,18 @@
  */
 @SuppressWarnings("serial")
 public class MolecularTypeSpecsTableModel extends VCellSortTableModel<MolecularComponentPattern> implements java.beans.PropertyChangeListener {
-
+
+	// TODO: sas is null for molecules added late (after the application is created)
+	// TODO: add is2D flag here as a checkbox (var is SpeciesContextSpec) - membrane species may have it set to true, for compartment species is always false
+	// TODO: math is wrong for a model with a membrane species, saving model fails, see model aaa-SS-membrane, see issue #1097
 
 	private enum ColumnType {
 		COLUMN_SITE("Site"),
 		COLUMN_MOLECULE("Molecule"),
 		COLUMN_STRUCTURE("Location"),
 		COLUMN_STATE("Initial State"),
-		COLUMN_RADIUS("Radius"),
-		COLUMN_DIFFUSION("Diffusion Rate");
+		COLUMN_RADIUS("Radius (nm)"),
+		COLUMN_DIFFUSION("Diffusion Rate (um^2/s)");
 
 		public final String label;
 		private ColumnType(String label){

vcell-client/src/main/java/cbit/vcell/mapping/gui/SpeciesContextSpecsTableModel.java

@@ -16,6 +16,7 @@
 import java.util.List;
 import java.util.TreeSet;
 
+import cbit.vcell.model.Membrane;
 import org.vcell.model.rbm.SpeciesPattern;
 import org.vcell.util.Displayable;
 import org.vcell.util.gui.GuiUtils;
@@ -65,6 +66,7 @@ public enum ColumnType {
 		COLUMN_SPECIESCONTEXT("Species"),
 		COLUMN_STRUCTURE("Structure"),
 		COLUMN_DEPICTION("Depiction"),
+		COLUMN_IS2D("Is 2D"),
 		COLUMN_CLAMPED("Clamped"),
 		COLUMN_RULES("Rules"),
 		COLUMN_INITIAL("Initial Condition"),
@@ -142,6 +144,7 @@ public Class<?> getColumnClass(int column) {
 		case COLUMN_RULES:{
 			return RulesProvenance.class;
 		}
+		case COLUMN_IS2D:
 		case COLUMN_CLAMPED:
 		case COLUMN_WELLMIXED:
 		case COLUMN_FORCECONTINUOUS:{
@@ -163,21 +166,36 @@ public String getColumnName(int columnIndex){
 }
 
