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

Example 1 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity 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 PhysicalEntity

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

the class BioModelEditorPathwayDiagramPanel method collapse2Complex.

private GroupObject collapse2Complex(BioPaxObject bpObject) {
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    GroupObject groupObject = null;
    HashSet<BioPaxObject> hiddenobjects = new HashSet<BioPaxObject>();
    if (bpObject instanceof Complex) {
        // collapse components
        Complex complex = (Complex) bpObject;
        Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
        for (PhysicalEntity pe : complex.getComponents()) {
            if (bioPaxObjects.contains(pe)) {
                hiddenobjects.add(pe);
            }
        }
        if (hiddenobjects.size() > 0) {
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), ((Entity) bpObject).getName(), id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
        } else {
            // error message
            DialogUtils.showErrorDialog(this, "No Collapse action happened because the components of the complex, " + getEntityName(complex) + ", haven't been imported to pathway model.");
        }
    } else if (bpObject instanceof Protein || bpObject instanceof SmallMolecule) {
        Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
        ArrayList<String> name = new ArrayList<String>();
        List<BioPaxObject> parents = bioModel.getPathwayModel().getParents(bpObject);
        if (parents.isEmpty()) {
            DialogUtils.showErrorDialog(this, "No Collapse action happened because protein, " + getEntityName((Entity) bpObject) + ", doesn't involve in any complexes in the pathway data.");
            return null;
        }
        for (BioPaxObject bpo : bioModel.getPathwayModel().getParents(bpObject)) {
            if (bpo instanceof Complex && bioPaxObjects.contains(bpo)) {
                hiddenobjects.add(bpo);
                name.addAll(((Complex) bpo).getName());
                for (PhysicalEntity pe : ((Complex) bpo).getComponents()) {
                    if (bioPaxObjects.contains(pe)) {
                        hiddenobjects.add(pe);
                    }
                }
            }
        }
        if (hiddenobjects.size() > 0) {
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            if (name.size() == 0) {
                name.add(id);
            }
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), name, id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
        } else {
            // error message
            DialogUtils.showErrorDialog(this, "No Collapse action happened because complexes that relate to protein, " + getEntityName((Entity) bpObject) + ", haven't been imported to pathway model.");
        }
    }
    return groupObject;
}

Example 3 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity 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 4 with PhysicalEntity

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

the class BioModelEditorPathwayPanel method importPathway.

public void importPathway(boolean addComplexes, boolean addComponents, boolean addInteractions) {
    ArrayList<BioPaxObject> selectedBioPaxObjects = new ArrayList<BioPaxObject>();
    int[] rows = table.getSelectedRows();
    if (rows == null || rows.length == 0) {
        return;
    }
    for (int row : rows) {
        BioPaxObject bioPaxObject = tableModel.getValueAt(row);
        selectedBioPaxObjects.add(bioPaxObject);
    }
    PathwaySelectionExpander selectionExpander = new PathwaySelectionExpander();
    PathwayModel rawPathwayModel = pathwayData.getPathwayModel();
    if (addComplexes) {
        selectionExpander.forPhysicalEntitiesAddComplexes(rawPathwayModel, selectedBioPaxObjects);
    }
    if (addComponents) {
        selectionExpander.forComplexesAddComponents(rawPathwayModel, selectedBioPaxObjects);
    }
    if (addInteractions) {
        selectionExpander.forPhysicalEntitiesAddInteractions(rawPathwayModel, selectedBioPaxObjects);
    }
    selectionExpander.forInteractionsAddControls(rawPathwayModel, selectedBioPaxObjects);
    selectionExpander.forInteractionsAddParticipants(rawPathwayModel, selectedBioPaxObjects);
    PathwayModel selectedPathwayModel = new PathwayModel();
    HashSet<BioPaxObject> objectsToDelete = new HashSet<BioPaxObject>();
    for (BioPaxObject candidateObject : selectedBioPaxObjects) {
        // is the object in the current pathwayModel already?
        BioPaxObject keeperObject = bioModel.getPathwayModel().find(candidateObject);
        if (keeperObject == null) {
            // not found in the current pathwayModel, add it
            selectedPathwayModel.add(candidateObject);
        } else {
            // make a list with the objects we don't bring in because of duplication
            objectsToDelete.add(candidateObject);
        }
    }
    // we replace references to those objects within selectedPathwayModel with the real thing
    for (BioPaxObject bpObject : selectedPathwayModel.getBiopaxObjects()) {
        if (bpObject == null) {
            System.out.println("PathwayModel: null BioPaxObject.");
            continue;
        }
        for (BioPaxObject objectToDelete : objectsToDelete) {
            BioPaxObject keeperObject = bioModel.getPathwayModel().find(objectToDelete);
            // for now we only implemented this for InteractionParticipant entities of Conversions
            bpObject.replace(keeperObject);
        }
    }
    // we bring proteins, small molecules, etc that are components of a Complex
    ArrayList<PhysicalEntity> addList = new ArrayList<>();
    for (BioPaxObject bpo : selectedPathwayModel.getBiopaxObjects()) {
        if (bpo instanceof Complex) {
            Complex complex = (Complex) bpo;
            addComplexComponents(complex, addList, 0);
        }
    }
    for (PhysicalEntity pe : addList) {
        if (selectedPathwayModel.find(pe) == null) {
            selectedPathwayModel.add(pe);
        }
    }
    bioModel.getPathwayModel().merge(selectedPathwayModel);
    // jump the view to pathway diagram panel
    if (selectionManager != null) {
        selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE, ActiveViewID.pathway_diagram), selectedPathwayModel.getBiopaxObjects().toArray());
    }
}

Example 5 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity 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);
                }
            }
            for (MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(mt);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == mt) {
                            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);
}