private Node realizeNeigbour(Graph2D graph, Node node) {
Iterator<Node> iterator = new ComponentIterator(graph, node);
for (; iterator.hasNext(); ) {
Node next = iterator.next();
if (_viewModel.getEditorViewMap().containsKey(next)
&& !MonomerInfoUtils.isChemicalModifierPolymer(next)) {
Node mapped = _viewModel.getViewNode(next);
if (MonomerInfoUtils.is5Node(mapped, _graph)) {
continue;
}
_viewModel.putViewNode(node, mapped);
return mapped;
}
}
// this should never happen. We're doing this for safety
Node result =
createNode(MonomerInfoUtils.getMonomerID(node), ViewElementsConstructor.SIMPLE_NODE);
_viewModel.putViewNode(node, result);
return result;
}
private void addBranchToBranchEdge(
Edge currentEdge, Attachment sourceAttachment, Attachment targetAttachment) {
EdgeMap edgeTypeMap = (EdgeMap) _graph.getDataProvider(EdgeMapKeys.EDGE_INFO);
Node sourceNode = _viewModel.getViewNode(currentEdge.source());
Node targetNode = _viewModel.getViewNode(currentEdge.target());
Edge newEdge = _graph.createEdge(sourceNode, targetNode);
edgeTypeMap.set(
newEdge, new SViewEdgeInfo(EdgeType.BRANCH_BRANCH, sourceAttachment, targetAttachment));
sourceNode = getViewStartingNode(newEdge.source(), _graph);
targetNode = getViewStartingNode(newEdge.target(), _graph);
_viewModel.addComplentaryViewNodes(sourceNode, targetNode);
}
private Edge addSimpleEdge(Edge currentEdge) {
Node sourceFrom = currentEdge.source();
Node from = _viewModel.getViewNode(sourceFrom);
if (from == null) {
from = realizeNeigbour(_graph, sourceFrom);
}
Node sourceTo = currentEdge.target();
Node to = _viewModel.getViewNode(sourceTo);
if (to == null) {
to = realizeNeigbour(_graph, sourceTo);
}
Edge newEdge = _graph.createEdge(from, to);
return newEdge;
}
/**
* get the starting node of the sequence in where the current node is sitting in
*
* @deprecated use getViewStartingNode
* @param node
* @param graph
* @return
*/
@Deprecated
private Node getStartingNode(Node node, Graph2D graph) {
if (_viewModel.getStartingViewNodeList().contains(node)) {
return node;
} else {
NodeCursor pres = node.predecessors();
Edge edge;
Node currentNode = node;
EdgeMap edgeMap = (EdgeMap) graph.getDataProvider(EdgeMapKeys.EDGE_INFO);
Node preNode = currentNode;
while (pres.ok()) {
for (; pres.ok(); pres.next()) {
edge = currentNode.getEdge(pres.node());
EdgeType edgeType = ((SViewEdgeInfo) edgeMap.get(edge)).getType();
if ((edgeType == EdgeType.REGULAR) || (edgeType == EdgeType.MODIFIED_P)) {
currentNode = pres.node();
break;
}
}
if (currentNode != preNode) {
pres = currentNode.predecessors();
preNode = currentNode;
} else {
break;
}
}
if (_viewModel.getStartingViewNodeList().contains(currentNode)) {
return currentNode;
} else {
return null;
}
}
}
