use of org.vcell.pathway.sbpax.SBMeasurable in project vcell by virtualcell.
the class PathwayTableModel method hasMeasuredData.
private boolean hasMeasuredData(Interaction interaction) {
Set<SBEntity> subEntities = new HashSet<SBEntity>();
subEntities.add(interaction);
Set<Control> controls = BioPAXUtil.findAllControls(interaction, pathwayModel);
subEntities.addAll(controls);
subEntities = SBPAX3Util.extractAllEntities(subEntities);
for (SBEntity subEntity : subEntities) {
if (subEntity instanceof SBMeasurable) {
return true;
}
}
return false;
}
use of org.vcell.pathway.sbpax.SBMeasurable in project vcell by virtualcell.
the class BioPaxObjectPropertiesPanel method refreshInterface.
protected void refreshInterface() {
if (bioPaxObject == null) {
// sanity check
return;
}
ArrayList<BioPaxObjectProperty> propertyList = new ArrayList<BioPaxObjectProperty>();
if (!(bioPaxObject instanceof SBEntity)) {
tableModel.setData(propertyList);
return;
}
SBEntity sbEntity = (SBEntity) bioPaxObject;
if (!(sbEntity instanceof Entity)) {
tableModel.setData(propertyList);
return;
}
Entity entity = (Entity) sbEntity;
// entity::type
propertyList.add(new BioPaxObjectProperty("Type", bioPaxObject.getTypeLabel()));
if (lookupContains(entity)) {
propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (looking...)"));
} else if (entity.getFormalNames() != null && entity.getFormalNames().size() != 0) {
propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (" + entity.getFormalNames().get(0) + ")"));
} else if (entity.getName() != null && entity.getName().size() > 0) {
String displayName = entity.getName().get(0);
if (entity.getxRef() != null && entity.getxRef().size() > 0) {
displayName = displayName + " (double-click lookup)";
}
// entity::name
propertyList.add(new BioPaxObjectProperty("Name", displayName));
}
// entity::Link
for (RelationshipObject rObject : bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject)) {
BioModelEntityObject beObject = rObject.getBioModelEntityObject();
String sType = beObject.getDisplayType();
propertyList.add(new BioPaxObjectProperty("Linked physiology object (" + sType + ")", beObject.getName(), beObject));
}
if (entity instanceof PhysicalEntity) {
// ------------------------ PHYSICAL ENTITY -----------------------
PhysicalEntity physicalEntity = (PhysicalEntity) entity;
// physicalEntity::feature (***ignored***)
// physicalEntity::memberPhysicalEntity (***ignored***)
// physicalEntity::notFeature (***ignored***)
// TODO: extract the kinetic law, then the SBEntities, then the measurables, units, aso
boolean isReactionParticipant = BioPAXUtil.isReactionParticipant(physicalEntity, bioModel.getPathwayModel());
String role = "";
if (BioPAXUtil.isController(physicalEntity, bioModel.getPathwayModel())) {
role += "Controller";
if (isReactionParticipant) {
role += ", Participant";
}
} else if (isReactionParticipant) {
role += "Participant";
}
if (!role.isEmpty()) {
propertyList.add(new BioPaxObjectProperty("Role(s)", role));
}
if (!(physicalEntity instanceof SmallMolecule)) {
// physicalEntity::cellular location
CellularLocationVocabulary cellularLocation = physicalEntity.getCellularLocation();
if (cellularLocation != null && cellularLocation.getTerm() != null && cellularLocation.getTerm().size() > 0) {
propertyList.add(new BioPaxObjectProperty("Cellular Location", cellularLocation.getTerm().get(0), cellularLocation));
} else if (entity.getName() != null && entity.getName().size() > 1) {
String location = entity.getName().get(1);
if (location.contains("[") && location.contains("]")) {
location = location.substring(location.indexOf("[") + 1, location.indexOf("]"));
propertyList.add(new BioPaxObjectProperty("Cellular Location", location));
}
}
}
if (physicalEntity instanceof Complex) {
