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Merge pull request #1289 from virtualcell/dan-ss-duplicates
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Dan ss duplicates
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@danv61
danv61 authored Jun 27, 2024
2 parents f79503b + b9ae0b1 commit c7b81fb
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Showing 4 changed files with 196 additions and 27 deletions.
8 changes: 4 additions & 4 deletions vcell-core/src/main/java/cbit/vcell/mapping/LangevinMathMapping.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1155,7 +1155,7 @@ private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns
List<RbmObservable> observableList = model.getRbmModelContainer().getObservableList();
List<MolecularType> molecularTypeList = model.getRbmModelContainer().getMolecularTypeList();
for (MolecularType molecularType : molecularTypeList) {
Map<MolecularComponentPattern, LangevinParticleMolecularComponent> mcToLpmc = new LinkedHashMap<> ();
Map<MolecularComponentPattern, LangevinParticleMolecularComponent> mcpToLpmc = new LinkedHashMap<> ();
LangevinParticleMolecularType particleMolecularType = new LangevinParticleMolecularType(molecularType.getName());
SpeciesContextSpec scs = molecularTypeToSpeciesContextSpecMap.get(molecularType); // scs may be null for Sink and Source
if(scs != null) {
Expand Down Expand Up @@ -1187,7 +1187,7 @@ private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns
particleMolecularComponent.setCoordinate(sas.getCoordinate());
particleMolecularComponent.setRadius(sas.getRadius());
particleMolecularComponent.setDiffusionRate(sas.getDiffusionRate());
mcToLpmc.put(mcp, particleMolecularComponent);
mcpToLpmc.put(mcp, particleMolecularComponent);
}
particleMolecularType.addMolecularComponent(particleMolecularComponent);
}
Expand All @@ -1205,8 +1205,8 @@ private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns
}
for(MolecularInternalLinkSpec mils : internalLinkSet) {
Pair<MolecularComponentPattern, MolecularComponentPattern> link = mils.getLink();
LangevinParticleMolecularComponent one = mcToLpmc.get(link.one);
LangevinParticleMolecularComponent two = mcToLpmc.get(link.two);
LangevinParticleMolecularComponent one = mcpToLpmc.get(link.one);
LangevinParticleMolecularComponent two = mcpToLpmc.get(link.two);
// error: Cannot invoke "Object.equals(Object)" because "this.one" is null
Pair<LangevinParticleMolecularComponent, LangevinParticleMolecularComponent> pair = new Pair<> (one, two);
particleMolecularType.getInternalLinkSpec().add(pair);
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16 changes: 16 additions & 0 deletions vcell-core/src/main/java/cbit/vcell/mapping/MolecularInternalLinkSpec.java
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Original file line number Diff line number Diff line change
Expand Up @@ -183,6 +183,22 @@ public static Pair<MolecularComponentPattern, MolecularComponentPattern> getLink
}
return new Pair<MolecularComponentPattern, MolecularComponentPattern>(internalLink.fieldMolecularComponentPatternOne, internalLink.fieldMolecularComponentPatternTwo);
}
public void setLink(Pair<MolecularComponentPattern, MolecularComponentPattern> link) {
SpeciesContext sc = fieldSpeciesContextSpec.getSpeciesContext();
SpeciesPattern sp = sc.getSpeciesPattern();
MolecularTypePattern mtp = sp.getMolecularTypePatterns().get(0); // the one and only
for(MolecularComponentPattern mpc : mtp.getComponentPatternList()) {
if(mpc == link.one) { // linkOne comes first
fieldMolecularComponentPatternOne = link.one;
fieldMolecularComponentPatternTwo = link.two;
break;
} else if(mpc == link.two) { // linkTwo comes first
fieldMolecularComponentPatternOne = link.two;
fieldMolecularComponentPatternTwo = link.one;
break;
}
}
}
@Override
public boolean compareEqual(Matchable obj) {
if (obj == this) {
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12 changes: 10 additions & 2 deletions vcell-core/src/main/java/cbit/vcell/mapping/ReactionContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -290,7 +290,11 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
refreshAll();
}
if(evt.getSource().equals(getModel()) && evt.getPropertyName().equals(Model.PROPERTY_NAME_SPECIES_CONTEXT_SPECIES_PATTERN)) {
refreshSpeciesContextSpecsSpeciesPatterns(); // only for springsalad, because we care about the sites (site attributes spec, internal link spec)
if(evt.getNewValue() instanceof SpeciesContext) {
refreshSpeciesContextSpecsSpeciesPatterns((SpeciesContext)evt.getNewValue()); // only for springsalad, because we care about the sites (site attributes spec, internal link spec)
} else {
throw new RuntimeException("Expected 'SpeciesContext' instance");
}
}
if (evt.getSource().equals(getModel()) && evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST)){
; // do nothing
Expand Down Expand Up @@ -621,8 +625,12 @@ private void refreshSpeciesContextSpecs() throws MappingException {
}
}
}
private void refreshSpeciesContextSpecsSpeciesPatterns() {
private void refreshSpeciesContextSpecsSpeciesPatterns(SpeciesContext sc) {
if(sc == null) {
throw new RuntimeException("Unexpected 'null' SpeciesContext");
}
if(Application.SPRINGSALAD == simContext.getApplicationType()) {
// TODO: we should use the sc in 'initializeForSpringSaLaD()'
for(SpeciesContextSpec scs : fieldSpeciesContextSpecs) {
scs.initializeForSpringSaLaD(null);
}
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187 changes: 166 additions & 21 deletions vcell-core/src/main/java/cbit/vcell/mapping/SpeciesContextSpec.java
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Original file line number Diff line number Diff line change
Expand Up @@ -663,7 +663,13 @@ public void initializeForSpatial(){
}
}

