package org.gvt.action;
import org.eclipse.jface.action.Action;
import org.eclipse.jface.dialogs.MessageDialog;
import org.gvt.ChisioMain;
import org.gvt.gui.ItemSelectionRunnable;
import org.gvt.util.EntityHolder;
import org.gvt.gui.ItemSelectionDialog;
import org.gvt.model.BioPAXGraph;
import org.gvt.model.EntityAssociated;
import org.patika.mada.algorithm.AlgoRunner;
import org.patika.mada.graph.Node;
import org.patika.mada.util.CausativePath;
import org.patika.mada.util.ExperimentData;
import org.patika.mada.util.Path;
import java.util.*;
/**
* @author Ozgun Babur
*
* Copyright: Bilkent Center for Bioinformatics, 2007 - present
*/
public class SearchCausativePathsAction extends Action
{
private ChisioMain main;
private Set<Node> targets;
private BioPAXGraph pathwayGraph;
/**
* specifies if the causality search will be performed on the subject graph or current view
* graph.
*/
private boolean globalSearch;
/**
* Path ids to real paths.
*/
private Map<String, CausativePath> idMap;
/**
* Constructor
* @param main main application
* @param globalSearch search in the global (background) graph or only in the current view
*/
public SearchCausativePathsAction(ChisioMain main, boolean globalSearch)
{
super("Search Causative Paths" + (globalSearch ? " In Entire Model" : ""));
this.setToolTipText(this.getText());
this.main = main;
this.globalSearch = globalSearch;
}
public SearchCausativePathsAction(ChisioMain main, Set<Node> targets, boolean globalSearch)
{
this(main, globalSearch);
this.targets = targets;
}
public void run()
{
if (globalSearch && main.getRootGraph() == null) return;
if (!globalSearch && main.getPathwayGraph() == null) return;
if (main.getExperimentDataManager(ExperimentData.EXPRESSION_DATA) == null)
{
MessageDialog.openError(main.getShell(), "No Expression Data Loaded!",
"Load experiment data to use this feature.");
return;
}
if (!main.getExperimentDataManager(ExperimentData.EXPRESSION_DATA).isInCompareMode())
{
MessageDialog.openError(main.getShell(), "Wrong Data Selection!",
"Causative paths can only be searched in data comparison mode.\n" +
"Go to \"Data Selection\" and compare some of the loaded experiments.");
return;
}
if (targets == null)
{
targets = new HashSet<Node>();
List selectedModel = main.getSelectedModel();
if (selectedModel != null)
{
for (Object o : selectedModel)
{
if (o instanceof Node)
{
targets.add((Node) o);
}
}
if (!targets.isEmpty() && globalSearch)
{
Map<EntityHolder, List<Node>> entityToNodeMap =
main.getRootGraph().getEntityToNodeMap();
ArrayList<Node> actors = new ArrayList<Node>(targets);
targets.clear();
for (Node actor : actors)
{
Node corresponding = (Node) actor.getLabel(BioPAXGraph.EXCISED_FROM);
if (corresponding instanceof EntityAssociated)
{
EntityHolder entity = ((EntityAssociated) corresponding).getEntity();
List<Node> nodeList = entityToNodeMap.get(entity);
for (Node node : nodeList)
{
targets.add(node);
}
}
}
}
}
}
// Prepare and run the algorithm
int limit = 10;
int k = 0;
int t = 0;
BioPAXGraph graph = globalSearch ? main.getRootGraph() : main.getPathwayGraph();
if (targets.isEmpty()) targets = null;
Map<Node, Map<Integer, List<CausativePath>>> allMap =
AlgoRunner.searchCausativePaths(graph, targets, limit, t, k);
// Search the paths map for each target and
// prepare the result paths to visualize
List<String> pathIDs = new ArrayList<String>();
idMap = new HashMap<String, CausativePath>();
// Collect all paths in a list to be used in excising the original graph and displaying the
// merge graph
List<Path> paths = new ArrayList<Path>();
for (Map<Integer, List<CausativePath>> integerListMap : allMap.values())
{
for (List<CausativePath> list : integerListMap.values())
{
paths.addAll(list);
}
}
// Open merge graph of result pathways in a new view
if (!paths.isEmpty() && globalSearch)
{
pathwayGraph = graph.excise(paths, false, true);
pathwayGraph.setName("Causative Paths");
main.createNewTab(pathwayGraph);
new CoSELayoutAction(main).run();
new ColorWithExperimentAction(main, pathwayGraph, ExperimentData.EXPRESSION_DATA).run();
for (Path path : paths)
{
path.replaceElements(pathwayGraph);
}
}
// If this is a local search then we will show result on the same result
if (!globalSearch)
{
pathwayGraph = graph;
}
for (Node target : allMap.keySet())
{
Map<Integer, List<CausativePath>> pathsMap = allMap.get(target);
if (pathsMap != null)
{
for (int i = 1; i <= limit; i++)
{
List<CausativePath> pathList = pathsMap.get(i);
if (pathList != null)
{
for (CausativePath path : pathList)
{
String id = path.toString();
if (pathIDs.contains(id))
{
int j = 2;
String nextID;
do
{
nextID = id + " (" + (j++) + ")";
}
while (pathIDs.contains(nextID));
id = nextID;
}
pathIDs.add(id);
idMap.put(id, path);
}
}
}
}
}
if (!pathIDs.isEmpty())
{
// Open a dialog so that user selected the specific path to visualize
ItemSelectionDialog dialog = new ItemSelectionDialog(main.getShell(),
250,
"Path Selection Dialog",
"Select path to visualize",
pathIDs, new ArrayList<String>(), false, false, new Runner());
dialog.setUpdateUponSelection(true);
dialog.setDoSort(false);
String lastItem = dialog.open();
if (lastItem == null || !lastItem.equals(ItemSelectionDialog.NONE))
{
dialog.runAsIfSelected(ItemSelectionDialog.NONE);
}
}
else
{
MessageDialog.openInformation(main.getShell(), "No results!",
"No causative paths found.");
}
targets = null;
pathwayGraph = null;
}
private class Runner implements ItemSelectionRunnable
{
private String lastID;
public void run(Collection<String> selectedTerms)
{
if (selectedTerms.isEmpty())
{
return;
}
String id = selectedTerms.iterator().next();
run(id);
}
public void run(String id)
{
if (id.equals(lastID))
{
return;
}
if (lastID != null)
{
idMap.get(lastID).removeInferenceData();
idMap.get(lastID).highlight(false);
}
if (id.equals(ItemSelectionDialog.NONE))
{
if (pathwayGraph.getLastAppliedColoring() != null)
{
pathwayGraph.representDataOnActors(pathwayGraph.getLastAppliedColoring());
}
else
{
pathwayGraph.removeRepresentations();
}
lastID = null;
return;
}
idMap.get(id).associateInferenceData();
idMap.get(id).highlight(true);
pathwayGraph.representDataOnActors(CausativePath.INFERENCE_DATA_KEY);
lastID = id;
}
}
}