Complex complex = (Complex) physicalEntity;
// complex::components
for (PhysicalEntity pe : complex.getComponents()) {
propertyList.add(new BioPaxObjectProperty("Component", getEntityName(pe), pe));
}
} else if (physicalEntity instanceof Protein) {
// Protein protein = (Protein)entity;
// protein::entity reference (***ignored***)
} else if (physicalEntity instanceof SmallMolecule) {
SmallMolecule sm = (SmallMolecule) physicalEntity;
EntityReference er = sm.getEntityReference();
if (er != null && !er.getName().isEmpty() && er.getName().get(0) != null && !er.getName().get(0).isEmpty()) {
propertyList.add(new BioPaxObjectProperty("Entity Reference", er.getName().get(0)));
ArrayList<Xref> xrefList = er.getxRef();
for (Xref xref : xrefList) {
propertyList.add(new BioPaxObjectProperty(" Xref", xref.getDb() + ":" + xref.getId(), xref));
}
}
} else if (physicalEntity instanceof Dna) {
// dna::entityReference (***ignored***)
} else if (physicalEntity instanceof DnaRegion) {
// dnaRegion::entityReference (***ignored***)
} else if (physicalEntity instanceof Rna) {
// rna::entityReference (***ignored***)
} else if (physicalEntity instanceof RnaRegion) {
// rnaRegion::entityReference (***ignored***)
}
} else if (entity instanceof Interaction) {
// --------------------------- INTERACTION -------------------
Interaction interaction = (Interaction) entity;
// interaction::interactionType
for (InteractionVocabulary interactionVocabulary : interaction.getInteractionTypes()) {
if (interactionVocabulary.getTerm().size() > 0) {
propertyList.add(new BioPaxObjectProperty("Interaction Type", interactionVocabulary.getTerm().get(0), interactionVocabulary));
}
}
// interaction::participants
for (InteractionParticipant interactionParticipant : interaction.getParticipants()) {
PhysicalEntity physicalEntity = interactionParticipant.getPhysicalEntity();
String physicalEntityName = physicalEntity.getName().size() > 0 ? physicalEntity.getName().get(0) : physicalEntity.getIDShort();
String cellularLocation = "";
if (physicalEntity.getCellularLocation() != null) {
cellularLocation = physicalEntity.getCellularLocation().getTerm().size() > 0 ? " [" + physicalEntity.getCellularLocation().getTerm().get(0) + "]" : "";
}
propertyList.add(new BioPaxObjectProperty(interactionParticipant.getLevel3PropertyName(), physicalEntityName + cellularLocation, physicalEntity));
}
// get the controllers for interactions
// we always need this because there's no guarantee we'll have kinetic laws
// for instance pathway commons doesn't have quantitative information
Set<String> controllersNames = getControllersNames(interaction);
if (controllersNames.size() > 0) {
for (String str : controllersNames) {
// String tooltip = "<html>how many of these 12 M <br>average size 1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
String tooltip = "";
propertyList.add(new BioPaxObjectProperty("Controlled by", str, interaction, tooltip));
}
}
// get the kinetic laws (if any)
Set<Control> controls = BioPAXUtil.getControlsOfInteraction(interaction, bioModel.getPathwayModel());
for (Control control : controls) {
ArrayList<SBEntity> sbEntities = control.getSBSubEntity();
for (SBEntity sbE : sbEntities) {
// the only SBSubEntities allowed in a control are kinetic laws
if (sbE.getID().contains("kineticLaw")) {
String str = new String();
if (control.getPhysicalControllers() != null) {
str += " for Controller(s): ";
for (PhysicalEntity ep : control.getPhysicalControllers()) {
if (ep.getName().size() > 0) {
str += ep.getName().get(0);
} else {
str += ep.getIDShort();
}
str += " ";
}
}
String sDetails = "";
ArrayList<SBVocabulary> sbTerms = sbE.getSBTerm();
for (SBVocabulary sbv : sbTerms) {
// type of kinetic law
String str1 = sbv.getID();
str1 = str1.substring(str1.lastIndexOf('#') + 1);
