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




 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