edu.iastate.metnet.graphmodel
Class ChemicalReactionMetaphor

java.lang.Object
  edu.iastate.metnet.graphmodel.AbstractGraphMetaphor
      edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

All Implemented Interfaces:

IGraphMetaphor

public class ChemicalReactionMetaphor
extends AbstractGraphMetaphor

flux analysis on this

• collect all valid edges
• collect all valid interaction nodes (including hidden transport node)
• get the component graph or subsystem
• pop up dialog with table which displays the sub-system (in combobox) and corresponding interaction, and rates field, and freedom hint (require user continue input)
• set up the linear equation system and solve it
• metaphor the sub-system with the solution

Author:

Jie Li

Field Summary

(package private) java.lang.Integer	currentBlockID current focus blockunit, if null, none is selected
(package private) org.apache.commons.collections.map.MultiKeyMap	currentBlockIDSubSystemMap since node is not always same hash I have to create another map say currentBlockIDSubSystemMap, the key is (blockid, blockunittype)
(package private) java.lang.Object[]	currentCells current graph cells in the jgraph instance
(package private) org.jgraph.JGraph	currentGraph current jgraph instance
(package private) java.util.Map	currentIntermediumMap hold the information of the intermedium compound the key is node->{blockid, incomingreactionids, outgoingreactionids, subsystem, }
(package private) java.util.Map	currentNodeSubSystemMap node and their corresponding sub-system-id
(package private) java.util.Map	currentValidEdgeMap edges covered by current chemical reaction set
(package private) java.util.Map	currentValidNodeMap current chemical reaction nodes and their substrate nodes
(package private) static org.apache.log4j.Logger	logger log4j facility
(package private) java.util.Map	reactionRateMap hold the chemical reaction rates
(package private) int	subSystem current sub-system label, if 0, none is selected

Fields inherited from class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

DEFAULT_BACKGROUND, DEFAULT_FOREGROUND, DEFAULT_LINE_WIDTH

Constructor Summary

ChemicalReactionMetaphor()

Method Summary

java.util.List	collectInteractionIDListInSubSystem(java.lang.Integer subSystem) collect the interaction in the sub-system
int	computeDegreeOfFreedom(int totalChemicalReactionCount, int providedRateCount) compute the degree of the freedom of the linear equation system.
java.lang.Integer	getCurrentBlockID()
org.apache.commons.collections.map.MultiKeyMap	getCurrentBlockIDSubSystemMap()
java.util.Map	getCurrentIntermediumMap()
java.util.Map	getCurrentNodeSubSystemMap()
java.util.Map	getCurrentValidEdgeMap()
java.util.Map	getCurrentValidNodeMap()
java.util.Map	getReactionRateMap()
int	getSubSystem()
void	run(org.jgraph.JGraph graph, java.lang.Object[] cells) make the graph black and white
void	runGlobalMetaphor(org.jgraph.JGraph graph, java.lang.Object[] cells) label all valid interaction as red
void	runPartialMetaphor(org.jgraph.JGraph graph, java.lang.Object[] cells, int subSystem) visualize the selected sub-system, for simplicity, we only change the color of the node, and ignore all edges.
void	runSpecialMetaphor(org.jgraph.JGraph graph, java.lang.Object[] cells, java.lang.Integer selectedBlockID) metaphor the selection as blue
void	runSpecialMetaphor(org.jgraph.JGraph graph, java.lang.Object[] cells, java.util.Map reactionRateMap) change the width of the reaction based on the rate
void	setCurrentBlockID(java.lang.Integer currentBlockID)
void	setCurrentBlockIDSubSystemMap(org.apache.commons.collections.map.MultiKeyMap currentBlockIDSubSystemMap)
void	setCurrentNodeSubSystemMap(java.util.Map nodeSubSystemMap)
void	setCurrentValidEdgeMap(java.util.Map validEdgeMap)
void	setCurrentValidNodeMap(java.util.Map validNodeMap)
void	setReactionRateMap(java.util.Map reactionRateMap)
void	setSubSystem(int subSystem)

Methods inherited from class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

autoSizeBox, changeEdgeColor, changeEdgeDualColor, changeEdgePattern, changeEdgeWidth, changeVertexBackgroundColor, changeVertexBorderColor, changeVertexBorderWidth, changeVertexDualColor, changeVertexForegroundColor, getEdgeType, getIncomingEdges, getIncomingNodes, getInteractionColorForEdge, getInteractionWidthForEdge, getIntersectionNodes, getLocationColorForVertex, getOutgoingEdges, getOutgoingNodes

Methods inherited from class java.lang.Object

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

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

subSystem

int subSystem

current sub-system label, if 0, none is selected

currentBlockID

java.lang.Integer currentBlockID

current focus blockunit, if null, none is selected

currentValidNodeMap

java.util.Map currentValidNodeMap

current chemical reaction nodes and their substrate nodes

currentValidEdgeMap

java.util.Map currentValidEdgeMap

edges covered by current chemical reaction set

currentNodeSubSystemMap

java.util.Map currentNodeSubSystemMap

node and their corresponding sub-system-id

currentBlockIDSubSystemMap

org.apache.commons.collections.map.MultiKeyMap currentBlockIDSubSystemMap

since node is not always same hash I have to create another map say currentBlockIDSubSystemMap, the key is (blockid, blockunittype)

currentGraph

org.jgraph.JGraph currentGraph

current jgraph instance

currentCells

java.lang.Object[] currentCells

current graph cells in the jgraph instance

reactionRateMap

java.util.Map reactionRateMap

hold the chemical reaction rates

currentIntermediumMap

java.util.Map currentIntermediumMap

hold the information of the intermedium compound the key is node->{blockid, incomingreactionids, outgoingreactionids, subsystem, }

