use of org.vcell.relationship.ConversionTableRow in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method createTableRow.
private ConversionTableRow createTableRow(BioPaxObject bpObject, String interactionId, String interactionLabel, String participantType, double stoich, HashSet<RelationshipObject> relationshipObjects) {
String location = "";
ConversionTableRow conversionTableRow = new ConversionTableRow(bpObject);
conversionTableRow.setInteractionId(interactionId);
conversionTableRow.setInteractionLabel(interactionLabel);
conversionTableRow.setParticipantType(participantType);
// stoichiometry and location
if (participantType.equals("Reactant") || participantType.equals("Product")) {
// stoichiometry
if (stoich != 0)
conversionTableRow.setStoich(stoich);
else
conversionTableRow.setStoich(1.0);
// location
// if(((PhysicalEntity)bpObject).getCellularLocation() != null && ((PhysicalEntity)bpObject).getCellularLocation().getTerm().size()>0)
// location = ((PhysicalEntity)bpObject).getCellularLocation().getTerm().get(0);
// else
location = bioModel.getModel().getStructures()[0].getName();
conversionTableRow.setLocation(location);
} else {
conversionTableRow.setStoich(1.0);
// else
if (bpObject instanceof Transport) {
if (bioModel.getModel().getMembranes().size() > 0)
location = bioModel.getModel().getMembranes().get(0).getName();
else
location = bioModel.getModel().getStructures()[0].getName();
} else
location = bioModel.getModel().getStructures()[0].getName();
conversionTableRow.setLocation(location);
}
// id
if (relationshipObjects == null) {
if (bpObject instanceof Entity) {
String id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
if (isValid(id))
conversionTableRow.setId(id);
else
conversionTableRow.setId(changeID(id));
}
} else {
String id = null;
for (RelationshipObject relationshipObject : relationshipObjects) {
if (relationshipObject.getBioModelEntityObject() instanceof MolecularType) {
id = relationshipObject.getBioModelEntityObject().getName();
location = "";
} else if (relationshipObject.getBioModelEntityObject().getStructure().getName().equalsIgnoreCase(location)) {
id = relationshipObject.getBioModelEntityObject().getName();
}
}
if (id != null) {
// the linked bmObject with the same location will be used
conversionTableRow.setId(id);
} else {
// a new bmObject will be created if no linked bmObject in the same location
if (bpObject instanceof Entity) {
id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
if (isValid(id))
conversionTableRow.setId(id);
else
conversionTableRow.setId(changeID(id));
}
}
}
return conversionTableRow;
}
use of org.vcell.relationship.ConversionTableRow in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method createTableRowForTransportParticipant.
private ConversionTableRow createTableRowForTransportParticipant(BioPaxObject bpObject, String interactionId, String interactionLabel, String participantType, double stoich, HashSet<RelationshipObject> relationshipObjects) {
String location = "";
ConversionTableRow conversionTableRow = new ConversionTableRow(bpObject);
conversionTableRow.setInteractionId(interactionId);
conversionTableRow.setInteractionLabel(interactionLabel);
conversionTableRow.setParticipantType(participantType);
// stoichiometry and location
Model model = bioModel.getModel();
StructureTopology structTopology = model.getStructureTopology();
if (participantType.equals("Reactant")) {
// stoichiometry
if (stoich != 0)
conversionTableRow.setStoich(stoich);
else
conversionTableRow.setStoich(1.0);
// else{
if (model.getMembranes().size() > 0)
location = structTopology.getOutsideFeature(model.getMembranes().get(0)).getName();
else
location = model.getStructures()[0].getName();
// }
conversionTableRow.setLocation(location);
} else if (participantType.equals("Product")) {
// stoichiometry
if (stoich != 0)
conversionTableRow.setStoich(stoich);
else
conversionTableRow.setStoich(1.0);
// else{
if (model.getMembranes().size() > 0)
location = structTopology.getInsideFeature(model.getMembranes().get(0)).getName();
else
location = model.getStructures()[0].getName();
// }
conversionTableRow.setLocation(location);
} else {
conversionTableRow.setStoich(1.0);
// else
if (bpObject instanceof Transport) {
if (model.getMembranes().size() > 0)
location = model.getMembranes().get(0).getName();
else
location = model.getStructures()[0].getName();
} else
location = model.getStructures()[0].getName();
conversionTableRow.setLocation(location);
}
// id
if (relationshipObjects == null) {
if (bpObject instanceof Entity) {
String id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
if (isValid(id))
conversionTableRow.setId(id);
else
conversionTableRow.setId(changeID(id));
}
} else {
String id = null;
for (RelationshipObject relationshipObject : relationshipObjects) {
if (relationshipObject.getBioModelEntityObject().getStructure().getName().equalsIgnoreCase(location)) {
id = relationshipObject.getBioModelEntityObject().getName();
}
}
if (id != null) {
// the linked bmObject with the same location will be used
conversionTableRow.setId(id);
} else {
// a new bmObject will be created if no linked bmObject in the same location
if (bpObject instanceof Entity) {
id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
if (isValid(id))
conversionTableRow.setId(id);
else
conversionTableRow.setId(changeID(id));
}
}
}
return conversionTableRow;
}
use of org.vcell.relationship.ConversionTableRow in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method refreshData.
