Examples with RelationshipObject org.vcell.relationship.RelationshipObject used on opensource projects

Example 11 with RelationshipObject

use of org.vcell.relationship.RelationshipObject 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 12 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class PathwayGraphModel method refreshRelationshipInfo.

protected void refreshRelationshipInfo(Shape shape) {
    if (shape instanceof BioPaxShape) {
        BioPaxShape bpShape = (BioPaxShape) shape;
        BioPaxObject bpObject = bpShape.getBioPaxObject();
        boolean hasRelationships = false;
        if (bioModel != null) {
            HashSet<RelationshipObject> relationships = bioModel.getRelationshipModel().getRelationshipObjects(bpObject);
            if (relationships.size() > 0) {
                hasRelationships = true;
            }
        }
        bpShape.setHasRelationships(hasRelationships);
    }
}

Example 13 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method showPhysiologyLinks.

private void showPhysiologyLinks() {
    BioPaxObject selectedBioPaxObject = getSelectedBioPaxObject();
    if (selectedBioPaxObject != null) {
        Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(selectedBioPaxObject);
        if (relationshipSet.size() > 0) {
            ArrayList<BioModelEntityObject> selectedBioModelEntityObjects = new ArrayList<BioModelEntityObject>();
            for (RelationshipObject re : relationshipSet) {
                BioModelEntityObject bioModelEntityObject = re.getBioModelEntityObject();
                selectedBioModelEntityObjects.add(bioModelEntityObject);
            }
            // if (selectedBioPaxObjects.get(0) instanceof ReactionStep) {
            // selectionManager.setActiveView(new ActiveView(null,DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions));
            // } else if (selectedBioPaxObjects.get(0) instanceof SpeciesContext) {
            // selectionManager.setActiveView(new ActiveView(null,DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species));
            // }
            selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram), selectedBioModelEntityObjects.toArray(new BioModelEntityObject[0]));
        }
    }
}

Example 14 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class BioModelEditorReactionTableModel method computeData.

protected ArrayList<ModelProcess> computeData() {
    ArrayList<ModelProcess> processList = new ArrayList<ModelProcess>();
    if (getModel() != null) {
        ModelProcess[] modelProcesses = getModel().getModelProcesses();
        if (searchText == null || searchText.length() == 0) {
            processList.addAll(Arrays.asList(modelProcesses));
        } else {
            String lowerCaseSearchText = searchText.toLowerCase();
            for (ModelProcess process : modelProcesses) {
                boolean bMatchRelationshipObj = false;
                if (process instanceof ReactionStep) {
                    ReactionStep reactionStep = (ReactionStep) process;
                    HashSet<RelationshipObject> relObjsHash = bioModel.getRelationshipModel().getRelationshipObjects(reactionStep);
                    for (RelationshipObject relObj : relObjsHash) {
                        if (relObj.getBioPaxObject() instanceof Entity) {
                            if (((Entity) relObj.getBioPaxObject()).getName().get(0).toLowerCase().contains(lowerCaseSearchText)) {
                                bMatchRelationshipObj = true;
                                break;
                            }
                        }
                    }
                }
                if (bMatchRelationshipObj || process.containsSearchText(lowerCaseSearchText)) {
                    if (!processList.contains(process)) {
                        processList.add(process);
                    }
                }
                if (process instanceof ReactionStep) {
                    // we also search in reaction step expression, for strings like "s1 + s2" or s1 -> s2
                    ModelProcessEquation mpe = new ModelProcessEquation(process, bioModel.getModel());
                    if (mpe.toString().toLowerCase().contains(lowerCaseSearchText)) {
                        if (!processList.contains(process)) {
                            processList.add(process);
                        }
                    }
                }
            }
        }
    }
    return processList;
}

Example 15 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class BioModelEditorSpeciesTableModel method computeData.

protected ArrayList<SpeciesContext> computeData() {
    ArrayList<SpeciesContext> speciesContextList = new ArrayList<SpeciesContext>();
    if (getModel() != null) {
        if (searchText == null || searchText.length() == 0) {
            speciesContextList.addAll(Arrays.asList(getModel().getSpeciesContexts()));
        } else {
            String lowerCaseSearchText = searchText.toLowerCase();
            for (SpeciesContext s : getModel().getSpeciesContexts()) {
                boolean bMatchRelationshipObj = false;
                HashSet<RelationshipObject> relObjsHash = bioModel.getRelationshipModel().getRelationshipObjects(s);
                for (RelationshipObject relObj : relObjsHash) {
                    if (relObj.getBioPaxObject() instanceof Entity) {
                        if (((Entity) relObj.getBioPaxObject()).getName().get(0).toLowerCase().contains(lowerCaseSearchText)) {
                            bMatchRelationshipObj = true;
                            break;
                        }
                    }
                }
                if (bMatchRelationshipObj || s.getName().toLowerCase().contains(lowerCaseSearchText) || s.getStructure().getName().toLowerCase().contains(lowerCaseSearchText)) {
                    speciesContextList.add(s);
                }
            }
        }
    }
    return speciesContextList;
}