Examples with Transport org.vcell.pathway.Transport used on opensource projects

Example 1 with Transport

use of org.vcell.pathway.Transport 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());
        }
    }
}

Example 2 with Transport

use of org.vcell.pathway.Transport 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;
}

Example 3 with Transport

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

the class PathwayReaderBiopax3 method addObjectTransport.

private Transport addObjectTransport(Element element) {
    Transport transport = new TransportImpl();
    addAttributes(transport, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentTransport(transport, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(transport);
    return transport;
}

Example 4 with Transport

use of org.vcell.pathway.Transport 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;
}

Example 5 with Transport

use of org.vcell.pathway.Transport 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);
}