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nroehnernroehner
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Fixed inference of total ordering of components during SBOL conversion and fixed bug with minimizing graph (deleting select blank edges).
1 parent 75d848a commit 770e60f

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2 files changed

+100
-47
lines changed

2 files changed

+100
-47
lines changed

‎src/main/java/knox/spring/data/neo4j/domain/NodeSpace.java‎

Lines changed: 11 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -830,15 +830,16 @@ public void deleteBlankEdges(Set<Edge> blankEdges) {
830830
}
831831

832832
public boolean deleteBlankEdge(Edge edge, HashMap<String, Set<Edge>> nodeIDToIncomingEdges) {
833-
if ((nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1 || edge.getTail().getNumEdges() == 1)
833+
if (((nodeIDToIncomingEdges.containsKey(edge.getHeadID()) && nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1)
834+
|| edge.getTail().getNumEdges() == 1)
834835
&& !edge.getTail().hasDiffNodeType(edge.getHead())
835836
&& (!edge.getTail().isAcceptNode() || edge.getHead().isAcceptNode()
836837
|| nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1)
837838
&& (!edge.getHead().isStartNode() || edge.getTail().isStartNode()
838839
|| edge.getTail().getNumEdges() == 1)
839840
&& (!edge.getTail().isStartNode()
840-
|| nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1
841-
|| !nodeIDToIncomingEdges.get(edge.getTailID()).isEmpty())) {
841+
|| (nodeIDToIncomingEdges.containsKey(edge.getHeadID()) && nodeIDToIncomingEdges.get(edge.getHeadID()).size() == 1)
842+
|| (nodeIDToIncomingEdges.containsKey(edge.getTailID()) && !nodeIDToIncomingEdges.get(edge.getTailID()).isEmpty()))) {
842843
edge.delete();
843844

844845
Set<Edge> headEdges = edge.getHead().removeEdges();
@@ -851,11 +852,13 @@ public boolean deleteBlankEdge(Edge edge, HashMap<String, Set<Edge>> nodeIDToInc
851852

852853
Set<Edge> incomingHeadEdges = new HashSet<Edge>();
853854

854-
for (Edge incomingHeadEdge : nodeIDToIncomingEdges.get(edge.getHeadID())) {
855-
if (incomingHeadEdge != edge) {
856-
incomingHeadEdge.setHead(edge.getTail());
857-
858-
incomingHeadEdges.add(incomingHeadEdge);
855+
if (nodeIDToIncomingEdges.containsKey(edge.getHeadID())) {
856+
for (Edge incomingHeadEdge : nodeIDToIncomingEdges.get(edge.getHeadID())) {
857+
if (incomingHeadEdge != edge) {
858+
incomingHeadEdge.setHead(edge.getTail());
859+
860+
incomingHeadEdges.add(incomingHeadEdge);
861+
}
859862
}
860863
}
861864

‎src/main/java/knox/spring/data/neo4j/sbol/SBOLConversion.java‎

Lines changed: 89 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -85,40 +85,41 @@ private List<NodeSpace> recurseVariableComponents(CombinatorialDerivation combin
8585
// order components by sequence constraints
8686
VariableComponent[] sortedVCs = sortVariableComponents(combinatorialDerivation);
8787
for (VariableComponent variableComponent : sortedVCs) {
88+
if (variableComponent != null) {
89+
// recurse through variant derivations
90+
Set<CombinatorialDerivation> variantDerivs = variableComponent.getVariantDerivations();
8891

89-
// recurse through variant derivations
90-
Set<CombinatorialDerivation> variantDerivs = variableComponent.getVariantDerivations();
92+
Boolean hasVariants = !variableComponent.getVariants().isEmpty() || !variableComponent.getVariantCollections().isEmpty();
9193

92-
Boolean hasVariants = !variableComponent.getVariants().isEmpty() || !variableComponent.getVariantCollections().isEmpty();
93-
94-
//handle structure for just repeats
95-
if (variantDerivs.size() == 1 && !hasVariants){
96-
for (CombinatorialDerivation cv : variantDerivs) {
97-
inputSpace.add(applyOperator(variableComponent.getOperator(), recurseVariableComponents(cv)));
94+
//handle structure for just repeats
95+
if (variantDerivs.size() == 1 && !hasVariants){
96+
for (CombinatorialDerivation cv : variantDerivs) {
97+
inputSpace.add(applyOperator(variableComponent.getOperator(), recurseVariableComponents(cv)));
98+
}
9899
}
99-
}
100100

101-
//else handle collapsed complex ORs
102-
else if (variantDerivs.size() > 0){
103-
List<NodeSpace> orSpace = new LinkedList<>();
104-
NodeSpace outputSpace = new NodeSpace();
101+
//else handle collapsed complex ORs
102+
else if (variantDerivs.size() > 0){
103+
List<NodeSpace> orSpace = new LinkedList<>();
104+
NodeSpace outputSpace = new NodeSpace();
105105

