org.biopax.paxtools.io.sbgn

Class SBGNLayoutManager

java.lang.Object

org.biopax.paxtools.io.sbgn.SBGNLayoutManager

public class SBGNLayoutManager
extends Object

SBGNLayoutManager Class: Applies layout by using ChiLay to Sbgn graph generated by paxtools.

Constructor Summary

Constructors

Constructor and Description
SBGNLayoutManager()

Method Summary

Modifier and Type	Method and Description
void	assignProcessAndLogicOpNodesToCompartment(org.sbgn.bindings.Sbgn sbgn) This method finds process nodes and logical operator nodes in sbgn map and assigns them to a compartment by using majority rule.
void	connectArcToPort(org.ivis.layout.sbgn.SbgnPDNode lPort, org.sbgn.bindings.Port vPort) This method connects the existing arcs to the newly created ports which are created by ChiLay and SBGNPD Layout.
org.sbgn.bindings.Sbgn	createLayout(org.sbgn.bindings.Sbgn sbgn) Applies CoSE layout to the given SBGN model.
void	createLEdges(List<org.sbgn.bindings.Arc> arcs, org.ivis.layout.Layout layout) Creates LNodes from Arcs of Sbgn and adds it to the passed layout object.
void	createLNode(VNode vNode, VNode parent, org.ivis.layout.Layout layout) Helper function for creating LNode objects from VNode objects and adds them to the given layout.
void	createVNodes(VCompound parent, List<org.sbgn.bindings.Glyph> glyphs) Recursively creates VNodes from Glyphs of Sbgn.
void	initPortIdToGlyphMap(List<org.sbgn.bindings.Glyph> glyphs) This method initializes map for glyphs and their respective ports.
boolean	isChildless(org.sbgn.bindings.Glyph targetGlyph) Returns true if a glyph includes child glyphs (state and info glyphs are out of count!)
void	populateCompartmentOccurencesMap(org.sbgn.bindings.Glyph targetGlyph, HashMap<String,Integer> compartmentIDandOccurenceMap) Updates a hashmap by incrementing the number of nodes in the compartment glyph that includes targetGlyph.
void	removePortsFromArcs(List<org.sbgn.bindings.Arc> arcs) This method replaces ports of arc objects with their owners.
void	setCompartmentRefForComplexMembers(org.sbgn.bindings.Glyph glyph, org.sbgn.bindings.Glyph compartment) This method recursively set compartmentRef fields of members of any complex glyphs as same as complex's compartmentRef
void	updateCompoundBounds(org.sbgn.bindings.Glyph parent, List<org.sbgn.bindings.Glyph> childGlyphs) Updates bounds of a compound node ( i.e.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SBGNLayoutManager

public SBGNLayoutManager()

Method Detail

createLayout

public org.sbgn.bindings.Sbgn createLayout(org.sbgn.bindings.Sbgn sbgn)

Applies CoSE layout to the given SBGN model.

Parameters:

sbgn - Sbgn object to which layout will be applied

Returns:

Laid out sbgn object

connectArcToPort

public void connectArcToPort(org.ivis.layout.sbgn.SbgnPDNode lPort,
                             org.sbgn.bindings.Port vPort)

This method connects the existing arcs to the newly created ports which are created by ChiLay and SBGNPD Layout.

Parameters:

lPort - l level port object.

vPort - v level port object.

assignProcessAndLogicOpNodesToCompartment

public void assignProcessAndLogicOpNodesToCompartment(org.sbgn.bindings.Sbgn sbgn)

This method finds process nodes and logical operator nodes in sbgn map and assigns them to a compartment by using majority rule.

Parameters:

sbgn - Given Sbgn map.

populateCompartmentOccurencesMap

public void populateCompartmentOccurencesMap(org.sbgn.bindings.Glyph targetGlyph,
                                             HashMap<String,Integer> compartmentIDandOccurenceMap)

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.

Parameters:

targetGlyph - glyph whose occurence will be updated in the given hashmap.

compartmentIDandOccurenceMap - Map that references number of nodes in a compartment by compartment ids .

updateCompoundBounds

public void updateCompoundBounds(org.sbgn.bindings.Glyph parent,
                                 List<org.sbgn.bindings.Glyph> childGlyphs)

Updates bounds of a compound node ( i.e. complex glyph ) from its children .

Parameters:

parent - compound glyph.

childGlyphs - related children of parent .

createVNodes

public void createVNodes(VCompound parent,
                         List<org.sbgn.bindings.Glyph> glyphs)

Recursively creates VNodes from Glyphs of Sbgn.

Parameters:

parent - Parent of the glyphs that are passed as second arguement.

glyphs - Glyphs that are child of parent which is passed as first arguement.

createLEdges

public void createLEdges(List<org.sbgn.bindings.Arc> arcs,
                         org.ivis.layout.Layout layout)

Creates LNodes from Arcs of Sbgn and adds it to the passed layout object.

Parameters:

arcs - List of arc objects from which the LEdges will be constructed for ChiLay Layout component.

layout - layout object to which the created LEdges added.

createLNode

public void createLNode(VNode vNode,
                        VNode parent,
                        org.ivis.layout.Layout layout)

Helper function for creating LNode objects from VNode objects and adds them to the given layout.

Parameters:

vNode - VNode object from which a corresponding LNode object will be created.

parent - parent of vNode, if not null vNode will be added to layout as child node.

layout - layout object to which the created LNodes added.

setCompartmentRefForComplexMembers

public void setCompartmentRefForComplexMembers(org.sbgn.bindings.Glyph glyph,
                                               org.sbgn.bindings.Glyph compartment)

This method recursively set compartmentRef fields of members of any complex glyphs as same as complex's compartmentRef

Parameters:

glyph - target glyph whose compartmentRef(compartment parameter) will be set.

compartment - compartmentRef value that will be set.

removePortsFromArcs

public void removePortsFromArcs(List<org.sbgn.bindings.Arc> arcs)

This method replaces ports of arc objects with their owners.

Parameters:

arcs - Arc list of SBGN model

initPortIdToGlyphMap

public void initPortIdToGlyphMap(List<org.sbgn.bindings.Glyph> glyphs)

This method initializes map for glyphs and their respective ports.

Parameters:

glyphs - Glyph list of SBGN model

isChildless

public boolean isChildless(org.sbgn.bindings.Glyph targetGlyph)

Returns true if a glyph includes child glyphs (state and info glyphs are out of count!)

Parameters:

targetGlyph - target glyph that will be queried.

Returns:

true/false