/**
* Constructor, defaults to undirected graph.
*
* @param nodes_list a <code>List</code> of <code>giny.model.Node</code> objects for which
* distances will be calculated
* @param distances the 2 dimensional array that will hold the calculated distances (possibly
* null)
* @param perspective the <code>giny.model.GraphPerspective</code> in which the nodes reside
* @deprecated Can't use this now that GraphPerspective uses root graph indices.
*/
public NodeDistances(List nodesList, CyNetwork network, Map nodeIndexToMatrixIndexMap) {
this.nodesList = nodesList;
this.nodeIndexToMatrixIndexMap = nodeIndexToMatrixIndexMap;
this.network = network;
distances = new int[nodesList.size()][];
directed = false;
}
/** {@inheritDoc} */
@Override
public Evidence[] mapEdgeToEvidence(Graph graph, Edge edge) {
if (graph == null) throw new NullPointerException("graph cannot be null");
if (edge == null) throw new NullPointerException("edge cannot be null");
if (edge.metadata == null) return new Evidence[0];
Object evidences = edge.metadata.get("evidences");
if (evidences == null || !(evidences instanceof List)) return new Evidence[0];
List<Map> evidenceMap = typedList(((List) evidences), Map.class);
List<Evidence> evidenceList = new ArrayList<Evidence>();
for (Map item : evidenceMap) {
@SuppressWarnings("unchecked")
Map<String, Object> evMap = (Map<String, Object>) item;
Evidence ev = new Evidence();
ev.belStatement = getOrEmptyString("bel_statement", evMap).replace("\\\"", "\"");
ev.summaryText = getOrEmptyString("summary_text", evMap);
Citation citation = new Citation();
@SuppressWarnings("unchecked")
Map<String, Object> citationMap = (Map<String, Object>) evMap.get("citation");
if (citationMap != null) {
citation.id = getOrEmptyString("id", citationMap);
citation.type = getOrEmptyString("type", citationMap);
citation.name = getOrEmptyString("name", citationMap);
}
ev.citation = citation;
BiologicalContext context = new BiologicalContext();
@SuppressWarnings("unchecked")
Map<String, Object> contextMap = (Map<String, Object>) evMap.get("biological_context");
if (contextMap != null) {
context.speciesCommonName = getOrEmptyString("species_common_name", contextMap);
context.ncbiTaxId = getOrZero("ncbi_tax_id", contextMap);
Set<String> varying = new HashSet<String>(contextMap.keySet());
varying.removeAll(asList("species_common_name", "ncbi_tax_id"));
for (String key : varying) {
context.variedAnnotations.put(key, contextMap.get(key));
}
ev.biologicalContext = context;
}
evidenceList.add(ev);
}
return evidenceList.toArray(new Evidence[evidenceList.size()]);
}
/** {@inheritDoc} */
@Override
public Evidence[] mapFromTable(CyEdge edge, CyTable table) {
if (edge == null) throw new NullPointerException("edge cannot be null");
if (table == null) throw new NullPointerException("table cannot be null");
Set<String> nonAnnotationColumns =
new HashSet<String>(
asList(
CyNetwork.SUID,
NETWORK_SUID,
NETWORK_NAME,
EDGE_SUID,
BEL_STATEMENT,
SUMMARY_TEXT,
CITATION_ID,
CITATION_NAME,
CITATION_TYPE,
SPECIES));
Collection<CyRow> evidenceRows = table.getMatchingRows(EDGE_SUID, edge.getSUID());
List<Evidence> evidences = new ArrayList<Evidence>(evidenceRows.size());
if (!evidenceRows.isEmpty()) {
for (CyRow evRow : evidenceRows) {
Evidence e = new Evidence();
e.belStatement = evRow.get(BEL_STATEMENT, String.class);
e.summaryText = evRow.get(SUMMARY_TEXT, String.class);
e.citation = new Citation();
e.citation.id = evRow.get(CITATION_ID, String.class);
e.citation.name = evRow.get(CITATION_NAME, String.class);
e.citation.type = evRow.get(CITATION_TYPE, String.class);
e.biologicalContext = new BiologicalContext();
e.biologicalContext.speciesCommonName = evRow.get(SPECIES, String.class);
e.biologicalContext.variedAnnotations = new HashMap<String, Object>();
for (Entry<String, Object> columnValue : evRow.getAllValues().entrySet()) {
if (nonAnnotationColumns.contains(columnValue.getKey())) continue;
e.biologicalContext.variedAnnotations.put(columnValue.getKey(), columnValue.getValue());
}
evidences.add(e);
}
}
return evidences.toArray(new Evidence[evidences.size()]);
}
/**
* Calculates the node distances.
*
* @return the <code>int[][]</code> array of calculated distances or null if the task was canceled
* or there was an error
*/
public int[][] calculate() {
int currentProgress = 0;
this.maxValue = distances.length;
CyNode[] nodes = new CyNode[nodesList.size()];
// TODO: REMOVE
// System.err.println( "Calculating all node distances.. for: "
// +nodesList.size()+" and "+nodes.length );
// We don't have to make new Integers all the time, so we store the index
// Objects in this array for reuse.
Integer[] integers = new Integer[nodes.length];
// Fill the nodes array with the nodes in their proper index locations.
