org.biopax.paxtools.io.sbgn.SBGNLayoutManager Maven / Gradle / Ivy
package org.biopax.paxtools.io.sbgn;
import java.util.*;
import org.ivis.layout.*;
import org.ivis.layout.sbgn.SbgnPDNode;
import org.ivis.layout.sbgn.SbgnProcessNode;
import org.ivis.layout.sbgn.SbgnPDLayout;
import org.sbgn.bindings.Arc;
import org.sbgn.bindings.Port;
import org.sbgn.bindings.Glyph;
import org.sbgn.bindings.Sbgn;
import org.sbgn.bindings.Bbox;
/**
* Chilay COSE layout of an SBGN PD graph.
*
* @author: Istemi Bahceci, rodche (refactoring)
*/
class SBGNLayoutManager
{
// Layout and root objects
private Layout layout;
private VCompound root;
// mapping between view and layout level
private HashMap viewToLayout;
private HashMap layoutToView;
private HashMap glyphToVNode;
private HashMap idToGLyph;
private HashMap idToCompartmentGlyphs;
private HashMap portIDToOwnerGlyph;
private HashMap idToArcs;
/**
* Applies CoSE layout to the given SBGN PD model.
*
* @param sbgn model where layout is performed and stored
*/
public void createLayout(final Sbgn sbgn)
{
viewToLayout = new HashMap();
glyphToVNode = new HashMap();
idToGLyph = new HashMap();
idToCompartmentGlyphs = new HashMap();
portIDToOwnerGlyph = new HashMap();
layoutToView = new HashMap();
idToArcs = new HashMap();
// Using the Compound Spring Embedder layout algorithm
layout = new SbgnPDLayout();
// This list holds the glyphs that will be deleted after corresponding glyph is added to child glyph of another glyph.
ArrayList deletedList = new ArrayList();
LGraphManager graphMgr = layout.getGraphManager();
graphMgr.addRoot(); //TODO: why is it here (some initialisation)?..
root = new VCompound(new Glyph());
// Detect compartment glyphs and put them in a hashmap;
// also set compartment glyphs of members of complexes.
for (Glyph g: sbgn.getMap().getGlyph())
{
if(g.getClazz().equals("compartment")) {
idToCompartmentGlyphs.put(g.getId(), g);
}
//Set compartmentRef to all children of a Complex node.
Glyph compartment = (Glyph)g.getCompartmentRef();
if(compartment != null && g.getClazz().equals("complex")) {
setCompartmentRefForComplexMembers(g, compartment, new HashSet());
}
}
// Nest glyphs inside compartment glyphs according to their compartmentRef.
for (Glyph g: sbgn.getMap().getGlyph())
{
Glyph containerCompartment = (Glyph)g.getCompartmentRef();
if(containerCompartment != null) {
idToCompartmentGlyphs.get(containerCompartment.getId()).getGlyph().add(g);
deletedList.add(g);
}
}
// Delete the duplicate glyphs, after they are moved to corresponding compartment glyph.
for (Glyph g: deletedList) {
sbgn.getMap().getGlyph().remove(g);
}
// initialize the map for keeping ports and their owner glyphs
// with entries like:
initPortIdToGlyphMap(sbgn.getMap().getGlyph());
//Remove ports from source and target field of ports
//replace them with owner glyphs of these ports
removePortsFromArcs(sbgn.getMap().getArc());
// Assign logical operator and Process nodes to compartment
assignProcessAndLogicOpNodesToCompartment(sbgn);
// Create Vnodes for ChiLay layout component
createVNodes(root, sbgn.getMap().getGlyph());
for (VNode vNode: root.children) {
createLNode(vNode, null);
}
// Create LEdges for ChiLay layout component
createLEdges(sbgn.getMap().getArc());
graphMgr.updateBounds(); //TODO: why is it called here and again after the layout is done?