 private void refreshColumns(){
+	SimulationContext simContext = getSimulationContext();
 	columns.clear();
 	columns.addAll(Arrays.asList(ColumnType.values())); // initialize to all columns
-	if (getSimulationContext() == null || !getSimulationContext().isStoch()){
+	if(simContext == null) {
+		columns.remove(ColumnType.COLUMN_IS2D);
 		columns.remove(ColumnType.COLUMN_FORCECONTINUOUS);
+		columns.remove(ColumnType.COLUMN_WELLMIXED);
+		columns.remove(ColumnType.COLUMN_DIFFUSION);
+		columns.remove(ColumnType.COLUMN_CLAMPED);
+		columns.remove(ColumnType.COLUMN_RULES);
+		return;
+	}
+	if(!simContext.getApplicationType().equals(SimulationContext.Application.SPRINGSALAD)) {
+		columns.remove(ColumnType.COLUMN_IS2D);
 	}
-	if (getSimulationContext() == null || getSimulationContext().getGeometry().getDimension() == 0){
+	if (!simContext.isStoch()){
+		columns.remove(ColumnType.COLUMN_FORCECONTINUOUS);
+	}
+	if (simContext.getGeometry().getDimension() == 0){
+		columns.remove(ColumnType.COLUMN_IS2D);
 		columns.remove(ColumnType.COLUMN_WELLMIXED);
 		columns.remove(ColumnType.COLUMN_DIFFUSION);
 	}
-	if (getSimulationContext() == null || getSimulationContext().isRuleBased()) {
+	if (simContext.isRuleBased()) {
 		// the NFSim simulator used for rule-based doesn't accept clamped or force continuous
+		columns.remove(ColumnType.COLUMN_IS2D);
 		columns.remove(ColumnType.COLUMN_CLAMPED);
 		columns.remove(ColumnType.COLUMN_FORCECONTINUOUS);
 	}
-	if (getSimulationContext() == null || getSimulationContext().getApplicationType().equals(SimulationContext.Application.SPRINGSALAD)) {
+	if (simContext.getApplicationType().equals(SimulationContext.Application.SPRINGSALAD)) {
 		columns.remove(ColumnType.COLUMN_DIFFUSION);
 		columns.remove(ColumnType.COLUMN_FORCECONTINUOUS);
 		columns.remove(ColumnType.COLUMN_WELLMIXED);
@@ -225,8 +243,11 @@ public Object getValueAt(int row, int col) {
 			case COLUMN_DEPICTION:{
 				return scSpec.getSpeciesContext().getSpeciesPattern();
 			}
+			case COLUMN_IS2D: {
+				return scSpec.getIs2D();
+			}
 			case COLUMN_CLAMPED:{
-				return new Boolean(scSpec.isConstant());
+				return scSpec.isConstant();
 			}
 			case COLUMN_RULES:{
 				return null;
@@ -251,7 +272,7 @@ public Object getValueAt(int row, int col) {
 				}
 			}
 			case COLUMN_FORCECONTINUOUS:{
-				return new Boolean(scSpec.isForceContinuous());
+				return scSpec.isForceContinuous();
 			}
 			default:{
 				return null;
@@ -283,6 +304,16 @@ public boolean isCellEditable(int rowIndex, int columnIndex) {
 		case COLUMN_DEPICTION:{
 			return false;
 		}
+		case COLUMN_IS2D:{
+			if(!bEditable) {
+				return false;
+			}
+			Structure structure = speciesContextSpec.getSpeciesContext().getStructure();
+			if(structure instanceof Membrane) {
+				return true;
+			}
+			return false;
+		}
 		case COLUMN_CLAMPED:{
 			if(!bEditable) {
 				return false;	// the table wants this column un-editable
@@ -528,6 +559,16 @@ public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
 	SpeciesContextSpec scSpec = getValueAt(rowIndex);
 	ColumnType columnType = columns.get(columnIndex);
 	switch (columnType){
+		case COLUMN_IS2D: {
+			boolean is2D = ((Boolean)aValue).booleanValue();
+			if(is2D) {
+				scSpec.setIs2D(true);
+			} else {
+				scSpec.setIs2D(false);
+			}
+			fireTableRowsUpdated(rowIndex,rowIndex);
+			break;
+		}
 		case COLUMN_CLAMPED:{
 			boolean bFixed = ((Boolean)aValue).booleanValue();
 			if (bFixed){
@@ -659,27 +700,36 @@ public int compare(SpeciesContextSpec speciesContextSpec1, SpeciesContextSpec sp
 						return name2.compareToIgnoreCase(name1);
 					}
 				}
+				case COLUMN_IS2D: {
+					Boolean bIs2D1 = speciesContextSpec1.getIs2D();
+					Boolean bIs2D2 = speciesContextSpec2.getIs2D();
+					if (ascending){
+						return bIs2D1.compareTo(bIs2D2);
+					}else{
+						return bIs2D2.compareTo(bIs2D1);
+					}
+				}
 				case COLUMN_CLAMPED : {
-					Boolean bClamped1 = new Boolean(speciesContextSpec1.isConstant());
-					Boolean bClamped2 = new Boolean(speciesContextSpec2.isConstant());
+					Boolean bClamped1 = speciesContextSpec1.isConstant();
+					Boolean bClamped2 = speciesContextSpec2.isConstant();
 					if (ascending){
 						return bClamped1.compareTo(bClamped2);
 					}else{
 						return bClamped2.compareTo(bClamped1);
 					}
 				}
 				case COLUMN_FORCECONTINUOUS : {
-					Boolean bForceContinuous1 = new Boolean(speciesContextSpec1.isForceContinuous());
-					Boolean bForceContinuous2 = new Boolean(speciesContextSpec2.isForceContinuous());
+					Boolean bForceContinuous1 = speciesContextSpec1.isForceContinuous();
+					Boolean bForceContinuous2 = speciesContextSpec2.isForceContinuous();
 					if (ascending){
 						return bForceContinuous1.compareTo(bForceContinuous2);
 					}else{
 						return bForceContinuous2.compareTo(bForceContinuous1);
 					}
 				}
 				case COLUMN_WELLMIXED : {
-					Boolean bWellMixed1 = new Boolean(speciesContextSpec1.isWellMixed());
-					Boolean bWellMixed2 = new Boolean(speciesContextSpec2.isWellMixed());
+					Boolean bWellMixed1 = speciesContextSpec1.isWellMixed();
+					Boolean bWellMixed2 = speciesContextSpec2.isWellMixed();
 					if (ascending){
 						return bWellMixed1.compareTo(bWellMixed2);
 					}else{

