Search in sources :

Example 1 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class PathwayMapping method createReactionStepFromPathway.

/*
	 * for reaction:
	 * 1. annotate the selected vcell object using linked pathway conversion
	 * 2. add non-existing speciesContexts from linked pathway conversion
	 * 3. add links between relative vcell objects and pathway objects
	 * Questions:
	 * - how to deal with the case that the reaction is existing in the model?
	 * 		+ add it in no matter what? 
	 * 				(this is the version we have now: 
	 * 					add the duplicated reactions in without name changing, 
	 * 				 	all duplicated reactions share the same participant objects)
	 *      + just modify the existing one?
	 */
private void createReactionStepFromPathway(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, boolean addSubunits) throws Exception {
    // annotate the selected vcell object using linked pathway object
    // add non-existing speciesContexts from linked pathway conversion
    ReactionParticipant[] rpArray = parseReaction(reactionStep, bioModel, relationshipObject);
    // create a hashtable for interaction Participants
    Hashtable<String, BioPaxObject> participantTable = new Hashtable<String, BioPaxObject>();
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getLeft()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getRight()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (ReactionParticipant rp : rpArray) {
        SpeciesContext speciesContext = rp.getSpeciesContext();
        if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
            // if the speciesContext is not existed, then add it to the bioModel and link it to the corresponding pathway object
            if (bioModel.getModel().getSpecies(speciesContext.getName()) == null) {
                bioModel.getModel().addSpecies(speciesContext.getSpecies());
            }
            bioModel.getModel().addSpeciesContext(speciesContext);
            RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
            bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
        } else {
            // if it is in the bioModel, then check whether it links to pathway object or not
            HashSet<RelationshipObject> linkedReObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioModel.getModel().getSpeciesContext(speciesContext.getName()));
            if (linkedReObjects != null) {
                boolean isLinked = false;
                for (RelationshipObject reObject : linkedReObjects) {
                    if (reObject.getBioPaxObject() == participantTable.get(speciesContext.getName())) {
                        isLinked = true;
                        break;
                    }
                }
                if (!isLinked) {
                    RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                    bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
                }
            } else {
                RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
            }
        }
    }
    (reactionStep).setReactionParticipants(rpArray);
    // add Control to the reaction
    if (process.getControl() != null) {
        for (InteractionParticipant pe : process.getControl().getParticipants()) {
            SpeciesContext newSpeciescontext = createSpeciesContextFromBioPaxObject(bioModel, pe.getPhysicalEntity(), addSubunits);
            (reactionStep).addReactionParticipant(new Catalyst(null, reactionStep, newSpeciescontext));
        }
    }
    addKinetics(reactionStep, process);
}
Also used : BioPaxObject(org.vcell.pathway.BioPaxObject) Hashtable(java.util.Hashtable) SpeciesContext(cbit.vcell.model.SpeciesContext) Conversion(org.vcell.pathway.Conversion) PhysicalEntity(org.vcell.pathway.PhysicalEntity) InteractionParticipant(org.vcell.pathway.InteractionParticipant) ReactionParticipant(cbit.vcell.model.ReactionParticipant) Catalyst(cbit.vcell.model.Catalyst)

Example 2 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method importIntoModel.