// Apply layout
layout.runLayout();
graphMgr.updateBounds();
// Here if any SbgnProcessNode node is returned from SBGNPD Layout
// this means that we will have two additional port info. We should
// add this information to libSbgn objects
for(Object lNode: layout.getAllNodes())
{
if( (LNode)lNode instanceof SbgnProcessNode)
{
//Set geometry of corresponding node
VNode vNode = layoutToView.get(((SbgnProcessNode) lNode).label);
Bbox tempBbox = vNode.glyph.getBbox();
tempBbox.setX((float)(((SbgnProcessNode) lNode).getLeft()));
tempBbox.setY((float) (((SbgnProcessNode) lNode).getTop()));
vNode.glyph.setBbox(tempBbox);
//Created port objects in layout level
SbgnPDNode inputLPort = ((SbgnProcessNode) lNode).getInputPort();
SbgnPDNode outputLPort = ((SbgnProcessNode) lNode).getOutputPort();
// New port objects
Port inputPort = new Port();
Port outputPort = new Port();
// Set port attributes
inputPort.setX((float) (inputLPort.getCenterX()));
inputPort.setY((float)(inputLPort.getCenterY()));
inputPort.setId(inputLPort.label);
outputPort.setX((float)(outputLPort.getCenterX()));
outputPort.setY((float) (outputLPort.getCenterY()));
outputPort.setId((outputLPort.label));
//Clear existing ports !
vNode.glyph.getPort().clear();
//Connect existing arcs to newly created ports
//These ports are created by ChiLay and SBGNPD Layout
connectArcToPort(inputLPort, inputPort);
connectArcToPort(outputLPort, outputPort);
//Add ports to the corresponding glyph
vNode.glyph.getPort().add(inputPort);
vNode.glyph.getPort().add(outputPort);
}
}
// Update the bounds
for (VNode vNode: root.children) {
updateCompoundBounds(vNode.glyph, vNode.glyph.getGlyph());
}
// Clear inside of the compartmentGlyphs
for (Glyph compGlyph: idToCompartmentGlyphs.values()) {
//Again add the members of compartments
for(Glyph memberGlyph: compGlyph.getGlyph() ) {
sbgn.getMap().getGlyph().add(memberGlyph);
}
compGlyph.getGlyph().clear();
}
}
/**
* This method connects the existing arcs to the newly created
* ports which are created by ChiLay and SBGNPD Layout.
* @param lPort l level port object.
* @param vPort v level port object.
* */
private void connectArcToPort(SbgnPDNode lPort, Port vPort)
{
//Iterate over the edges of l level port
for (Object e: (lPort.getEdges()))
{
//Ignore rigid edges
if(((LEdge)e).type.equals("rigid edge"))
continue;
//Determine the if vPort is source or target
Arc arc = idToArcs.get(((LEdge)e).label);
if( lPort.label.equals(((LEdge)e).getSource().label ))
{
arc.setSource(vPort);
}
else if ( lPort.label.equals(((LEdge)e).getTarget().label ) )
{
arc.setTarget(vPort);
}
}
}
/**
* This method finds process nodes and logical operator nodes in sbgn map and assigns them to a compartment by using majority rule.
* @param sbgn Given Sbgn map.
* */
private void assignProcessAndLogicOpNodesToCompartment(Sbgn sbgn)
{
// Create a hashmap for keeping a node( generally logical operators and process nodes ) and its neighbours.
// TreeMap value of the hash map keeps track of compartment nodes that includes neighbours of the node by String id and
// Integer value holds the number of occurences of that compartment among the neighbours of the node as parent.
HashMap > nodetoNeighbours = new HashMap>();
List glyphList = sbgn.getMap().getGlyph();
List arcList = sbgn.getMap().getArc();
// Keeps track of process and logical operator nodes that will be assigned to a compartment.
