Author: scooter
Date: 2011-02-02 20:00:39 -0800 (Wed, 02 Feb 2011)
New Revision: 24007
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java
Log:
Arg!! Cytoscape.getNetwork() wants a CyNetwork identifier, which is not
the same thing as a title...
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/AbstractGraphObjectHandler.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -67,17 +67,22 @@
super(ns);
}
- protected CyNetwork getNetwork(String command, Map<String, Object>
args) throws CyCommandException {
- String netName = getArg(command, "network", args);
- if (netName == null || netName.equals("current"))
- return Cytoscape.getCurrentNetwork();
+ protected CyNetwork getNetwork(String command, Map<String, Object> args)
throws CyCommandException {
+ String netName = getArg(command, "network", args);
+ if (netName == null || netName.equalsIgnoreCase("current"))
+ return Cytoscape.getCurrentNetwork();
+ return getNetwork(command, netName);
+ }
- CyNetwork net = Cytoscape.getNetwork(netName);
- if (net == Cytoscape.getNullNetwork())
- throw new
CyCommandException(namespace.getNamespaceName()+": no such network "+netName);
+ protected CyNetwork getNetwork(String command, String title) throws
CyCommandException {
+ Set<CyNetwork>networks = Cytoscape.getNetworkSet();
+ for (CyNetwork net: networks) {
+ if (net.getTitle().equalsIgnoreCase(title))
+ return net;
+ }
+ throw new CyCommandException(namespace.getNamespaceName()+" "+command+":
no such network "+title);
+ }
- return net;
- }
protected String makeNodeList(Collection<CyNode>nodes) {
String nodeList = "";
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/GroupNamespace.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -47,6 +47,7 @@
import cytoscape.groups.CyGroupManager;
import cytoscape.layout.Tunable;
import cytoscape.logger.CyLogger;
+import cytoscape.logger.CyLogger;
import cytoscape.view.CyNetworkView;
import java.util.ArrayList;
@@ -173,12 +174,7 @@
return result;
CyNetwork network = Cytoscape.getCurrentNetwork();
- String networkName = getArg(command, NETWORK, args);
- if (networkName != null) {
- network = Cytoscape.getNetwork(networkName);
- if (network == null)
- throw new CyCommandException("group:
can't find network '"+networkName+"'");
- }
+ network = getNetwork(CREATE, args);
if (args.containsKey(VIEWER)) {
String viewer = (String)args.get(VIEWER);
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkNamespace.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -62,7 +62,7 @@
/**
* XXX FIXME XXX Description
*/
-public class NetworkNamespace extends AbstractCommandHandler {
+public class NetworkNamespace extends AbstractGraphObjectHandler {
static String NETWORK = "network";
// Commands
@@ -111,13 +111,7 @@
if (netName == null)
throw new CyCommandException("network: need the
name of the network to destroy");
- CyNetwork net = Cytoscape.getCurrentNetwork();
- if (!netName.equalsIgnoreCase(CURRENT))
- net = Cytoscape.getNetwork(netName);
-
- if (net == null)
- throw new CyCommandException("network: the
network '"+netName+"' doesn't exist");
-
+ CyNetwork net = getNetwork(DESTROY, args);
Cytoscape.destroyNetwork(net);
// Return the current network
@@ -133,9 +127,7 @@
throw new CyCommandException("network: need a
network name to make current");
// Get the network
- CyNetwork net = Cytoscape.getNetwork(netName);
- if (net == null)
- throw new CyCommandException("network: network
'"+netName+"' doesn't exist");
+ CyNetwork net = getNetwork(MAKECURRENT, netName);
Cytoscape.setCurrentNetwork(netName);
result.addMessage("network: set current network to
"+netName);
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/NetworkViewNamespace.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -56,6 +56,7 @@
import java.util.Map;
import java.util.Set;
+import coreCommands.namespaces.AbstractGraphObjectHandler;
import coreCommands.namespaces.networkView.ExportNetworkView;
/**
@@ -147,17 +148,9 @@
return result;
