edu.iastate.metnet.graphmodel
Class FCMetaphor

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

All Implemented Interfaces:

IGraphMetaphor

public class FCMetaphor
extends AbstractGraphMetaphor

default metaphor
• (nodeType = RNA) maps to (shape = rectangular)
• (nodeType = Protein) maps to (shape = diamond)
• (nodeType = Compound) maps to (shape = ecclipse)
• (location = cytosol) maps to (node fill color = 0xFFFFCC)
• (location = mitochondria*) maps to (node fill color = pink)
• (location = microbody) maps to (node fill color = grey)
• (location = plastid*) maps to (node fill color = green)
• (location = apoplast) maps to (node fill color = 0x6699FF)
• (location = nucleus) maps to (node outline color = yellow)
• (location = thylakoids*) maps to (node outline color = green)
• (edgeType = Catalysis) maps to (line thickness = medium)
• (edgeType = Catalysis) maps to (line color = blue)
• (edgeType = Enzymatic) maps to (line thickness = medium)
• (edgeType = OR) maps to (line thickness = medium-narrow)
• (edgeType = OR) maps to (line color = yellow)
• (edgeType = Regulation/Positive regulation) maps to (line color = green)
• (edgeType = Regulation/Positive regulation) maps to (line thickness = medium-narrow)
• (edgeType = Regulation/Negative regulation) maps to (line color = red)
• (edgeType = Regulation/Negative regulation) maps to (line thickness = medium-narrow)
• (certainty = indirect evidence) maps to (line type = dash-dot)
• (certainty = several line*) maps to (line type = dotted)
• (certainty = wild hypo*) maps to (line type = dotted)

Author:

Jie Li

Field Summary

(package private) java.util.Set	derivedNodeSet derived system nodes also need to be highlighted
(package private) static org.apache.log4j.Logger	logger log4j facility
(package private) java.util.Set	originalNodeSet original system node need to be red colored

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

DEFAULT_BACKGROUND, DEFAULT_FOREGROUND, DEFAULT_LINE_WIDTH

Constructor Summary

FCMetaphor()
default constructor

FCMetaphor(java.util.Collection nodeList)
default constructor

FCMetaphor(java.util.Collection originalNodeList, java.util.Collection derivedNodeList)
default constructor

Method Summary

void	run(org.jgraph.JGraph graph, java.lang.Object[] cells) color the graph according to FCModeler

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

originalNodeSet

java.util.Set originalNodeSet

original system node need to be red colored

derivedNodeSet

java.util.Set derivedNodeSet

derived system nodes also need to be highlighted

Constructor Detail

FCMetaphor

public FCMetaphor()

default constructor

FCMetaphor

public FCMetaphor(java.util.Collection nodeList)

default constructor

FCMetaphor

public FCMetaphor(java.util.Collection originalNodeList,
                  java.util.Collection derivedNodeList)

default constructor

Method Detail

run

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

color the graph according to FCModeler

Specified by:

run in interface IGraphMetaphor

Overrides:

run in class AbstractGraphMetaphor

Parameters:

graph - the graph

cells - all the cells