vcell-client/src/main/java/cbit/vcell/math/gui/MathDescEditor.java

@@ -536,7 +536,8 @@ private static Set<String> getAutoCompletionWords() {
 		autoCompletionWords.add(VCML.ParticleDriftZ);
 		autoCompletionWords.add(VCML.Subtype);		
 		autoCompletionWords.add(VCML.TransitionCondition);		
-		autoCompletionWords.add(VCML.BondLength);		
+		autoCompletionWords.add(VCML.BondLength);
+		autoCompletionWords.add(VCML.Is2D);
 		autoCompletionWords.add(VCML.Links);		
 		autoCompletionWords.add(VCML.LinkSeparator);		
 		autoCompletionWords.add(VCML.ParticleComponentRadius);		
@@ -850,6 +851,7 @@ public static Set<String> getkeywords() {
 		keywords.add(VCML.TransitionCondition);
 		keywords.add(VCML.BondLength);
 		keywords.add(VCML.Links);
+		keywords.add(VCML.Is2D);
 		keywords.add(VCML.ParticleComponentRadius);
 		keywords.add(VCML.ParticleComponentDiffusionRate);
 		keywords.add(VCML.ParticleComponentLocation);

vcell-client/src/main/java/org/vcell/model/springsalad/gui/MolecularStructuresPanel.java

@@ -520,7 +520,7 @@ public Component getTableCellRendererComponent(JTable table, Object value, boole
 		gbc.gridy = 5;
 		gbc.anchor = GridBagConstraints.SOUTH;
 		gbc.insets = new Insets(2, 2, 2, 2);
-		sitesPanel.add(new JLabel(" X: "), gbc);
+		sitesPanel.add(new JLabel(" X (nm) "), gbc);
 
 		gbc = new GridBagConstraints();
 		gbc.gridx = 1;
@@ -536,7 +536,7 @@ public Component getTableCellRendererComponent(JTable table, Object value, boole
 		gbc.gridy = 5;
 		gbc.anchor = GridBagConstraints.SOUTH;
 		gbc.insets = new Insets(2, 2, 2, 2);
-		sitesPanel.add(new JLabel(" Y: "), gbc);
+		sitesPanel.add(new JLabel(" Y (nm) "), gbc);
 
 		gbc = new GridBagConstraints();
 		gbc.gridx = 3;
@@ -552,7 +552,7 @@ public Component getTableCellRendererComponent(JTable table, Object value, boole
 		gbc.gridy = 5;
 		gbc.anchor = GridBagConstraints.SOUTH;
 		gbc.insets = new Insets(2, 2, 2, 2);
-		sitesPanel.add(new JLabel(" Z: "), gbc);
+		sitesPanel.add(new JLabel(" Z (nm) "), gbc);
 
 		gbc = new GridBagConstraints();
 		gbc.gridx = 5;

vcell-core/src/main/java/cbit/vcell/mapping/AbstractStochMathMapping.java

@@ -106,6 +106,7 @@ protected void addInitialConditions(Domain domain, SpeciesContextSpec[] speciesC
 				// species initial values (either function or constant)
 				//
 				for (int i = 0; i < speciesContextSpecs.length; i++){
+
 					SpeciesContextSpec.SpeciesContextSpecParameter initParam = null;//can be concentration or amount
 					Expression iniExp = null;
 					StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());

vcell-core/src/main/java/cbit/vcell/mapping/LangevinMathMapping.java

@@ -99,10 +99,6 @@
  */
 public class LangevinMathMapping extends AbstractStochMathMapping {
 
-/**
- * @param model cbit.vcell.model.Model
- * @param geometry cbit.vcell.geometry.Geometry
- */
 protected LangevinMathMapping(SimulationContext simContext, MathMappingCallback callback, NetworkGenerationRequirements networkGenerationRequirements) {
 	super(simContext, callback, networkGenerationRequirements);
 }
@@ -1100,7 +1096,8 @@ private List<ParticleObservable> addObservables(
 				}else{
 					particleObservableType = ParticleObservable.ObservableType.Species; 
 				}
-				ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(observableCountParameter, geometryClass),domain,particleObservableType);
+				Domain d = new Domain(geometryClass);
+				ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(observableCountParameter, geometryClass),d,particleObservableType);
 
