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Fixed inference of total ordering of components during SBOL conversio…
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…n and fixed bug with minimizing graph (deleting select blank edges).
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@nroehner
nroehner committed Jan 13, 2020
1 parent 75d848a commit 770e60f
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Showing 2 changed files with 100 additions and 47 deletions.
19 changes: 11 additions & 8 deletions src/main/java/knox/spring/data/neo4j/domain/NodeSpace.java
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Original file line number Diff line number Diff line change
Expand Up @@ -830,15 +830,16 @@ public void deleteBlankEdges(Set<Edge> blankEdges) {
}

public boolean deleteBlankEdge(Edge edge, HashMap<String, Set<Edge>> nodeIDToIncomingEdges) {
if ((nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1 || edge.getTail().getNumEdges() == 1)
if (((nodeIDToIncomingEdges.containsKey(edge.getHeadID()) && nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1)
|| edge.getTail().getNumEdges() == 1)
&& !edge.getTail().hasDiffNodeType(edge.getHead())
&& (!edge.getTail().isAcceptNode() || edge.getHead().isAcceptNode()
|| nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1)
&& (!edge.getHead().isStartNode() || edge.getTail().isStartNode()
|| edge.getTail().getNumEdges() == 1)
&& (!edge.getTail().isStartNode()
|| nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1
|| !nodeIDToIncomingEdges.get(edge.getTailID()).isEmpty())) {
|| (nodeIDToIncomingEdges.containsKey(edge.getHeadID()) && nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1)
|| (nodeIDToIncomingEdges.containsKey(edge.getTailID()) && !nodeIDToIncomingEdges.get(edge.getTailID()).isEmpty()))) {
edge.delete();

Set<Edge> headEdges = edge.getHead().removeEdges();
Expand All @@ -851,11 +852,13 @@ public boolean deleteBlankEdge(Edge edge, HashMap<String, Set<Edge>> nodeIDToInc

Set<Edge> incomingHeadEdges = new HashSet<Edge>();

for (Edge incomingHeadEdge : nodeIDToIncomingEdges.get(edge.getHeadID())) {
if (incomingHeadEdge != edge) {
incomingHeadEdge.setHead(edge.getTail());

incomingHeadEdges.add(incomingHeadEdge);
if (nodeIDToIncomingEdges.containsKey(edge.getHeadID())) {
for (Edge incomingHeadEdge : nodeIDToIncomingEdges.get(edge.getHeadID())) {
if (incomingHeadEdge != edge) {
incomingHeadEdge.setHead(edge.getTail());

incomingHeadEdges.add(incomingHeadEdge);
}
}
}

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128 changes: 89 additions & 39 deletions src/main/java/knox/spring/data/neo4j/sbol/SBOLConversion.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,40 +85,41 @@ private List<NodeSpace> recurseVariableComponents(CombinatorialDerivation combin
// order components by sequence constraints
VariableComponent[] sortedVCs = sortVariableComponents(combinatorialDerivation);
for (VariableComponent variableComponent : sortedVCs) {
if (variableComponent != null) {
// recurse through variant derivations
Set<CombinatorialDerivation> variantDerivs = variableComponent.getVariantDerivations();

// recurse through variant derivations
Set<CombinatorialDerivation> variantDerivs = variableComponent.getVariantDerivations();
Boolean hasVariants = !variableComponent.getVariants().isEmpty() || !variableComponent.getVariantCollections().isEmpty();

Boolean hasVariants = !variableComponent.getVariants().isEmpty() || !variableComponent.getVariantCollections().isEmpty();

//handle structure for just repeats
if (variantDerivs.size() == 1 && !hasVariants){
for (CombinatorialDerivation cv : variantDerivs) {
inputSpace.add(applyOperator(variableComponent.getOperator(), recurseVariableComponents(cv)));
//handle structure for just repeats
if (variantDerivs.size() == 1 && !hasVariants){
for (CombinatorialDerivation cv : variantDerivs) {
inputSpace.add(applyOperator(variableComponent.getOperator(), recurseVariableComponents(cv)));
}
}
}

