Author: scooter
Date: 2009-11-24 15:17:49 -0800 (Tue, 24 Nov 2009)
New Revision: 18572
Added:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeListUtils.java
Removed:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AbstractCommand.java
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AttributeUtils.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/EdgeNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/LayoutNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkViewNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/PropertyNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/QuitNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/SessionNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/VizMapNamespace.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/CreateNetwork.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ExportNetwork.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ImportNetwork.java
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/networkView/ExportNetworkView.java
Log:
Moved AbstractCommand into the core
Deleted:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AbstractCommand.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AbstractCommand.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AbstractCommand.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -1,218 +0,0 @@
-/* vim: set ts=2: */
-/**
- * Copyright (c) 2007 The Regents of the University of California.
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions, and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above
- * copyright notice, this list of conditions, and the following
- * disclaimer in the documentation and/or other materials provided
- * with the distribution.
- * 3. Redistributions must acknowledge that this software was
- * originally developed by the UCSF Computer Graphics Laboratory
- * under support by the NIH National Center for Research Resources,
- * grant P41-RR01081.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
- * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
- * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
- * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
- * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
- * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
- * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
- * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- */
-package coreCommands.namespaces;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import cytoscape.CyNetwork;
-import cytoscape.CyNode;
-import cytoscape.Cytoscape;
-import cytoscape.command.CyCommandException;
-import cytoscape.command.CyCommandHandler;
-import cytoscape.command.CyCommandManager;
-import cytoscape.command.CyCommandNamespace;
-import cytoscape.command.CyCommandResult;
-import cytoscape.data.CyAttributes;
-import cytoscape.layout.Tunable;
-
-/**
- * The layout command handles all requests to layout the current network.
- * For efficiency reasons, this should be done assuming we're in headless
- * mode.
- */
-public abstract class AbstractCommand implements CyCommandHandler {
- protected Map<String, List<Tunable>> settingsMap = null;
- protected CyCommandNamespace namespace = null;
-
- /**
- * Override if this handler supports subcommands
- */
- public List<String> getCommands() { return new
ArrayList(settingsMap.keySet()); }
-
- /**
- * Override to return the arguments supported for a specific command
- */
- public List<String> getArguments(String command) {
- if (!settingsMap.containsKey(command)) {
- return null;
- }
-
- List<String> argList = new ArrayList();
- for (Tunable t: settingsMap.get(command)) {
- argList.add(t.getName());
- }
- return argList;
- }
-
- /**
- * Override to return the current values for a specific command
- */
- public Map<String, Object> getSettings(String command) {
- Map<String, Object> kvSettings = createKVSettings(command);
- if (kvSettings != null)
- return kvSettings;
- return null;
- }
-
- /**
- * Override to return the Tunables supported for a specific command
- */
- public Map<String, Tunable> getTunables(String command) {
- if (settingsMap.containsKey(command)) {
- Map<String, Tunable> tunableMap = new HashMap();
- for (Tunable t: settingsMap.get(command)) {
- tunableMap.put(t.getName(), t);
- }
- return tunableMap;
- }
- return null;
- }
-
- /**
- * Override if the commands support Tunables directly (recommended)
- */
- public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
- return execute(command, createKVMap(args));
- }
-
- protected void addSetting(String command) {
- if (settingsMap == null)
- settingsMap = new HashMap();
- if (!settingsMap.containsKey(command)) {
- settingsMap.put(command, new ArrayList());
- CyCommandManager.register(namespace, command,
(CyCommandHandler)this);
- }
- }
-
- protected void addSetting(String command, String vKey) {
- addSetting(command, vKey, null);
- }
-
- protected void addSetting(String command, String vKey, String value) {
- Tunable t = new Tunable(vKey, vKey, Tunable.STRING, value);
- addSetting(command, t);
- }
-
- protected void addSetting(String command, Tunable t) {
- if (settingsMap == null)
- settingsMap = new HashMap();
-
- if (!settingsMap.containsKey(command)) {
- settingsMap.put(command, new ArrayList());
- CyCommandManager.register(namespace, command, this);
- }
-
- List<Tunable> tList = settingsMap.get(command);
- tList.add(t);
- }
-
- /**
- * This method is useful for converting from Tunable lists to key-value
settings
- */
- protected Map<String, Object> createKVSettings(String command) {
- if (!settingsMap.containsKey(command)) return null;
- return createKVMap(settingsMap.get(command));
- }
-
- protected Map<String, Object> createKVMap(Collection<Tunable> tList) {
- Map<String, Object> kvSettings = new HashMap();
- for (Tunable t: tList) {
- Object v = t.getValue();
- if (v != null)
- kvSettings.put(t.getName(), v.toString());
- else
- kvSettings.put(t.getName(), null);
- }
- return kvSettings;
- }
-
- /**
- * Some additional utility routines
- */
-
- protected String getArg(String command, String key,
Map<String,Object>args) {
- // Do we have the key in our settings map?