 				switch (rbmObservable.getSequence()){
 					case Multimolecular:{
@@ -1131,7 +1128,8 @@ private List<ParticleObservable> addObservables(
 			if (mathMappingParameter instanceof SpeciesCountParameter){
 				SpeciesCountParameter speciesCountParameter = (SpeciesCountParameter)mathMappingParameter;
 				ParticleObservable.ObservableType particleObservableType = ParticleObservable.ObservableType.Species;
-				ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(speciesCountParameter, geometryClass),domain,particleObservableType);
+				Domain d = new Domain(geometryClass);
+				ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(speciesCountParameter, geometryClass),d,particleObservableType);
 				particleObservable.setSequence(Sequence.Multimolecular);
 				SpeciesPattern speciesPattern = speciesCountParameter.getSpeciesContext().getSpeciesPattern();
 				VolumeParticleSpeciesPattern vpsp = speciesPatternMap.get(speciesPattern);
@@ -1153,6 +1151,10 @@ private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns
 			Map<MolecularComponentPattern, LangevinParticleMolecularComponent> mcToLpmc = new LinkedHashMap<> ();
 			LangevinParticleMolecularType particleMolecularType = new LangevinParticleMolecularType(molecularType.getName());
 			SpeciesContextSpec scs = molecularTypeToSpeciesContextSpecMap.get(molecularType);	// scs may be null for Sink and Source
+			if(scs != null) {
+				boolean is2D = scs.getIs2D();
+				particleMolecularType.setIs2D(is2D);
+			}
 			for (MolecularComponent molecularComponent : molecularType.getComponentList()) {
 				String pmcName = molecularComponent.getName();
 				String pmcId = particleMolecularType.getName() + "_" + molecularComponent.getName();
@@ -1231,7 +1233,18 @@ private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns
 		HashMap<SpeciesPattern,VolumeParticleSpeciesPattern> speciesPatternMap = new HashMap<SpeciesPattern, VolumeParticleSpeciesPattern>();
 		String speciesPatternName = "speciesPattern0";
 		for (SpeciesPattern speciesPattern : speciesPatternStructureMap.keySet()) {
-			VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = new VolumeParticleSpeciesPattern(speciesPatternName,domain,speciesPatternStructureMap.get(speciesPattern).getName());
+			Structure structure = speciesPatternStructureMap.get(speciesPattern);
+			StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(structure);
+			GeometryClass gc = sm.getGeometryClass();
+			SubDomain sd = mathDesc.getSubDomain(gc.getName());
+			Domain d = new Domain(sd);
+
+			// TODO: other useful code
+//			Structure structures[] = getSimulationContext().getGeometryContext().getModel().getStructures();
+//			GeometryClass[] geometryClass = getSimulationContext().getGeometryContext().getGeometry().getGeometryClasses();
+//			Structure[] mappedStructures = getSimulationContext().getGeometryContext().getStructuresFromGeometryClass(geometryClass[i]);
+
+			VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = new VolumeParticleSpeciesPattern(speciesPatternName, d, structure.getName());
 
 			for (MolecularTypePattern molecularTypePattern : speciesPattern.getMolecularTypePatterns()){
 				ParticleMolecularType particleMolecularType = mathDesc.getParticleMolecularType(molecularTypePattern.getMolecularType().getName());
@@ -1393,8 +1406,10 @@ protected void refreshVariables() throws MappingException {
 			throw new MappingException(e.getMessage());
 		}
 		//we always add variables, all species are independent variables, no matter they are constant or not.
-		String countMathSymbol = getMathSymbol(spCountParm, getSimulationContext().getGeometryContext().getStructureMapping(scs.getSpeciesContext().getStructure()).getGeometryClass());
-		scm.setVariable(new VolumeParticleVariable(countMathSymbol,defaultDomain));
+		GeometryClass gc = getSimulationContext().getGeometryContext().getStructureMapping(scs.getSpeciesContext().getStructure()).getGeometryClass();
+		String countMathSymbol = getMathSymbol(spCountParm, gc);
+		Domain d = new Domain(gc);
+		scm.setVariable(new VolumeParticleVariable(countMathSymbol,d));
 		mathSymbolMapping.put(scm.getSpeciesContext(),scm.getVariable().getName());
 	}
 

vcell-core/src/main/java/cbit/vcell/mapping/SpeciesContextSpec.java

@@ -443,8 +443,17 @@ public void targetPropertyChange(PropertyChangeEvent evt){
     private Boolean bWellMixed = DEFAULT_WELL_MIXED;
     private Boolean bForceContinuous = DEFAULT_FORCECONTINUOUS;
 