ArrayList targetNodes = new ArrayList();
//Iterate over glyphs of sbgn map
for(Glyph glyph: glyphList)
{
// Here logical operator nodes and process nodes are interested !
if(glyph.getClazz().equals("process") ||glyph.getClazz().equals("omitted process")||glyph.getClazz().equals( "uncertain process") || glyph.getClazz().equals("phenotype")||
glyph.getClazz().equals("association") || glyph.getClazz().equals("dissociation") ||glyph.getClazz().equals("and")||glyph.getClazz().equals("or")||glyph.getClazz().equals("not"))
{
// Add a new value to hash map and also store the node as target node
String processGlyphID = glyph.getId();
String rootID = "root";
nodetoNeighbours.put(processGlyphID, new HashMap());
targetNodes.add(glyph);
// Iterate over arc list
for(Arc arc: arcList)
{
Glyph target = null;
Glyph source = null;
// If source and target of node is port find its owner glyph ! else just assign it.
if(arc.getSource() instanceof Port)
source = portIDToOwnerGlyph.get(((Port)arc.getSource()).getId());
else
source = (Glyph)arc.getSource();
if(arc.getTarget() instanceof Port)
target = portIDToOwnerGlyph.get(((Port)arc.getTarget()).getId());
else
target = (Glyph)arc.getTarget();
// If source of any arc is our node, then target must be neighbour of this node !
if(source.getId().equals(processGlyphID))
{
populateCompartmentOccurencesMap(target, nodetoNeighbours.get(processGlyphID));
}
// same as target part !!
else if(target.getId().equals(processGlyphID))
{
populateCompartmentOccurencesMap(source, nodetoNeighbours.get(processGlyphID));
}
}
}
}
//Finally assign nodes to compartments by majority rule
for(Glyph glyph: targetNodes)
{
String id = glyph.getId();
HashMap compartmentsOfTargetNode = nodetoNeighbours.get(id);
// Finally sort the hashmap to obtain the compartment that includes majority of the neighbours of the targetNode
List> entries = new LinkedList>(compartmentsOfTargetNode.entrySet());
Collections.sort(entries, new Comparator>() {
@Override
public int compare(Map.Entry o1, Map.Entry o2)
{
return -(o1.getValue().compareTo(o2.getValue()));
}
});
if(entries.size() > 0)
{
// if the process belongs to root do not make any changes
if(entries.get(0).getKey().equals("root"))
continue;
Glyph compartment = idToCompartmentGlyphs.get(entries.get(0).getKey());
//Set compartmentRef of process glyph also!
glyph.setCompartmentRef(compartment);
compartment.getGlyph().add(glyph);
//Remove it from sbgn also
sbgn.getMap().getGlyph().remove(glyph);
}
}
}
/**
* Updates a hashmap by incrementing the number of nodes in the compartment glyph that includes targetGlyph.
* It is assumed that given hashmap includes compartment ids' as keys and number of nodes as values.This method
* is an utility method that will be used to populate a hashmap while determining the compartment node of a process
* node by majority rule.
*
* @param targetGlyph glyph whose occurence will be updated in the given hashmap.
* @param compartmentIDandOccurenceMap Map that references number of nodes in a compartment by compartment ids .
* */
private void populateCompartmentOccurencesMap(Glyph targetGlyph, HashMap compartmentIDandOccurenceMap)
{
String rootID = "root";
// if compartment ref of targetGlyph node is not null, increment its occurence by 1
if(targetGlyph.getCompartmentRef() != null)
{
Glyph containerCompartment = (Glyph)targetGlyph.getCompartmentRef();
String compartmentID = containerCompartment.getId();
Integer compartmentOccurrenceValue = compartmentIDandOccurenceMap.get(compartmentID);
if( compartmentOccurrenceValue != null)
{
compartmentIDandOccurenceMap.put(compartmentID, compartmentOccurrenceValue + 1);
}
else
compartmentIDandOccurenceMap.put(compartmentID, 1);
}
// else targetGlyph is in root graph so increment root graphs counter value by 1
else
{
Integer compartmentOccurrenceValue = compartmentIDandOccurenceMap.get(rootID);
if( compartmentOccurrenceValue != null)
{
compartmentIDandOccurenceMap.put(rootID, compartmentOccurrenceValue + 1);
}
else
compartmentIDandOccurenceMap.put(rootID, 1);
}
}
/**
* Updates bounds of a compound node ( i.e. complex glyph ) from its children .
