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

Example 51 with BioPaxObject

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

the class PathwayGrouping method findGroupAncestor.

public BioPaxObject findGroupAncestor(Map<BioPaxObject, BioPaxObject> groupMap, BioPaxObject bpObject) {
    BioPaxObject ancestor = groupMap.get(bpObject);
    if (ancestor == null)
        return bpObject;
    else {
        BioPaxObject temp = groupMap.get(ancestor);
        while (temp != null) {
            ancestor = temp;
            temp = groupMap.get(ancestor);
        }
        return ancestor;
    }
}

Example 52 with BioPaxObject

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

the class PathwayGrouping method updateBioPaxObjectList.

// get a list of independent biopax Objects including groupObjects
public Set<BioPaxObject> updateBioPaxObjectList(PathwayModel pathwayModel) {
    Set<BioPaxObject> clonedOriginalList = new HashSet<BioPaxObject>(pathwayModel.getBiopaxObjects());
    Set<BioPaxObject> removedList = new HashSet<BioPaxObject>();
    for (BioPaxObject bpObject : clonedOriginalList) {
        if (bpObject instanceof GroupObject) {
            GroupObject gObject = (GroupObject) bpObject;
            for (BioPaxObject bpo : gObject.getGroupedObjects()) {
                removedList.add(bpo);
            }
        }
    }
    clonedOriginalList.removeAll(removedList);
    return clonedOriginalList;
}

Example 53 with BioPaxObject

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

the class PathwayGrouping method updateGroupableList.

private HashSet<BioPaxObject> updateGroupableList(PathwayModel pathwayModel, HashSet<BioPaxObject> bpObjects) {
    HashSet<BioPaxObject> groupable = new HashSet<BioPaxObject>();
    Map<BioPaxObject, BioPaxObject> groupMap = pathwayModel.getGroupMap();
    // the group object should be a tree structure. so we will group the parents of the selected objects together.
    for (BioPaxObject bpObject : bpObjects) {
        groupable.add(findGroupAncestor(groupMap, bpObject));
    }
    return groupable;
}