public void initializeForSpringSaLaD(MolecularType molecularType){
public void initializeForSpringSaLaD(MolecularType molecularType) {
// we need to make sure that the mcp in the siteAttributesMap:
// Map<MolecularComponentPattern, SiteAttributesSpec> siteAttributesMap = scs.getSiteAttributesMap();
// are the same as the authoritative mcp from the physiology:
// scs -> sc -> sp -> mtp -> mcp, mcp,...

// step 1: we solve the scs -> sc -> sp -> mtp -> mcp, mcp sequence
if(getSpeciesContext() != null) {
SpeciesPattern sp = getSpeciesContext().getSpeciesPattern();
if (sp == null) {
Expand All @@ -679,37 +685,91 @@ public void initializeForSpringSaLaD(MolecularType molecularType){
// molecularType != null and molecularType == mt : this molecule has a different
// number of components or a different component order
List<MolecularComponent> componentList = mt.getComponentList();

// step 1.1: superficial sanity check, before changing anything
final String saMapExceptionPrefix = "SiteAttributeMap of SpeciesContextSpec of Species '" + getSpeciesContext().getName() + "' ";
if(siteAttributesMap == null || siteAttributesMap.isEmpty()) {
; // do nothing, map is empty, initialization phase
} else { // if map not empty, now we need to check
// we don't fire exceptions, size mismatch may be correct if we delete or add sites to a molecule
if (siteAttributesMap.size() > componentList.size()) {
System.out.println(saMapExceptionPrefix + "has obsolete attributes");
} else if (siteAttributesMap.size() < componentList.size()) {
System.out.println(saMapExceptionPrefix + "has missing attributes");
} else {
for (MolecularComponent mc : componentList) {
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
if (!siteAttributesMap.containsKey(mcp)) {
System.out.println(saMapExceptionPrefix + "mismatching key found (MolecularComponentPattern)");
}
}
}
}
// here the work is being done
//
// step 2: build the set of "old" mcp from the siteAttributesMap
Set<MolecularComponentPattern> oldMcpSet = new LinkedHashSet<> ();
for(Map.Entry<MolecularComponentPattern, SiteAttributesSpec> entry : siteAttributesMap.entrySet()) {
oldMcpSet.add(entry.getKey());
}

// step 3.1: hard compare (instance match) of the authoritative mcp (from the physiology) with the mcp in siteAttributesMap
for (MolecularComponent mc : componentList) {
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
if (siteAttributesMap.containsKey(mcp)) {
oldMcpSet.remove(mcp); // perfect instance match between physiology and siteAttributesMap, stays as is
}
}
// step 3.2: soft compare (using compareEqual)
// Set <MolecularComponentPattern> mcpToAdd = new LinkedHashSet<> (); // new mcp instances to add
Set <MolecularComponentPattern> mcpToRemove = new LinkedHashSet<> (); // obsolete instances of mcp to be replaced by the new above
for (MolecularComponent mc : componentList) {
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
if (siteAttributesMap.containsKey(mcp)) {
continue; // dealt with it already
}
for(MolecularComponentPattern mcpOld : oldMcpSet) {
if(mcp.compareEqual(mcpOld)) {
// mcpToAdd.add(mcp);
mcpToRemove.add(mcpOld);
// we recover the sas from the obsolete mcpOld and transfer it to the new mcp
// since we do not loop through siteAttributesMap we can add right here
SiteAttributesSpec sas = siteAttributesMap.get(mcpOld);
siteAttributesMap.put(mcp, sas);
siteAttributesMap.remove(mcpOld);
break; // can't be more than one
}
}
}
oldMcpSet.removeAll(mcpToRemove); // remove the old mcp we have just dealt with