}
- String netName = getArg(command, NETWORK, args);
- if (netName == null) {
- throw new CyCommandException("networkview: "+command+"
requires network argument");
- }
- if (!netName.equalsIgnoreCase(CURRENT)) {
- net = Cytoscape.getNetwork(netName);
- if (net == null)
- throw new CyCommandException("networkview:
can't find network: "+netName);
- if (!viewMap.containsKey(netName) &&
!command.equals("create"))
- throw new CyCommandException("networkview:
can't find view for network: "+netName);
- }
+ net = getNetwork(command, args);
+ if (!viewMap.containsKey(net.getIdentifier()) &&
!command.equals("create"))
+ throw new CyCommandException("networkview: can't find
view for network: "+net.getTitle());
if (command.equals(CREATE)) {
CyNetworkView view = Cytoscape.createNetworkView(net);
@@ -166,16 +159,16 @@
} else if (command.equals(MAKECURRENT)) {
Cytoscape.setCurrentNetworkView(net.getIdentifier());
- result.addMessage("networkview: set network view for
"+net.getIdentifier()+" as current");
+ result.addMessage("networkview: set network view for
"+net.getTitle()+" as current");
} else if (command.equals(FIT)) {
CyNetworkView view = viewMap.get(net.getIdentifier());
view.fitContent();
- result.addMessage("networkview: fit view to content for
"+net.getIdentifier());
+ result.addMessage("networkview: fit view to content for
"+net.getTitle());
} else if (command.equals(UPDATE)) {
CyNetworkView view = viewMap.get(net.getIdentifier());
view.updateView();
- result.addMessage("networkview: view
'"+net.getIdentifier()+"' updated");
+ result.addMessage("networkview: view
'"+net.getTitle()+"' updated");
} else if (command.equals(FOCUS)) {
CyNetworkView view = viewMap.get(net.getIdentifier());
@@ -183,7 +176,7 @@
if (nodes == null || nodes.length() == 0) {
((DingNetworkView) view).fitSelected();
view.updateView();
- result.addMessage("networkview: focused
'"+net.getIdentifier()+"' on selected nodes/edges");
+ result.addMessage("networkview: focused
'"+net.getTitle()+"' on selected nodes/edges");
} else {
// get the list of nodes
List<CyNode> nodeList = getNodeList(net,
result, args);
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddEdgeNetwork.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -81,16 +81,13 @@
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
- String netName = getArg(command, NETWORK, args);
- if (netName == null)
- throw new CyCommandException("network: need a network
name to add the edges to");
+ CyNetwork network = getNetwork(command, args);
- CyNetwork network = Cytoscape.getNetwork(netName);
- if (network == null)
- throw new CyCommandException("network: no such network
"+netName);
-
List<CyEdge> edgeList = getEdgeList(network, result, args,
true);
- result.addMessage("Added "+edgeList.size()+" edge(s) to network
"+netName);
+ for (CyEdge edge: edgeList) {
+ network.addEdge(edge);
+ }
+ result.addMessage("Added "+edgeList.size()+" edge(s) to network
"+network.getTitle());
return result;
}
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/AddNodeNetwork.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -80,17 +80,15 @@
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
- String netName = getArg(command, NETWORK, args);
- if (netName == null)
- throw new CyCommandException("network: need a network
name to add the nodes to");
+ CyNetwork network = getNetwork(command, args);
- CyNetwork network = Cytoscape.getNetwork(netName);
- if (network == null)
- throw new CyCommandException("network: no such network
"+netName);
-
List<CyNode> nodeList = getNodeList(network, result, args,
true);
- result.addMessage("Added "+nodeList.size()+" node(s) to network
"+netName);
+ for (CyNode node: nodeList) {
+ network.addNode(node);
+ }
+ result.addMessage("Added "+nodeList.size()+" node(s) to network
"+network.getTitle());
+
return result;
}
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/CreateNetwork.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -110,9 +110,7 @@