//else handle collapsed complex ORs
else if (variantDerivs.size() > 0){
List<NodeSpace> orSpace = new LinkedList<>();
NodeSpace outputSpace = new NodeSpace();
//else handle collapsed complex ORs
else if (variantDerivs.size() > 0){
List<NodeSpace> orSpace = new LinkedList<>();
NodeSpace outputSpace = new NodeSpace();

if (hasVariants){
orSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template)); //add variants
}
if (hasVariants){
orSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template)); //add variants
}

for (CombinatorialDerivation cv : variantDerivs) {
orSpace.add(applyOperator(OperatorType.ONE, recurseVariableComponents(cv)));
}
for (CombinatorialDerivation cv : variantDerivs) {
orSpace.add(applyOperator(OperatorType.ONE, recurseVariableComponents(cv)));
}

OROperator.apply(orSpace, outputSpace); //"or" all the elements in the list
List<NodeSpace> tempSpace = new LinkedList<>();
tempSpace.add(outputSpace);
inputSpace.add(applyOperator(variableComponent.getOperator(), tempSpace));
}
OROperator.apply(orSpace, outputSpace); //"or" all the elements in the list
List<NodeSpace> tempSpace = new LinkedList<>();
tempSpace.add(outputSpace);
inputSpace.add(applyOperator(variableComponent.getOperator(), tempSpace));
}

else if (hasVariants){
inputSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template));
else if (hasVariants){
inputSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template));
}
}
}

Expand All @@ -128,20 +129,69 @@ else if (hasVariants){
private VariableComponent[] sortVariableComponents(CombinatorialDerivation combinatorialDerivation){
//make ordered components from sequence constraints
List<Component> orderedComponents = new ArrayList<>();
Set<SequenceConstraint> seqConstraints = combinatorialDerivation.getTemplate().getSequenceConstraints();

ComponentDefinition template = combinatorialDerivation.getTemplate();
Set<SequenceConstraint> seqConstraints = template.getSequenceConstraints();

//check if total ordering
Set<URI> subjectURIs = new HashSet<URI>();
Set<URI> objectURIs = new HashSet<URI>();

Set<URI> firstURI = new HashSet<URI>();
Set<URI> lastURI = new HashSet<URI>();

HashMap<URI,URI> precedesMap = new HashMap<URI,URI>();

for (SequenceConstraint constraint : seqConstraints) {
//subject precedes object
Component subject = constraint.getSubject();
Component object = constraint.getObject();
int subIndex = orderedComponents.indexOf(subject);
int objIndex = orderedComponents.indexOf(object);
if (subIndex == -1 && objIndex == -1){
orderedComponents.add(subject);
orderedComponents.add(object);
}else if(subIndex > -1){
orderedComponents.add(subIndex+1, object);
}else if(objIndex > -1){
orderedComponents.add(objIndex, subject);
if (constraint.getRestriction().equals(RestrictionType.PRECEDES)) {
subjectURIs.add(constraint.getSubjectURI());
objectURIs.add(constraint.getObjectURI());

firstURI.add(constraint.getSubjectURI());
lastURI.add(constraint.getObjectURI());

precedesMap.put(constraint.getSubjectURI(), constraint.getObjectURI());
}
}

firstURI.removeAll(objectURIs);
lastURI.removeAll(subjectURIs);

boolean totalOrdering;

if (firstURI.size() == 1 && lastURI.size() == 1) {
URI currentURI = firstURI.iterator().next();

orderedComponents.add(template.getComponent(currentURI));

while (precedesMap.containsKey(currentURI)) {
currentURI = precedesMap.get(currentURI);

orderedComponents.add(template.getComponent(currentURI));
}

totalOrdering = currentURI.equals(lastURI.iterator().next());
} else {
totalOrdering = false;
}

if (!totalOrdering) {
orderedComponents.clear();

for (SequenceConstraint constraint : seqConstraints) {
//subject precedes object
Component subject = constraint.getSubject();
Component object = constraint.getObject();
int subIndex = orderedComponents.indexOf(subject);
int objIndex = orderedComponents.indexOf(object);
if (subIndex == -1 && objIndex == -1){
orderedComponents.add(subject);
orderedComponents.add(object);
}else if(subIndex > -1){
orderedComponents.add(subIndex+1, object);
}else if(objIndex > -1){
orderedComponents.add(objIndex, subject);
}
}
}

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