fr.systemsbiology.cyni
Interface CyCyniMetric

All Known Implementing Classes:

AbstractCyniMetric

public interface CyCyniMetric

An interface specific to Cyni metrics.

Method Summary

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
Double	getMetric(CyniTable table1, CyniTable table2, int indexBase, List<Integer> indexToCompare) The implementation of the metric.
String	getName() Returns the computer-readable name of the Cyni Metric.
List<String>	getTagsList() The list of tags that define 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

Method Detail

getMetric

Double getMetric(CyniTable table1,
                 CyniTable table2,
                 int indexBase,
                 List<Integer> indexToCompare)

The implementation of the metric. This method takes two sets of data and calculate a measurement.

Parameters:

table1 - The cyniTable where there is the first element to compare.

table2 - The cyniTable where there is the second element to compare.

indexBase - The index of the element in the first CyniTable that will be compared.

indexToCompare - The list of indexes of the elements in the second CyniTable that will compared

Returns:

the result of the measurement

getName

String getName()

Returns the computer-readable name of the Cyni Metric. To get a human readable name, use toString().

Returns:

The computer-readable name of the metric.

getTagsList

List<String> getTagsList()

The list of tags that define this metric

Returns:

the list of tags

getCyniTable

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

Returns:

the new extended CyniTable

initMetric

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.

setParameters

void setParameters(Map<String,Object> params)

It sets the metric's parameters

Parameters:

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