public void importIntoModel() {
    if (bioModel == null) {
        return;
    }
    String warningMessage = "";
    String warningMessage2 = "";
    int warningCount = 0;
    int warningCount2 = 0;
    String infoMessage = "";
    ArrayList<BioPaxObject> importedBPObjects = new ArrayList<BioPaxObject>();
    warningMessage = "The following pathway object(s) have been associated with object(s) in the physiology model:\n";
    warningMessage2 = "The following transport reaction(s) will NOT be converted to the physiology model:\n";
    warningCount = 0;
    warningCount2 = 0;
    infoMessage = "The following pathway object(s) have been coverted in the physiology model:\n\n";
    boolean hasMembrane = false;
    if (bioModel.getModel().getMembranes().size() > 0)
        hasMembrane = true;
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
    // convert group Object to regular biopaxObjects
    for (BioPaxObject bpo : getSelectedBioPaxObjects()) {
        if (bpo instanceof GroupObject) {
            selected.addAll(((GroupObject) bpo).computeGroupedBioPaxObjects());
        } else {
            selected.add(bpo);
        }
    }
    for (BioPaxObject bpo : selected) {
        if (bpo instanceof Conversion) {
            if (bpo instanceof Transport && !hasMembrane) {
                warningCount2++;
                if (((Conversion) bpo).getName().size() > 0)
                    warningMessage2 += "\nTransport: \'" + ((Conversion) bpo).getName().get(0) + "\'\n";
                else
                    warningMessage2 += "\nTransport: \'" + ((Conversion) bpo).getIDShort() + "\'\n";
            } else if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                importedBPObjects.add(bpo);
            } else {
                warningCount++;
                if (((Conversion) bpo).getName().size() > 0)
                    warningMessage += "\nReaction: \'" + ((Conversion) bpo).getName().get(0) + "\' =>\n";
                else
                    warningMessage += "\nReaction: \'" + ((Conversion) bpo).getIDShort() + "\' =>\n";
                for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                    warningMessage += "\t=> \'" + r.getBioModelEntityObject().getName() + "\'\n";
                }
            }
        } else if (bpo instanceof PhysicalEntity) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                importedBPObjects.add(bpo);
            } else {
                warningCount++;
                if (((PhysicalEntity) bpo).getName().size() > 0)
                    warningMessage += "\nSpecies: \'" + ((PhysicalEntity) bpo).getName().get(0) + "\' =>\n";
                else
                    warningMessage += "\nSpecies: \'" + ((PhysicalEntity) bpo).getIDShort() + "\' =>\n";
                for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                    warningMessage += "\t=> \'" + r.getBioModelEntityObject().getName() + "\'\n";
                }
            }
        }
    }
    // create import panel
    conversionPanel = new ConversionPanel();
    conversionPanel.setBioModel(bioModel);
    conversionPanel.setSelectionManager(getSelectionManager());
    // show warning message
    warningMessage2 += "\nNO membrane structures available in the physiology model.\n";
    if (warningCount2 > 0) {
        DialogUtils.showWarningDialog(conversionPanel, warningMessage2);
    }
    warningMessage += "\nThey will NOT be converted to the physiology model.\n";
    if (warningCount > 0) {
        DialogUtils.showWarningDialog(conversionPanel, warningMessage);
    }
    if (importedBPObjects.size() == 0) {
        return;
    }
    // set the selected objects to be the validly imported biopaxObject set
    conversionPanel.setBioPaxObjects(importedBPObjects);
    int returnCode = DialogUtils.showComponentOKCancelDialog(this, conversionPanel, "Import into Physiology");
    if (returnCode == JOptionPane.OK_OPTION) {
        PathwayMapping pathwayMapping = new PathwayMapping();
        try {
            // function I:
            // pass the table rows that contains user edited values to create Vcell object
            pathwayMapping.createBioModelEntitiesFromBioPaxObjects(bioModel, conversionPanel.getTableRows(), conversionPanel.isAddSubunits());
            for (BioPaxObject bpo : importedBPObjects) {
                if (bpo instanceof Conversion) {
                    infoMessage += "Reaction: \t\'";
                    for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                        infoMessage += r.getBioModelEntityObject().getName() + "\'\n";
                    }
                    infoMessage += "\n";
                } else if (bpo instanceof PhysicalEntity) {
                    infoMessage += "Species: \t\'";
                    for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                        infoMessage += r.getBioModelEntityObject().getName() + "\'\n";
                    }
                    infoMessage += "\n";
                }
            }
            DialogUtils.showInfoDialog(this, infoMessage);
            // jump the view to reaction diagram panel
            if (selectionManager != null) {
                selectionManager.setActiveView(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram));
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            DialogUtils.showErrorDialog(this, "Errors occur when converting pathway objects to VCell bioModel objects.\n" + e.getMessage());
        }
    }
}
Also used : PathwayMapping(org.vcell.relationship.PathwayMapping) BioPaxObject(org.vcell.pathway.BioPaxObject) ArrayList(java.util.ArrayList) GroupObject(org.vcell.pathway.GroupObject) ActiveView(cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView) Conversion(org.vcell.pathway.Conversion) RelationshipObject(org.vcell.relationship.RelationshipObject) ZoomRangeException(cbit.gui.graph.GraphResizeManager.ZoomRangeException) UtilCancelException(org.vcell.util.UtilCancelException) PhysicalEntity(org.vcell.pathway.PhysicalEntity) Transport(org.vcell.pathway.Transport) HashSet(java.util.HashSet)

Example 3 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class BioPaxRelationshipTableModel method refreshData.

