org.biopax.paxtools.io.sif.level3

Class ActivityNetworkAnalyzer

java.lang.Object

org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer

Deprecated.

public class ActivityNetworkAnalyzer
extends Object

This class analyzes the network to predict the effect of modifications on PEs on their activity. NOTE: This method is experimental and makes several assumptions based on the existing data sources. It might not work universally or return unexpected results for untested data sets. Use with caution.

Author:

Emek Demir

Constructor Summary

Constructors

Constructor and Description
ActivityNetworkAnalyzer() Deprecated.

Method Summary

Modifier and Type	Method and Description
void	analyzeStates(Model model) Deprecated. Given a model this method will analyze the states and populate the stateChangeMap and extendedControls maps.
Set<PEStateChange>	getAllStates(EntityReference er) Deprecated.
Set<SimplePhysicalEntity>	getPrecedingStates(SimplePhysicalEntity spe) Deprecated.
Set<SimplePhysicalEntity>	getSucceedingStates(SimplePhysicalEntity spe) Deprecated.
void	writeStateNetworkAnalysis(OutputStream out) Deprecated. This method writes out the results of the stateNetworkAnalysis for each detected state change.

Methods inherited from class java.lang.Object

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

Constructor Detail

ActivityNetworkAnalyzer

public ActivityNetworkAnalyzer()

Deprecated.

Method Detail

analyzeStates

public void analyzeStates(Model model)

Deprecated.

Given a model this method will analyze the states and populate the stateChangeMap and extendedControls maps.

Parameters:

model - to be analyzed.

getPrecedingStates

public Set<SimplePhysicalEntity> getPrecedingStates(SimplePhysicalEntity spe)

Deprecated.

Parameters:

spe - a physical entity but complex

Returns:

all preceding states of a SimplePhysicalEntity. Preceding states are other spes of the same EntityReference that are converted into this spe in one conversion.

getAllStates

public Set<PEStateChange> getAllStates(EntityReference er)

Deprecated.

getSucceedingStates

public Set<SimplePhysicalEntity> getSucceedingStates(SimplePhysicalEntity spe)

Deprecated.

Parameters:

spe - a physical entity but complex

Returns:

all succeeding states of a SimplePhysicalEntity. Preceding states are other spes of the same EntityReference that this spe is converted into in one conversion.

writeStateNetworkAnalysis

public void writeStateNetworkAnalysis(OutputStream out)
                               throws IOException

Deprecated.

This method writes out the results of the stateNetworkAnalysis for each detected state change.

Parameters:

out - output stream

Throws:

IOException - when an I/O error happens