org.cytoscape.command

Interface StringToModel

public interface StringToModel

The service implementing StringToModel provides a common mechanism for converting command arguments into Cytoscape model elements. For example, the command: nodes select network=current nodelist="name:gene1,name:gene2" could be handled as follows:

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

Module: command-executor-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>command-executor-api</artifactId>
</dependency>

Method Summary

Modifier and Type	Method and Description
List<CyEdge>	getEdgeList(CyNetwork net, String edgelist) Convert a string request for a edgelist into a list of CyEdges.
CyNetwork	getNetwork(String strNet) Convert a string request for a network into a CyNetwork.
List<CyNode>	getNodeList(CyNetwork net, String nodelist) Convert a string request for a nodelist into a list of CyNodes.
List<CyRow>	getRowList(CyTable table, String rowlist) Convert a string request for a rowlist into a list of CyRows.
CyTable	getTable(String strTable) Convert a string request for a table into a CyTable.

Method Detail

getNetwork

CyNetwork getNetwork(String strNet)

Convert a string request for a network into a CyNetwork. This method may be used to find a network with a given name or the current network. Future implementations might accept other columns to search on.

Parameters:

strNet - the name of the network to return or "current"

Returns:

the returned CyNetwork or null if the name doesn't exist

getTable

CyTable getTable(String strTable)

Convert a string request for a table into a CyTable. This method may be used to find a table with a given name or the current table. Future implementations might accept other columns to search on.

Parameters:

strTable - the name of the table to return or "current"

Returns:

the returned CyTable or null if the name doesn't exist

getNodeList

List<CyNode> getNodeList(CyNetwork net,
                         String nodelist)

Convert a string request for a nodelist into a list of CyNodes. This method may be used to find selected nodes, or nodes matching a particular column by using the pattern "column:value". If no column is specified, it is assumed that the column is the NAME column. No wildcarding or regular expression matching is supported at this time. The following special keywords are also recognized: all return all nodes in this network selected return all selected nodes in this network unselected return all unselected nodes in this network

Parameters:

net - the CyNetwork to search through. If null, use the current network

nodelist - the string representing the nodelist

Returns:

a list of CyNodes or null if nothing matched

getEdgeList

List<CyEdge> getEdgeList(CyNetwork net,
                         String edgelist)

Convert a string request for a edgelist into a list of CyEdges. This method may be used to find selected edges, or edges matching a particular column by using the pattern "column:value". If no column is specified, it is assumed that the column is the NAME column. No wildcarding or regular expression matching is supported at this time. The following special keywords are also recognized: all return all edges in this network selected return all selected edges in this network unselected return all unselected edges in this network

Parameters:

net - the CyNetwork to search through. If null, use the current network

edgelist - the string representing the edgelist

Returns:

a list of CyEdges or null if nothing matched

getRowList

List<CyRow> getRowList(CyTable table,
                       String rowlist)

Convert a string request for a rowlist into a list of CyRows. This method may be used to find all rows, or rows matching a particular column by using the pattern "column:value". If no column is specified, it is assumed that the column is the NAME column. No wildcarding or regular expression matching is supported at this time. The following special keywords are also recognized: all return all edges in this network

Parameters:

table - the CyTable to search through.

rowlist - the string representing the rowlist

Returns:

a list of CyRows or null if nothing matched