// int index;
CyNode from_node;
for (int i = 0; i < nodes.length; i++) {
from_node = (CyNode) nodesList.get(i);
if (from_node == null) {
continue;
}
int index = ((Integer) nodeIndexToMatrixIndexMap.get(from_node.getSUID())).intValue();
// index = ((Integer) nodeIndexToMatrixIndexMap.get(new
// Integer(from_node.getRootGraphIndex()))).intValue();
if ((index < 0) || (index >= nodes.length)) {
System.err.println(
"WARNING: GraphNode \""
+ from_node
+ "\" has an index value that is out of range: "
+ index
+ ". Graph indices should be maintained such "
+ "that no index is unused.");
return null;
}
if (nodes[index] != null) {
System.err.println(
"WARNING: GraphNode \""
+ from_node
+ "\" has an index value ( "
+ index
+ " ) that is the same as "
+ "that of another GraphNode ( \""
+ nodes[index]
+ "\" ). Graph indices should be maintained such "
+ "that indices are unique.");
return null;
}
nodes[index] = from_node;
Integer in = new Integer(index);
integers[index] = in;
}
LinkedList queue = new LinkedList();
boolean[] completed_nodes = new boolean[nodes.length];
Iterator neighbors;
CyNode to_node;
CyNode neighbor;
int neighbor_index;
int to_node_distance;
int neighbor_distance;
for (int from_node_index = 0; from_node_index < nodes.length; from_node_index++) {
if (this.interrupted) {
// The task was canceled
this.distances = null;
return this.distances;
}
from_node = nodes[from_node_index];
if (from_node == null) {
// Make the distances in this row all Integer.MAX_VALUE.
if (distances[from_node_index] == null) {
distances[from_node_index] = new int[nodes.length];
}
Arrays.fill(distances[from_node_index], Integer.MAX_VALUE);
continue;
}
// TODO: REMOVE
// System.err.print( "Calculating node distances from graph node " +
// from_node );
// System.err.flush();
// Make the distances row and initialize it.
if (distances[from_node_index] == null) {
distances[from_node_index] = new int[nodes.length];
}
Arrays.fill(distances[from_node_index], Integer.MAX_VALUE);
distances[from_node_index][from_node_index] = 0;
// Reset the completed nodes array.
Arrays.fill(completed_nodes, false);
// Add the start node to the queue.
queue.add(integers[from_node_index]);
while (!(queue.isEmpty())) {
if (this.interrupted) {
// The task was canceled
this.distances = null;
return this.distances;
}
int index = ((Integer) queue.removeFirst()).intValue();
if (completed_nodes[index]) {
continue;
}
completed_nodes[index] = true;
to_node = nodes[index];
to_node_distance = distances[from_node_index][index];
if (index < from_node_index) {
// Oh boy. We've already got every distance from/to this node.
int distance_through_to_node;
for (int i = 0; i < nodes.length; i++) {
if (distances[index][i] == Integer.MAX_VALUE) {
continue;
}
distance_through_to_node = to_node_distance + distances[index][i];
if (distance_through_to_node <= distances[from_node_index][i]) {
// Any immediate neighbor of a node that's already been
// calculated for that does not already have a shorter path
// calculated from from_node never will, and is thus complete.
if (distances[index][i] == 1) {
completed_nodes[i] = true;
}
distances[from_node_index][i] = distance_through_to_node;
}
} // End for every node, update the distance using the distance from
// to_node.
// So now we don't need to put any neighbors on the queue or
// anything, since they've already been taken care of by the previous
// calculation.
continue;
} // End if to_node has already had all of its distances calculated.
neighbors = getNeighbors(to_node).iterator();
// neighbors = perspective.neighborsList(to_node).iterator();
while (neighbors.hasNext()) {
if (this.interrupted) {
this.distances = null;
return this.distances;
}
neighbor = (CyNode) neighbors.next();
neighbor_index = ((Integer) nodeIndexToMatrixIndexMap.get(neighbor.getSUID())).intValue();
// neighbor_index = ((Integer) nodeIndexToMatrixIndexMap.get(new
// Integer(neighbor.getRootGraphIndex()))).intValue();
// If this neighbor was not in the incoming List, we cannot include
// it in any paths.
if (nodes[neighbor_index] == null) {
distances[from_node_index][neighbor_index] = Integer.MAX_VALUE;
continue;
}
if (completed_nodes[neighbor_index]) {
// We've already done everything we can here.
continue;
}
neighbor_distance = distances[from_node_index][neighbor_index];
if ((to_node_distance != Integer.MAX_VALUE)
&& (neighbor_distance > (to_node_distance + 1))) {
distances[from_node_index][neighbor_index] = (to_node_distance + 1);
queue.addLast(integers[neighbor_index]);
}
// TODO: REMOVE
// System.out.print( "." );
// System.out.flush();
} // For each of the next nodes' neighbors
// TODO: REMOVE
// System.out.print( "|" );
// System.out.flush();
} // For each to_node, in order of their (present) distances
// TODO: REMOVE
/*
System.err.println( "done." );
*/
// Calculate Percentage. This must be a value between 0..100.
int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
// Estimate Time Remaining
long timeRemaining = maxValue - currentProgress;
// Update the Task Monitor.
// This automatically updates the UI Component w/ progress bar.
if (taskMonitor != null) {
taskMonitor.setProgress(percentComplete);
taskMonitor.setStatusMessage(
"Calculating Node Distances: " + currentProgress + "of " + maxValue);
// taskMonitor.setEstimatedTimeRemaining(timeRemaining);
}
currentProgress++;
} // For each from_node
// TODO: REMOVE
// System.err.println( "..Done calculating all node distances." );
return distances;
} // calculate