{
String pName = getArg(command, PARENT, args);
if (pName != null) {
- parent = Cytoscape.getNetwork(pName);
- if (parent == null)
- throw new CyCommandException("network:
parent network "+pName+" doesn't exist");
+ parent = getNetwork(command, pName);
}
}
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ExportNetwork.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -52,6 +52,8 @@
import cytoscape.logger.CyLogger;
import cytoscape.view.CyNetworkView;
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
import java.io.File;
import java.io.FileWriter;
@@ -64,7 +66,7 @@
/**
* XXX FIXME XXX Description
*/
-public class ExportNetwork extends AbstractCommandHandler {
+public class ExportNetwork extends AbstractGraphObjectHandler {
static String NETWORK = "network";
// Commands
@@ -110,11 +112,9 @@
CyNetwork net = Cytoscape.getCurrentNetwork();
CyNetworkView view = Cytoscape.getCurrentNetworkView();
if (!netName.equalsIgnoreCase(CURRENT)) {
- net = Cytoscape.getNetwork(netName);
- view = Cytoscape.getNetworkView(netName);
+ net = getNetwork(command, netName);
+ view = Cytoscape.getNetworkView(net.getIdentifier());
}
- if (net == null)
- throw new CyCommandException("network: the network
'"+netName+"' doesn't exist");
ret_val[0] = net;
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/network/ImportNetwork.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -49,6 +49,8 @@
import cytoscape.logger.CyLogger;
import cytoscape.view.CyNetworkView;
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
import java.io.File;
import java.io.FileWriter;
@@ -63,7 +65,7 @@
/**
* XXX FIXME XXX Description
*/
-public class ImportNetwork extends AbstractCommandHandler {
+public class ImportNetwork extends AbstractGraphObjectHandler {
static String NETWORK = "network";
// Commands
@@ -119,9 +121,7 @@
{
String pName = getArg(command, PARENT, args);
if (pName != null) {
- parent = Cytoscape.getNetwork(pName);
- if (parent == null)
- throw new CyCommandException("network:
parent network "+pName+" doesn't exist");
+ parent = getNetwork(command, pName);
}
}
Modified:
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java
===================================================================
---
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java
2011-02-03 00:42:36 UTC (rev 24006)
+++
cytoscape/trunk/coreplugins/CoreCommands/src/main/java/coreCommands/namespaces/networkView/ExportNetworkView.java
2011-02-03 04:00:39 UTC (rev 24007)
@@ -58,6 +58,8 @@
import ding.view.DGraphView;
+import coreCommands.namespaces.AbstractGraphObjectHandler;
+
import java.io.File;
import java.io.FileOutputStream;
@@ -71,7 +73,7 @@
/**
* XXX FIXME XXX Description
*/
-public class ExportNetworkView extends AbstractCommandHandler {
+public class ExportNetworkView extends AbstractGraphObjectHandler {
private static String NETWORKVIEW = "networkview";
private static String EXPORT = "export";
@@ -110,17 +112,9 @@
Map<String, CyNetworkView> viewMap =
Cytoscape.getNetworkViewMap();
CyNetwork net = Cytoscape.getCurrentNetwork();
- String netName = getArg(command, NETWORK, args);
- if (netName == null) {
- throw new CyCommandException("networkview: "+command+"
requires network argument");
- }
- if (!netName.equalsIgnoreCase(CURRENT)) {
- net = Cytoscape.getNetwork(netName);
- if (net == null)
- throw new CyCommandException("networkview:
can't find network: "+netName);
- if (!viewMap.containsKey(netName) &&
!command.equals("create"))
- throw new CyCommandException("networkview:
can't find view for network: "+netName);
- }
+ net = getNetwork(command, args);
+ if (!viewMap.containsKey(net.getIdentifier()) &&
!command.equals("create"))
+ throw new CyCommandException("networkview: can't find
view for network: "+net.getTitle());
CyNetworkView view = viewMap.get(net.getIdentifier());
float zoom = Float.parseFloat(getArg(command, ZOOM, args));
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