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

Example 41 with BioPaxObject

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

the class PhysiologyRelationshipTableModel method getValueAt.

public Object getValueAt(int iRow, int iCol) {
    PhysiologyRelationshipTableRow entitySelectionTableRow = getValueAt(iRow);
    BioPaxObject bpObject = entitySelectionTableRow.getBioPaxObject();
    switch(iCol) {
        case iColSelected:
            {
                return entitySelectionTableRow.selected();
            }
        case iColEntity:
            {
                return getLabel(bpObject);
            }
        case iColType:
            {
                return getType(bpObject);
            }
        default:
            {
                return null;
            }
    }
}

Example 42 with BioPaxObject

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

the class PhysiologyRelationshipTableModel method refreshData.

private void refreshData() {
    ArrayList<PhysiologyRelationshipTableRow> pathwayObjectList = new ArrayList<PhysiologyRelationshipTableRow>();
    if (bioModel != null) {
        HashSet<RelationshipObject> relationshipObjects = null;
        if (bioModelEntityObject != null) {
            relationshipObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
        }
        List<PhysiologyRelationshipTableRow> allPathwayObjectList = new ArrayList<PhysiologyRelationshipTableRow>();
        for (BioPaxObject bpObject1 : bioModel.getPathwayModel().getBiopaxObjects()) {
            if ((bpObject1 instanceof PhysicalEntity && (bioModelEntityObject == null || bioModelEntityObject instanceof SpeciesContext)) || (bpObject1 instanceof Conversion && (bioModelEntityObject == null || bioModelEntityObject instanceof ModelProcess)) || (bpObject1 instanceof PhysicalEntity && (bioModelEntityObject == null || bioModelEntityObject instanceof MolecularType))) {
                PhysiologyRelationshipTableRow entityRow = new PhysiologyRelationshipTableRow(bpObject1);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioPaxObject() == entityRow.getBioPaxObject()) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allPathwayObjectList.add(entityRow);
                }
            }
        }
        if (searchText == null || searchText.length() == 0) {
            pathwayObjectList.addAll(allPathwayObjectList);
        } else {
            for (PhysiologyRelationshipTableRow rs : allPathwayObjectList) {
                BioPaxObject bpObject = rs.getBioPaxObject();
                String lowerCaseSearchText = searchText.toLowerCase();
                if (getLabel(bpObject).toLowerCase().contains(lowerCaseSearchText) || getType(bpObject).toLowerCase().contains(lowerCaseSearchText)) {
                    pathwayObjectList.add(rs);
                }
            }
        }
    }
    setData(pathwayObjectList);
    GuiUtils.flexResizeTableColumns(ownerTable);
}

Example 43 with BioPaxObject

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

the class RelationshipObject method createRelationshipObject.

public static RelationshipObject createRelationshipObject(VCID bioModelObjectID, VCID bioPaxObjectID, IdentifiableProvider provider) {
    if (bioModelObjectID == null || bioPaxObjectID == null) {
        return null;
    }
    BioModelEntityObject bmo = (BioModelEntityObject) provider.getIdentifiableObject(bioModelObjectID);
    BioPaxObject bpo = (BioPaxObject) provider.getIdentifiableObject(bioPaxObjectID);
    return new RelationshipObject(bmo, bpo);
}

Example 44 with BioPaxObject

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

the class PathwayReaderBiopax3 method addAttributes.

private void addAttributes(BioPaxObject bioPaxObject, Element element) {
    int count = 0;
    for (Object attr : element.getAttributes()) {
        Attribute attribute = (Attribute) attr;
        if (attribute.getName().equals("ID")) {
            if (bioPaxObject instanceof RdfObjectProxy) {
                showUnexpected(attribute);
            } else {
                String uri = context.unAbbreviateURI(element, attribute.getValue());
                bioPaxObject.setID(uri);
                count++;
            }
        } else if (attribute.getName().equals("resource")) {
            if (bioPaxObject instanceof RdfObjectProxy) {
                String uri = context.unRelativizeURI(element, attribute.getValue());
                bioPaxObject.setID(uri);
                count++;
            } else {
                showUnexpected(attribute);
            }
        } else if (attribute.getName().equals("about")) {
            if (bioPaxObject instanceof RdfObjectProxy) {
                // TODO: can this ever happen?
                String uri = context.unRelativizeURI(element, attribute.getValue());
                bioPaxObject.setID(uri);
                count++;
            } else {
                String uri = context.unRelativizeURI(element, attribute.getValue());
                bioPaxObject.setID(uri);
                count++;
            }
        } else if (attribute.getName().equals("nodeID")) {
            if (bioPaxObject instanceof RdfObjectProxy) {
                // TODO: can this ever happen?
                ((RdfObjectProxy) bioPaxObject).setID(attribute.getValue());
                count++;
            } else {
                bioPaxObject.setID(attribute.getValue());
                count++;
            }
        } else {
            showUnexpected(attribute);
        }
    }
    if (count < 1) {
        System.out.println(element + " has neither ID nor resource attributes.");
    }
    if (count > 1) {
        System.out.println(element + " has multiple ID and/or resource attributes.");
    }
}

Example 45 with BioPaxObject

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

the class BioPAXPathwayModelTreeNode method getNewChildren.

public List<BioPAXTreeNode> getNewChildren() {
    Set<BioPaxObject> objects = getPathwayModel().getBiopaxObjects();
    Map<Class<?>, Set<BioPaxObject>> subclassMap = BioPAXTreeMaker.divideBySubclasses(BioPaxObject.class, objects);
    List<BioPAXTreeNode> childrenNew = new ArrayList<BioPAXTreeNode>();
    for (Map.Entry<Class<?>, Set<BioPaxObject>> entry : subclassMap.entrySet()) {
        Class<?> subclass = entry.getKey();
        Set<BioPaxObject> objectsOfSubclass = entry.getValue();
        List<BioPaxObject> objectsOfSubclassList = new ArrayList<BioPaxObject>();
        objectsOfSubclassList.addAll(objectsOfSubclass);
        childrenNew.add(new BioPAXObjectListTreeNode<BioPaxObject>(getPathwayModel(), objectsOfSubclassList, subclass, this));
    }
    // for(BioPaxObject object : objects) {
    // children.add(
    // new BioPAXMessageTreeNode(getPathwayModel(), object.toString(), this));
    // }
    // TODO
    int nObjects = pathwayModel.getBiopaxObjects().size();
    Pathway topLevelPathway = pathwayModel.getTopLevelPathway();
    if (topLevelPathway != null) {
        List<String> nameList = topLevelPathway.getName();
        if (nameList != null && !nameList.isEmpty()) {
        }
    }
    labelText = nObjects + " objects";
    return childrenNew;
}