// step 3.3: whatever is left in the oldMcpSet doesn't exist anymore in the authoritative mcp list,
// could be a mc that has been deleted
for(MolecularComponentPattern mcpOld : oldMcpSet) {
siteAttributesMap.remove(mcpOld);
}
oldMcpSet.clear();

// step 3.4: we add any new instance of authoritative mcp not there yet, and we initialize with default sas
for (MolecularComponent mc : componentList) {
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
if (siteAttributesMap.containsKey(mcp)) {
continue; // this is set, nothing to do
continue; // exists, already dealt with
}
SiteAttributesSpec sas = siteAttributesMap.get(mcp);
if (sas == null || sas.getMolecularComponentPattern() == null) {
sas = new SiteAttributesSpec(this, mcp, getSpeciesContext().getStructure());
siteAttributesMap.put(mcp, sas);
}
}
// at this point the siteAttributesMap should be fully reconstructed

if (getInternalLinkSet().isEmpty()) {
for (int i = 0; i < componentList.size() - 1; i++) {
MolecularComponent mcOne = componentList.get(i);
MolecularComponent mcTwo = componentList.get(i + 1);
MolecularComponentPattern mcpOne = mtp.getMolecularComponentPattern(mcOne);
MolecularComponentPattern mcpTwo = mtp.getMolecularComponentPattern(mcTwo);
MolecularInternalLinkSpec link = new MolecularInternalLinkSpec(this, mcpOne, mcpTwo);
// TODO: set x,y,z instead, link will be computed
// link.setLinkLength(2.0);
internalLinkSet.add(link);
}
}
// sanity checks (the current (up to date) instances can be obtained
// sanity checks, after (the current (up to date) instances can be obtained
// only via SpeciesContext -> SpeciesPattern -> MolecularTypePattern -> MolecularComponentPattern
// all the site attribute map elements and all internal link set elements must use the right instances of these mcp
// if(molecularType == null) {
// return; // we don't need to do sanity check when we start clean (do we? does it hurt if we do? can it possibly fail?)
// }
String saMapExceptionPrefix = "SiteAttributeMap of SpeciesContextSpec of Species '" + getSpeciesContext().getName() + "' ";
if(siteAttributesMap.size() > componentList.size()) {
throw new RuntimeException(saMapExceptionPrefix + "has obsolete attributes");
} else if(siteAttributesMap.size() < componentList.size()) {
Expand All @@ -722,22 +782,107 @@ public void initializeForSpringSaLaD(MolecularType molecularType){
}
}
}
String ilSetExceptionPrefix = "InternalLinkSet of SpeciesContextSpec of Species '" + getSpeciesContext().getName() + "' ";
// we build set of authoritative MolecularComponentPattern from the SpeciesPattern
// ======== dealing with the links ====================================================
//
// if the list is empty, we just add a full set of default links
if (getInternalLinkSet().isEmpty()) {
for (int i = 0; i < componentList.size() - 1; i++) {
MolecularComponent mcOne = componentList.get(i);
MolecularComponent mcTwo = componentList.get(i + 1);
MolecularComponentPattern mcpOne = mtp.getMolecularComponentPattern(mcOne);
MolecularComponentPattern mcpTwo = mtp.getMolecularComponentPattern(mcTwo);
MolecularInternalLinkSpec link = new MolecularInternalLinkSpec(this, mcpOne, mcpTwo);
// TODO: set x,y,z instead, link will be computed
// link.setLinkLength(2.0);
internalLinkSet.add(link);
}
return; // initial initialization done, nothing else to do
}

// step 1.1: build the set of "old" mcp and mils from the siteAttributesMap
oldMcpSet = new LinkedHashSet<> (); // Set<MolecularComponentPattern>
for(MolecularInternalLinkSpec oldMils : getInternalLinkSet()) {
MolecularComponentPattern mcpOne = oldMils.getMolecularComponentPatternOne();
MolecularComponentPattern mcpTwo = oldMils.getMolecularComponentPatternTwo();
oldMcpSet.add(mcpOne);
oldMcpSet.add(mcpTwo);
}
// step 1.2: we build set of authoritative MolecularComponentPattern from the SpeciesPattern
Set<MolecularComponentPattern> authoritativeMcpSet = new LinkedHashSet<>();
for (MolecularComponent mc : componentList) {
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
authoritativeMcpSet.add(mcp);
}
// we can't assume how many links we have, even 0 is possible if we deleted them manually