System.out.println(str1);
SBOTerm sboT = SBOListEx.sboMap.get(str1);
sDetails += "<font color=\"#660000\"><b>" + sboT.getName() + "</b></font>" + " " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
sDetails += "<br>";
}
ArrayList<SBEntity> klProperties = sbE.getSBSubEntity();
for (SBEntity klProperty : klProperties) {
if (klProperty instanceof SBMeasurable) {
SBMeasurable m = (SBMeasurable) klProperty;
String str1 = "";
String str2 = "";
String str3 = "";
if (m.hasTerm()) {
str1 += m.extractSBOTermAsString();
}
if (m.hasNumber()) {
str2 += m.getNumber().get(0);
}
if (m.hasUnit()) {
str3 += m.extractSBOUnitAsString();
}
// str1 is an SBO id, for example "SBO:0000064"
SBOTerm sboT = SBOListEx.sboMap.get(str1);
sDetails += sboT.getSymbol() + " (" + sboT.getName() + ")" + "<font color=\"#660000\"><b>" + str2 + str3 + "</b></font>" + " " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
} else {
sDetails = klProperty.getIDShort() + " " + klProperty.getTypeLabel();
}
sDetails += "<br>";
}
// String tooltip = "<html>how many of these 12 M <br>average size 1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
String tooltip = "";
BioPaxObjectProperty bpop = new BioPaxObjectProperty("Kinetic Law" + str, sbE.getID(), sbE, tooltip);
bpop.setDetails(sDetails);
propertyList.add(bpop);
}
}
}
if (interaction instanceof Control) {
// TODO: is this ever being called?
Control c = (Control) interaction;
// catalysis::controlled
Interaction controlledInteraction = c.getControlledInteraction();
if (controlledInteraction != null) {
String controlledName = controlledInteraction.getIDShort();
if (controlledInteraction.getName().size() > 0) {
controlledName = controlledInteraction.getName().get(0);
}
propertyList.add(new BioPaxObjectProperty("Controlled Interaction", controlledName, controlledInteraction));
}
}
} else if (entity instanceof GroupObject) {
// ---------------------- GROUP OBJECT ------------------
GroupObject groupObject = (GroupObject) entity;
for (BioPaxObject bpo : groupObject.getGroupedObjects()) {
propertyList.add(new BioPaxObjectProperty("Element::" + bpo.getTypeLabel(), getEntityName((Entity) bpo), bpo));
}
}
// entity::comments
for (String comment : entity.getComments()) {
propertyList.add(new BioPaxObjectProperty("Comment", comment));
}
// entity::xRef
ArrayList<Xref> xrefList = ((Entity) bioPaxObject).getxRef();
for (Xref xref : xrefList) {
if (xref instanceof UnificationXref) {
propertyList.add(new BioPaxObjectProperty("Xref", xref.getDb() + ":" + xref.getId(), xref));
}
}
for (Xref xref : xrefList) {
if (xref instanceof RelationshipXref) {
propertyList.add(new BioPaxObjectProperty("Xref (related)", xref.getDb() + ":" + xref.getId(), xref));
}
}
for (Xref xref : xrefList) {
if (xref instanceof PublicationXref) {
propertyList.add(new BioPaxObjectProperty("Publication", xref.getDb() + ":" + xref.getId(), xref));
}
}
// for(SBVocabulary sbVocab : sbEntity.getSBTerm()) {
// propertyList.add(new BioPaxObjectProperty("SBO Term", SBPAXLabelUtil.makeLabel(sbVocab)));
// }
// if(sbEntity instanceof Interaction) {
// // TODO: this goes away
// Interaction interaction = (Interaction) sbEntity;
// Set<SBEntity> subEntities = new HashSet<SBEntity>();
// subEntities.add(interaction);
// Set<Control> controls = BioPAXUtil.findAllControls(interaction, bioModel.getPathwayModel());
// subEntities.addAll(controls);
// subEntities = SBPAX3Util.extractAllEntities(subEntities);
// for(SBEntity subEntity : subEntities) {
// if(subEntity instanceof SBMeasurable) {
// propertyList.add(new BioPaxObjectProperty("Measured quantity", SBPAXLabelUtil.makeLabel(subEntity)));
// }
// }
// }
tableModel.setData(propertyList);
}
use of org.vcell.pathway.sbpax.SBMeasurable in project vcell by virtualcell.
