Author: mes
Date: 2009-12-01 12:16:48 -0800 (Tue, 01 Dec 2009)
New Revision: 18625
Added:
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/NodeCommandCollection.java
Modified:
csplugins/trunk/ucsd/mes/coreCommands2/build.xml
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/CoreCommands.java
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/AbstractCommand.java
Log:
updated to reflect new API
Modified: csplugins/trunk/ucsd/mes/coreCommands2/build.xml
===================================================================
--- csplugins/trunk/ucsd/mes/coreCommands2/build.xml 2009-12-01 20:14:54 UTC
(rev 18624)
+++ csplugins/trunk/ucsd/mes/coreCommands2/build.xml 2009-12-01 20:16:48 UTC
(rev 18625)
@@ -1,5 +1,5 @@
<?xml version = "1.0"?>
-<project name = "coreCommands" default = "jar" basedir = ".">
+<project name = "coreCommands" default = "all" basedir = ".">
<property name = "src" location = "src"/>
<property name = "build" location = "build"/>
@@ -45,6 +45,9 @@
</jar>
</target>
+ <target name = "all" depends="jar" >
+ </target>
+
<target name = "run" depends="jar" description = "Run under development">
<java classname = "cytoscape.CyMain" classpathref = "classpath"
fork = "true" maxmemory = "1g">
Modified:
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/CoreCommands.java
===================================================================
--- csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/CoreCommands.java
2009-12-01 20:14:54 UTC (rev 18624)
+++ csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/CoreCommands.java
2009-12-01 20:16:48 UTC (rev 18625)
@@ -34,6 +34,7 @@
import cytoscape.Cytoscape;
import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandNamespace;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.CytoscapeInit;
import cytoscape.logger.CyLogger;
@@ -54,27 +55,37 @@
// Register our built-ins -- these should really be
// provided directly by the core...
try {
- CyCommandManager.register(new SelectEdgeCommand());
- CyCommandManager.register(new DeselectEdgeCommand());
- CyCommandManager.register(new
GetEdgeAttributeCommand());
- CyCommandManager.register(new
ImportEdgeAttributesCommand());
- CyCommandManager.register(new
SetEdgeAttributeCommand());
- CyCommandManager.register(new
GetSelectedEdgesCommand());
+ CyCommandNamespace selectNS =
CyCommandManager.reserveNamespace("edge");
+ CyCommandManager.register(selectNS, new
SelectEdgeCommand());
+ CyCommandManager.register(selectNS, new
DeselectEdgeCommand());
+ CyCommandManager.register(selectNS, new
GetEdgeAttributeCommand());
+ CyCommandManager.register(selectNS, new
ImportEdgeAttributesCommand());
+ CyCommandManager.register(selectNS, new
SetEdgeAttributeCommand());
+ CyCommandManager.register(selectNS, new
GetSelectedEdgesCommand());
- CyCommandManager.register(new NetworkCreateCommand());
- CyCommandManager.register(new NetworkImportCommand());
+ CyCommandNamespace networkNS =
CyCommandManager.reserveNamespace("network");
+ CyCommandManager.register(networkNS, new
NetworkCreateCommand());
+ CyCommandManager.register(networkNS, new
NetworkImportCommand());
// CyCommandManager.register(new NetworkViewCommand());
-// CyCommandManager.register(new NodeCommand());
// CyCommandManager.register(new PropertyCommand());
// CyCommandManager.register(new SessionCommand());
// CyCommandManager.register(new VizMapCommand());
- CyCommandManager.register(new
GetDefaultLayoutCommand());
- CyCommandManager.register(new
GetCurrentLayoutCommand());
- CyCommandManager.register(new
ApplyDefaultLayoutCommand());
+ CyCommandNamespace layoutNS =
CyCommandManager.reserveNamespace("layout");
+ CyCommandManager.register(layoutNS, new
GetDefaultLayoutCommand());
+ CyCommandManager.register(layoutNS, new
GetCurrentLayoutCommand());
+ CyCommandManager.register(layoutNS, new
ApplyDefaultLayoutCommand());
for ( CyLayoutAlgorithm alg : CyLayouts.getAllLayouts()
)
- CyCommandManager.register(new
ApplyLayoutCommand(alg));