// step 2: make a corresponding map between oldMcp and authoritative mcp
Map <MolecularComponentPattern, MolecularComponentPattern> oldToNewMcp = new LinkedHashMap<> ();
Set<MolecularComponentPattern> mcpToRemoveSet = new LinkedHashSet<> (); // these will be removed from authoritativeMcpSet
// step 2.1: hard compare (instance match) of the authoritative mcp (from the physiology) with the mcp in siteAttributesMap
for(MolecularComponentPattern oldMcp : oldMcpSet) {
if (authoritativeMcpSet.contains(oldMcp)) {
oldToNewMcp.put(oldMcp, oldMcp);
mcpToRemoveSet.add(oldMcp);
}
}
// once we have an instance match we don't want to again try a compareEqual() match,
// which will obviously succed and risk producing duplicates
authoritativeMcpSet.removeAll(mcpToRemoveSet);
oldMcpSet.removeAll(mcpToRemoveSet);
mcpToRemoveSet.clear();

// step 2.2: soft compare, using compareEqual()
for(MolecularComponentPattern oldMcp : oldMcpSet) {
for(MolecularComponentPattern newMcp : authoritativeMcpSet) {
if(oldMcp.compareEqual(newMcp)) {
oldToNewMcp.put(oldMcp, newMcp);
mcpToRemoveSet.add(newMcp);
}
}
}
// everything that matched one way or another is dealt with, whatever remains is unlinked sites
// perhaps a newly added site
authoritativeMcpSet.removeAll(mcpToRemoveSet);
oldMcpSet.removeAll(mcpToRemoveSet);
mcpToRemoveSet.clear();
// any mcp still present in the authoritativeMcpSet was newly added
// not sure if we need to do anything about it
if(!authoritativeMcpSet.isEmpty()) {
System.out.println("Unlinked mcp in authoritativeMcpSet");
}

// step 3: we iterate through the internal link set, we replace all mcs with the new mcs in oldToNewMcp
// any mcp not found there was deleted, we must delete the link containing it
Set<MolecularInternalLinkSpec> linksToRemove = new LinkedHashSet<> ();
for(MolecularInternalLinkSpec oldMils : getInternalLinkSet()) {
Pair<MolecularComponentPattern, MolecularComponentPattern> link = oldMils.getLink();
MolecularComponentPattern mcpOne = oldMils.getMolecularComponentPatternOne();
MolecularComponentPattern mcpTwo = oldMils.getMolecularComponentPatternTwo();
if(!oldToNewMcp.containsKey(mcpOne) || !oldToNewMcp.containsKey(mcpTwo)) {
linksToRemove.add(oldMils);
} else {
Pair<MolecularComponentPattern, MolecularComponentPattern> newLink = new Pair(oldToNewMcp.get(mcpOne), oldToNewMcp.get(mcpTwo));
oldMils.setLink(newLink);
}
}
getInternalLinkSet().removeAll(linksToRemove);

String ilSetExceptionPrefix = "InternalLinkSet of SpeciesContextSpec of Species '" + getSpeciesContext().getName() + "' ";
// step 4: sanity check on links (after)
// step 4.1: we build a new authoritativeMcpSet2 (the old authoritativeMcpSet still contains mcp that are unlinked)
Set<MolecularComponentPattern> authoritativeMcpSet2 = new LinkedHashSet<>();
for (MolecularComponent mc : componentList) {
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
authoritativeMcpSet2.add(mcp);
}
// step 4.2: we can't assume how many links we have, even 0 is possible if we deleted them manually
// hoever, any mcp instance present in a link must be valid (present in the authoritativeMcpSet)
for(MolecularInternalLinkSpec link : getInternalLinkSet()) {
MolecularComponentPattern mcpOne = link.getMolecularComponentPatternOne();
MolecularComponentPattern mcpTwo = link.getMolecularComponentPatternTwo();
if(!authoritativeMcpSet.contains(mcpOne)) {
if(!authoritativeMcpSet2.contains(mcpOne)) {
throw new RuntimeException(ilSetExceptionPrefix + "has invalid MolecularComponentPattern instance");
}
if(!authoritativeMcpSet.contains(mcpTwo)) {
if(!authoritativeMcpSet2.contains(mcpTwo)) {
throw new RuntimeException(ilSetExceptionPrefix + "has invalid MolecularComponentPattern instance");
}
}
Expand Down

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