- String value = null;
-
- if (settingsMap.containsKey(command)) {
- List<Tunable> tL = settingsMap.get(command);
- for (Tunable t: tL) {
- if (t.getName().equals(key)) {
- Object v = t.getValue();
- if (v != null)
- value = v.toString();
- break;
- }
- }
- }
-
- if (args == null || args.size() == 0 || !args.containsKey(key))
- return value;
-
- return args.get(key).toString();
- }
-
- protected static List<CyNode> getNodeList(CyNetwork net,
CyCommandResult result,
- Map<String, Object> args) {
- if (args == null || args.size() == 0)
- return null;
-
- List<CyNode> retList = new ArrayList();
- if (args.containsKey("nodelist")) {
- String[] nodes =
args.get("nodelist").toString().split(",");
- for (int nodeIndex = 0; nodeIndex < nodes.length;
nodeIndex++) {
- addNode(net, nodes[nodeIndex], retList, result);
- }
- } else if (args.containsKey("node")) {
- String nodeName = args.get("node").toString();
- addNode(net, nodeName, retList, result);
- } else {
- return null;
- }
- return retList;
- }
-
- protected static void addNode(CyNetwork net, String nodeName,
List<CyNode> list, CyCommandResult result) {
- CyNode node = Cytoscape.getCyNode(nodeName, false);
- if (node == null)
- result.addError("node: can't find node "+nodeName);
- else
- list.add(node);
- return;
- }
-
-}
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AttributeUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AttributeUtils.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/AttributeUtils.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -37,6 +37,7 @@
import cytoscape.data.CyAttributes;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/EdgeNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/EdgeNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/EdgeNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -35,6 +35,7 @@
import cytoscape.CyEdge;
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -76,26 +77,25 @@
private static String VALUE = "value";
protected EdgeNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(DESELECT, EDGE);
- addSetting(DESELECT, EDGELIST);
- // addSetting("export attributes", "file");
- // addSetting("export attributes", "attribute");
- // addSetting("find", "expression");
- addSetting(GETATTR, EDGE);
- addSetting(GETATTR, EDGELIST);
- addSetting(GETATTR, NAME);
- addSetting(GETSEL, NETWORK, "current");
- addSetting(IMPORTATTR, FILE);
- addSetting(SELECT, EDGE);
- addSetting(SELECT, EDGELIST);
- addSetting(SETATTR, EDGE);
- addSetting(SETATTR, EDGELIST);
- addSetting(SETATTR, NAME);
- addSetting(SETATTR, VALUE);
+ addArgument(DESELECT, EDGE);
+ addArgument(DESELECT, EDGELIST);
+ // addArgument("export attributes", "file");
+ // addArgument("export attributes", "attribute");
+ // addArgument("find", "expression");
+ addArgument(GETATTR, EDGE);
+ addArgument(GETATTR, EDGELIST);
+ addArgument(GETATTR, NAME);
+ addArgument(GETSEL, NETWORK, "current");
+ addArgument(IMPORTATTR, FILE);
+ addArgument(SELECT, EDGE);
+ addArgument(SELECT, EDGELIST);
+ addArgument(SETATTR, EDGE);
+ addArgument(SETATTR, EDGELIST);
+ addArgument(SETATTR, NAME);
+ addArgument(SETATTR, VALUE);
// Handle table import????