106-
if (hasVariants){
107-
orSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template)); //add variants
108-
}
106+
if (hasVariants){
107+
orSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template)); //add variants
108+
}
109109

110-
for (CombinatorialDerivation cv : variantDerivs) {
111-
orSpace.add(applyOperator(OperatorType.ONE, recurseVariableComponents(cv)));
112-
}
110+
for (CombinatorialDerivation cv : variantDerivs) {
111+
orSpace.add(applyOperator(OperatorType.ONE, recurseVariableComponents(cv)));
112+
}
113113

114-
OROperator.apply(orSpace, outputSpace); //"or" all the elements in the list
115-
List<NodeSpace> tempSpace = new LinkedList<>();
116-
tempSpace.add(outputSpace);
117-
inputSpace.add(applyOperator(variableComponent.getOperator(), tempSpace));
118-
}
114+
OROperator.apply(orSpace, outputSpace); //"or" all the elements in the list
115+
List<NodeSpace> tempSpace = new LinkedList<>();
116+
tempSpace.add(outputSpace);
117+
inputSpace.add(applyOperator(variableComponent.getOperator(), tempSpace));
118+
}
119119

120-
else if (hasVariants){
121-
inputSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template));
120+
else if (hasVariants){
121+
inputSpace.add(createNodeSpaceFromVariableComponent(variableComponent, template));
122+
}
122123
}
123124
}
124125

@@ -128,20 +129,69 @@ else if (hasVariants){
128129
private VariableComponent[] sortVariableComponents(CombinatorialDerivation combinatorialDerivation){
129130
//make ordered components from sequence constraints
130131
List<Component> orderedComponents = new ArrayList<>();
131-
Set<SequenceConstraint> seqConstraints = combinatorialDerivation.getTemplate().getSequenceConstraints();
132+
133+
ComponentDefinition template = combinatorialDerivation.getTemplate();
134+
Set<SequenceConstraint> seqConstraints = template.getSequenceConstraints();
135+
136+
//check if total ordering
137+
Set<URI> subjectURIs = new HashSet<URI>();
138+
Set<URI> objectURIs = new HashSet<URI>();
139+
140+
Set<URI> firstURI = new HashSet<URI>();
141+
Set<URI> lastURI = new HashSet<URI>();
142+
143+
HashMap<URI,URI> precedesMap = new HashMap<URI,URI>();
144+
132145
for (SequenceConstraint constraint : seqConstraints) {
133-
//subject precedes object
134-
Component subject = constraint.getSubject();
135-
Component object = constraint.getObject();
136-
int subIndex = orderedComponents.indexOf(subject);
137-
int objIndex = orderedComponents.indexOf(object);
138-
if (subIndex == -1 && objIndex == -1){
139-
orderedComponents.add(subject);
140-
orderedComponents.add(object);
141-
}else if(subIndex > -1){
142-
orderedComponents.add(subIndex+1, object);
143-
}else if(objIndex > -1){
144-
orderedComponents.add(objIndex, subject);
146+
if (constraint.getRestriction().equals(RestrictionType.PRECEDES)) {
147+
subjectURIs.add(constraint.getSubjectURI());
148+
objectURIs.add(constraint.getObjectURI());
149+
150+
firstURI.add(constraint.getSubjectURI());
151+
lastURI.add(constraint.getObjectURI());
152+
153+
precedesMap.put(constraint.getSubjectURI(), constraint.getObjectURI());
154+
}
155+
}
156+
157+
firstURI.removeAll(objectURIs);
158+
lastURI.removeAll(subjectURIs);
159+
160+
boolean totalOrdering;
161+
162+
if (firstURI.size() == 1 && lastURI.size() == 1) {
163+
URI currentURI = firstURI.iterator().next();
164+
165+
orderedComponents.add(template.getComponent(currentURI));
166+
167+
while (precedesMap.containsKey(currentURI)) {
168+
currentURI = precedesMap.get(currentURI);
169+
170+
orderedComponents.add(template.getComponent(currentURI));
171+
}
172+
173+
totalOrdering = currentURI.equals(lastURI.iterator().next());
174+
} else {
175+
totalOrdering = false;
176+
}
177+
178+
if (!totalOrdering) {
179+
orderedComponents.clear();
180+
181+
for (SequenceConstraint constraint : seqConstraints) {
182+
//subject precedes object
183+
Component subject = constraint.getSubject();
184+
Component object = constraint.getObject();
185+
int subIndex = orderedComponents.indexOf(subject);
186+
int objIndex = orderedComponents.indexOf(object);
187+
if (subIndex == -1 && objIndex == -1){
188+
orderedComponents.add(subject);
189+
orderedComponents.add(object);
190+
}else if(subIndex > -1){
191+
orderedComponents.add(subIndex+1, object);
192+
}else if(objIndex > -1){
193+
orderedComponents.add(objIndex, subject);
194+
}
145195
}
146196
}
147197

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