the class SBPAXKineticsExtractor method extractKineticsExactMatch.
public static boolean extractKineticsExactMatch(ReactionStep reaction, Process process) throws ExpressionException, PropertyVetoException {
// we try a perfect match first based on the existence of a SBOTerm in the kinetic law
if (process.getControl() == null) {
// no control means no kinetic law - nothing more to do
return true;
}
Control control = process.getControl();
ArrayList<SBEntity> sbEntities = control.getSBSubEntity();
for (SBEntity sbE : sbEntities) {
// the only SBSubEntities allowed in a control are kinetic laws
if (sbE.getID().contains("kineticLaw")) {
// build list of the parameters of this kinetic law in sboParams
// params of this kinetic law
ArrayList<SBOParam> sboParams = new ArrayList<SBOParam>();
ArrayList<SBEntity> subEntities = sbE.getSBSubEntity();
for (SBEntity subEntity : subEntities) {
if (subEntity instanceof SBMeasurable) {
SBMeasurable m = (SBMeasurable) subEntity;
if (!m.hasTerm()) {
// we don't know what to do with a measurable with no SBTerm
break;
}
String termName = m.extractSBOTermAsString();
SBOTerm sboT = SBOListEx.sboMap.get(termName);
System.out.println(" " + sboT.getIndex() + " " + sboT.getName());
SBOParam sboParam = matchSBOParam(sboT);
if (m.hasNumber()) {
double number = m.getNumber().get(0);
sboParam.setNumber(number);
}
if (m.hasUnit()) {
String unit = m.extractSBOUnitAsString();
sboParam.setUnit(unit);
}
sboParams.add(sboParam);
}
}
// find if a kinetic law type exists and if not guesstimate one based on parameters
// simple rule: if we have a Km param it's MM, otherwise it's mass action
ArrayList<SBVocabulary> sbTerms = sbE.getSBTerm();
if (sbTerms.isEmpty()) {
// return false;
SBVocabulary sbTerm = new SBVocabulary();
ArrayList<String> termNames = new ArrayList<String>();
String id;
SBOParam kMichaelis = extractMichaelisForwardParam(sboParams);
if (kMichaelis == null) {
// mass action rate law
id = new String("SBO:0000012");
} else {
// irreversible Henri-Michaelis-Menten rate law
id = new String("SBO:0000029");
}
// termNames.add(id);
// sbTerm.setTerm(termNames);
sbTerm.setID(id);
sbTerms.add(sbTerm);
}
System.out.println(" kinetic law ID: " + sbTerms.get(0).getID());
// identify the kinetic law type (mass action, michaelis menten, etc) and bring it in vCell
for (SBVocabulary sbv : sbTerms) {
// use for loop even though we only expect 1 SBTerm
// SBVocabulary id, used to retrieve the kinetic law type
String vocabularyID = sbv.getID();
SBOTerm sboT = SBOUtil.getSBOTermFromVocabularyId(vocabularyID);
System.out.println(vocabularyID + " " + sboT.getName());
SBOParam kForward;
SBOParam kCat;
SBOParam vM;
SBOParam kReverse;
SBOParam kMichaelis;
Kinetics kinetics;
MappedKinetics current = matchSBOKineticLaw(sboT);
switch(current) {
case SBO_0000069:
case SBO_0000432:
// some kinetic laws unknown to vCell will fall through to this category
// honestly i don't know what to do with them
System.out.println("GeneralKinetics");
// TODO: what to do here?
return true;
case SBO_0000012:
case SBO_0000078:
System.out.println("MassActionKinetics - reversible");
kForward = extractKForwardParam(sboParams);
kReverse = extractKReverseParam(sboParams);
kinetics = new MassActionKinetics(reaction);
reaction.setKinetics(kinetics);
setKForwardParam(reaction, kForward, kinetics);
setKReverseParam(reaction, kReverse, kinetics);
return true;
case SBO_0000043:
System.out.println("MassActionKinetics - zeroth order irreversible, Kr <- 0 ");
kForward = extractKForwardParam(sboParams);
kinetics = new MassActionKinetics(reaction);
// TODO: what to do here?