+ CyCommandManager.register(layoutNS, new
ApplyLayoutCommand(alg));
+ CyCommandNamespace nodeNS =
CyCommandManager.reserveNamespace("node");
+ CyCommandManager.register(nodeNS, new
NodeCommandCollection("select"));
+ CyCommandManager.register(nodeNS, new
NodeCommandCollection("deselect"));
+ CyCommandManager.register(nodeNS, new
NodeCommandCollection("get selected"));
+ CyCommandManager.register(nodeNS, new
NodeCommandCollection("get attribute"));
+ CyCommandManager.register(nodeNS, new
NodeCommandCollection("set attribute"));
+ CyCommandManager.register(nodeNS, new
NodeCommandCollection("import attributes"));
+
} catch (Exception e) {
logger.error(e.getMessage(),e);
}
Modified:
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/AbstractCommand.java
===================================================================
---
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/AbstractCommand.java
2009-12-01 20:14:54 UTC (rev 18624)
+++
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/AbstractCommand.java
2009-12-01 20:16:48 UTC (rev 18625)
@@ -188,4 +188,8 @@
return;
}
+ public String toString() {
+ return namespace + " " + commandName;
+ }
+
}
Added:
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/NodeCommandCollection.java
===================================================================
---
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/NodeCommandCollection.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/coreCommands2/src/coreCommands/commands/NodeCommandCollection.java
2009-12-01 20:16:48 UTC (rev 18625)
@@ -0,0 +1,234 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2009 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.commands;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandResult;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * XXX FIXME XXX Description
+ */
+public class NodeCommandCollection extends AbstractCommand {
+
+
+ public NodeCommandCollection(final String commandName ) {
+ super("node",commandName);
+
+ // Define our settings
+ if ( commandName.equals("deselect") ) {
+ addSetting("node");
+ addSetting("nodeList");
+ } else if ( commandName.equals("get attribute") ) {
+ addSetting("node");
+ addSetting("nodelist");
+ addSetting("name");
+ } else if ( commandName.equals("get selected") ) {
+ addSetting("network", "current");
+ } else if ( commandName.equals("import attributes") ) {
+ addSetting("file");
+ } else if ( commandName.equals("select") ) {
+ addSetting("node");
+ addSetting("nodeList");
+ } else if ( commandName.equals("set attribute") ) {
+ addSetting("node");
+ addSetting("nodelist");
+ addSetting("name");
+ addSetting("value");
+ addSetting("type");
+ }
+ }
+
+ public CyCommandResult execute(Map<String, String>args) throws
CyCommandException {
+ // simple pass through to old code
+ return execute(getCommandName(), args);
+ }
+
+ private CyCommandResult execute(String command, Map<String,
String>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ // Import node attributes from a file
+ if ("import attributes".equals(command)) {
+ String fileName = getArg("file", args);
+ if (fileName == null)
+ throw new CyCommandException("node: filename is
required to import attributes");
+ try {
+ File file = new File(fileName);
+ Cytoscape.loadAttributes(new String[] {
file.getAbsolutePath() },
+ new String[] {});
+ result.addMessage("node: attributes imported
from "+file.getAbsolutePath());
+ } catch (Exception e) {
+ throw new CyCommandException("node: unable to
import attributes: "+e.getMessage());
+ }
+
+ // Export node attributes to a file
+ // } else if ("export attributes".equals(command)) {
+
+ // Select some ndoes
+ } else if ("select".equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ throw new CyCommandException("node: nothing to
select");
+ net.setSelectedNodeState(nodeList, true);
+ result.addMessage("node: selected "+nodeList.size()+"
nodes");
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // de-select some ndoes