* @param parent compound glyph.
* @param childGlyphs related children of parent .
* */
private void updateCompoundBounds(Glyph parent,List childGlyphs)
{
float PAD = (float) 2.0;
float minX = Float.MAX_VALUE; float minY = Float.MAX_VALUE;
float maxX = Float.MIN_VALUE; float maxY = Float.MIN_VALUE;
for (Glyph tmpGlyph:childGlyphs)
{
if(!tmpGlyph.getClazz().equals("unit of information") && !tmpGlyph.getClazz().equals("state variable") )
{
if(tmpGlyph.getGlyph().size() > 0)
updateCompoundBounds(tmpGlyph, tmpGlyph.getGlyph());
float w = tmpGlyph.getBbox().getW();
float h = tmpGlyph.getBbox().getH();
// Verify MIN and MAX x/y again:
minX = Math.min(minX, (tmpGlyph.getBbox().getX()));
minY = Math.min(minY, (tmpGlyph.getBbox().getY()));
maxX = Math.max(maxX, (tmpGlyph.getBbox().getX())+w);
maxY = Math.max(maxY, (tmpGlyph.getBbox().getY())+h);
if (minX == Float.MAX_VALUE) minX = 0;
if (minY == Float.MAX_VALUE) minY = 0;
if (maxX == Float.MIN_VALUE) maxX = 0;
if (maxY == Float.MIN_VALUE) maxY = 0;
parent.getBbox().setX(minX - PAD);
parent.getBbox().setY(minY - PAD);
parent.getBbox().setW(maxX - parent.getBbox().getX() + PAD);
parent.getBbox().setH(maxY - parent.getBbox().getY() + PAD);
}
}
}
/**
* Recursively creates VNodes from Glyphs of Sbgn.
*
* @param parent Parent of the glyphs that are passed as second arguement.
* @param glyphs Glyphs that are child of parent which is passed as first arguement.
*
* */
private void createVNodes(VCompound parent,List glyphs)
{
for(Glyph glyph: glyphs )
{
if (!glyph.getClazz().equals("state variable") && !glyph.getClazz().equals("unit of information") )
{
if(glyph.getClazz().equals("process"))
{
VCompound v = new VCompound(glyph);
}
if(!isChildless(glyph))
{
VCompound v = new VCompound(glyph);
idToGLyph.put(glyph.getId(), glyph);
glyphToVNode.put(glyph, v);
parent.children.add(v);
createVNodes(v, glyph.getGlyph());
}
else
{
VNode v = new VNode(glyph);
idToGLyph.put(glyph.getId(), glyph);
glyphToVNode.put(glyph, v);
parent.children.add(v);
}
}
}
}
/**
* Creates LNodes from Arcs of Sbgn and adds it to the passed layout object.
*
* @param arcs List of arc objects from which the LEdges will be constructed for ChiLay Layout component.
*
* */
private void createLEdges(List arcs)
{
for(Arc arc: arcs )
{
LEdge lEdge = layout.newEdge(null);
lEdge.type = arc.getClazz();
lEdge.label = arc.getId();
LNode sourceLNode = viewToLayout.get(glyphToVNode.get(arc.getSource()));
LNode targetLNode = viewToLayout.get(glyphToVNode.get(arc.getTarget()));
idToArcs.put(arc.getId(), arc);
// Add edge to the layout
layout.getGraphManager().add(lEdge, sourceLNode, targetLNode);
}
}
/**
* Helper function for creating LNode objects from VNode objects and adds them to the given layout.
