fr.systemsbiology.cyni
Class AbstractCyniMetric

java.lang.Object
  fr.systemsbiology.cyni.AbstractCyniMetric

All Implemented Interfaces:

CyCyniMetric

public abstract class AbstractCyniMetric
extends Object
implements CyCyniMetric

The AbstractCyniMetrics provides a basic implementation of a cyni metric TaskFactory.

Constructor Summary

AbstractCyniMetric(String computerName, String humanName)
The Constructor.

Method Summary

protected void	addTag(String tag) It adds a tags to the list of tags that define that metric
CyniTable	getCyniTable(org.cytoscape.model.CyTable table, String[] attributes, boolean transpose, boolean ignoreMissing, boolean selectedOnly) It produces a CyniTable with methods specific for this metric
String	getName() A computer readable name used to differentiate the metrics.
List<String>	getTagsList() The list of tags of this metric
void	initMetric() It initializes the metric and after this method the metric is ready to start calculating measurements.
void	setParameters(Map<String,Object> params) It sets the metric's parameters
String	toString() Used to get the user-visible name of the cyni Metric.

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.systemsbiology.cyni.CyCyniMetric

getMetric

Constructor Detail

AbstractCyniMetric

public AbstractCyniMetric(String computerName,
                          String humanName)

The Constructor.

Parameters:

computerName - a computer readable name used to differentiate the metrics.

humanName - a user visible name of the metric.

Method Detail

getName

public String getName()

A computer readable name used to differentiate the metrics.

Specified by:

getName in interface CyCyniMetric

Returns:

a computer readable name used to differentiate the metrics.

toString

public String toString()

Used to get the user-visible name of the cyni Metric.

Overrides:

toString in class Object

Returns:

the user-visible name of the cyni Metric.

addTag

protected void addTag(String tag)

It adds a tags to the list of tags that define that metric

getCyniTable

public CyniTable getCyniTable(org.cytoscape.model.CyTable table,
                              String[] attributes,
                              boolean transpose,
                              boolean ignoreMissing,
                              boolean selectedOnly)

It produces a CyniTable with methods specific for this metric

Specified by:

getCyniTable in interface CyCyniMetric

Returns:

the new extended CyniTable

getTagsList

public List<String> getTagsList()

The list of tags of this metric

Specified by:

getTagsList in interface CyCyniMetric

Returns:

the list of types

initMetric

public void initMetric()

It initializes the metric and after this method the metric is ready to start calculating measurements. If there are parameters to be set, they should be set before calling this method.

Specified by:

initMetric in interface CyCyniMetric

setParameters

public void setParameters(Map<String,Object> params)

It sets the metric's parameters

Specified by:

setParameters in interface CyCyniMetric

Parameters:

params - The map that maps the name of the parameter with the actual variable