Package org.cytoscape.command
Interface StringToModel
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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:@Tunable(description="Network to select", context="nongui") String network; @Tunable(description="List of nodes to select", context="nongui") String nodelist; public run(TaskMonitor mon) { CyNetwork net = stringToModel.getNetwork(network); List<CyNode> nodeList = stringToModel.getNodeList(net, nodelist); // Actually select the nodes... }
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>
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.
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Field Summary
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description List<CyEdge>
getEdgeList(CyNetwork net, String edgelist)
Convert a string request for a edgelist into a list ofCyEdge
s.CyNetwork
getNetwork(String strNet)
Convert a string request for a network into aCyNetwork
.CyNetworkView
getNetworkView(String strNetView)
Convert a string request for a network view into aCyNetworkView
.List<CyNode>
getNodeList(CyNetwork net, String nodelist)
Convert a string request for a nodelist into a list ofCyNode
s.List<CyRow>
getRowList(CyTable table, String rowlist)
Convert a string request for a rowlist into a list ofCyRow
s.CyTable
getTable(String strTable)
Convert a string request for a table into aCyTable
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Field Detail
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_CY_NETWORK_DESC
static final String _CY_NETWORK_DESC
- See Also:
- Constant Field Values
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_CY_NETWORK_VIEW_DESC
static final String _CY_NETWORK_VIEW_DESC
- See Also:
- Constant Field Values
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_CY_LIST_DESC
static final String _CY_LIST_DESC
- See Also:
- Constant Field Values
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_CY_ROW_DESC
static final String _CY_ROW_DESC
- See Also:
- Constant Field Values
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CY_NETWORK_LONG_DESCRIPTION
static final String CY_NETWORK_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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CY_NETWORK_EXAMPLE_STRING
static final String CY_NETWORK_EXAMPLE_STRING
- See Also:
- Constant Field Values
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CY_NETWORK_VIEW_LONG_DESCRIPTION
static final String CY_NETWORK_VIEW_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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CY_NETWORK_VIEW_EXAMPLE_STRING
static final String CY_NETWORK_VIEW_EXAMPLE_STRING
- See Also:
- Constant Field Values
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TABLE_LONG_DESCRIPTION
static final String TABLE_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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ROW_LONG_DESCRIPTION
static final String ROW_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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COLUMN_LONG_DESCRIPTION
static final String COLUMN_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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VALUE_LONG_DESCRIPTION
static final String VALUE_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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ROW_EXAMPLE
static final String ROW_EXAMPLE
- See Also:
- Constant Field Values
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COLUMN_EXAMPLE
static final String COLUMN_EXAMPLE
- See Also:
- Constant Field Values
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VALUE_EXAMPLE
static final String VALUE_EXAMPLE
- See Also:
- Constant Field Values
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TABLE_TITLE_LONG_DESCRIPTION
static final String TABLE_TITLE_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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TABLE_TITLE_EXAMPLE
static final String TABLE_TITLE_EXAMPLE
- See Also:
- Constant Field Values
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KEY_TYPE_LONG_DESCRIPTION
static final String KEY_TYPE_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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KEY_TYPE_EXAMPLE
static final String KEY_TYPE_EXAMPLE
- See Also:
- Constant Field Values
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CY_NODE_LIST_LONG_DESCRIPTION
static final String CY_NODE_LIST_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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CY_NODE_LIST_EXAMPLE_STRING
static final String CY_NODE_LIST_EXAMPLE_STRING
- See Also:
- Constant Field Values
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CY_EDGE_LIST_LONG_DESCRIPTION
static final String CY_EDGE_LIST_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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CY_EDGE_LIST_EXAMPLE_STRING
static final String CY_EDGE_LIST_EXAMPLE_STRING
- See Also:
- Constant Field Values
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CY_ROW_LIST_LONG_DESCRIPTION
static final String CY_ROW_LIST_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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GROUP_NAME_LONG_DESCRIPTION
static final String GROUP_NAME_LONG_DESCRIPTION
Group terms- See Also:
- Constant Field Values
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GROUP_NAME_EXAMPLE_STRING
static final String GROUP_NAME_EXAMPLE_STRING
- See Also:
- Constant Field Values
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GROUP_NAME_EXAMPLE_STRING2
static final String GROUP_NAME_EXAMPLE_STRING2
- See Also:
- Constant Field Values
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GROUP_LIST_LONG_DESCRIPTION
static final String GROUP_LIST_LONG_DESCRIPTION
- See Also:
- Constant Field Values
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GROUP_LIST_EXAMPLE_STRING
static final String GROUP_LIST_EXAMPLE_STRING
- See Also:
- Constant Field Values
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Method Detail
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getNetwork
CyNetwork getNetwork(String strNet)
Convert a string request for a network into aCyNetwork
. 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
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getNetworkView
CyNetworkView getNetworkView(String strNetView)
Convert a string request for a network view into aCyNetworkView
. This method may be used to find a network view with a given name or the current network view. Future implementations might accept other columns to search on.- Parameters:
strNetView
- the name of the network view to return or "current"- Returns:
- the returned CyNetworkView or null if the name doesn't exist
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getTable
CyTable getTable(String strTable)
Convert a string request for a table into aCyTable
. 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
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getNodeList
List<CyNode> getNodeList(CyNetwork net, String nodelist)
Convert a string request for a nodelist into a list ofCyNode
s. 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 networknodelist
- the string representing the nodelist- Returns:
- a list of CyNodes or null if nothing matched
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getEdgeList
List<CyEdge> getEdgeList(CyNetwork net, String edgelist)
Convert a string request for a edgelist into a list ofCyEdge
s. 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 networkedgelist
- the string representing the edgelist- Returns:
- a list of CyEdges or null if nothing matched
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getRowList
List<CyRow> getRowList(CyTable table, String rowlist)
Convert a string request for a rowlist into a list ofCyRow
s. 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
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