private void refreshData() {
    ArrayList<BioPaxRelationshipTableRow> entityRows = new ArrayList<BioPaxRelationshipTableRow>();
    if (bioModel != null) {
        HashSet<RelationshipObject> relationshipObjects = null;
        if (bioPaxObject != null) {
            relationshipObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject);
        }
        List<BioPaxRelationshipTableRow> allEntityRows = new ArrayList<BioPaxRelationshipTableRow>();
        if (bioPaxObject instanceof Conversion) {
            for (ReactionStep rs : bioModel.getModel().getReactionSteps()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
            for (ReactionRule rr : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rr);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rr) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        } else if (bioPaxObject instanceof PhysicalEntity) {
            for (SpeciesContext rs : bioModel.getModel().getSpeciesContexts()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        }
        if (searchText == null || searchText.length() == 0) {
            entityRows.addAll(allEntityRows);
        } else {
            for (BioPaxRelationshipTableRow rs : allEntityRows) {
                BioModelEntityObject object = rs.getBioModelEntityObject();
                String lowerCaseSearchText = searchText.toLowerCase();
                if (object.getName().toLowerCase().contains(lowerCaseSearchText) || object.getTypeLabel().toLowerCase().contains(lowerCaseSearchText)) {
                    entityRows.add(rs);
                }
            }
        }
    }
    setData(entityRows);
    GuiUtils.flexResizeTableColumns(ownerTable);
}
Also used : ReactionRule(cbit.vcell.model.ReactionRule) ArrayList(java.util.ArrayList) SpeciesContext(cbit.vcell.model.SpeciesContext) BioModelEntityObject(cbit.vcell.model.BioModelEntityObject) RelationshipObject(org.vcell.relationship.RelationshipObject) Conversion(org.vcell.pathway.Conversion) PhysicalEntity(org.vcell.pathway.PhysicalEntity) ReactionStep(cbit.vcell.model.ReactionStep)

Example 4 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class PathwayGraphModel method refreshControl.

private void refreshControl(Control control) {
    Interaction controlledInteraction = control.getControlledInteraction();
    if (controlledInteraction instanceof Conversion) {
        List<InteractionParticipant> physicalControllers = control.getParticipants();
        if (physicalControllers != null) {
            Conversion conversion = (Conversion) controlledInteraction;
            BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(conversion);
            if (ancestorObject == conversion) {
                // conversion was not grouped
                BioPaxConversionShape conversionShape = (BioPaxConversionShape) getShapeFromModelObject(conversion);
                if (conversionShape != null) {
                    for (InteractionParticipant participant : physicalControllers) {
                        refreshParticipant(conversionShape, participant);
                    }
                }
            } else {
                if (ancestorObject instanceof GroupObject) {
                    // conversion has been grouped
                    GroupObject groupObject = (GroupObject) ancestorObject;
                    for (InteractionParticipant participant : physicalControllers) {
                        refreshGroupInteraction(groupObject, participant);
                    }
                }
            }
        }
    }
}
Also used : Interaction(org.vcell.pathway.Interaction) MolecularInteraction(org.vcell.pathway.MolecularInteraction) BioPaxObject(org.vcell.pathway.BioPaxObject) InteractionParticipant(org.vcell.pathway.InteractionParticipant) GroupObject(org.vcell.pathway.GroupObject) Conversion(org.vcell.pathway.Conversion)

Example 5 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class PathwayGraphModel method refreshAll.