}
@@ -109,6 +109,10 @@
*/
public String getHandlerName() { return EDGE; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/LayoutNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/LayoutNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/LayoutNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -33,6 +33,7 @@
package coreCommands.namespaces;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -47,6 +48,7 @@
import cytoscape.view.CyNetworkView;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -61,24 +63,23 @@
private static String DEFAULT = "default";
protected LayoutNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(GETCURRENT);
- addSetting(GETDEFAULT);
- addSetting(DEFAULT);
+ addArgument(GETCURRENT);
+ addArgument(GETDEFAULT);
+ addArgument(DEFAULT);
// Get the list of layouts from the layout manager
for (CyLayoutAlgorithm alg: CyLayouts.getAllLayouts()) {
String layout = alg.getName();
LayoutProperties props = alg.getSettings();
if (props == null) {
- addSetting(layout);
+ addArgument(layout);
continue;
}
for (Tunable t: props.getTunables())
- addSetting(layout, t);
+ addArgument(layout, t);
}
}
@@ -91,6 +92,10 @@
*/
public String getHandlerName() { return LAYOUT; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -35,6 +35,7 @@
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -50,6 +51,7 @@
import cytoscape.view.CyNetworkView;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -79,14 +81,13 @@
static String TYPE = "type";
protected NetworkNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(DESTROY, NAME);
- addSetting(GETCURRENT);
- addSetting(LIST);
- addSetting(MAKECURRENT, NAME);
+ addArgument(DESTROY, NAME);
+ addArgument(GETCURRENT);
+ addArgument(LIST);
+ addArgument(MAKECURRENT, NAME);
}
@@ -98,6 +99,10 @@
*/
public String getHandlerName() { return NETWORK; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkViewNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkViewNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NetworkViewNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -37,6 +37,7 @@
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -49,6 +50,7 @@
import cytoscape.view.InternalFrameComponent;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -78,27 +80,26 @@
static String SCALE = "scale";
public NetworkViewNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(CREATE, NETWORK, CURRENT);
- addSetting(GETCURRENT);
- // addSetting("get size", "network", "current");
- addSetting(FIT, NETWORK, CURRENT);
- addSetting(FOCUS, NODELIST);
- addSetting(FOCUS, NETWORK, CURRENT);
- addSetting(LIST);
- addSetting(MAKECURRENT, NETWORK);
- // addSetting("set window", "network", "current");
- // addSetting("set window", "x");
- // addSetting("set window", "y");
- // addSetting("set window", "height");
- // addSetting("set window", "width");
- addSetting(UPDATE, NETWORK, CURRENT);
- addSetting(ZOOM, FACTOR, "2.0");
- addSetting(ZOOM, SCALE);
- addSetting(ZOOM, NETWORK, CURRENT);
+ addArgument(CREATE, NETWORK, CURRENT);
+ addArgument(GETCURRENT);
+ // addArgument("get size", "network", "current");
+ addArgument(FIT, NETWORK, CURRENT);
+ addArgument(FOCUS, NODELIST);
+ addArgument(FOCUS, NETWORK, CURRENT);
+ addArgument(LIST);
+ addArgument(MAKECURRENT, NETWORK);
+ // addArgument("set window", "network", "current");
+ // addArgument("set window", "x");
+ // addArgument("set window", "y");
+ // addArgument("set window", "height");
+ // addArgument("set window", "width");
+ addArgument(UPDATE, NETWORK, CURRENT);
+ addArgument(ZOOM, FACTOR, "2.0");
+ addArgument(ZOOM, SCALE);
+ addArgument(ZOOM, NETWORK, CURRENT);
}
@@ -110,6 +111,10 @@
*/
public String getHandlerName() { return NETWORKVIEW; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Map<String, CyNetworkView> viewMap =
Cytoscape.getNetworkViewMap();
@@ -169,7 +174,7 @@
result.addMessage("networkview: focused
'"+net.getIdentifier()+"' on selected nodes/edges");
} else {
// get the list of nodes
- List<CyNode> nodeList = getNodeList(net,
result, args);
+ List<CyNode> nodeList =
NodeListUtils.getNodeList(net, result, args);
// Remember our currently selected nodes and
edges
List<CyNode>selNodes = new
ArrayList(net.getSelectedNodes());
Added:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeListUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeListUtils.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeListUtils.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -0,0 +1,90 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2007 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package coreCommands.namespaces;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandResult;
+
+/**
+ * This is a utility class that contains some methods that help with the
handling of
+ * node and node list parameters. A node list is denoted by the key
<b>nodelist</b>
+ * and the a string value with a simple comma-separated list of node
identifiers. A
+ * node is denoted by the key <b>node</b> and a single node identifier.