*
* @param vNode VNode object from which a corresponding LNode object will be created.
* @param parent parent of vNode, if not null vNode will be added to layout as child node.
* */
private void createLNode(VNode vNode, VNode parent)
{
LNode lNode = ((SbgnPDLayout)layout).newNode(vNode);
lNode.type = vNode.glyph.getClazz();
lNode.label = vNode.glyph.getId();
LGraph rootLGraph = layout.getGraphManager().getRoot();
//Add corresponding nodes to corresponding maps
viewToLayout.put(vNode, lNode);
layoutToView.put(lNode.label,vNode);
// if the vNode has a parent, add the lNode as a child of the parent l-node.
// otherwise, add the node to the root graph.
if (parent != null)
{
LNode parentLNode = viewToLayout.get(parent);
parentLNode.getChild().add(lNode);
}
else
{
rootLGraph.add(lNode);
}
lNode.setLocation(vNode.glyph.getBbox().getX(), vNode.glyph.getBbox().getY());
if (vNode instanceof VCompound)
{
VCompound vCompound = (VCompound) vNode;
// add new LGraph to the graph manager for the compound node
layout.getGraphManager().add(layout.newGraph(null), lNode);
// for each VNode in the node set create an LNode
for (VNode vChildNode: vCompound.getChildren())
{
createLNode(vChildNode, vCompound);
}
}
else
{
lNode.setWidth(vNode.glyph.getBbox().getW());
lNode.setHeight(vNode.glyph.getBbox().getH());
}
}
/**
* Recursively sets compartmentRef fields of members of a complex glyph
* to the same value as complex's compartment.
*
* @param glyph target glyph where compartmentRef(compartment parameter) will be set.
* @param compartment compartmentRef value that will be set.
* @param visited (initially an empty set of) previously processed glyphs, to escape infinite loops
* */
private void setCompartmentRefForComplexMembers(final Glyph glyph, final Glyph compartment,
final Set visited)
{
if(!visited.add(glyph))
return;
glyph.setCompartmentRef(compartment);
if(glyph.getGlyph().size() > 0) {
for(Glyph g: glyph.getGlyph() ) {
setCompartmentRefForComplexMembers(g, compartment, visited);
}
}
}
/**
* This method replaces ports of arc objects with their owners.
* @param arcs Arc list of SBGN model
* */
private void removePortsFromArcs(List arcs)
{
for(Arc arc: arcs )
{
// If source is port, first clear port indicators else retrieve it from hashmaps
if (arc.getSource() instanceof Port )
{
Glyph source = portIDToOwnerGlyph.get(((Port)arc.getSource()).getId());
arc.setSource(source);
}
// If target is port, first clear port indicators else retrieve it from hashmaps
if (arc.getTarget() instanceof Port)
{
Glyph target = portIDToOwnerGlyph.get(((Port)arc.getTarget()).getId());
arc.setTarget(target);
}
}
}
/**
* This method initializes map for glyphs and their respective ports.
* @param glyphs Glyph list of SBGN model
* */
private void initPortIdToGlyphMap(List glyphs)
{
for(Glyph glyph: glyphs)
{
for(Port p: glyph.getPort())
{
portIDToOwnerGlyph.put(p.getId(), glyph );
}
if(glyph.getGlyph().size() > 0)
initPortIdToGlyphMap(glyph.getGlyph());
}
}
/**
* Returns true if a glyph includes child glyphs (state and info glyphs are out of count!)
* @param targetGlyph target glyph that will be queried.
* @return true/false
* */
private boolean isChildless(Glyph targetGlyph)
{
boolean checker = true;
for(Glyph glyph: targetGlyph.getGlyph() )
{
if ( !glyph.getClazz().equals("state variable") && !glyph.getClazz().equals("unit of information") )
{
checker = false;
break;
}
}
return checker;
}
}
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