private void refreshData() {
if (bioModel == null || bioModel.getPathwayModel() == null || bioPaxObjects == null) {
setData(null);
return;
}
// function I :: get selected objects only
// create ConversionTableRow objects
allPathwayObjectList = new ArrayList<ConversionTableRow>();
convertedBPObjects = new HashSet<BioPaxObject>();
printObjects(bioPaxObjects);
BioModel.printBpModelObjects(bioModel.getPathwayModel().getBiopaxObjects());
// BioModel.printBpRelationshipObjects(bioModel.getRelationshipModel().getBioPaxObjects()); // derived; the bpObjects that are part of a relationship
BioModel.printRelationships(bioModel.getRelationshipModel().getRelationshipObjects());
System.out.println("----------------------------------------------------------------------");
for (BioPaxObject bpo : bioPaxObjects) {
if (bpo instanceof Conversion) {
if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
Conversion conversion = (Conversion) bpo;
ArrayList<String> nameList = conversion.getName();
String interactionId = conversion.getID();
String interactionLabel = nameList.isEmpty() ? conversion.getIDShort() : nameList.get(0);
ConversionTableRow newConversionTableRow = createTableRow(conversion, interactionId, interactionLabel, "Conversion", 1.0, null);
allPathwayObjectList.add(newConversionTableRow);
convertedBPObjects.add(bpo);
ArrayList<Stoichiometry> stoichiometryList = conversion.getParticipantStoichiometry();
// stoichiometryMap problem:
// how to deal with the case that the same object occurs on both left and right sides
HashMap<PhysicalEntity, Double> stoichiometryMap = createStoichiometryMap(stoichiometryList);
// reactant
for (BioPaxObject bpObject1 : conversion.getLeft()) {
Double stoich = 1.0;
if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
}
ConversionTableRow conversionTableRow;
if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
if (conversion instanceof Transport)
conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
else
conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
} else {
if (conversion instanceof Transport)
conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
else
conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
}
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(bpObject1);
}
// product
for (BioPaxObject bpObject1 : conversion.getRight()) {
Double stoich = 1.0;
if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
}
ConversionTableRow conversionTableRow;
if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
if (conversion instanceof Transport)
conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
else
conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
} else {
if (conversion instanceof Transport)
conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
else
conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
}
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(bpObject1);
}
// control
for (BioPaxObject bpObject : bioModel.getPathwayModel().getBiopaxObjects()) {
if (bpObject instanceof Control) {
Control control = (Control) bpObject;
if (control instanceof Catalysis) {
// catalysis
if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
for (PhysicalEntity pe : ((Catalysis) control).getPhysicalControllers()) {
ConversionTableRow conversionTableRow;
if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, null);
} else {
conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
}
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(pe);
}
}
} else {
// other control types
if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
for (PhysicalEntity pe : control.getPhysicalControllers()) {
ConversionTableRow conversionTableRow;
if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, null);
} else {
conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
}
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(pe);
}
}
}
}
}
}
} else if (bpo instanceof Catalysis) {
for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
if (!convertedBPObjects.contains(pe)) {
ConversionTableRow conversionTableRow;
if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, null);
} else {
conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
}
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(pe);
}
}
for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
// TODO
}
} else if (bpo instanceof Control) {
for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
if (!convertedBPObjects.contains(pe)) {
ConversionTableRow conversionTableRow;
if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, null);
} else {
conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
}
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(pe);
}
}
for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
// TODO
}
}
}
// 2nd pass - entities selected as themselves
for (BioPaxObject bpo : bioPaxObjects) {
if (bpo instanceof PhysicalEntity) {
if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
PhysicalEntity physicalEntityObject = (PhysicalEntity) bpo;
// we add standalone selected entities, only if they were not already added as part of any reaction
if (!convertedBPObjects.contains(physicalEntityObject)) {
ConversionTableRow conversionTableRow = createTableRow(physicalEntityObject, "", "", "", 1.0, null);
allPathwayObjectList.add(conversionTableRow);
convertedBPObjects.add(physicalEntityObject);
}
}
}
}
// apply text search function for particular columns
ArrayList<ConversionTableRow> pathwayObjectList = new ArrayList<ConversionTableRow>();
if (searchText == null || searchText.length() == 0) {
pathwayObjectList.addAll(allPathwayObjectList);
} else {
String lowerCaseSearchText = searchText.toLowerCase();
for (ConversionTableRow rs : allPathwayObjectList) {
BioPaxObject bpObject = rs.getBioPaxObject();
if (rs.interactionLabel().toLowerCase().contains(lowerCaseSearchText) || rs.participantType().toLowerCase().contains(lowerCaseSearchText) || getLabel(bpObject).toLowerCase().contains(lowerCaseSearchText) || getType(bpObject).toLowerCase().contains(lowerCaseSearchText)) {
pathwayObjectList.add(rs);
}
}
}
setData(pathwayObjectList);
GuiUtils.flexResizeTableColumns(ownerTable);
}
use of org.vcell.relationship.ConversionTableRow in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method isCellEditable.
public boolean isCellEditable(int iRow, int iCol) {
ConversionTableRow conversonTableRow = getValueAt(iRow);
boolean editable = true;
if (conversonTableRow.participantType().equals("Conversion") || conversonTableRow.participantType().equals("")) {
editable = false;
}
// only allow users to edit the stoich and location
return ((iCol == iColStoich && editable) || iCol == iColLocation || iCol == iColID);
}
use of org.vcell.relationship.ConversionTableRow in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method getValueAt.
public Object getValueAt(int iRow, int iCol) {
ConversionTableRow conversionTableRow = getValueAt(iRow);
BioPaxObject bpObject = conversionTableRow.getBioPaxObject();
switch(iCol) {
case iColInteraction:
{
return conversionTableRow.interactionLabel();
}
case iColParticipant:
{
return conversionTableRow.participantType();
}
case iColEntity:
{
return getLabel(bpObject);
}
case iColType:
{
return getType(bpObject);
}
case iColStoich:
{
return conversionTableRow.stoich();
}
case iColID:
{
return conversionTableRow.id();
}
case iColLocation:
{
return conversionTableRow.location();
}
default:
{
return null;
}
}
}
Aggregations