+ */
+public class NodeListUtils {
+
+ /**
+ * This method is used to handle both <b>nodelist</b> and <b>node</b>
parameters.
+ *
+ * @param net the network we are currently dealing with
+ * @param result the CyCommandResult to store our values in
+ * @param args the argument list we're use to look for <b>nodelist</b>
and
+ * <b>node</b> arguments.
+ * @return the list of CyNode objects we found that matched the
arguments
+ */
+ public static List<CyNode> getNodeList(CyNetwork net, CyCommandResult
result,
+ Map<String, Object> args) {
+ if (args == null || args.size() == 0)
+ return null;
+
+ List<CyNode> retList = new ArrayList();
+ if (args.containsKey("nodelist")) {
+ String[] nodes =
args.get("nodelist").toString().split(",");
+ for (int nodeIndex = 0; nodeIndex < nodes.length;
nodeIndex++) {
+ addNode(net, nodes[nodeIndex], retList, result);
+ }
+ } else if (args.containsKey("node")) {
+ String nodeName = args.get("node").toString();
+ addNode(net, nodeName, retList, result);
+ } else {
+ return null;
+ }
+ return retList;
+ }
+
+ private static void addNode(CyNetwork net, String nodeName,
List<CyNode> list, CyCommandResult result) {
+ CyNode node = Cytoscape.getCyNode(nodeName, false);
+ if (node == null)
+ result.addError("node: can't find node "+nodeName);
+ else
+ list.add(node);
+ return;
+ }
+
+}
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/NodeNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -35,6 +35,7 @@
import cytoscape.CyNetwork;
import cytoscape.CyNode;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -76,27 +77,26 @@
private static String TYPE = "type";
public NodeNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(DESELECT, NODE);
- addSetting(DESELECT, NODELIST);
- // addSetting("export attributes", "file");
- // addSetting("export attributes", "attribute");
- // addSetting("find", "expression");
- addSetting(GETATTR, NODE);
- addSetting(GETATTR, NODELIST);
- addSetting(GETATTR, NAME);
- addSetting(GETSEL, NETWORK, "current");
- addSetting(IMPORTATTR, FILE);
- addSetting(SELECT, NODE);
- addSetting(SELECT, NODELIST);
- addSetting(SETATTR, NODE);
- addSetting(SETATTR, NODELIST);
- addSetting(SETATTR, NAME);
- addSetting(SETATTR, VALUE);
- addSetting(SETATTR, TYPE);
+ addArgument(DESELECT, NODE);
+ addArgument(DESELECT, NODELIST);
+ // addArgument("export attributes", "file");
+ // addArgument("export attributes", "attribute");
+ // addArgument("find", "expression");
+ addArgument(GETATTR, NODE);
+ addArgument(GETATTR, NODELIST);
+ addArgument(GETATTR, NAME);
+ addArgument(GETSEL, NETWORK, "current");
+ addArgument(IMPORTATTR, FILE);
+ addArgument(SELECT, NODE);
+ addArgument(SELECT, NODELIST);
+ addArgument(SETATTR, NODE);
+ addArgument(SETATTR, NODELIST);
+ addArgument(SETATTR, NAME);
+ addArgument(SETATTR, VALUE);
+ addArgument(SETATTR, TYPE);
}
@@ -108,6 +108,10 @@
*/
public String getHandlerName() { return NODE; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
@@ -131,7 +135,7 @@
// Select some ndoes
} else if (SELECT.equals(command)) {
CyNetwork net = getNetwork(command, args);
- List<CyNode> nodeList = getNodeList(net, result, args);
+ List<CyNode> nodeList = NodeListUtils.getNodeList(net,
result, args);
if (nodeList == null)
throw new CyCommandException("node: nothing to
select");
net.setSelectedNodeState(nodeList, true);
@@ -144,7 +148,7 @@
} else if (DESELECT.equals(command)) {
CyNetwork net = getNetwork(command, args);
try {
- List<CyNode> nodeList = getNodeList(net,
result, args);
+ List<CyNode> nodeList =
NodeListUtils.getNodeList(net, result, args);
if (nodeList == null)
throw new CyCommandException("node:
nothing to deselect");
@@ -177,7 +181,7 @@
else if (nodeAttributes.getType(attrName) ==
CyAttributes.TYPE_UNDEFINED)
throw new CyCommandException("node: attribute
'name' does not exist");
- List<CyNode> nodeList = getNodeList(net, result, args);
+ List<CyNode> nodeList = NodeListUtils.getNodeList(net,
result, args);
if (nodeList == null)
nodeList = net.nodesList();
@@ -201,7 +205,7 @@
if (attrName == null || value == null)
throw new CyCommandException("node: attribute