Constructor Detail

ChemicalReactionMetaphor

public ChemicalReactionMetaphor()

Method Detail

setCurrentNodeSubSystemMap

public void setCurrentNodeSubSystemMap(java.util.Map nodeSubSystemMap)

Parameters:

nodeSubSystemMap - The nodeSubSystem to set.

setCurrentValidEdgeMap

public void setCurrentValidEdgeMap(java.util.Map validEdgeMap)

Parameters:

validEdgeMap - The validEdgeMap to set.

setCurrentValidNodeMap

public void setCurrentValidNodeMap(java.util.Map validNodeMap)

Parameters:

validNodeMap - The validNodeMap to set.

runGlobalMetaphor

public void runGlobalMetaphor(org.jgraph.JGraph graph,
                              java.lang.Object[] cells)

label all valid interaction as red

runPartialMetaphor

public void runPartialMetaphor(org.jgraph.JGraph graph,
                               java.lang.Object[] cells,
                               int subSystem)

visualize the selected sub-system, for simplicity, we only change the color of the node, and ignore all edges. we did not hold the subsystem for those edges

Parameters:

graph - the jgraph instance

cells - the graph cell in the jgraph instance

subSystem - the selected sub-system

runSpecialMetaphor

public void runSpecialMetaphor(org.jgraph.JGraph graph,
                               java.lang.Object[] cells,
                               java.lang.Integer selectedBlockID)

metaphor the selection as blue

Parameters:

graph - the jgraph instance

cells - the graph cells in the jgraph instance

selectedBlockID - the selected blockunit id

runSpecialMetaphor

public void runSpecialMetaphor(org.jgraph.JGraph graph,
                               java.lang.Object[] cells,
                               java.util.Map reactionRateMap)

change the width of the reaction based on the rate

Parameters:

graph -

cells -

reactionRateMap -

run

public void run(org.jgraph.JGraph graph,
                java.lang.Object[] cells)

Description copied from class: AbstractGraphMetaphor

make the graph black and white

Specified by:

run in interface IGraphMetaphor

Overrides:

run in class AbstractGraphMetaphor

Parameters:

graph - the jgraph instance

cells - the selected cells or all cells

getSubSystem

public int getSubSystem()

Returns:

Returns the subSystem.

setSubSystem

public void setSubSystem(int subSystem)

Parameters:

subSystem - The subSystem to set.

getCurrentNodeSubSystemMap

public java.util.Map getCurrentNodeSubSystemMap()

Returns:

Returns the nodeSubSystem.

getCurrentValidEdgeMap

public java.util.Map getCurrentValidEdgeMap()

Returns:

Returns the validEdgeMap.

getCurrentValidNodeMap

public java.util.Map getCurrentValidNodeMap()

Returns:

Returns the validNodeMap.

collectInteractionIDListInSubSystem

public java.util.List collectInteractionIDListInSubSystem(java.lang.Integer subSystem)

collect the interaction in the sub-system

Parameters:

subSystem - the subsystem

Returns:

the interaction id list

getCurrentBlockID

public java.lang.Integer getCurrentBlockID()

Returns:

Returns the currentBlockID.

setCurrentBlockID

public void setCurrentBlockID(java.lang.Integer currentBlockID)

Parameters:

currentBlockID - The currentBlockID to set.

getReactionRateMap

public java.util.Map getReactionRateMap()

Returns:

Returns the reactionRateMap.

setReactionRateMap

public void setReactionRateMap(java.util.Map reactionRateMap)

Parameters:

reactionRateMap - The reactionRateMap to set.

computeDegreeOfFreedom

public int computeDegreeOfFreedom(int totalChemicalReactionCount,
                                  int providedRateCount)

compute the degree of the freedom of the linear equation system. only zero degree system is determined and potentially solvable.

suppose

• x is the number of the total chemical reactions in the sub-system
• y is the number of intermdium compounds in the sub-system
• z is the number of the chemical reactions that user provides the rates
• d is the degree of freedom

then
d = x - (y + z)

Parameters:

totalChemicalReactionCount - total checmical reaction count

providedRateCount - provided rate parameter count

Returns:

the degree of the freedom

getCurrentBlockIDSubSystemMap

public org.apache.commons.collections.map.MultiKeyMap getCurrentBlockIDSubSystemMap()

Returns:

Returns the currentBlockIDSubSystemMap.

setCurrentBlockIDSubSystemMap

public void setCurrentBlockIDSubSystemMap(org.apache.commons.collections.map.MultiKeyMap currentBlockIDSubSystemMap)

Parameters:

currentBlockIDSubSystemMap - The currentBlockIDSubSystemMap to set.

getCurrentIntermediumMap

public java.util.Map getCurrentIntermediumMap()

Returns:

Returns the currentIntermediumMap.