return true;
case SBO_0000044:
System.out.println("MassActionKinetics - first order irreversible, Kr <- 0 ");
kForward = extractKForwardParam(sboParams);
kinetics = new MassActionKinetics(reaction);
reaction.setKinetics(kinetics);
setKForwardParam(reaction, kForward, kinetics);
return true;
case SBO_0000028:
case SBO_0000029:
System.out.println("HMM_IRRKinetics");
// TODO: make kCat global variable, set its number and unit in annotation
// TODO: make vM global variable, set its number and unit in annotation
// get the numbers, if present (may be null)
kMichaelis = extractMichaelisForwardParam(sboParams);
vM = extractVMForwardParam(sboParams, process);
kCat = extractKCatForwardParam(sboParams);
kinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
try {
// TODO: create expression only if kCat != null, otherwise use vM directly (if != null) otherwise ???
kinetics.reading(true);
setVMForwardParamAsExpression(reaction, kCat, kinetics);
} finally {
kinetics.reading(false);
}
reaction.setKinetics(kinetics);
setMichaelisForwardParam(reaction, kMichaelis, kinetics);
return true;
case SBO_0000438:
System.out.println("HMMREVKinetics");
kinetics = new HMM_REVKinetics((SimpleReaction) reaction);
return true;
default:
// TODO: guessing happens above - if we have nothing by now we need to raise runtime exception
// change the code below !!!
System.out.println("Unable to match the SBOTerm with any compatible kinetic law.");
// found unmapped kinetic law, we'll try to guess a match
return false;
}
}
}
}
// no SBTerm found so we cannot know for sure the kinetic law, we'll have to guess it
return false;
}
use of org.vcell.pathway.sbpax.SBMeasurable in project vcell by virtualcell.
the class PathwayReaderBiopax3 method addObjectSBMeasurable.
private SBMeasurable addObjectSBMeasurable(Element element) {
if (element.getChildren().size() == 0) {
SBMeasurableProxy proxy = new SBMeasurableProxy();
addAttributes(proxy, element);
pathwayModel.add(proxy);
return proxy;
}
SBMeasurable sbSubEntity = new SBMeasurable();
addAttributes(sbSubEntity, element);
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
if (!addContentSBMeasurable(sbSubEntity, element, childElement)) {
showUnexpected(childElement);
}
}
}
pathwayModel.add(sbSubEntity);
return sbSubEntity;
}
use of org.vcell.pathway.sbpax.SBMeasurable in project vcell by virtualcell.
the class PathwayProducerBiopax3 method addContentSBMeasurable.
private Element addContentSBMeasurable(BioPaxObject bpObject, Element element) {
element = addContentUtilityClass(bpObject, element);
SBMeasurable ob = (SBMeasurable) bpObject;
Element tmpElement = null;
if (ob.getUnit() != null && ob.getUnit().size() > 0) {
List<UnitOfMeasurement> list = ob.getUnit();
for (UnitOfMeasurement item : list) {
tmpElement = new Element("hasUnit", sbx3);
String id = item.getID();
if (URIUtil.isAbsoluteURI(id)) {
tmpElement.setAttribute("resource", context.relativizeURI(tmpElement, id), rdf);
} else {
tmpElement.setAttribute("nodeID", id, rdf);
}
mustPrintObject(item);
element.addContent(tmpElement);
}
}
if (ob.getSBTerm() != null && ob.getSBTerm().size() > 0) {
List<SBVocabulary> list = ob.getSBTerm();
for (SBVocabulary item : list) {
tmpElement = new Element("sbTerm", sbx3);
addIDToProperty(tmpElement, item);
mustPrintObject(item);
element.addContent(tmpElement);
}
}
if (ob.getNumber() != null && ob.getNumber().size() > 0) {
List<Double> list = ob.getNumber();
for (Double item : list) {
tmpElement = new Element("hasNumber", sbx3);
tmpElement.setAttribute("datatype", schemaDouble, rdf);
tmpElement.setText(item.toString());
element.addContent(tmpElement);
}
}
return element;
}
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