'name' and 'value' are required");
- List<CyNode> nodeList = getNodeList(net, result, args);
+ List<CyNode> nodeList = NodeListUtils.getNodeList(net,
result, args);
if (nodeList == null)
nodeList = net.nodesList();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/PropertyNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/PropertyNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/PropertyNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -34,6 +34,7 @@
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -44,6 +45,7 @@
import cytoscape.view.CyNetworkView;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -63,14 +65,13 @@
static String VALUE = "value";
public PropertyNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(SET, NAME);
- addSetting(SET, VALUE);
- addSetting(GET, NAME);
- addSetting(CLEAR, NAME);
+ addArgument(SET, NAME);
+ addArgument(SET, VALUE);
+ addArgument(GET, NAME);
+ addArgument(CLEAR, NAME);
}
@@ -82,6 +83,10 @@
*/
public String getHandlerName() { return PROPERTY; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Properties props = CytoscapeInit.getProperties();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/QuitNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/QuitNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/QuitNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -34,6 +34,7 @@
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -44,6 +45,7 @@
import cytoscape.view.CyNetworkView;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -55,8 +57,8 @@
public class QuitNamespace extends AbstractCommand {
public QuitNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
- addSetting("");
+ super(ns);
+ addArgument("");
}
@@ -68,11 +70,14 @@
*/
public String getHandlerName() { return namespace.getNamespaceName(); }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ System.exit(0);
+ return null;
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
- CyCommandResult result = new CyCommandResult();
-
System.exit(0);
- return result;
+ return null;
}
public static CyCommandHandler register(String namespace) throws
RuntimeException {
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/SessionNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/SessionNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/SessionNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -33,6 +33,7 @@
package coreCommands.namespaces;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -47,6 +48,7 @@
import java.io.File;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -64,12 +66,12 @@
static String FILE = "file";
public SessionNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
+
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(OPEN, FILE);
- addSetting(NEW);
- addSetting(SAVE, FILE);
+ addArgument(OPEN, FILE);
+ addArgument(NEW);
+ addArgument(SAVE, FILE);
}
@@ -81,6 +83,10 @@
*/
public String getHandlerName() { return SESSION; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/VizMapNamespace.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/VizMapNamespace.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/VizMapNamespace.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -33,6 +33,7 @@
package coreCommands.namespaces;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -47,6 +48,7 @@
import java.io.File;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -67,13 +69,12 @@
static String FILE = "file";
public VizMapNamespace(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(APPLY, STYLE, "default");
+ addArgument(APPLY, STYLE, "default");
- addSetting(IMPORT, FILE, null);
+ addArgument(IMPORT, FILE, null);
}
@@ -85,6 +86,10 @@
*/
public String getHandlerName() { return VIZMAP; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
if (command.equals(STYLE)) {
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/CreateNetwork.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/CreateNetwork.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/CreateNetwork.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -35,6 +35,7 @@