+ } else if ("deselect".equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ try {
+ List<CyNode> nodeList = getNodeList(net,
result, args);
+ if (nodeList == null)
+ throw new CyCommandException("node:
nothing to deselect");
+
+ net.setSelectedNodeState(nodeList, false);
+ result.addMessage("node: deselected
"+nodeList.size()+" nodes");
+ } catch (CyCommandException e) {
+ // deselect everything
+ net.unselectAllNodes();
+ result.addMessage("node: deselected all nodes");
+ }
+
+ if (net == Cytoscape.getCurrentNetwork()) {
+ Cytoscape.getCurrentNetworkView().updateView();
+ }
+
+ // return the list of currently selected nodes
+ } else if ("get selected".equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ Set<CyNode>nodes = net.getSelectedNodes();
+ result.addMessage("node: returned "+nodes.size()+"
selected nodes");
+ result.addResult("nodes", makeNodeList(nodes));
+
+ // Get attribute values
+ } else if ("get attribute".equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes nodeAttributes =
Cytoscape.getNodeAttributes();
+ String attrName = getArg("name", args);
+ if (attrName == null)
+ throw new CyCommandException("node: attribute
'name' is required");
+ else if (nodeAttributes.getType(attrName) ==
CyAttributes.TYPE_UNDEFINED)
+ throw new CyCommandException("node: attribute
'name' does not exist");
+
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ nodeList = net.nodesList();
+
+ byte attributeType = nodeAttributes.getType(attrName);
+ result.addResult("attribute type", attributeType);
+ result.addMessage("node: values for '"+attrName+"'
attribute:");
+ for (CyNode node: nodeList) {
+ if
(nodeAttributes.hasAttribute(node.getIdentifier(), attrName)) {
+ Object attr =
nodeAttributes.getAttribute(node.getIdentifier(), attrName);
+ result.addResult(node.getIdentifier(),
attr);
+ result.addMessage("
"+node.getIdentifier()+"='"+AttributeUtils.attributeToString(attr,
attributeType)+"'");
+ }
+ }
+
+ // Set attribute values
+ } else if ("set attribute".equals(command)) {
+ CyNetwork net = getNetwork(command, args);
+ CyAttributes nodeAttributes =
Cytoscape.getNodeAttributes();
+ String attrName = getArg("name", args);
+ String value = getArg("value", args);
+ if (attrName == null || value == null)
+ throw new CyCommandException("node: attribute
'name' and 'value' are required");
+
+ List<CyNode> nodeList = getNodeList(net, result, args);
+ if (nodeList == null)
+ nodeList = net.nodesList();
+
+ String typeName = getArg("type", args);
+ byte attributeType = nodeAttributes.getType(attrName);
+ if (attributeType == CyAttributes.TYPE_UNDEFINED &&
typeName == null)
+ attributeType = CyAttributes.TYPE_STRING;
+ else if (attributeType == CyAttributes.TYPE_UNDEFINED
&& typeName != null) {
+ attributeType =
AttributeUtils.attributeStringToByte(typeName);
+ }
+
+ int count = 0;
+ int nodeCount = nodeList.size();
+ for (CyNode node: nodeList) {
+ String id = node.getIdentifier();
+ if (AttributeUtils.setAttribute(result, "node",
nodeAttributes, attributeType, id, attrName, value))
+ count++;
+ }
+ result.addMessage("node: set "+count+" attributes (out
of "+nodeCount+")");
+
+ // find nodes based on an expression
+ } else if ("find".equals(command)) {
+ }
+
+ return result;
+ }
+
+ private CyNetwork getNetwork(String command, Map<String, String> args)
throws CyCommandException {
+ String netName = getArg("network", args);
+ if (netName == null || netName.equals("current"))
+ return Cytoscape.getCurrentNetwork();
+
+ CyNetwork net = Cytoscape.getNetwork(netName);
+ if (net == Cytoscape.getNullNetwork())
+ throw new CyCommandException("node: no such network
"+netName);
+ return net;
+ }
+
+ private String makeNodeList(Collection<CyNode>nodes) {
+ String nodeList = "";
+ if (nodes == null || nodes.size() == 0)
+ return nodeList;
+
+ for (CyNode node: nodes) {
+ nodeList += node.getIdentifier()+",";
+ }
+ return nodeList.substring(0, nodeList.length()-1);
+ }
+}
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