@Override
public void refreshAll() {
    if (pathwayModel == null) {
        clearAllShapes();
        fireGraphChanged();
        return;
    }
    unwantedShapes = new HashSet<Shape>();
    unwantedShapes.addAll(getShapes());
    pathwayContainerShape = (PathwayContainerShape) getShapeFromModelObject(pathwayModel);
    if (pathwayContainerShape == null) {
        pathwayContainerShape = new PathwayContainerShape(this, pathwayModel);
        pathwayContainerShape.getSpaceManager().setSize(400, 300);
        addShape(pathwayContainerShape);
    }
    unwantedShapes.remove(pathwayContainerShape);
    Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(pathwayModel.getDisplayableBioPaxObjectList());
    for (BioPaxObject bpObject : bioPaxObjects) {
        BioPaxShape bpObjectShape = (BioPaxShape) getShapeFromModelObject(bpObject);
        if (bpObjectShape == null) {
            if (bpObject instanceof Conversion) {
                bpObjectShape = new BioPaxConversionShape((Conversion) bpObject, this);
            } else if (bpObject instanceof MolecularInteraction) {
                bpObjectShape = new BioPaxMolecularInteractionShape((MolecularInteraction) bpObject, this);
            } else if (bpObject instanceof Protein) {
                bpObjectShape = new BioPaxProteinShape((Protein) bpObject, this);
            } else if (bpObject instanceof Complex) {
                bpObjectShape = new BioPaxComplexShape((Complex) bpObject, this);
            } else if (bpObject instanceof SmallMolecule) {
                bpObjectShape = new BioPaxSmallMoleculeShape((SmallMolecule) bpObject, this);
            } else if (bpObject instanceof Dna) {
                bpObjectShape = new BioPaxDnaShape((Dna) bpObject, this);
            } else if (bpObject instanceof Rna) {
                bpObjectShape = new BioPaxRnaShape((Rna) bpObject, this);
            } else if (bpObject instanceof PhysicalEntity) {
                bpObjectShape = new BioPaxPhysicalEntityShape((PhysicalEntity) bpObject, this);
            } else if (bpObject instanceof GroupObject) {
                bpObjectShape = new BioPaxGroupShape((GroupObject) bpObject, this);
            } else {
                bpObjectShape = new BioPaxObjectShape(bpObject, this);
            }
            if (!(bpObject instanceof Control)) {
                // the Control objects will not be displayed on the diagram
                pathwayContainerShape.addChildShape(bpObjectShape);
                addShape(bpObjectShape);
            }
            Dimension shapeSize = bpObjectShape.getSpaceManager().getSize();
            Rectangle boundary = getContainerLayout().getBoundaryForAutomaticLayout(pathwayContainerShape);
            int xPos = boundary.x + random.nextInt(boundary.width - shapeSize.width);
            int yPos = boundary.y + random.nextInt(boundary.height - shapeSize.height);
            bpObjectShape.setAbsPos(xPos, yPos);
        }
        unwantedShapes.remove(bpObjectShape);
    }
    for (BioPaxObject bpObject : bioPaxObjects) {
        if (bpObject instanceof Conversion) {
            refreshInteraction((Conversion) bpObject);
        } else if (bpObject instanceof MolecularInteraction) {
            refreshInteraction((MolecularInteraction) bpObject);
        } else if (bpObject instanceof Control) {
            refreshControl((Control) bpObject);
        } else if (bpObject instanceof GroupObject) {
            refreshGroupObject((GroupObject) bpObject);
        }
    }
    for (Shape unwantedShape : unwantedShapes) {
        removeShape(unwantedShape);
    }
    refreshRelationshipInfo();
    fireGraphChanged();
}
Also used : EdgeShape(cbit.gui.graph.EdgeShape) Shape(cbit.gui.graph.Shape) Rna(org.vcell.pathway.Rna) BioPaxObject(org.vcell.pathway.BioPaxObject) Rectangle(java.awt.Rectangle) Complex(org.vcell.pathway.Complex) Control(org.vcell.pathway.Control) MolecularInteraction(org.vcell.pathway.MolecularInteraction) HashSet(java.util.HashSet) GroupObject(org.vcell.pathway.GroupObject) Dimension(java.awt.Dimension) Conversion(org.vcell.pathway.Conversion) Protein(org.vcell.pathway.Protein) PhysicalEntity(org.vcell.pathway.PhysicalEntity) SmallMolecule(org.vcell.pathway.SmallMolecule) Dna(org.vcell.pathway.Dna)

Aggregations

Conversion (org.vcell.pathway.Conversion)13 BioPaxObject (org.vcell.pathway.BioPaxObject)10 PhysicalEntity (org.vcell.pathway.PhysicalEntity)9 ArrayList (java.util.ArrayList)7 GroupObject (org.vcell.pathway.GroupObject)6 SpeciesContext (cbit.vcell.model.SpeciesContext)4 RelationshipObject (org.vcell.relationship.RelationshipObject)4 HashSet (java.util.HashSet)3 Control (org.vcell.pathway.Control)3 InteractionParticipant (org.vcell.pathway.InteractionParticipant)3 MolecularInteraction (org.vcell.pathway.MolecularInteraction)3 BioModelEntityObject (cbit.vcell.model.BioModelEntityObject)2 Catalyst (cbit.vcell.model.Catalyst)2 Product (cbit.vcell.model.Product)2 Reactant (cbit.vcell.model.Reactant)2 ReactionParticipant (cbit.vcell.model.ReactionParticipant)2 ReactionRule (cbit.vcell.model.ReactionRule)2 ReactionStep (cbit.vcell.model.ReactionStep)2 Dimension (java.awt.Dimension)2 Element (org.jdom.Element)2