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandNamespace;
@@ -44,12 +45,11 @@
import cytoscape.logger.CyLogger;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import coreCommands.namespaces.AbstractCommand;
-
/**
* XXX FIXME XXX Description
*/
@@ -65,13 +65,12 @@
static String PARENT = "parent";
public CreateNetwork(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(CREATE, NAME, "NewNetwork");
- addSetting(CREATE, CREATEVIEW, "true");
- addSetting(CREATE, PARENT);
+ addArgument(CREATE, NAME, "NewNetwork");
+ addArgument(CREATE, CREATEVIEW, "true");
+ addArgument(CREATE, PARENT);
}
@@ -83,6 +82,10 @@
*/
public String getHandlerName() { return CREATE; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ExportNetwork.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ExportNetwork.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ExportNetwork.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -35,6 +35,7 @@
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandNamespace;
@@ -55,12 +56,11 @@
import java.io.FileWriter;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import coreCommands.namespaces.AbstractCommand;
-
/**
* XXX FIXME XXX Description
*/
@@ -83,13 +83,12 @@
static String SIF = "sif";
public ExportNetwork(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(EXPORT, NAME , CURRENT);
- addSetting(EXPORT, FILE);
- addSetting(EXPORT, TYPE, XGMML);
+ addArgument(EXPORT, NAME , CURRENT);
+ addArgument(EXPORT, FILE);
+ addArgument(EXPORT, TYPE, XGMML);
}
@@ -101,6 +100,10 @@
*/
public String getHandlerName() { return EXPORT; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ImportNetwork.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ImportNetwork.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/network/ImportNetwork.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -35,6 +35,7 @@
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandNamespace;
@@ -54,12 +55,11 @@
import java.net.URI;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import coreCommands.namespaces.AbstractCommand;
-
/**
* XXX FIXME XXX Description
*/
@@ -82,13 +82,12 @@
static String SIF = "sif";
public ImportNetwork(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(IMPORT, FILE);
- addSetting(IMPORT, CREATEVIEW, "true");
- addSetting(IMPORT, PARENT);
+ addArgument(IMPORT, FILE);
+ addArgument(IMPORT, CREATEVIEW, "true");
+ addArgument(IMPORT, PARENT);
}
@@ -100,6 +99,10 @@
*/
public String getHandlerName() { return IMPORT; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Modified:
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/networkView/ExportNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/networkView/ExportNetworkView.java
2009-11-24 23:10:36 UTC (rev 18571)
+++
csplugins/trunk/ucsf/scooter/coreCommands/src/coreCommands/namespaces/networkView/ExportNetworkView.java
2009-11-24 23:17:49 UTC (rev 18572)
@@ -37,6 +37,8 @@
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
+
+import cytoscape.command.AbstractCommand;
import cytoscape.command.CyCommandException;
import cytoscape.command.CyCommandHandler;
import cytoscape.command.CyCommandManager;
@@ -58,14 +60,14 @@
import java.io.File;
import java.io.FileOutputStream;
+
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import coreCommands.namespaces.AbstractCommand;
-
/**
* XXX FIXME XXX Description
*/
@@ -89,14 +91,13 @@
private static String BMP = "bmp";
public ExportNetworkView(CyCommandNamespace ns) {
- this.namespace = ns;
+ super(ns);
// Define our subcommands
- settingsMap = new HashMap();
- addSetting(EXPORT, FILE);
- addSetting(EXPORT, NETWORK, CURRENT);
- addSetting(EXPORT, TYPE, PNG);
- addSetting(EXPORT, ZOOM, "1.0");
+ addArgument(EXPORT, FILE);
+ addArgument(EXPORT, NETWORK, CURRENT);
+ addArgument(EXPORT, TYPE, PNG);
+ addArgument(EXPORT, ZOOM, "1.0");
}
@@ -108,6 +109,10 @@
*/
public String getHandlerName() { return EXPORT; }
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
Map<String, CyNetworkView> viewMap =
Cytoscape.getNetworkViewMap();
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