-    private Set<MolecularInternalLinkSpec> internalLinkSet = new LinkedHashSet<>();            // SpringSaLaD
+    // SpringSaLaD specific entities
+    private Set<MolecularInternalLinkSpec> internalLinkSet = new LinkedHashSet<>();
     private Map<MolecularComponentPattern, SiteAttributesSpec> siteAttributesMap = new LinkedHashMap<>();
+    // is2D flag, used by the solver for collision / overlapping calculations, exact meaning uncertain
+    // membrane species may have it set to true, for compartment species is always false
+    // for now we have it hardcoded to false and non-editable
+    // TODO: slowly add it to export and persistence, eventually make it editable for membrane species
+    // Obs: it's really an attribute of a MolecularTypePattern, or even better of a so called "MolecularTypePatternSpec",
+    //      but since all species in SS are single molecule by design it's okay to have it here
+    // TODO: add getIs2DSQL() and readIs2DSQL(), similar to getSiteAttributesSQL(), readSiteAttributesSQL
+    private boolean is2D = false;
 
     protected transient java.beans.VetoableChangeSupport vetoPropertyChange;
     private SpeciesContextSpecParameter[] fieldParameters = null;
@@ -1927,6 +1936,12 @@ void setSpeciesContextReference(SpeciesContext sc) throws MappingException{
         }
     }
 
+    public void setIs2D(boolean is2D) {
+        this.is2D = is2D;
+    }
+    public boolean getIs2D() {
+        return this.is2D;
+    }
 
     /**
      * This method was created by a SmartGuide.

vcell-core/src/main/java/cbit/vcell/math/LangevinParticleMolecularType.java

@@ -16,7 +16,8 @@
 
 @SuppressWarnings("serial")
 public class LangevinParticleMolecularType extends ParticleMolecularType {
-
+
+	private boolean is2D = false;
 	private Set<Pair<LangevinParticleMolecularComponent, LangevinParticleMolecularComponent>> internalLinkSpec = new LinkedHashSet<> ();
 
 
@@ -43,6 +44,7 @@ public String getVCML() {
 		if (getComponentList().size() == 0 && getAnchorList().size() == 0) {
 			buffer.append(" "+VCML.EndBlock+"\n");
 		} else {
+			buffer.append("\n        " + VCML.Is2D + "  " + getIs2D());
 			if(internalLinkSpec.size() > 0) {
 				buffer.append("\n        " + VCML.Links + "  " + VCML.BeginBlock);
 				for(Pair<LangevinParticleMolecularComponent, LangevinParticleMolecularComponent> pair : internalLinkSpec) {
@@ -74,6 +76,10 @@ public void read(CommentStringTokenizer tokens) throws MathFormatException {
 			if (token.equalsIgnoreCase(VCML.EndBlock)) {
 				break;
 			}
+			if(token.equalsIgnoreCase(VCML.Is2D)) {
+				token = tokens.nextToken();
+				setIs2D(Boolean.getBoolean(token));
+			}
 			if (token.equalsIgnoreCase(VCML.Links)) {
 				token = tokens.nextToken();
 				if (!token.equalsIgnoreCase(VCML.BeginBlock)){
@@ -124,5 +130,11 @@ public Set<Pair<LangevinParticleMolecularComponent, LangevinParticleMolecularCom
 	public void setInternalLinkSpec(Set<Pair<LangevinParticleMolecularComponent, LangevinParticleMolecularComponent>> internalLinkSpec) {
 		this.internalLinkSpec = internalLinkSpec;
 	}
-
+
+	public boolean getIs2D() {
+		return is2D;
+	}
+	public void setIs2D(boolean is2D) {
+		this.is2D = is2D;
+	}
 }

vcell-core/src/main/java/cbit/vcell/math/VCML.java

@@ -216,6 +216,7 @@ public class VCML {
 
 	public final static String LangevinParticleJumpProcess		= "LangevinParticleJumpProcess"; // Langevin particle
 	public final static String LangevinParticleMolecularType	= "LangevinParticleMolecularType";
+	public final static String Is2D						= "Is2D";
 	public final static String Subtype					= "Subtype"; // particle Langevin / SpringSaLaD
 	public final static String TransitionCondition		= "TransitionCondition"; // particle Langevin / SpringSaLaD
 	public final static String BondLength				= "BondLength"; // particle Langevin / SpringSaLaD